title: 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.).
authors.affiliation: Department of Biology, Hong Kong Baptist University, Hong Kong, P. R. China.
authors.forename: Yanjie
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Division of Life Sciences, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, P. R. China.
authors.forename: Jin
authors.initials: J
authors.lastname: Sun
authors.affiliation: Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa, 237-0061, Japan.
authors.forename: Chong
authors.initials: C
authors.lastname: Chen
authors.affiliation: Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa, 237-0061, Japan.
authors.forename: Hiromi K
authors.initials: HK
authors.lastname: Watanabe
authors.affiliation: CAS Key Laboratory of Marginal Sea Geology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, P. R. China.
authors.forename: Dong
authors.initials: D
authors.lastname: Feng
authors.affiliation: College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, P. R. China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Department of Biology, Hong Kong Baptist University, Hong Kong, P. R. China.
authors.forename: Jill M Y
authors.initials: JM
authors.lastname: Chiu
authors.affiliation: Division of Life Sciences, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, P. R. China.
authors.forename: Pei-Yuan
authors.initials: PY
authors.lastname: Qian
authors.affiliation: Department of Biology, Hong Kong Baptist University, Hong Kong, P. R. China.
authors.forename: Jian-Wen
authors.initials: JW
authors.lastname: Qiu
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D000595:Amino Acid Sequence; D000596:Amino Acids / Q000235:genetics; D000818:Animals; D000845:Annelida / Q000235:genetics* / Q000502:physiology*; D001482:Base Composition / Q000235:genetics; D005075:Biological Evolution; D003062:Codon / Q000235:genetics; D020869:Gene Expression Profiling; D063990:Gene Ontology; D020131:Genes, Duplicate; D006454:Hemoglobins / Q000737:chemistry; D058977:Molecular Sequence Annotation; D009792:Oceans and Seas; D010802:Phylogeny; D012641:Selection, Genetic; D013045:Species Specificity; D059467:Transcriptome / Q000235:genetics*; D014867:Water
chemical_list: D000596:Amino Acids; D003062:Codon; D006454:Hemoglobins; D014867:Water