Adaptation and evolution of deep-sea scale worms (Annelida: Polynoidae): insights from transcriptome comparison with a shallow-water species

Abstract

Polynoid scale worms (Polynoidae, Annelida) invaded deep-sea chemosynthesis-based ecosystems approximately 60 million years ago, but little is known about their genetic adaptation to the extreme deep-sea environment. In this study, we reported the first two transcriptomes of deep-sea polynoids (Branchipolynoe pettiboneae, Lepidonotopodium sp.) and compared them with the transcriptome of a shallow-water polynoid (Harmothoe imbricata). We determined codon and amino acid usage, positive selected genes, highly expressed genes and putative duplicated genes. Transcriptome assembly produced 98,806 to 225,709 contigs in the three species. There were more positively charged amino acids (i.e., histidine and arginine) and less negatively charged amino acids (i.e., aspartic acid and glutamic acid) in the deep-sea species. There were 120 genes showing clear evidence of positive selection. Among the 10% most highly expressed genes, there were more hemoglobin genes with high expression levels in both deep-sea species. The duplicated genes related to DNA recombination and metabolism, and gene expression were only enriched in deep-sea species. Deep-sea scale worms adopted two strategies of adaptation to hypoxia in the chemosynthesis-based habitats (i.e., rapid evolution of tetra-domain hemoglobin in Branchipolynoe or high expression of single-domain hemoglobin in Lepidonotopodium sp.).

Figure 1. Contig length distribution in the assembled transcriptomes of B. pettiboneae, Lepidonotopodium sp. and H. imbricata.

Figure 2. Gene Ontology (GO) distribution of annotated genes in the transcriptomes of B. pettiboneae, Lepidonotopodium sp. and H. imbricata.

Genes are grouped into three main functional categories: biological process, cellular component and molecular function. The left abscissa indicates the percentage and right one shows the number of annotated genes. One gene may have match in multiple GO terms.

Figure 3. Biological functions of positively selected genes in pair-wise comparisons among the three species of scale worms.

Figure 4. Comparison of highly expressed genes in B. pettiboneae, Lepidonotopodium sp. and H. imbricata.

(a) Percentage of genes participated in different cellular processes. Each datum shows the percentage each gene group to all top 10% highly expressed genes. (b) Expression level for gene groups participated in different cellular processes. Each datum shows the percentage of average FPKM value of a gene group to average FPKM value of all top 10% highly expressed genes.

Figure 5. Comparison of putatively duplicated genes in three species of scale worms.

(a) Gene Ontology (GO) distribution of putatively duplicated genes in the three species. The triangles stand for groups only present in B. pettiboneae; the squares for groups only present in Lepidonotopodium sp.; the pentagons for groups present in both deep-sea species. (b) Significantly enriched biological process GO terms of putatively duplicated genes only present in both deep-sea species (highlighted in yellow). Boxes framed in red show terminal GO terms in both deep-sea species. Data in parentheses include the number of genes associated with the listed GO term in B. pettiboneae (first number) and Lepidonotopodium sp. (second number). A dash in parenthesis indicates absence of the gene. Arrows represent the connection between two enriched GO terms at different levels. Only selected significantly enriched GO branches in deep-sea species are shown to illustrate the interspecific differences with shallow-water species.

Figure 6. Phylogenetic tree of potential hemoglobin sequences from scale worms.

Sequences from Lumbricus and Glycera served as outgroups. Numbers above branches represent MP/ML bootstrap values based on 1,000 iterations, with 100 (indicated using an asterisk) as the highest value. Bootstrap values below 50 are shown only as a short dash due to the weak support. Sequences from deep-sea species are highlighted in red color.

Figure 7. Alignment of hemoglobin sequences from deep-sea polynoids.

The sequences with a blue background are tetra-domain hemoglobins from three species of Branchipolynoe. Green letters above sequences indicate the positions of the heme pocket residues in tetra-domain hemoglobin. Red letters indicate the positions of conserved amino acid residues in all hemoglobin domains. Black letters show the positions of conserved amino acids in all hemoglobins from deep-sea polynoids. Orange letters show the positions of conserved amino acids in tetra-domain hemoglobins. The asterisks show positive selected sites in tetra-domain hemoglobins. SD: single-domain; TD: tetra-domain; Bse: B. seepensis; Bsy: B. symmytilida; Bpe: B. pettiboneae; Lepw: Lepidonotopodium williamsae; Branchipc: Branchiplicatus cupreus; Branchins: Branchinotogluma segonzaci; Branchint: Branchinotogluma trifurcus.