http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–3 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2015.1007329
MITOGENOME ANNOUNCEMENT
The complete mitogenome of the freshwater fairy shrimp Streptocephalus sirindhornae (Crustacea: Anostraca: Streptocephalidae) Xue-Chen Liu1, Hua-Wei Li2, Usuma Jermnak3, and Jin-Shu Yang1 1
Mitochondrial DNA Downloaded from informahealthcare.com by McMaster University on 03/02/15 For personal use only.
Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, PR China, 2School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, PR China, and 3 Department of Pharmacology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand Abstract
Keywords
In this study, we amplified, sequenced and analyzed the complete mitogenome of the freshwater fairy shrimp Streptocephalus sirindhornae (Crustacea: Anostraca: Streptocephalidae). The full-length of the S. sirindhornae mitogenome is a circular molecule of 16,887 bp in size with an A + T content of 64.5%. It has the largest putative control region (2794 bp) with the lowest A + T content (62.6%) for all determined branchiopod mitogenomes. The genome consisted of 37 genes that are involved in the respiration chain as well as the mitochondrial translation system. The S. sirindhornae mitogenome exhibits an identical gene arrangement as the Artemia pattern, which shows translocation and inversion of two transfer-RNA genes compared to the pancrustacean ancestral pattern. This is by far the first determined mitogenome of a freshwater fairy shrimp. The results of our study will provide significant data for reconstructing the consensus Branchiopoda tree of life.
Anostraca, mitochondrial genome, Streptocephalidae, Streptocephalus sirindhornae
Streptocephalus sirindhornae, the first freshwater anostracan from Thailand, is wide-spread in the northeast of the country where it is remarkably distributed in episodic waters (Sanoamuang et al., 2000). S. sirindhornae was also found in a dry pond of the southwest China (Sun & Yang, 2008, personal communication). It is regarded as a nutritionally adequate food for postlarvae of the giant freshwater prawn Macrobrachium rosenbergii and can enhance the carotenoid contents in the prawn (Sriputhorn & Sanoamuang, 2011). Resting eggs of the fairy shrimp was obtained from the Applied Taxonomic Research Center, Faculty of Science, Khon Kaen University, Thailand. DNA was extracted from 50 mg of eggs by a conventional proteinase K/phenol/chloroform method. We used versatile primers LCO1490/HCO2198 and 16Sar/16Sbr to amplify partial fragments of the mitogenome. According to the partial sequences, we designed gene-specific primers to amplify two longer mtDNA fragments, and both of them were determined by random sequencing their shot-gun DNA libraries. We assembled, annotated and deposited the mitogenome in GenBank under the accession number KP273593. The full-length of the S. sirindhornae mitogenome is 16,887 bp, composed of 37 genes that encode subunits of respiration-chain complexes as well as structural and functional RNAs in mitochondrion (Figure 1). The total A + T content of the genome is 64.5%, which is typical within the Anostraca (62.3– 71.5%). Its putative control region is 2794 bp in length, that is the Correspondence: Jin-Shu 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 3 January 2015 Accepted 10 January 2015 Published online 19 February 2015
largest within the Branchiopoda (467–1932 bp), A + T content (62.6%) of which is the lowest for all branchiopod mitogenomes determined to date (64.0–74.6%). There are two major adjacent overlaps between genes: atp8 and atp6 share seven nucleotides, while nad4 and nad4L share eight nucleotides. The 13 proteincoding genes have several forms of start codon: ATG (cob, cox2, cox3, nad1 and nad4), ATT (atp8, nad2, nad3, nad4L and nad6), TTG (cox1 and nad5) and GTG (atp6). TAA (atp6, atp8, nad2 and nad4L)/TAG (nad3) or TA (nad6)/T (cob, cox1–3, nad1, nad4 and nad5) serve as complete or incomplete terminal codons. There are seven mitogenomes that have been determined to date in the class Branchiopoda, and two arranging patterns of mitochondrial genes have been identified. One is shared by four Phyllopoda species (Daphnia pulex, Triops australiensis, T. cancriformis and T. longicaudatus), which is considered as the pancrustacean ancestral pattern (Cook et al., 2005). The S. sirindhornae mitogenome exhibits a mitochondrial gene order identical to the second arrangement that is shared by three Artemia species (Zhang et al., 2013). Compared to the pancrustacean ancestral pattern, in the Artemia + Streptocephalus pattern trnI and trnQ translocated from between the control region and trnM to between trnW and trnC, where trnI underwent an extra inversion from the positive strand to the negative strand. Freshwater fairy shrimps constitute important part of taxonomy of anostracans. Our result is by far the first mitogenome of this lineage. It enriches the extremely imbalanced sampling of not only anostrancan but also branchiopod mitogenomes. More and more information of mtDNA within this elegant taxonomic group is needed to eventually build the consensus Branchiopoda tree of life.
X.-C. Liu et al.
Mitochondrial DNA, Early Online: 1–3
Mitochondrial DNA Downloaded from informahealthcare.com by McMaster University on 03/02/15 For personal use only.
2
Figure 1. Mitochondrial genome of Streptocephalus sirindhornae. Genes blocks are filled with different textures as the cutline shows below. The nucleotide numbering begins from cox1. Clockwise or counterclockwise transcribed genes are located outside or inside the circle, respectively. Inner ring indicates GC contents 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 4L; rrnS and rrnL, small and large subunit rRNAs; trnX, tRNAs, where X indicates the one-letter abbreviation of the corresponding amino acid. OGDRAW generated the original graphical organization, and the final figure was modified manually.
DOI: 10.3109/19401736.2015.1007329
Declaration of interest The authors declare no conflicts of interest. This work was supported by the 863 Program of China (2012AA092103) and the National Natural Sciences Foundation of China (41376133).
References
Mitochondrial DNA Downloaded from informahealthcare.com by McMaster University on 03/02/15 For personal use only.
Cook CE, Yue QY, Akam M. (2005). Mitochondrial genomes suggest that hexapods and crustaceans are mutually paraphyletic. Proc R Soc B 272:1295–304.
Streptocephalus sirindhornae mitogenome
3
Sanoamuang L, Murugan G, Weekers PHH, Dumont HJ. (2000). Streptocephalus sirindhornae, new species of freshwater fairy shrimp (Anostraca) from Thailand. J Crust Biol 20:559–65. Sriputhorn K, Sanoamuang L. (2011). Fairy shrimp (Streptocephalus sirindhornae) as live feed improve growth and carotenoid contents of giant freshwater prawn Macrobrachium rosenbergii. Int J Zool Res 7: 138–46. Zhang HX, Luo QB, Sun J, Liu F, Wu G, Yu J, Wang WW. (2013). Mitochondrial genome sequences of Artemia tibetiana and Artemia urmiana: Assessing molecular changes for high plateau adaptation. Sci China Life Sci 56:440–52.
MITOGENOME ANNOUNCEMENT
The complete mitogenome of the freshwater fairy shrimp Streptocephalus sirindhornae (Crustacea: Anostraca: Streptocephalidae) Xue-Chen Liu1, Hua-Wei Li2, Usuma Jermnak3, and Jin-Shu Yang1 1
Mitochondrial DNA Downloaded from informahealthcare.com by McMaster University on 03/02/15 For personal use only.
Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, PR China, 2School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, PR China, and 3 Department of Pharmacology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand Abstract
Keywords
In this study, we amplified, sequenced and analyzed the complete mitogenome of the freshwater fairy shrimp Streptocephalus sirindhornae (Crustacea: Anostraca: Streptocephalidae). The full-length of the S. sirindhornae mitogenome is a circular molecule of 16,887 bp in size with an A + T content of 64.5%. It has the largest putative control region (2794 bp) with the lowest A + T content (62.6%) for all determined branchiopod mitogenomes. The genome consisted of 37 genes that are involved in the respiration chain as well as the mitochondrial translation system. The S. sirindhornae mitogenome exhibits an identical gene arrangement as the Artemia pattern, which shows translocation and inversion of two transfer-RNA genes compared to the pancrustacean ancestral pattern. This is by far the first determined mitogenome of a freshwater fairy shrimp. The results of our study will provide significant data for reconstructing the consensus Branchiopoda tree of life.
Anostraca, mitochondrial genome, Streptocephalidae, Streptocephalus sirindhornae
Streptocephalus sirindhornae, the first freshwater anostracan from Thailand, is wide-spread in the northeast of the country where it is remarkably distributed in episodic waters (Sanoamuang et al., 2000). S. sirindhornae was also found in a dry pond of the southwest China (Sun & Yang, 2008, personal communication). It is regarded as a nutritionally adequate food for postlarvae of the giant freshwater prawn Macrobrachium rosenbergii and can enhance the carotenoid contents in the prawn (Sriputhorn & Sanoamuang, 2011). Resting eggs of the fairy shrimp was obtained from the Applied Taxonomic Research Center, Faculty of Science, Khon Kaen University, Thailand. DNA was extracted from 50 mg of eggs by a conventional proteinase K/phenol/chloroform method. We used versatile primers LCO1490/HCO2198 and 16Sar/16Sbr to amplify partial fragments of the mitogenome. According to the partial sequences, we designed gene-specific primers to amplify two longer mtDNA fragments, and both of them were determined by random sequencing their shot-gun DNA libraries. We assembled, annotated and deposited the mitogenome in GenBank under the accession number KP273593. The full-length of the S. sirindhornae mitogenome is 16,887 bp, composed of 37 genes that encode subunits of respiration-chain complexes as well as structural and functional RNAs in mitochondrion (Figure 1). The total A + T content of the genome is 64.5%, which is typical within the Anostraca (62.3– 71.5%). Its putative control region is 2794 bp in length, that is the Correspondence: Jin-Shu 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 3 January 2015 Accepted 10 January 2015 Published online 19 February 2015
largest within the Branchiopoda (467–1932 bp), A + T content (62.6%) of which is the lowest for all branchiopod mitogenomes determined to date (64.0–74.6%). There are two major adjacent overlaps between genes: atp8 and atp6 share seven nucleotides, while nad4 and nad4L share eight nucleotides. The 13 proteincoding genes have several forms of start codon: ATG (cob, cox2, cox3, nad1 and nad4), ATT (atp8, nad2, nad3, nad4L and nad6), TTG (cox1 and nad5) and GTG (atp6). TAA (atp6, atp8, nad2 and nad4L)/TAG (nad3) or TA (nad6)/T (cob, cox1–3, nad1, nad4 and nad5) serve as complete or incomplete terminal codons. There are seven mitogenomes that have been determined to date in the class Branchiopoda, and two arranging patterns of mitochondrial genes have been identified. One is shared by four Phyllopoda species (Daphnia pulex, Triops australiensis, T. cancriformis and T. longicaudatus), which is considered as the pancrustacean ancestral pattern (Cook et al., 2005). The S. sirindhornae mitogenome exhibits a mitochondrial gene order identical to the second arrangement that is shared by three Artemia species (Zhang et al., 2013). Compared to the pancrustacean ancestral pattern, in the Artemia + Streptocephalus pattern trnI and trnQ translocated from between the control region and trnM to between trnW and trnC, where trnI underwent an extra inversion from the positive strand to the negative strand. Freshwater fairy shrimps constitute important part of taxonomy of anostracans. Our result is by far the first mitogenome of this lineage. It enriches the extremely imbalanced sampling of not only anostrancan but also branchiopod mitogenomes. More and more information of mtDNA within this elegant taxonomic group is needed to eventually build the consensus Branchiopoda tree of life.
X.-C. Liu et al.
Mitochondrial DNA, Early Online: 1–3
Mitochondrial DNA Downloaded from informahealthcare.com by McMaster University on 03/02/15 For personal use only.
2
Figure 1. Mitochondrial genome of Streptocephalus sirindhornae. Genes blocks are filled with different textures as the cutline shows below. The nucleotide numbering begins from cox1. Clockwise or counterclockwise transcribed genes are located outside or inside the circle, respectively. Inner ring indicates GC contents 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 4L; rrnS and rrnL, small and large subunit rRNAs; trnX, tRNAs, where X indicates the one-letter abbreviation of the corresponding amino acid. OGDRAW generated the original graphical organization, and the final figure was modified manually.
DOI: 10.3109/19401736.2015.1007329
Declaration of interest The authors declare no conflicts of interest. This work was supported by the 863 Program of China (2012AA092103) and the National Natural Sciences Foundation of China (41376133).
References
Mitochondrial DNA Downloaded from informahealthcare.com by McMaster University on 03/02/15 For personal use only.
Cook CE, Yue QY, Akam M. (2005). Mitochondrial genomes suggest that hexapods and crustaceans are mutually paraphyletic. Proc R Soc B 272:1295–304.
Streptocephalus sirindhornae mitogenome
3
Sanoamuang L, Murugan G, Weekers PHH, Dumont HJ. (2000). Streptocephalus sirindhornae, new species of freshwater fairy shrimp (Anostraca) from Thailand. J Crust Biol 20:559–65. Sriputhorn K, Sanoamuang L. (2011). Fairy shrimp (Streptocephalus sirindhornae) as live feed improve growth and carotenoid contents of giant freshwater prawn Macrobrachium rosenbergii. Int J Zool Res 7: 138–46. Zhang HX, Luo QB, Sun J, Liu F, Wu G, Yu J, Wang WW. (2013). Mitochondrial genome sequences of Artemia tibetiana and Artemia urmiana: Assessing molecular changes for high plateau adaptation. Sci China Life Sci 56:440–52.
