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. 2019 May 31:8:e45017.
doi: 10.7554/eLife.45017.

The genomes of polyextremophilic cyanidiales contain 1% horizontally transferred genes with diverse adaptive functions

Alessandro W Rossoni  1 , Dana C Price  2 , Mark Seger  3 , Dagmar Lyska  1 , Peter Lammers  3 , Debashish Bhattacharya  4 , Andreas Pm Weber  1
Affiliations

The genomes of polyextremophilic cyanidiales contain 1% horizontally transferred genes with diverse adaptive functions

Alessandro W Rossoni et al. Elife. .

Abstract

The role and extent of horizontal gene transfer (HGT) in eukaryotes are hotly disputed topics that impact our understanding of the origin of metabolic processes and the role of organelles in cellular evolution. We addressed this issue by analyzing 10 novel Cyanidiales genomes and determined that 1% of their gene inventory is HGT-derived. Numerous HGT candidates share a close phylogenetic relationship with prokaryotes that live in similar habitats as the Cyanidiales and encode functions related to polyextremophily. HGT candidates differ from native genes in GC-content, number of splice sites, and gene expression. HGT candidates are more prone to loss, which may explain the absence of a eukaryotic pan-genome. Therefore, the lack of a pan-genome and cumulative effects fail to provide substantive arguments against our hypothesis of recurring HGT followed by differential loss in eukaryotes. The maintenance of 1% HGTs, even under selection for genome reduction, underlines the importance of non-endosymbiosis related foreign gene acquisition.

Keywords: Cyanidiales; evolution; evolutionary biology; genome; horizontal gene transfer; lateral gene transfer; red algae.

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Conflict of interest statement

AR, DP, MS, DL, PL, DB, AW No competing interests declared

Figures

Figure 1.
Figure 1.. Geographic origin and habitat description of the analyzed Cyanidiales strains.
Available reference genomes are marked with an asterisk (*), whereas ‘na’ indicates missing information.
Figure 2.
Figure 2.. Species tree of the 13 analyzed extremophilic Cyanidiales genomes using mesophilic red (Porphyra umbilicalis, Porphyridium purpureum) and green algae (Ostreococcus tauri, Chlamydomonas reinhardtii) as outgroups.
IQTREE was used to infer a single maximum-likelihood phylogeny based on orthogroups containing single-copy representative proteins from at least 12 of the 17 taxa (13 Cyanidiales + 4 Others). Each orthogroup alignment represented one partition with unlinked models of protein evolution chosen by IQTREE. Consensus tree branch support was determined by 2000 rapid bootstraps. All nodes in this tree had 100% bootstrap support, and are therefore not shown. Divergence time estimates are taken from Yang et al. (2016). Similarity is derived from the average one-way best blast hit protein identity (minimum protein identity threshold = 30%). The minimal protein identity between two strains was 65.4%, measured between g. sulphuraria SAG21.92, which represent the second most distant sampling locations (12,350 km). Similar lineage boundaries were obtained for the C. merolae samples (66.4% protein identity), which are separated by only 1150 km.
Figure 3.
Figure 3.. Differential gene expression of G. sulphuraria 074W.
(A) and C. merolae 10D (B), here measured as log fold change (logFC) vs transcription rate (logCPM). Differentially expressed genes are colored red (quasi-likelihood (QL) F-test, Benjamini-Hochberg, p <= 0.01). HGT candidates are shown as large circles. The blue dashes indicate the average logCPM of the dataset. Although HGT candidates are not significantly more or less expressed than native genes, they react significantly stronger to temperature changes in G. sulphuraria 074W (‘more red than black dots'). This is not the case in high CO2 treated C. merolae 10D.
Figure 4.
Figure 4.. Comparative analysis of the 96 OGs potentially derived from HGT.
(A) OG count vs. the number of Cyanidiales species contained in an OG (=OG size). Only genes from the sequenced genomes were considered (13 species). A total of 60 OGs are exclusive to the Galdieria lineage (11 species), 23 OGs are exclusive to the Cyanidioschyzon lineage (two species), and 13 OGs are shared by both lineages. A total of 46/96 HGT events seem to be affected by later gene erosion/partial fixation. (B) OG-wise PID between HGT candidates vs. their potential non-eukaryotic donors. Point size represents the number of sequenced species contained in each OG. Because only two genomes of Cyanidioschyzon were sequenced, the maximum point size for this lineage is 2. The whiskers span minimum and maximum shared PID of each OG. The PID within Cyanidiales HGTs vs. PID between Cyanidiales HGTs and their potential non-eukaryotic donors is positively correlated (Kendall's tau coefficient, p=0.000747), showing evolutionary constraints that are gene function dependent, rather than time-dependent. (C) Density curve of average PID towards potential non-eukaryotic donors. The area under each curve is equal to 1. The average PID of HGT candidates found in both lineages (‘ancient HGT’, left dotted line) is ~5% lower than the average PID of HGT candidates exclusive to Galdieria or Cyandioschyzon (‘recent HGT’, right dotted lines). This difference is not significant (pairwise Wilcoxon rank-sum test, Benjamini-Hochberg, p>0.05). (D) Presence/Absence pattern (green/white) of Cyanidiales species in HGT OGs. Some patterns strictly follow the branching structure of the species tree. They represent either recent HGTs that affect a monophyletic subset of the Galdieria lineage, or are the last eukaryotic remnants of an ancient gene that was eroded through differential loss. In other cases, the presence/absence pattern of Galdieria species is random and conflicts with the Galdieria lineage phylogeny. HGT would assume either multiple independent acquisitions of the same HGT candidate, or a partial fixation of the HGT candidate in the lineage, while still allowing for gene erosion. According to DL, these are the last existing paralogs of an ancient gene, whose erosion within the eukaryotic kingdom is nearly complete.
Figure 5.
Figure 5.. The analysis of OGs containing HGT candidates revealed different patterns of HGT acquisition.
Some OGs contain genes that are shared by all Cyanidiales, whereas others are unique to the Galdieria or Cyanidioschyzon lineage. In some cases, HGT appears to have replaced the eukaryotic genes in one lineage, whereas the other lineage maintained the eukaryotic ortholog. Here, some examples of OG phylogenies are shown, which were simplified for ease of presentation. The first letter of the tip labels indicates the kingdom. A = Archaea (yellow), B = Bacteria (blue), E = Eukaryota (green). Branches containing Cyanidiales sequences are highlited in red. (A) Example of an ancient HGT that occurred before Galdieria and Cyanidioschyzon split into separate lineages. As such, both lineages are monophyletic (e.g., OG0001476). (B) HGT candidates are unique to the Galdieria lineage (e.g. OG0001760). (C) HGT candidates are unique to the Cyanidioschyzon lineage (e.g. OG0005738). (D) Galdieria and Cyanidioschyzon HGT candidates are derived from different HGT events and share monophyly with different non-eukaryotic organisms (e.g., OG0003085). (E) Galdieria HGT candidates cluster with non-eukaryotes, whereas the Cyanidioschyzon lineage clusters with eukaryotes (e.g., OG0001542). (F) Cyanidioschyzon HGT candidates cluster with non-eukaryotes, whereas the Galdieria lineage clusters with eukaryotes (e.g., OG0006136).
Figure 5—figure supplement 1.
Figure 5—figure supplement 1.. Sequence tree of orthogroup OG0001476.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 2.
Figure 5—figure supplement 2.. Sequence tree of orthogroup OG0001486.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 3.
Figure 5—figure supplement 3.. Sequence tree of orthogroup OG0001509.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 4.
Figure 5—figure supplement 4.. Sequence tree of orthogroup OG0001513.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 5.
Figure 5—figure supplement 5.. Sequence tree of orthogroup OG0001542.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 6.
Figure 5—figure supplement 6.. Sequence tree of orthogroup OG0001613.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 7.
Figure 5—figure supplement 7.. Sequence tree of orthogroup OG0001658.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 8.
Figure 5—figure supplement 8.. Sequence tree of orthogroup OG0001760.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 9.
Figure 5—figure supplement 9.. Sequence tree of orthogroup OG0001807.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 10.
Figure 5—figure supplement 10.. Sequence tree of orthogroup OG0001810.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 11.
Figure 5—figure supplement 11.. Sequence tree of orthogroup OG0001929.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 12.
Figure 5—figure supplement 12.. Sequence tree of orthogroup OG0001938.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 13.
Figure 5—figure supplement 13.. Sequence tree of orthogroup OG0001955.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 14.
Figure 5—figure supplement 14.. Sequence tree of orthogroup OG0001976.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 15.
Figure 5—figure supplement 15.. Sequence tree of orthogroup OG0001994.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 16.
Figure 5—figure supplement 16.. Sequence tree of orthogroup OG0002036.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 17.
Figure 5—figure supplement 17.. Sequence tree of orthogroup OG0002051.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 18.
Figure 5—figure supplement 18.. Sequence tree of orthogroup OG0002191.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 19.
Figure 5—figure supplement 19.. Sequence tree of orthogroup OG0002305.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 20.
Figure 5—figure supplement 20.. Sequence tree of orthogroup OG0002337.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 21.
Figure 5—figure supplement 21.. Sequence tree of orthogroup OG0002431.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 22.
Figure 5—figure supplement 22.. Sequence tree of orthogroup OG0002483.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 23.
Figure 5—figure supplement 23.. Sequence tree of orthogroup OG0002574.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 24.
Figure 5—figure supplement 24.. Sequence tree of orthogroup OG0002578.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 25.
Figure 5—figure supplement 25.. Sequence tree of orthogroup OG0002609.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 26.
Figure 5—figure supplement 26.. Sequence tree of orthogroup OG0002676.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 27.
Figure 5—figure supplement 27.. Sequence tree of orthogroup OG0002727.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 28.
Figure 5—figure supplement 28.. Sequence tree of orthogroup OG0002785.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 29.
Figure 5—figure supplement 29.. Sequence tree of orthogroup OG0002871.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 30.
Figure 5—figure supplement 30.. Sequence tree of orthogroup OG0002896.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 31.
Figure 5—figure supplement 31.. Sequence tree of orthogroup OG0002999.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 32.
Figure 5—figure supplement 32.. Sequence tree of orthogroup OG0003085.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 33.
Figure 5—figure supplement 33.. Sequence tree of orthogroup OG0003250.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 34.
Figure 5—figure supplement 34.. Sequence tree of orthogroup OG0003367.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 35.
Figure 5—figure supplement 35.. Sequence tree of orthogroup OG0003441.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 36.
Figure 5—figure supplement 36.. Sequence tree of orthogroup OG0003539.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 37.
Figure 5—figure supplement 37.. Sequence tree of orthogroup OG0003777.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 38.
Figure 5—figure supplement 38.. Sequence tree of orthogroup OG0003782.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 39.
Figure 5—figure supplement 39.. Sequence tree of orthogroup OG0003834.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 40.
Figure 5—figure supplement 40.. Sequence tree of orthogroup OG0003846.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 41.
Figure 5—figure supplement 41.. Sequence tree of orthogroup OG0003856.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 42.
Figure 5—figure supplement 42.. Sequence tree of orthogroup OG0003901.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 43.
Figure 5—figure supplement 43.. Sequence tree of orthogroup OG0003905.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 44.
Figure 5—figure supplement 44.. Sequence tree of orthogroup OG0003907.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 45.
Figure 5—figure supplement 45.. Sequence tree of orthogroup OG0003929.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 46.
Figure 5—figure supplement 46.. Sequence tree of orthogroup OG0003954.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 47.
Figure 5—figure supplement 47.. Sequence tree of orthogroup OG0004030.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 48.
Figure 5—figure supplement 48.. Sequence tree of orthogroup OG0004102.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 49.
Figure 5—figure supplement 49.. Sequence tree of orthogroup OG0004142.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 50.
Figure 5—figure supplement 50.. Sequence tree of orthogroup OG0004203.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 51.
Figure 5—figure supplement 51.. Sequence tree of orthogroup OG0004258.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 52.
Figure 5—figure supplement 52.. Sequence tree of orthogroup OG0004339.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 53.
Figure 5—figure supplement 53.. Sequence tree of orthogroup OG0004392.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 54.
Figure 5—figure supplement 54.. Sequence tree of orthogroup OG0004405.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 55.
Figure 5—figure supplement 55.. Sequence tree of orthogroup OG0004486.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 56.
Figure 5—figure supplement 56.. Sequence tree of orthogroup OG0004658.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 57.
Figure 5—figure supplement 57.. Sequence tree of orthogroup OG0005083.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 58.
Figure 5—figure supplement 58.. Sequence tree of orthogroup OG0005087.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 59.
Figure 5—figure supplement 59.. Sequence tree of orthogroup OG0005153.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 60.
Figure 5—figure supplement 60.. Sequence tree of orthogroup OG0005224.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 61.
Figure 5—figure supplement 61.. Sequence tree of orthogroup OG0005235.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 62.
Figure 5—figure supplement 62.. Sequence tree of orthogroup OG0005280.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 63.
Figure 5—figure supplement 63.. Sequence tree of orthogroup OG0005479.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 64.
Figure 5—figure supplement 64.. Sequence tree of orthogroup OG0005540.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 65.
Figure 5—figure supplement 65.. Sequence tree of orthogroup OG0005561.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 66.
Figure 5—figure supplement 66.. Sequence tree of orthogroup OG0005596.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 67.
Figure 5—figure supplement 67.. Sequence tree of orthogroup OG0005683.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 68.
Figure 5—figure supplement 68.. Sequence tree of orthogroup OG0005694.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 69.
Figure 5—figure supplement 69.. Sequence tree of orthogroup OG0005738.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 70.
Figure 5—figure supplement 70.. Sequence tree of orthogroup OG0005963.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 71.
Figure 5—figure supplement 71.. Sequence tree of orthogroup OG0005984.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 72.
Figure 5—figure supplement 72.. Sequence tree of orthogroup OG0006136.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 73.
Figure 5—figure supplement 73.. Sequence tree of orthogroup OG0006143.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 74.
Figure 5—figure supplement 74.. Sequence tree of orthogroup OG0006191.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 75.
Figure 5—figure supplement 75.. Sequence tree of orthogroup OG0006251.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 76.
Figure 5—figure supplement 76.. Sequence tree of orthogroup OG0006252.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 77.
Figure 5—figure supplement 77.. Sequence tree of orthogroup OG0006435.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 78.
Figure 5—figure supplement 78.. Sequence tree of orthogroup OG0006482.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 79.
Figure 5—figure supplement 79.. Sequence tree of orthogroup OG0006498.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 80.
Figure 5—figure supplement 80.. Sequence tree of orthogroup OG0006623.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 81.
Figure 5—figure supplement 81.. Sequence tree of orthogroup OG0006670.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 82.
Figure 5—figure supplement 82.. Sequence tree of orthogroup OG0007051.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 83.
Figure 5—figure supplement 83.. Sequence tree of orthogroup OG0007123.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 84.
Figure 5—figure supplement 84.. Sequence tree of orthogroup OG0007346.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 85.
Figure 5—figure supplement 85.. Sequence tree of orthogroup OG0007383.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 86.
Figure 5—figure supplement 86.. Sequence tree of orthogroup OG0007550.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 87.
Figure 5—figure supplement 87.. Sequence tree of orthogroup OG0007551.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 88.
Figure 5—figure supplement 88.. Sequence tree of orthogroup OG0007596.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 89.
Figure 5—figure supplement 89.. Sequence tree of orthogroup OG0008189.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 90.
Figure 5—figure supplement 90.. Sequence tree of orthogroup OG0008334.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 91.
Figure 5—figure supplement 91.. Sequence tree of orthogroup OG0008335.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 92.
Figure 5—figure supplement 92.. Sequence tree of orthogroup OG0008579.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 93.
Figure 5—figure supplement 93.. Sequence tree of orthogroup OG0008680.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 94.
Figure 5—figure supplement 94.. Sequence tree of orthogroup OG0008822.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 95.
Figure 5—figure supplement 95.. Sequence tree of orthogroup OG0008898.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 5—figure supplement 96.
Figure 5—figure supplement 96.. Sequence tree of orthogroup OG0008996.
The tree is based on amino acid sequences. Archaea (yellow), Bacteria (blue), Cyanidiales (red), Eukaryotes including other red algae (green). Branches containing Cyanidiales sequences are highlited in red.
Figure 6.
Figure 6.. HGT vs. non-HGT orthogroup comparisons.
(A) Maximum PID of Cyanidiales genes in native (blue) and HGT (yellow) orthogroups when compared to non-eukaryotic sequences in each OG. The red lines denote the 70% PID threshold for assembly artifacts according to ‘the 70% rule’. Dots located in the top-right corner depict the 73 OGs that appear to contradict this rule, plus the 5 HGT candidates that score higher than 70%. 18/73 of those OGs are not derived from EGT or contamination within eukaryotic assemblies. (B) Density curve of average PID towards non-eukaryotic species in the same orthogroup (potential non-eukaryotic donors in case of HGT candidates). The area under each curve is equal to 1. The average PID of HGT candidates (left dotted line) is 6.1% higher than the average PID of native OGs also containing non-eukaryotic species (right dotted line). This difference is significant (Wilcoxon rank-sum test, p>0.01). (C) Distribution of OG-sizes (=number of Galdieria species present in each OG) between the native and HGT dataset. A total of 80% of the HGT OGs and 89% of the native OGs are present in either ≤10 species, or ≤2 species. Whereas 52.5% of the native gene set is conserved in ≤10 Galdieria strains, only 36.1% of the HGT candidates are conserved. In contrast, about 50% of the HGT candidates are present in only one Galdieria strain. (D) Pairwise OG-size comparison between HGT OGs and native OGs. A significantly higher PID when compared to non-eukaryotic sequences was measured in the HGT OGs at OG-sizes of 1 and 11 (Wilcoxon rank-sum test, BH, p<0.01). No evidence of cumulative effects was detected in the HGT dataset. However, the fewer Galdieria species that are contained in one OG, the higher the average PID when compared to non-eukaryotic species in the same tree (Jonckheere-Terpstra, p<0.01) in the native dataset.
Figure 7.
Figure 7.. Cyanidiales live in hostile habitats, necessitating a broad range of adaptations to polyextremophily.
The majority of the 96 HGT-impacted OGs were annotated and putative functions identified (in the image, colored fields are from HGT, whereas gray fields are native functions). The largest number of HGT candidates is involved in carbon and amino acid metabolism, especially in the Galdieria lineage. The excretion of lytic enzymes and the high number of importers (protein/AA symporter, glycerol/H2O symporter) within the HGT dataset suggest a preference for import and catabolic function.
Appendix 1—figure 1.
Appendix 1—figure 1.. Raw read length distribution of the sequenced Cyanidiales strains.
The strains were sequenced in 2016/2017 using PacBio’s RS2 sequencing technology and P6-C4 chemistry (the only exception being C. merolae Soos, which was sequenced as pilot study using P4-C2 chemistry in 2014). Seven strains, namely G. sulphuraria 5572, G. sulphuraria 002, G. sulphuraria SAG21.92, G. sulphuraria Azora, G. sulphuraria MtSh, G. sulphuraria RT22 and G. sulphuraria MS1 were sequenced at the University of Maryland Institute for Genome Sciences (Baltimore, USA). The remaining three strains, G. sulphuraria YNP5578.1, G. phlegrea Soos and C. merolae Soos, were sequenced at the Max-Planck-Institut für Pflanzenzüchtungsforschung (Cologne, Germany).
Appendix 3—figure 1.
Appendix 3—figure 1.. %GC – Galdieria sulphuraria 074W: (Left) Violin plot showing the %GC distribution across native transcripts and HGT candidates.
(Mid) Cumulative %GC distribution of transcripts. Red line shows the average, blue line a normal distribution based on the average value. (Right) Ranking all transcripts based upon their %GC content. Red ‘*' demarks HGT candidates. As the %GC content was normally distributed, students test was applied for the determination of significant differences between the native gene and the HGT candidate subset.
Appendix 3—figure 2.
Appendix 3—figure 2.. %GC – Galdieria sulphuraria MS1: (Left) Violin plot showing the %GC distribution across native transcripts and HGT candidates.
(Mid) Cumulative %GC distribution of transcripts. Red line shows the average, blue line a normal distribution based on the average value. (Right) Ranking all transcripts based upon their %GC content. Red ‘*' demarks HGT candidates. As the %GC content was normally distributed, students test was applied for the determination of significant differences between the native gene and the HGT candidate subset.
Appendix 3—figure 3.
Appendix 3—figure 3.. %GC – Galdieria sulphuraria RT22: (Left) Violin plot showing the %GC distribution across native transcripts and HGT candidates.
(Mid) Cumulative %GC distribution of transcripts. Red line shows the average, blue line a normal distribution based on the average value. (Right) Ranking all transcripts based upon their %GC content. Red ‘*' demarks HGT candidates. As the %GC content was normally distributed, students test was applied for the determination of significant differences between the native gene and the HGT candidate subset.
Appendix 3—figure 4.
Appendix 3—figure 4.. %GC – Galdieria sulphuraria SAG21: (Left) Violin plot showing the %GC distribution across native transcripts and HGT candidates.
(Mid) Cumulative %GC distribution of transcripts. Red line shows the average, blue line a normal distribution based on the average value. (Right) Ranking all transcripts based upon their %GC content. Red ‘*' demarks HGT candidates. As the %GC content was normally distributed, students test was applied for the determination of significant differences between the native gene and the HGT candidate subset.
Appendix 3—figure 5.
Appendix 3—figure 5.. %GC – Galdieria sulphuraria Mount Shasta (MtSh): (Left) Violin plot showing the %GC distribution across native transcripts and HGT candidates.
(Mid) Cumulative %GC distribution of transcripts. Red line shows the average, blue line a normal distribution based on the average value. (Right) Ranking all transcripts based upon their %GC content. Red ‘*' demarks HGT candidates. As the %GC content was normally distributed, students test was applied for the determination of significant differences between the native gene and the HGT candidate subset.
Appendix 3—figure 6.
Appendix 3—figure 6.. Galdieria sulphuraria Azora: (Left) Violin plot showing the %GC distribution across native transcripts and HGT candidates.
(Mid) Cumulative %GC distribution of transcripts. Red line shows the average, blue line a normal distribution based on the average value. (Right) Ranking all transcripts based upon their %GC content. Red ‘*' demarks HGT candidates. As the %GC content was normally distributed, students test was applied for the determination of significant differences between the native gene and the HGT candidate subset.
Appendix 3—figure 7.
Appendix 3—figure 7.. %GC – Galdieria sulphuraria Mount Shasta YNP5578.1: (Left) Violin plot showing the %GC distribution across native transcripts and HGT candidates.
(Mid) Cumulative %GC distribution of transcripts. Red line shows the average, blue line a normal distribution based on the average value. (Right) Ranking all transcripts based upon their %GC content. Red ‘*' demarks HGT candidates. As the %GC content was normally distributed, students test was applied for the determination of significant differences between the native gene and the HGT candidate subset.
Appendix 3—figure 8.
Appendix 3—figure 8.. %GC – Galdieria sulphuraria 5572: (Left) Violin plot showing the %GC distribution across native transcripts and HGT candidates.
(Mid) Cumulative %GC distribution of transcripts. Red line shows the average, blue line a normal distribution based on the average value. (Right) Ranking all transcripts based upon their %GC content. Red ‘*' demarks HGT candidates. As the %GC content was normally distributed, students test was applied for the determination of significant differences between the native gene and the HGT candidate subset.
Appendix 3—figure 9.
Appendix 3—figure 9.. %GC – Galdieria sulphuraria 002: (Left) Violin plot showing the %GC distribution across native transcripts and HGT candidates.
(Mid) Cumulative %GC distribution of transcripts. Red line shows the average, blue line a normal distribution based on the average value. (Right) Ranking all transcripts based upon their %GC content. Red ‘*' demarks HGT candidates. As the %GC content was normally distributed, students test was applied for the determination of significant differences between the native gene and the HGT candidate subset.
Appendix 3—figure 10.
Appendix 3—figure 10.. %GC – Galdieria phlegrea Soos: (Left) Violin plot showing the %GC distribution across native transcripts and HGT candidates.
(Mid) Cumulative %GC distribution of transcripts. Red line shows the average, blue line a normal distribution based on the average value. (Right) Ranking all transcripts based upon their %GC content. Red ‘*' demarks HGT candidates. As the %GC content was normally distributed, students test was applied for the determination of significant differences between the native gene and the HGT candidate subset.
Appendix 3—figure 11.
Appendix 3—figure 11.. %GC – Galdieria phlegrea DBV009: (Left) Violin plot showing the %GC distribution across native transcripts and HGT candidates.
(Mid) Cumulative %GC distribution of transcripts. Red line shows the average, blue line a normal distribution based on the average value. (Right) Ranking all transcripts based upon their %GC content. Red ‘*' demarks HGT candidates. As the %GC content was normally distributed, students test was applied for the determination of significant differences between the native gene and the HGT candidate subset.
Appendix 3—figure 12.
Appendix 3—figure 12.. %GC – Cyanidioschyzon merolae Soos: (Left) Violin plot showing the %GC distribution across native transcripts and HGT candidates.
(Mid) Cumulative %GC distribution of transcripts. Red line shows the average, blue line a normal distribution based on the average value. (Right) Ranking all transcripts based upon their %GC content. Red ‘*' demarks HGT candidates. As the %GC content was normally distributed, students test was applied for the determination of significant differences between the native gene and the HGT candidate subset.
Appendix 3—figure 13.
Appendix 3—figure 13.. %GC – Cyanidioschyzon merolae 10D: (Left) Violin plot showing the %GC distribution across native transcripts and HGT candidates.
(Mid) Cumulative %GC distribution of transcripts. Red line shows the average, blue line a normal distribution based on the average value. (Right) Ranking all transcripts based upon their %GC content. Red ‘*' demarks HGT candidates. As the %GC content was normally distributed, students test was applied for the determination of significant differences between the native gene and the HGT candidate subset.
Appendix 4—figure 1.
Appendix 4—figure 1.. Exon/Intron – Galdieria sulphuraria 074W: (Left) Mid) Cumulative %GC distribution of transcripts.
Red line shows the average, blue line a normal distribution based on the average value. The data is categorical (genes have either one, two, three etc. exons) and does not follow a normal distribution. (Mid) Ranking all transcripts based upon their number of exons. Red ‘*' demarks HGT candidates. As the number of exons was not normally distributed, transcripts were ranked by number of exons. In order to resolve the high number of tied ranks (e.g. many transcripts have two exons) a bootstrap was implied by which the rank of transcripts sharing the same number of exons was randomly assigned 1000 times. Wilcoxon-Mann-Whitney-Test applied for the determination of significant rank differences between the native gene and the HGT candidate subset. (Right) Violin plot showing the number of exons per transcript distribution across native transcripts and HGT candidates.
Appendix 4—figure 2.
Appendix 4—figure 2.. Exon/Intron – Galdieria sulphuraria MS1: (Left) Mid) Cumulative %GC distribution of transcripts.
Red line shows the average, blue line a normal distribution based on the average value. The data is categorical (genes have either one, two, three etc. exons) and does not follow a normal distribution. (Mid) Ranking all transcripts based upon their number of exons. Red ‘*' demarks HGT candidates. As the number of exons was not normally distributed, transcripts were ranked by number of exons. In order to resolve the high number of tied ranks (e.g. many transcripts have two exons) a bootstrap was implied by which the rank of transcripts sharing the same number of exons was randomly assigned 1000 times. Wilcoxon-Mann-Whitney-Test applied for the determination of significant rank differences between the native gene and the HGT candidate subset. (Right) Violin plot showing the number of exons per transcript distribution across native transcripts and HGT candidates.
Appendix 4—figure 3.
Appendix 4—figure 3.. Exon/Intron – Galdieria sulphuraria RT22: (Left) Mid) Cumulative %GC distribution of transcripts.
Red line shows the average, blue line a normal distribution based on the average value. The data is categorical (genes have either one, two, three etc. exons) and does not follow a normal distribution. (Mid) Ranking all transcripts based upon their number of exons. Red ‘*' demarks HGT candidates. As the number of exons was not normally distributed, transcripts were ranked by number of exons. In order to resolve the high number of tied ranks (e.g. many transcripts have two exons) a bootstrap was implied by which the rank of transcripts sharing the same number of exons was randomly assigned 1000 times. Wilcoxon-Mann-Whitney-Test applied for the determination of significant rank differences between the native gene and the HGT candidate subset. (Right) Violin plot showing the number of exons per transcript distribution across native transcripts and HGT candidates.
Appendix 4—figure 4.
Appendix 4—figure 4.. Exon/Intron – Galdieria sulphuraria SAG21: (Left) Mid) Cumulative %GC distribution of transcripts.
Red line shows the average, blue line a normal distribution based on the average value. The data is categorical (genes have either one, two, three etc. exons) and does not follow a normal distribution. (Mid) Ranking all transcripts based upon their number of exons. Red ‘*' demarks HGT candidates. As the number of exons was not normally distributed, transcripts were ranked by number of exons. In order to resolve the high number of tied ranks (e.g. many transcripts have two exons) a bootstrap was implied by which the rank of transcripts sharing the same number of exons was randomly assigned 1000 times. Wilcoxon-Mann-Whitney-Test applied for the determination of significant rank differences between the native gene and the HGT candidate subset. (Right) Violin plot showing the number of exons per transcript distribution across native transcripts and HGT candidates.
Appendix 4—figure 5.
Appendix 4—figure 5.. Exon/Intron – Galdieria sulphuraria MtSh: (Left) Mid) Cumulative %GC distribution of transcripts.
Red line shows the average, blue line a normal distribution based on the average value. The data is categorical (genes have either one, two, three etc. exons) and does not follow a normal distribution. (Mid) Ranking all transcripts based upon their number of exons. Red ‘*' demarks HGT candidates. As the number of exons was not normally distributed, transcripts were ranked by number of exons. In order to resolve the high number of tied ranks (e.g. many transcripts have two exons) a bootstrap was implied by which the rank of transcripts sharing the same number of exons was randomly assigned 1000 times. Wilcoxon-Mann-Whitney-Test applied for the determination of significant rank differences between the native gene and the HGT candidate subset. (Right) Violin plot showing the number of exons per transcript distribution across native transcripts and HGT candidates.
Appendix 4—figure 6.
Appendix 4—figure 6.. Exon/Intron – Galdieria sulphuraria Azora: (Left) Mid) Cumulative %GC distribution of transcripts.
Red line shows the average, blue line a normal distribution based on the average value. The data is categorical (genes have either one, two, three etc. exons) and does not follow a normal distribution. (Mid) Ranking all transcripts based upon their number of exons. Red ‘*' demarks HGT candidates. As the number of exons was not normally distributed, transcripts were ranked by number of exons. In order to resolve the high number of tied ranks (e.g. many transcripts have two exons) a bootstrap was implied by which the rank of transcripts sharing the same number of exons was randomly assigned 1000 times. Wilcoxon-Mann-Whitney-Test applied for the determination of significant rank differences between the native gene and the HGT candidate subset. (Right) Violin plot showing the number of exons per transcript distribution across native transcripts and HGT candidates.
Appendix 4—figure 7.
Appendix 4—figure 7.. Exon/Intron – Galdieria sulphuraria YNP5578.1: (Left) Mid) Cumulative %GC distribution of transcripts.
Red line shows the average, blue line a normal distribution based on the average value. The data is categorical (genes have either one, two, three etc. exons) and does not follow a normal distribution. (Mid) Ranking all transcripts based upon their number of exons. Red ‘*' demarks HGT candidates. As the number of exons was not normally distributed, transcripts were ranked by number of exons. In order to resolve the high number of tied ranks (e.g. many transcripts have two exons) a bootstrap was implied by which the rank of transcripts sharing the same number of exons was randomly assigned 1000 times. Wilcoxon-Mann-Whitney-Test applied for the determination of significant rank differences between the native gene and the HGT candidate subset. (Right) Violin plot showing the number of exons per transcript distribution across native transcripts and HGT candidates.
Appendix 4—figure 8.
Appendix 4—figure 8.. Exon/Intron – Galdieria sulphuraria 5572: (Left) Mid) Cumulative %GC distribution of transcripts.
Red line shows the average, blue line a normal distribution based on the average value. The data is categorical (genes have either one, two, three etc. exons) and does not follow a normal distribution. (Mid) Ranking all transcripts based upon their number of exons. Red ‘*' demarks HGT candidates. As the number of exons was not normally distributed, transcripts were ranked by number of exons. In order to resolve the high number of tied ranks (e.g. many transcripts have two exons) a bootstrap was implied by which the rank of transcripts sharing the same number of exons was randomly assigned 1000 times. Wilcoxon-Mann-Whitney-Test applied for the determination of significant rank differences between the native gene and the HGT candidate subset. (Right) Violin plot showing the number of exons per transcript distribution across native transcripts and HGT candidates.
Appendix 4—figure 9.
Appendix 4—figure 9.. Exon/Intron – Galdieria sulphuraria 002: (Left) Mid) Cumulative %GC distribution of transcripts.
Red line shows the average, blue line a normal distribution based on the average value. The data is categorical (genes have either one, two, three etc. exons) and does not follow a normal distribution. (Mid) Ranking all transcripts based upon their number of exons. Red ‘*' demarks HGT candidates. As the number of exons was not normally distributed, transcripts were ranked by number of exons. In order to resolve the high number of tied ranks (e.g. many transcripts have two exons) a bootstrap was implied by which the rank of transcripts sharing the same number of exons was randomly assigned 1000 times. Wilcoxon-Mann-Whitney-Test applied for the determination of significant rank differences between the native gene and the HGT candidate subset. (Right) Violin plot showing the number of exons per transcript distribution across native transcripts and HGT candidates.
Appendix 4—figure 10.
Appendix 4—figure 10.. Exon/Intron – Galdieria phlegrea Soos: (Left) Mid) Cumulative %GC distribution of transcripts.
Red line shows the average, blue line a normal distribution based on the average value. The data is categorical (genes have either one, two, three etc. exons) and does not follow a normal distribution. (Mid) Ranking all transcripts based upon their number of exons. Red ‘*' demarks HGT candidates. As the number of exons was not normally distributed, transcripts were ranked by number of exons. In order to resolve the high number of tied ranks (e.g. many transcripts have two exons) a bootstrap was implied by which the rank of transcripts sharing the same number of exons was randomly assigned 1000 times. Wilcoxon-Mann-Whitney-Test applied for the determination of significant rank differences between the native gene and the HGT candidate subset. (Right) Violin plot showing the number of exons per transcript distribution across native transcripts and HGT candidates.
Appendix 4—figure 11.
Appendix 4—figure 11.. Exon/Intron – Cyanidioschyzon merolae Soos: (Left) Mid) Cumulative %GC distribution of transcripts.
Red line shows the average, blue line a normal distribution based on the average value. The data is categorical (genes have either one, two, three etc. exons) and does not follow a normal distribution. (Mid) Ranking all transcripts based upon their number of exons. Red ‘*” demarks HGT candidates. As the number of exons was not normally distributed, transcripts were ranked by number of exons. In order to resolve the high number of tied ranks (e.g. many transcripts have two exons) a bootstrap was implied by which the rank of transcripts sharing the same number of exons was randomly assigned 1000 times. Wilcoxon-Mann-Whitney-Test applied for the determination of significant rank differences between the native gene and the HGT candidate subset. (Right) Violin plot showing the number of exons per transcript distribution across native transcripts and HGT candidates..
Appendix 4—figure 12.
Appendix 4—figure 12.. Exon/Intron – Cyanidioschyzon merolae 074W: (Left) Mid) Cumulative %GC distribution of transcripts.
Red line shows the average, blue line a normal distribution based on the average value. The data is categorical (genes have either one, two, three etc. exons) and does not follow a normal distribution. (Mid) Ranking all transcripts based upon their number of exons. Red ‘*' demarks HGT candidates. As the number of exons was not normally distributed, transcripts were ranked by number of exons. In order to resolve the high number of tied ranks (e.g. many transcripts have two exons) a bootstrap was implied by which the rank of transcripts sharing the same number of exons was randomly assigned 1000 times. Wilcoxon-Mann-Whitney-Test applied for the determination of significant rank differences between the native gene and the HGT candidate subset. (Right) Violin plot showing the number of exons per transcript distribution across native transcripts and HGT candidates.
Appendix 5—figure 1.
Appendix 5—figure 1.. Best Blast Hit between each of the 13 Cyanidiales species and their most similar non-eukaryotic Ortholog in each OG-phylogeny.
Values are given as average percent protein identity between Cyanidiales and non-eukaryotic ortholog. White boxes represent missing Cyanidiales orthologs.
See this image and copyright information in PMC

Comment in

  • Adapting for life in the extreme.
    Kobras CM, Falush D. Kobras CM, et al. Elife. 2019 Jul 15;8:e48999. doi: 10.7554/eLife.48999. Elife. 2019. PMID: 31305242 Free PMC article.

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