http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.963804
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Hyriopsis cumingii (Unionoida: Unionidae): genome description and related phylogenetic analyses Min Wei1, Shoubao Yang2, Peng Yu1, and Quan Wan1 College of Animal Science and Technology, Anhui Agricultural University, Hefei, P.R. China and 2College of Life Sciences, Shaoxing University, Shaoxing, P.R. China
Mitochondrial DNA Downloaded from informahealthcare.com by Lakehead University on 03/14/15 For personal use only.
1
Abstract
Keywords
Hyriopsis cumingii is a freshwater pearl mussel in china, easily identified by a big sail-like bulging at back edge of the mussel. In the present study, we reported the complete mitochondrial genome of H. cumingii. It was 16,958 bp in length, and it contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes. Besides, we conducted alignment with other two different individuals of H. cumingii and phylogenetic analysis with closely related species.
Hyriopsis cumingii, mitochondrial genome, phylogenetic analyses, sequencing
Hyriopsis cumingii is a freshwater pearl mussel in China, easily identified by a big sail-like bulging at back edge of the mussel. It was mostly found in shallow lakes and rivers with muddy bottom in the provinces of Hunan, Hubei, Anhui, Zhejiang, Jiangxi and Jiangsu in China, and it contributed over 95% of total freshwater pearl production in China. In recent years, the pearl production increased, while the quality of cultured freshwater pearl was getting worse. Consequently, it was necessary to determine the complete mitochondrial genome of H. cumingii and identify its phylogenetic relationships for Selective Breeding of fine varieties. The two different individuals of the same species were designated HC2010-M (HM347668) and HC2008-F (NC-011763), respectively. All data were analyzed by DNASTAR 7.10 software (Madison, WI) and the phylogenetic tree was constructed by Mega 5.0 software (Tempe, AZ). The M-shape complete mitochondrial genome of H. cumingii (designated AAU-HC2014-M) was 16,958 bp in length, submitted in GenBank database with the accession number KM393224. It consisted of 13 protein-coding genes (ND2, ND3, CYTB, ND5, ND1, ND6, ND4, ND4L, ATP8, ATP6, COX3, COX1 and COX2), 2 rRNA genes (12S rRNA and 16S rRNA) and 22 tRNA genes (Table 1). The mitochondrial genes order arrangement of H. cumingii was identical to that of Hyriopsis schlegeli, but different from vertebrates and other published freshwater bivalves. It demonstrated that the mitochondrial genes order arrangement of invertebrates was not conservative (Wolstenholme, 1992). Besides, most of the tRNA genes and two rRNA genes were encoded on the light strand (L-strand)
History Received 1 September 2014 Accepted 7 September 2014 Published online 25 September 2014
except for tRNAAsp and tRNAHis genes, but most of the proteincoding genes were encoded on the heavy strand (H-strand) with the exception of ND2, ND1, CYTB and ND6 (Table 1), which also differed from that of vertebrates. Only four overlaps were observed between: ND2-tRNAMet, tRNATyr-16S rRNA, tRNAProCYTB and ND4-ND4L, sharing 1, 2, 9 and 8 bp, respectively. After alignment, 17 variable sites (14 base substitutions and 3 indels) were determined between AAU-HC2014-M and HC2010M, accounting for 0.11% of the complete mitogenome sites, and these base substitutions were distributed in five protein-coding genes (CYTB, ND5, ND1, COX3 and COX2) and non-coding intergenic spacers. Besides, 3 indels were also observed in noncoding intergenic spacers. In comparation with HC2008-F, 577 variable sites (including 536 substitutions and 41 indels) were observed, accounting for 3.62% of the complete mitogenome sites. It demonstrated that there was a few of variances between M-shape mussels, while more variances between M-shape and F-shape mussel (Obata et al., 2006). The phylogenetic tree was constructed based on complete mitogenome sequences from H. cumingii (AAU-HC2014-M, HC2010-M and HC2008-F), Cristaria plicata (NC_012716), H. schlegeli (NC_015110), Lampsilis ornata (AY365193), Pyganodon grandis (FJ809755) and Quadrula quadrula (FJ809751) by the maximum parsimony method (Tamura et al., 2011; figure not shown and can be available if request). The result revealed that H. cumingii (AAU-HC2014-M, HC2010-M and HC2008-F) and H. schlegeli are closely related species due to the formation of a monophyletic group with high bootstrap support value.
Correspondence: Quan Wan, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, P.R. China. Tel/Fax: +86 55 65786397. E-mail: [email protected]
2
M. Wei et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Organization of the mitochondrial genome of H. cumingii.
Mitochondrial DNA Downloaded from informahealthcare.com by Lakehead University on 03/14/15 For personal use only.
Position
Size
Codon
Gene
From
To
Nucleotide (bp)
AA
Start
Stop
ND2 tRNAMet ND3 tRNAAla tRNASer(UCA) tRNAGlu tRNATrp tRNAArg 12S rRNA tRNALys tRNAThr tRNATyr 16S rRNA tRNALeu(CUA) tRNAAsn tRNAPro Cyt b tRNAPhe ND5 tRNAGln tRNACys tRNAIle tRNAVal tRNALeu(UUA) ND1 tRNAGly ND6 ND4 ND4L ATP8 tRNAAsp ATP6 COX3 COX1 COX2 tRNAHis tRNASer(UCU)
1 966 1146 1605 1678 1768 2251 2317 2380 3216 3282 3347 3408 4693 4771 4838 4893 6061 6169 8097 8172 8242 8308 8370 8433 9342 9424 9959 11,298 11,615 11,765 11,831 12,547 13,339 14,887 15,663 15,876
966 1031 1502 1669 1741 1831 2312 2378 3212 3281 3342 3409 4691 4755 4835 4901 6047 6133 7896 8160 8235 8305 8369 8432 9329 9402 9912 11,305 11,594 11,764 11,827 12,538 13,326 14,880 15,567 15,726 15,945
966 66 357 65 64 64 62 62 833 66 61 63 1284 63 65 64 1155 73 1728 64 64 64 62 63 897 61 489 1347 297 150 63 708 780 1542 681 64 70
321
ATG
TAG
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Obata M, Kamiya C, Kawamura K, Komaru A. (2006). Sperm mitochondrial DNA transmission to both male and female offspring in the blue mussel Mytilus galloprovincialis. Dev Growth Differ 48: 253–61.
Anti codon CAT
118
ATG
TAG TGC TGA TTC TCA TCG TTT TGT GTA TAG GTT TGG
384
ATT
TAA
575
GTG
TAA
GAA TTG GCA GAT TAC TAA 298
ATC
TAG
162 448 98 49
ATT ATT ATG ATG
TAA TAA TAG TAA
235 259 513 226
ATG ATG TTG ATG
TAA TAG TAG TAG
TCC
GTC
GTG TCT
Intergenic nucleotides 1 114 102 8 26 419 4 1 3 0 4 2 1 15 2 9 13 35 200 11 6 2 0 0 12 21 46 8 20 0 3 8 12 6 95 149
Strand L L H L L L L L L L L L L L L L L L H L L L L L L L L H H H H H H H H H L
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. (2011). MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–9. Wolstenholme DR. (1992). Animal mitochondrial DNA: Structure and evolution. In: Wolstenholme DR, Jeon KW, editors. International review of cytology. Mitochondrial genomes. San Diego: Academic Press. p 173–216.
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Hyriopsis cumingii (Unionoida: Unionidae): genome description and related phylogenetic analyses Min Wei1, Shoubao Yang2, Peng Yu1, and Quan Wan1 College of Animal Science and Technology, Anhui Agricultural University, Hefei, P.R. China and 2College of Life Sciences, Shaoxing University, Shaoxing, P.R. China
Mitochondrial DNA Downloaded from informahealthcare.com by Lakehead University on 03/14/15 For personal use only.
1
Abstract
Keywords
Hyriopsis cumingii is a freshwater pearl mussel in china, easily identified by a big sail-like bulging at back edge of the mussel. In the present study, we reported the complete mitochondrial genome of H. cumingii. It was 16,958 bp in length, and it contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes. Besides, we conducted alignment with other two different individuals of H. cumingii and phylogenetic analysis with closely related species.
Hyriopsis cumingii, mitochondrial genome, phylogenetic analyses, sequencing
Hyriopsis cumingii is a freshwater pearl mussel in China, easily identified by a big sail-like bulging at back edge of the mussel. It was mostly found in shallow lakes and rivers with muddy bottom in the provinces of Hunan, Hubei, Anhui, Zhejiang, Jiangxi and Jiangsu in China, and it contributed over 95% of total freshwater pearl production in China. In recent years, the pearl production increased, while the quality of cultured freshwater pearl was getting worse. Consequently, it was necessary to determine the complete mitochondrial genome of H. cumingii and identify its phylogenetic relationships for Selective Breeding of fine varieties. The two different individuals of the same species were designated HC2010-M (HM347668) and HC2008-F (NC-011763), respectively. All data were analyzed by DNASTAR 7.10 software (Madison, WI) and the phylogenetic tree was constructed by Mega 5.0 software (Tempe, AZ). The M-shape complete mitochondrial genome of H. cumingii (designated AAU-HC2014-M) was 16,958 bp in length, submitted in GenBank database with the accession number KM393224. It consisted of 13 protein-coding genes (ND2, ND3, CYTB, ND5, ND1, ND6, ND4, ND4L, ATP8, ATP6, COX3, COX1 and COX2), 2 rRNA genes (12S rRNA and 16S rRNA) and 22 tRNA genes (Table 1). The mitochondrial genes order arrangement of H. cumingii was identical to that of Hyriopsis schlegeli, but different from vertebrates and other published freshwater bivalves. It demonstrated that the mitochondrial genes order arrangement of invertebrates was not conservative (Wolstenholme, 1992). Besides, most of the tRNA genes and two rRNA genes were encoded on the light strand (L-strand)
History Received 1 September 2014 Accepted 7 September 2014 Published online 25 September 2014
except for tRNAAsp and tRNAHis genes, but most of the proteincoding genes were encoded on the heavy strand (H-strand) with the exception of ND2, ND1, CYTB and ND6 (Table 1), which also differed from that of vertebrates. Only four overlaps were observed between: ND2-tRNAMet, tRNATyr-16S rRNA, tRNAProCYTB and ND4-ND4L, sharing 1, 2, 9 and 8 bp, respectively. After alignment, 17 variable sites (14 base substitutions and 3 indels) were determined between AAU-HC2014-M and HC2010M, accounting for 0.11% of the complete mitogenome sites, and these base substitutions were distributed in five protein-coding genes (CYTB, ND5, ND1, COX3 and COX2) and non-coding intergenic spacers. Besides, 3 indels were also observed in noncoding intergenic spacers. In comparation with HC2008-F, 577 variable sites (including 536 substitutions and 41 indels) were observed, accounting for 3.62% of the complete mitogenome sites. It demonstrated that there was a few of variances between M-shape mussels, while more variances between M-shape and F-shape mussel (Obata et al., 2006). The phylogenetic tree was constructed based on complete mitogenome sequences from H. cumingii (AAU-HC2014-M, HC2010-M and HC2008-F), Cristaria plicata (NC_012716), H. schlegeli (NC_015110), Lampsilis ornata (AY365193), Pyganodon grandis (FJ809755) and Quadrula quadrula (FJ809751) by the maximum parsimony method (Tamura et al., 2011; figure not shown and can be available if request). The result revealed that H. cumingii (AAU-HC2014-M, HC2010-M and HC2008-F) and H. schlegeli are closely related species due to the formation of a monophyletic group with high bootstrap support value.
Correspondence: Quan Wan, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, P.R. China. Tel/Fax: +86 55 65786397. E-mail: [email protected]
2
M. Wei et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Organization of the mitochondrial genome of H. cumingii.
Mitochondrial DNA Downloaded from informahealthcare.com by Lakehead University on 03/14/15 For personal use only.
Position
Size
Codon
Gene
From
To
Nucleotide (bp)
AA
Start
Stop
ND2 tRNAMet ND3 tRNAAla tRNASer(UCA) tRNAGlu tRNATrp tRNAArg 12S rRNA tRNALys tRNAThr tRNATyr 16S rRNA tRNALeu(CUA) tRNAAsn tRNAPro Cyt b tRNAPhe ND5 tRNAGln tRNACys tRNAIle tRNAVal tRNALeu(UUA) ND1 tRNAGly ND6 ND4 ND4L ATP8 tRNAAsp ATP6 COX3 COX1 COX2 tRNAHis tRNASer(UCU)
1 966 1146 1605 1678 1768 2251 2317 2380 3216 3282 3347 3408 4693 4771 4838 4893 6061 6169 8097 8172 8242 8308 8370 8433 9342 9424 9959 11,298 11,615 11,765 11,831 12,547 13,339 14,887 15,663 15,876
966 1031 1502 1669 1741 1831 2312 2378 3212 3281 3342 3409 4691 4755 4835 4901 6047 6133 7896 8160 8235 8305 8369 8432 9329 9402 9912 11,305 11,594 11,764 11,827 12,538 13,326 14,880 15,567 15,726 15,945
966 66 357 65 64 64 62 62 833 66 61 63 1284 63 65 64 1155 73 1728 64 64 64 62 63 897 61 489 1347 297 150 63 708 780 1542 681 64 70
321
ATG
TAG
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Obata M, Kamiya C, Kawamura K, Komaru A. (2006). Sperm mitochondrial DNA transmission to both male and female offspring in the blue mussel Mytilus galloprovincialis. Dev Growth Differ 48: 253–61.
Anti codon CAT
118
ATG
TAG TGC TGA TTC TCA TCG TTT TGT GTA TAG GTT TGG
384
ATT
TAA
575
GTG
TAA
GAA TTG GCA GAT TAC TAA 298
ATC
TAG
162 448 98 49
ATT ATT ATG ATG
TAA TAA TAG TAA
235 259 513 226
ATG ATG TTG ATG
TAA TAG TAG TAG
TCC
GTC
GTG TCT
Intergenic nucleotides 1 114 102 8 26 419 4 1 3 0 4 2 1 15 2 9 13 35 200 11 6 2 0 0 12 21 46 8 20 0 3 8 12 6 95 149
Strand L L H L L L L L L L L L L L L L L L H L L L L L L L L H H H H H H H H H L
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. (2011). MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–9. Wolstenholme DR. (1992). Animal mitochondrial DNA: Structure and evolution. In: Wolstenholme DR, Jeon KW, editors. International review of cytology. Mitochondrial genomes. San Diego: Academic Press. p 173–216.
