Comparative mitochondrial genomic analyses of three chemosynthetic vesicomyid clams from deep-sea habitats

Ecology and Evolution
Helu LiuHaibin Zhang

Abstract

Vesicomyid clams of the subfamily Pliocardinae are among the dominant chemosymbiotic bivalves found in sulfide-rich deep-sea habitats. Plastic morphologies and present molecular data could not resolve taxonomic uncertainties. The complete mitochondrial (mt) genomes will provide more data for comparative studies on molecular phylogeny and systematics of this taxonomically uncertain group, and help to clarify generic classifications. In this study, we analyze the features and evolutionary dynamics of mt genomes from three Archivesica species (Archivesica sp., Ar. gigas and Ar. pacifica) pertaining to subfamily Pliocardinae. Sequence coverage is nearly complete for the three newly sequenced mt genomes, with only the control region and some tRNA genes missing. Gene content, base composition, and codon usage are highly conserved in these pliocardiin species. Comparative analysis revealed the vesicomyid have a relatively lower ratio of Ka/Ks, and all 13 protein-coding genes (PGCs) are under strong purifying selection with a ratio of Ka/Ks far lower than one. Minimal changes in gene arrangement among vesicomyid species are due to the translocation trnaG in Isorropodon fossajaponicum. Additional tRNA genes were detected between trnaG a...Continue Reading

References

Jan 1, 1992·International Review of Cytology·D R Wolstenholme
Apr 2, 1999·Nucleic Acids Research·J L Boore
Feb 23, 2000·Journal of Molecular Evolution·A S PeekR C Vrijenhoek
Mar 3, 2004·Proceedings of the National Academy of Sciences of the United States of America·Swaine L ChenHarley H McAdams
Sep 1, 2005·Marine Biotechnology·Coren A Milbury, Patrick M Gaffney
May 29, 2007·Genomics, Proteomics & Bioinformatics·Zhang ZhangJun Yu
Nov 24, 2007·Bioinformatics·Dean Laslett, Björn Canbäck
Apr 9, 2010·PloS One·Elena M Krylova, Heiko Sahling
Nov 26, 2010·Nature Reviews. Genetics·Joshua B Plotkin, Grzegorz Kudla
Dec 18, 2010·Genome Génome / Conseil National De Recherches Canada·Xiaodong XuZiniu Yu
Feb 22, 2011·Bioinformatics·Diego DarribaDavid Posada
Aug 1, 2012·Nature Methods·Diego DarribaDavid Posada
Sep 22, 2012·Molecular Ecology·Ronald S Burton, Felipe S Barreto
Oct 16, 2015·Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis·Helu LiuRobert C Vrijenhoek
Mar 24, 2016·Molecular Biology and Evolution·Sudhir KumarKoichiro Tamura

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PCR

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