A genome resource for the marine annelid Platynereis spp

Abstract

The marine annelid Platynereis dumerilii is a model organism used in many research areas including evolution and development, neurobiology, ecology and regeneration. Here we present the genomes of P. dumerilii (laboratory culture reference and a single individual assembly) and of the closely related P. massiliensis and P. megalops (single individual assembly) to facilitate comparative genomic approaches and help explore Platynereis biology. We used long-read sequencing technology and chromosomal-conformation capture along with extensive transcriptomic resources to obtain and annotate a draft genome assembly of ~ 1.47 Gbp for P. dumerilii, of which more than half represent repeat elements. We predict around 29,000 protein-coding genes, with relatively large intron sizes, over 38,000 non-coding genes, and 105 miRNA loci. We further explore the high genetic variation (~ 3% heterozygosity) within the Platynereis species complex. Gene ontology reveals the most variable loci to be associated with pigmentation, development and immunity. The current work sets the stage for further development of Platynereis genomic resources.

Keywords: Platynereis; Platynereis dumerilii; Annelid; Evo-devo; Genome; Model organism; Spiralia.

Fig. 1

Platynereis dumerilii genome within Spiralia. A phylogenetic tree of major Spiralia/Lophotrochozoa groups, with the sequenced and ‘annotated’ annelid genome size estimates highlighted [30]. The genome sizes are based off genome assemblies or DNA nuclei staining methods. The Platynereis dumerilii genome size was previously estimated as 1 Gbp [31], this study estimates it to be ~ 1.47 Gbp, Helobdella robusta and Capitella teleta values were taken from [28], the Eisenia fetida genome size estimates were taken from [32, 33], the Streblospio benedictii measurements were taken from [29], the Dimorphilus gyrociliatus genome size from [25] and the Owenia fusiformis’ from [26]

Fig. 2

A chromosomal scale P. dumerilii genome assembly. A Hi-C contact map of all 330 P. dumerilii scaffolds. Highlighted in green are the 8 scaffolds that make up 50% of the assembly, in magenta at the 14 scaffolds (which may correspond to the 14 chromosomes of P. dumerilii), and in blue are the 28 scaffolds amounting to 80% of the assembly

Fig. 3

The repeat-element landscape in P. dumerilii. A, a doughnut plot illustrating the percentages of repeat and non-repeat elements found in the P. dumerilii genome. Percentages are of the total assembly (i.e. 49.43% of the entire genome is annotated as non-repetitive; yellow). B annelids – whose relationships are shown in a phylogenetic tree – genomic repeat-element landscape. C the distribution of intra – vs – inter-genic P. dumerilii repeat elements. D counts of repeat elements represented as scatterplots within annotated intragenic regions of the P. dumerilii genome. E an example gene locus (XLOC_041197) and its flanking regions on scaffold_3 highlighting repeat-element tracks (dark-blue) with the 5’ and 3’ UTRs (light-purple and green tracks respectively), exons (dark-orange track), introns (pink tracks) and the CDS (green tracks). F proportion of repeat-element families and their occupancy at different intragenic regions. G proportion of repeat-element specific RNA-seq reads mapping to intra – vs – inter-genic sites in P. dumerilii. H proportion of RNA-seq reads mapping to intra – vs – inter-genic sites within specific RE types, colored according to the same legend in panel F

Fig. 4

The protein coding repertoire in annelids. A Annelid protein coding gene sizes plotted in log₁₀ scale. The n values represent the total number of protein-coding genes that were measured for gene size, spanning the actual gene locus i.e. exons, introns and UTRs. The longest isoforms per gene were selected for the analysis. B Proportion of annelid protein-coding genes in orthogroups

Fig. 5

Evolutionarily conserved miRNA gene families and clusters in P. dumerilii. A gain and loss of miRNA families within the annelid species as annotated in MirGeneDB. Several novel miRNA families are organized into clusters, as shown below the tree, and color-coded accordingly. B distribution of phylogenetically conserved miRNA gene clusters in selected bilaterian phyla from the MirGeneDB database. The tree, next to the species names, reflects the lophotrochozoan clade phylogeny [69]. The names of the miRNA clusters are defined by the miRNA genes, separated by underscores (_), and are listed at the top of the figure. Since the order of miRNA genes in genomic clusters can vary between species, the nomenclature follows three hierarchical criteria: 1. The gene order in the P. dumerilii genome; 2. The most common arrangement in the analyzed species 3. Alphabetical order, when the first two criteria cannot be fulfilled. When the same miRNA gene name is repeated in the cluster, it indicates the presence of multiple copies, with uncertain homology, of the correspondent gene family. If the cluster name ends with three dots (…), more copies of the last listed gene are present. The number of copies can vary between species. When the cluster ends with an asterisk followed by a number (*¹), it indicates that the gene cluster expanded in another phylogenetic clade. Therefore, it is shown twice in the figure. miRNA clusters are grouped and ordered according to their phylogenetic conservation, with the respective clades indicated just below the clusters. C right panel, the Mir-10 genes in the Hox cluster of P. dumerilii compared to other bilaterian taxa. Protein-encoding genes are shown using the colored boxes, while miRNAs are with the red triangles. In both cases, the direction of transcription is indicated by the triangle's apex. The tree indicates the acquisition of novel Mir-10-P1 paralogues in each clade. A red X indicates the loss of the miRNA. The expansion of Mir-10-P1 genes within the Hox cluster of annelids often occurs at the same or similar locations of other novel miRNAs in other taxa. This includes the evolution of Mir-196 in vertebrates (human silhouette) and Iab-4 (fruit fly silhouette) in arthropods near or within the posterior or Abd-B genes, a phenomenon known as genomic parallelism [63] (indicated with the arrows). C left panel, sequence evolution of the mature miRNA of the mir-10 family in P. dumerilii compared to other taxa. The seed sequence (nucleotides 2–8) and the 3'complementary region (nucleotides 13–16) are highlighted with colors

Fig. 6

Genomic and transcriptomic variation analyses on wild sampled P. dumerilii. A global map of sites of P. dumerilii mRNA sampling. B histogram of raw mRNA-seq genome mapping percentages. C proportion of In/Del overlaps identified from the different Platynereis samples. D gene feature abundance/occupancy of SNPs and In/Dels from mRNA-seq reads accessed from P. dumerilii lab cultures. E SNP and In/Del counts from the same position on the genome correlation for the top 5,000 most variable genes (i.e. genes that showed the most variation in SNP and In/Del counts across the different sites). F GO-term enrichment analysis of the top 5,000 variable genes

Fig. 7

Comparison of three Platynereis species. Oxford dotplot comparison of the three Platynereis species genome assemblies. White homologies of most of the scaffolds can be identified, within scaffold inversions are common and present in all species

Fig. 8

Bilaterian Ancestral Linkage Group (bALG) fusion-with-mixing (FWM) events towards and within Errantia. Mapping of FWM events detected in this study onto the most up-to-date annelid-mollusc tree. Highlighted are the FWM events detected in annelid species belonging to specific groups within Sedentaria (orange) and Errantia (pink). Also see Suppl. Figure 16 for example bALGs