Bivalve-specific gene expansion in the pearl oyster genome: implications of adaptation to a sessile lifestyle

• Main Authors: Takeuchi, Takeshi, Koyanagi, Ryo, Fuki Gyoja, Kanda, Miyuki, Hisata, Kanako, Fujie, Manabu, Goto, Hiroki, Yamasaki, Shinichi, Kiyohito Nagai, Morino, Yoshiaki, Miyamoto, Hiroshi, Endo, Kazuyoshi, Endo, Hirotoshi, Nagasawa, Hiromichi, Shigeharu Kinoshita, Asakawa, Shuichi, Shugo Watabe, Satoh, Noriyuki, Kawashima, Takeshi
• Format: Article in Journal/Newspaper
• Language: unknown
• Published: Figshare 2016
• Subjects: Biochemistry; Genetics; FOS Biological sciences; Molecular Biology; Evolutionary Biology; Ecology; 69999 Biological Sciences not elsewhere classified; Marine Biology; Inorganic Chemistry; FOS Chemical sciences; 110309 Infectious Diseases; FOS Health sciences; 60506 Virology; Pacific; Crassostrea gigas; Pacific oyster
• Online Access: https://dx.doi.org/10.6084/m9.figshare.c.3610172; https://figshare.com/collections/Bivalve-specific_gene_expansion_in_the_pearl_oyster_genome_implications_of_adaptation_to_a_sessile_lifestyle/3610172

Abstract Introduction Bivalve molluscs have flourished in marine environments, and many species constitute important aquatic resources. Recently, whole genome sequences from two bivalves, the pearl oyster, Pinctada fucata, and the Pacific oyster, Crassostrea gigas, have been decoded, making it possible to compare genomic sequences among molluscs, and to explore general and lineage-specific genetic features and trends in bivalves. In order to improve the quality of sequence data for these purposes, we have updated the entire P. fucata genome assembly. Results We present a new genome assembly of the pearl oyster, Pinctada fucata (version 2.0). To update the assembly, we conducted additional sequencing, obtaining accumulated sequence data amounting to 193Ă the P. fucata genome. Sequence redundancy in contigs that was caused by heterozygosity was removed in silico, which significantly improved subsequent scaffolding. Gene model version 2.0 was generated with the aid of manual gene annotations supplied by the P. fucata research community. Comparison of mollusc and other bilaterian genomes shows that gene arrangements of Hox, ParaHox, and Wnt clusters in the P. fucata genome are similar to those of other molluscs. Like the Pacific oyster, P. fucata possesses many genes involved in environmental responses and in immune defense. Phylogenetic analyses of heat shock protein70 and C1q domain-containing protein families indicate that extensive expansion of genes occurred independently in each lineage. Several gene duplication events prior to the split between the pearl oyster and the Pacific oyster are also evident. In addition, a number of tandem duplications of genes that encode shell matrix proteins are also well characterized in the P. fucata genome. Conclusions Both the Pinctada and Crassostrea lineages have expanded specific gene families in a lineage-specific manner. Frequent duplication of genes responsible for shell formation in the P. fucata genome explains the diversity of mollusc shell structures. These duplications reveal dynamic genome evolution to forge the complex physiology that enables bivalves to employ a sessile lifestyle in the intertidal zone.