title: The complete mitochondrial genome sequence of the tubeworm Lamellibrachia satsuma and structural conservation in the mitochondrial genome control regions of Order Sabellida.
abstract: The control region of the mitochondrial genomes shows high variation in conserved sequence organizations, which follow distinct evolutionary patterns in different species or taxa. In this study, we sequenced the complete mitochondrial genome of Lamellibrachia satsuma from the cold-seep region of Kagoshima Bay, as a part of whole genome study and extensively studied the structural features and patterns of the control region sequences. We obtained 15,037 bp of mitochondrial genome using Illumina sequencing and identified the non-coding AT-rich region or control region (354 bp, AT=83.9%) located between trnH and trnR. We found 7 conserved sequence blocks (CSB), scattered throughout the control region of L. satsuma and other taxa of Annelida. The poly-TA stretches, which commonly form the stem of multiple stem-loop structures, are most conserved in the CSB-I and CSB-II regions. The mitochondrial genome of L. satsuma encodes a unique repetitive sequence in the control region, which forms a unique secondary structure in comparison to Lamellibrachia luymesi. Phylogenetic analyses of all protein-coding genes indicate that L. satsuma forms a monophyletic clade with L. luymesi along with other tubeworms found in cold-seep regions (genera: Lamellibrachia, Escarpia, and Seepiophila). In general, the control region sequences of Annelida could be aligned with certainty within each genus, and to some extent within the family, but with a higher rate of variation in conserved regions.
authors.affiliation: Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Ansan 426-744, Republic of Korea; Department of Marine Biotechnology, Korea University of Science and Technology, Daejeon 305-333, Republic of Korea. Electronic address: patraajitkumar@gmail.com.
authors.forename: Ajit Kumar
authors.initials: AK
authors.lastname: Patra
authors.affiliation: Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Ansan 426-744, Republic of Korea. Electronic address: jichi9@kiost.ac.kr.
authors.forename: Yong Min
authors.initials: YM
authors.lastname: Kwon
authors.affiliation: Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Ansan 426-744, Republic of Korea; Department of Marine Biotechnology, Korea University of Science and Technology, Daejeon 305-333, Republic of Korea. Electronic address: sgkang@kiost.ac.kr.
authors.forename: Sung Gyun
authors.initials: SG
authors.lastname: Kang
authors.affiliation: Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka 237-0061, Japan. Electronic address: fujiwara@jamstec.go.jp.
authors.forename: Yoshihiro
authors.initials: Y
authors.lastname: Fujiwara
authors.affiliation: Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Ansan 426-744, Republic of Korea; Department of Marine Biotechnology, Korea University of Science and Technology, Daejeon 305-333, Republic of Korea; National Marine Biodiversity Institute of Korea, Seocheon 325-902, Republic of Korea. Electronic address: s-jkim@kiost.ac.kr.
authors.forename: Sang-Jin
authors.initials: SJ
authors.lastname: Kim
mesh_terms: D000818:Animals; D001483:Base Sequence; D003062:Codon; D004247:DNA / Q000235:genetics; D005786:Gene Expression Regulation / Q000502:physiology*; D054629:Genome, Mitochondrial / Q000235:genetics*; D010802:Phylogeny; D011077:Polychaeta / Q000145:classification / Q000235:genetics*; D012335:RNA, Ribosomal / Q000235:genetics; D012343:RNA, Transfer / Q000235:genetics
chemical_list: D003062:Codon; D012335:RNA, Ribosomal; D004247:DNA; D012343:RNA, Transfer
keywords: Control region; Lamellibrachia; Mitochondria; Phylogeny; Tubeworm