Insights from the genomes of 4 diploid Camelina spp

Abstract

Plant evolution has been a complex process involving hybridization and polyploidization making understanding the origin and evolution of a plant's genome challenging even once a published genome is available. The oilseed crop, Camelina sativa (Brassicaceae), has a fully sequenced allohexaploid genome with 3 unknown ancestors. To better understand which extant species best represent the ancestral genomes that contributed to C. sativa's formation, we sequenced and assembled chromosome level draft genomes for 4 diploid members of Camelina: C. neglecta C. hispida var. hispida, C. hispida var. grandiflora, and C. laxa using long and short read data scaffolded with proximity data. We then conducted phylogenetic analyses on regions of synteny and on genes described for Arabidopsis thaliana, from across each nuclear genome and the chloroplasts to examine evolutionary relationships within Camelina and Camelineae. We conclude that C. neglecta is closely related to C. sativa's sub-genome 1 and that C. hispida var. hispida and C. hispida var. grandiflora are most closely related to C. sativa's sub-genome 3. Further, the abundance and density of transposable elements, specifically Helitrons, suggest that the progenitor genome that contributed C. sativa's sub-genome 3 maybe more similar to the genome of C. hispida var. hispida than that of C. hispida var. grandiflora. These diploid genomes show few structural differences when compared to C. sativa's genome indicating little change to chromosome structure following allopolyploidization. This work also indicates that C. neglecta and C. hispida are important resources for understanding the genetics of C. sativa and potential resources for crop improvement.

Keywords: Brassicaceae; Camelina; allopolyploidy; chromosome evolution; genome evolution; phylogenomics.

Fig 1.

Species trees. These species trees were produced by ASTRAL-III using a multispecies coalescent model and trees produced by MrBayes for each fragment identified by bowtie 2’s alignment of sequence fragments from A. lyrata. These are grouped within 11 ABK groups that correspond to either whole ancestral chromosomes or chromosome arms that have been largely conserved. The ACK(s) included in each tree are indicated in the box to the left of each tree and the ancestral chromosome structure with division into ACK and ABK is shown in the lower right.

Fig. 2.

Density tree plots. Density tree plots of 1,000 randomly chosen tree estimated by StarBEAST2 for a set of a) fragment sequences, and b) genes, and c) 2 sets of reciprocal gene sequences.

Fig. 3.

Consensus networks. The consensus networks generated with PhyloNet using 1 set of reciprocal gene sequences (a) and the 3 most credible networks contributing to this consensus (b–d) with the percentage of credible networks represented.

Fig 4.

Trees from OrthoFinder. Phylogenetic trees generated by OrthoFinder based on in silico predictions of amino acids produced by AUGUSTUS. a) A consensus of 14,513 gene trees with an inferred root and b) a concatenated multiple sequence alignment of 7,401 shared, single-copy genes. Node labels indicate support values for each bipartition with the higher levels of support for the concatenated data expected for the type of analysis.

Fig. 5.

Chloroplast-based phylogeny. Phylogeny constructed from whole chloroplast alignment using MrBayes. Node labels indicate posterior probabilities.

Fig. 6.

Synteny plots with C. neglecta and C. sativa’s subgenomes 1 and 2. Plots indicating regions of synteny as indicated by nucmer between C. neglecta, with A. lyrata (a), C. sativa’s sub-genomes (b, c, e), and between A. lyrata and C. sativa’s sub-genomes (d, f). Plot (b) is colored by alignment with A. lyrata’s chromosomes, analogs for the ancestral chromosomes.

Fig. 7.

Synteny plots with C. hispida var. hispida, C. laxa, and C. sativa sub-genome 3. Plots indicating regions of synteny as indicated by nucmer among the diploid Camelina species C. hispida var. hispida and C. laxa with C. sativa’s sub-genomes (a, d, g, h) and with A. lyrata (b, e, i). Synteny between C. sativa sub-genomes and A. lyrata are shown for comparison (c, f). Plots (b) and (f) are colored by alignment with A. lyrata’s chromosomes, analogs for the ancestral chromosomes.

Fig. 8.

TE types and abundance. Types of TE in a) Camelina neglecta, b) C. laxa, c) C. hispida var. grandiflora, d) C. hispida var. hispida, e) Arabidopsis lyrata, f) C. sativa sub-genome 1, g) C. sativa sub-genome 2, and h) C. sativa sub-genome 3, as annotated by Extensive De novo Transposable Element (EDTA). Pie graphs are scaled by the percentage of the genome attributed to TEs which at highest is 49.6% for C. hispida var. hispida (d). Classification of TE type follows the unified classification system for eukaryotic TEs that uses a 3 letter code indicating class, order, and superfamily (34). Here, these are divided into 3 groups: DNA transposons (DNA), which includes Helitrons (DHH); LTR, which includes retrotransposons RLC (Copia) and RLG (Gypsy); and miniature-inverted transposable elements.

Fig. 9.

Helitron ideogram and abundance. a) Density of Helitrons identified by EAHelitron across the sub-genome 3 of C. sativa with the locations of Helitrons shared by C. hispida var. hispida, C. hispida var. grandiflora or both indicated and b) Venn diagram of the number of Helitrons shared among C. hispida var. hispida, C. hispida var. grandiflora, and C. sativa’s sub-genome 3.