http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–3 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2015.1007291
MITOGENOME ANNOUNCEMENT
The complete mitogenome of the Atlantic hydrothermal vent shrimp Rimicaris exoculata Williams & Rona 1986 (Crustacea: Decapoda: Alvinocarididae) Yan-Qin Yu1,2, Xiao-Li Liu1, Hua-Wei Li3, Bo Lu4, Yu-Peng Fan1, and Jin-Shu Yang1
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 02/10/15 For personal use only.
1
Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, PR China, 2Department of Clinical Laboratory, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, PR China, 3School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, PR China, and 4Second Institute of Oceanography, State Oceanic Administration, Hangzhou, Zhejiang, PR China Abstract
Keywords
In this study we completely determined and analyzed the mitochondrial genome of the Mid-Atlantic Ridge hydrothermal-vent shrimp Rimicaris exoculata (Crustacea: Decapoda: Alvinocarididae). The circular molecule is 15,902 bp in size with an AT content of 65.7%, composed of the same 37 mitochondrial genes as in all other known metazoan mitogenomes. Sequence composition of the R. exoculata mitogenome is exceptionally similar to that of its Indian-Ocean congener R. kairei, which suggests the fact that they might diverge at a quite recent age. The genome exhibits an ancestral pancrustacean arrangement of mitochondrial genes that presents only the translocation/inversion of trnL-UUR from the ancestral arthropod pattern. Determination of the R. exoculata mitogenome can help to resolve the consensus Decapoda tree of life. It also provides more genetic information available for phylogenetics as well as population genetics on this extensively studied species from hydrothermal vents.
Alvinocarididae, caridea, mitochondrial genome, Rimicaris exoculata
The alvinocarid shrimp Rimicaris exoculata is one of the most extensively investigated organisms from hydrothermal vents. Since its discovery at the Mid-Atlantic Ridge (Williams & Rona, 1986), at present it has two congeners: R. kairei (Watabe & Hashimoto, 2002) and R. hybisae (Nye et al., 2012) from the Central Indian Ridge and Caribbean, respectively. Although the mitochondrial gene fragment cox1 is widely used for systematic as well as biogeographic analyses of R. exoculata, no attempt to sequence its mitochondrial genome has been made to date. In this study we determined the complete sequence of the R. exoculata mitogenome and performed comparative analyses of its composition and arrangement. The shrimp was collected at the South Mid-Atlantic Ridge (SMAR) on 4 June 2011 during the cruise DY115-22V-SMARS024-TVG05 (15 S, 13 W, 2,741 m). The sample was stored in 80 C until required. We extracted DNA from abdominal muscle of one individual using the proteinase K/phenol/chloroform method. Partial fragments were amplified using the universal primer combinations LCO1490/HCO2198 and 16Sar/16Sbr. Two larger fragments were amplified by gene-specific primer designed according to the short sequences and subjected to random sequencing of shot-gun DNA libraries. Finally, the mitogenome was assembled, annotated, analyzed and deposited in GenBank under the accession number KP284529.
Correspondence: J. -S. Yang, Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, PR China. Tel: +86571-8820-6155. Fax: +86-571-8827-3176. E-mail: [email protected]
History Received 19 December 2014 Revised 19 December 2014 Accepted 30 December 2014 Published online 10 February 2015
The R. exoculata mitogenome is quite similar to that of its Indian-Ocean congener R. kairei (Yang et al., 2013). It is a circular molecule of 15,902 bp in size with an AT content of 65.7%. For R. kairei, the values are 15,900 bp and 65.8%. The sequence similarity between the two Rimicaris mitogenomes is as high as 98.0%. Furthermore, all parts of the two genomes (separate genes and control regions) show 93.8–100% identities. Their exceptionally close relationship indicates that they might diverge at a very recent age, even considering the fact that the Alvinocarididae itself has a quite short evolutionary history of 51.5–69.7 Ma (Yang et al., 2013). The R. exoculata mitogenome is composed of 37 genes encoding respiration-chain complexes as well as mitochondrial RNAs as in all other known metazoan mitogenomes (Figure 1). Of all 13 protein-coding genes, seven genes use ATG, four use ATT, one uses ACG, and one uses ATC as start codons. Stop condons appear as the complete TAA (six genes) and TAG (3), or the incomplete T (4) that can be completed by adding two 30 -A residues posttranscriptionally. The arrangement of the R. exoculata mitogenome exhibits an ancestral pancrustacean pattern (Cook et al., 2005) that is shared by all caridean mitogenomes determined to date. Compared to the ancestral arthropod arrangement, this pattern presents the trnLUUR translocation/inversion from between trnL-CUN and nad1 on the minus strand to between cox1 and cox2 on the plus strand, which is considered as a parsimonious event within pancrustaceans (Cook et al., 2005). Determination of the R. exoculata mitogenome not only helps us to finally reconstruct the consensus Decapoda tree of life, but also provides more genetic information available for
Y.-Q. Yu et al.
Mitochondrial DNA, Early Online: 1–3
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 02/10/15 For personal use only.
2
Figure 1. The Rimicaris exoculata mitogenome. Genes blocks are filled as the cutline shows below. Numbers in parentheses indicate nucleotides starting from cox1. Clockwise or counterclockwise transcribed genes reside outside or inside the circle, respectively. Inner ring shows the GC content graph of the mitogenome. Gene abbreviations: atp6 and atp8, ATP synthase subunits 6 and 8; cob, cytochrome b; cox1–3, cytochrome c oxidase subunits 1–3; nad1–6 and nad4L, NADH dehydrogenase subunits 1–6 and 4 L; rrnS and rrnL, small and large subunit rRNAs; trnX, tRNAs (X is the one-letter abbreviation of the corresponding amino acid). We used OGDRAW (Lohse et al., 2007) to generate the original graphical organization and later modified manually.
phylogenetics as well as population genetics on this hot-spot species from hydrothermal vents.
Declaration of interest This work was supported by the 863 Program of China (2012AA092103), the National Natural Sciences Foundation of China (41376133), and the
Natural Science Foundation of Zhejiang Province (LQ14H040005). The authors declare no conflicts of interest.
References Cook CE, Yue QY, Akam M. (2005). Mitochondrial genomes suggest that hexapods and crustaceans are mutually paraphyletic. Proc R Soc B 272:1295–304.
DOI: 10.3109/19401736.2015.1007291
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 02/10/15 For personal use only.
Lohse M, Drechsel O, Bock R. (2007). OrganellarGenomeDRAW (OGDRAW) - a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Curr Genet 52:267–74. Nye V, Copley J, Plouviez S. (2012). A new species of Rimicaris (Crustacea: Decapoda: Caridea: Alvinocarididae) from hydrothermal vent fields on the Mid-Cayman Spreading Centre, Caribbean. J Mar Biol Assoc UK 92:1057–72. Watabe H, Hashimoto J. (2002). A new species of the genus Rimicaris (Alvinocarididae: Caridea: Decapoda) from the active hydrothermal
The Rimicaris exoculata mitogenome
3
vent field, ‘‘Kairei Field’’, on the Central Indian Ridge, the Indian Ocean. Zool Sci 19:1167–74. Williams AB, Rona PA. (1986). Two new caridean shrimps (Bresiliidae) from a hydrothermal field on the Mid-Atlantic Ridge. J Crust Biol 6:446–62. Yang JS, Lu B, Chen DF, Yu YQ, Yang F, Nagasawa H, Tsuchida S, et al. (2013). When did decapods invade hydrothermal vents? Clues from the Western Pacific and Indian Oceans. Mol Biol Evol 30: 305–9.
MITOGENOME ANNOUNCEMENT
The complete mitogenome of the Atlantic hydrothermal vent shrimp Rimicaris exoculata Williams & Rona 1986 (Crustacea: Decapoda: Alvinocarididae) Yan-Qin Yu1,2, Xiao-Li Liu1, Hua-Wei Li3, Bo Lu4, Yu-Peng Fan1, and Jin-Shu Yang1
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 02/10/15 For personal use only.
1
Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, PR China, 2Department of Clinical Laboratory, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, PR China, 3School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, PR China, and 4Second Institute of Oceanography, State Oceanic Administration, Hangzhou, Zhejiang, PR China Abstract
Keywords
In this study we completely determined and analyzed the mitochondrial genome of the Mid-Atlantic Ridge hydrothermal-vent shrimp Rimicaris exoculata (Crustacea: Decapoda: Alvinocarididae). The circular molecule is 15,902 bp in size with an AT content of 65.7%, composed of the same 37 mitochondrial genes as in all other known metazoan mitogenomes. Sequence composition of the R. exoculata mitogenome is exceptionally similar to that of its Indian-Ocean congener R. kairei, which suggests the fact that they might diverge at a quite recent age. The genome exhibits an ancestral pancrustacean arrangement of mitochondrial genes that presents only the translocation/inversion of trnL-UUR from the ancestral arthropod pattern. Determination of the R. exoculata mitogenome can help to resolve the consensus Decapoda tree of life. It also provides more genetic information available for phylogenetics as well as population genetics on this extensively studied species from hydrothermal vents.
Alvinocarididae, caridea, mitochondrial genome, Rimicaris exoculata
The alvinocarid shrimp Rimicaris exoculata is one of the most extensively investigated organisms from hydrothermal vents. Since its discovery at the Mid-Atlantic Ridge (Williams & Rona, 1986), at present it has two congeners: R. kairei (Watabe & Hashimoto, 2002) and R. hybisae (Nye et al., 2012) from the Central Indian Ridge and Caribbean, respectively. Although the mitochondrial gene fragment cox1 is widely used for systematic as well as biogeographic analyses of R. exoculata, no attempt to sequence its mitochondrial genome has been made to date. In this study we determined the complete sequence of the R. exoculata mitogenome and performed comparative analyses of its composition and arrangement. The shrimp was collected at the South Mid-Atlantic Ridge (SMAR) on 4 June 2011 during the cruise DY115-22V-SMARS024-TVG05 (15 S, 13 W, 2,741 m). The sample was stored in 80 C until required. We extracted DNA from abdominal muscle of one individual using the proteinase K/phenol/chloroform method. Partial fragments were amplified using the universal primer combinations LCO1490/HCO2198 and 16Sar/16Sbr. Two larger fragments were amplified by gene-specific primer designed according to the short sequences and subjected to random sequencing of shot-gun DNA libraries. Finally, the mitogenome was assembled, annotated, analyzed and deposited in GenBank under the accession number KP284529.
Correspondence: J. -S. Yang, Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, PR China. Tel: +86571-8820-6155. Fax: +86-571-8827-3176. E-mail: [email protected]
History Received 19 December 2014 Revised 19 December 2014 Accepted 30 December 2014 Published online 10 February 2015
The R. exoculata mitogenome is quite similar to that of its Indian-Ocean congener R. kairei (Yang et al., 2013). It is a circular molecule of 15,902 bp in size with an AT content of 65.7%. For R. kairei, the values are 15,900 bp and 65.8%. The sequence similarity between the two Rimicaris mitogenomes is as high as 98.0%. Furthermore, all parts of the two genomes (separate genes and control regions) show 93.8–100% identities. Their exceptionally close relationship indicates that they might diverge at a very recent age, even considering the fact that the Alvinocarididae itself has a quite short evolutionary history of 51.5–69.7 Ma (Yang et al., 2013). The R. exoculata mitogenome is composed of 37 genes encoding respiration-chain complexes as well as mitochondrial RNAs as in all other known metazoan mitogenomes (Figure 1). Of all 13 protein-coding genes, seven genes use ATG, four use ATT, one uses ACG, and one uses ATC as start codons. Stop condons appear as the complete TAA (six genes) and TAG (3), or the incomplete T (4) that can be completed by adding two 30 -A residues posttranscriptionally. The arrangement of the R. exoculata mitogenome exhibits an ancestral pancrustacean pattern (Cook et al., 2005) that is shared by all caridean mitogenomes determined to date. Compared to the ancestral arthropod arrangement, this pattern presents the trnLUUR translocation/inversion from between trnL-CUN and nad1 on the minus strand to between cox1 and cox2 on the plus strand, which is considered as a parsimonious event within pancrustaceans (Cook et al., 2005). Determination of the R. exoculata mitogenome not only helps us to finally reconstruct the consensus Decapoda tree of life, but also provides more genetic information available for
Y.-Q. Yu et al.
Mitochondrial DNA, Early Online: 1–3
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 02/10/15 For personal use only.
2
Figure 1. The Rimicaris exoculata mitogenome. Genes blocks are filled as the cutline shows below. Numbers in parentheses indicate nucleotides starting from cox1. Clockwise or counterclockwise transcribed genes reside outside or inside the circle, respectively. Inner ring shows the GC content graph of the mitogenome. Gene abbreviations: atp6 and atp8, ATP synthase subunits 6 and 8; cob, cytochrome b; cox1–3, cytochrome c oxidase subunits 1–3; nad1–6 and nad4L, NADH dehydrogenase subunits 1–6 and 4 L; rrnS and rrnL, small and large subunit rRNAs; trnX, tRNAs (X is the one-letter abbreviation of the corresponding amino acid). We used OGDRAW (Lohse et al., 2007) to generate the original graphical organization and later modified manually.
phylogenetics as well as population genetics on this hot-spot species from hydrothermal vents.
Declaration of interest This work was supported by the 863 Program of China (2012AA092103), the National Natural Sciences Foundation of China (41376133), and the
Natural Science Foundation of Zhejiang Province (LQ14H040005). The authors declare no conflicts of interest.
References Cook CE, Yue QY, Akam M. (2005). Mitochondrial genomes suggest that hexapods and crustaceans are mutually paraphyletic. Proc R Soc B 272:1295–304.
DOI: 10.3109/19401736.2015.1007291
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 02/10/15 For personal use only.
Lohse M, Drechsel O, Bock R. (2007). OrganellarGenomeDRAW (OGDRAW) - a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Curr Genet 52:267–74. Nye V, Copley J, Plouviez S. (2012). A new species of Rimicaris (Crustacea: Decapoda: Caridea: Alvinocarididae) from hydrothermal vent fields on the Mid-Cayman Spreading Centre, Caribbean. J Mar Biol Assoc UK 92:1057–72. Watabe H, Hashimoto J. (2002). A new species of the genus Rimicaris (Alvinocarididae: Caridea: Decapoda) from the active hydrothermal
The Rimicaris exoculata mitogenome
3
vent field, ‘‘Kairei Field’’, on the Central Indian Ridge, the Indian Ocean. Zool Sci 19:1167–74. Williams AB, Rona PA. (1986). Two new caridean shrimps (Bresiliidae) from a hydrothermal field on the Mid-Atlantic Ridge. J Crust Biol 6:446–62. Yang JS, Lu B, Chen DF, Yu YQ, Yang F, Nagasawa H, Tsuchida S, et al. (2013). When did decapods invade hydrothermal vents? Clues from the Western Pacific and Indian Oceans. Mol Biol Evol 30: 305–9.
