http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.905852
MITOGENOME ANNOUNCEMENT
Complete maternal mitochondrial genome of freshwater mussel Anodonta lucida (Bivalvia: Unionidae: Anodontinae) Xue-Lin Song1,2, Shan Ouyang2, Chun-Hua Zhou1,2, and Xiao-Ping Wu1,2 Center for Watershed Ecology, Institute of Life Science, Nanchang University, Nanchang, People’s Republic of China, and 2School of Life Sciences and Food Engineering, Nanchang University, Nanchang, People’s Republic of China
Mitochondrial DNA Downloaded from informahealthcare.com by Universitaet Zuerich on 06/02/14 For personal use only.
1
Abstract
Keywords
The taxonomy of genus Anodonta is rather ambiguous, as it has great variation on the shell shape. Anodonta lucida is an endemic species of freshwater mussel in China, characterized by shining epidermis. The complete maternal mitochondrial genome of freshwater mussel A. lucida was first determined (GenBank accession no. KF667529). The genome is 16,285 bp long with an AT content of 64.02%. All the 37 typical animal mitochondrial genes are found, including 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. The genome also contains 24 unassigned regions, ranking from 1 to 830 bp in length, the largest of which is the putative control region (CR). The base composition of the genome is A (36.32%), G (13.01%), T (27.70%) and C (22.98%). Gene order is identical to other species of Unionidae except Gonideinae.
Anodonta lucida, freshwater mussel, mitochondrial genome
Convergent evolution is pervasive in freshwater mussels, and its shell shape is easily influenced by environmental factors, causing some difficulties in species identification. With great conchological variance, genus Anodonta has much confusion in taxonomy and is treated as one of the thorniest group by mollusk taxonomists. Anodonta lucida (Heude, 1877) is an endemic species of China distributed only in Jiangxi and Hunan province (Hu, 2005). This species has stable genetic character and distinct shining, fuscous epidermis (Simpson, 1900). Doubly uniparental inheritance (DUI) of mitochondrial DNA existing in Unionoida, Mytiloida and Veneroida (Doucet-Beaupre´ et al., 2012) has been confirmed. In DUI, there are two divergent gender-associated mitogenomes: maternal and paternal genome. The complete mitochondrial genome would provide useful information to ascertain the taxonomy of genus Anodonta and contribute to the protection of imperiled species. The specimens were collected alive from Da Yuan reservoir (Jiangxi Province, China), and stored at 80 C. Microscopic examination of gonad tissue was used to determine the mussel gender. The total genomic DNA was extracted from the mantle tissue of female individual, using TIANGEN TIANamp Marine Animals DNA Kit (Tiangen Biotech, Beijing, China). The entire mitogenome was amplified in three overlapping segments according to our previous studies (Huang et al., 2013a). The PCR fragments were sequenced by Sangon Biotech (Shanghai, China) using the primer-walking strategy. The complete maternal mitochondrial genome of A. lucida is 16,285 bp in length, consisting of 13 protein-coding genes,
Correspondence: Xiao-Ping Wu and Chun-Hua Zhou, School of Life Sciences and Food Engineering, Nanchang University, Nanchang, People’s Republic of China. Tel: 86-791-83969531. Fax: 86-79183969531. E-mail: [email protected] (X.-P. Wu); zhouchunhuajx@ hotmail.com (C.-H. Zhou)
History Received 10 March 2014 Accepted 15 March 2014 Published online 4 April 2014
22 tRNA genes, 2 rRNA genes and 1 putative control region (Table 1). The sequence had been deposited in GenBank with an accession number KF667529. The arrangement of the 37 genes is identical to other female freshwater mussels, except for Gonideinae species (e.g. Solenaia oleivora (Huang et al., 2013b)). Two types of mitochondrial gene arrangement have been reported, difference mainly occurring among COII12SrRNA. Anodonta lucida presents the gene order of COIIND3-H-A-S2-S1-E-ND2-M-W-R-12SrRNA, while Gonideinae species presents COII-H-S1-ND2-M-ND3-A-S2-E-W-R12SrRNA. The base composition of the genome was A (36.32%), G (13.01%), T (27.70%) and C (22.98%). The AT content was 64.02%, showing a moderate AT-rich specialty, which conforms to A or T codon preference of invertebrate mitogenome (Brown, 1985). Among the 37 genes, COI, COII, COIII, ND3, tRNAHis, tRNAasp, ND5, ND4, ND4L, ATP6 and ATP8 are encoded on heavy strand, while the rest 26 genes are encoded on light strand (Table 1). There are two overlapping regions, one is 39 bp between ND2 and tRNAMet, the other is 8 bp between ND4 and ND4L. All protein-coding genes start with the orthodox ATG codon, except for COI (TTG), Cob (ATT), ND5 (GTG), ND6 (ATT), ND4 (ATT), ND4L (GTG). All 13 protein-coding genes have the complete stop codon TAA or TAG. The 22 tRNA genes, ranking from 62 to 70 bp in size, have the typical cloverleaf structure. The 12SrRNA is 839 bp long with an A+T content of 63.05%, and 16SrRNA is 1281 bp long with an A+T content of 66.20%. The largest unassigned region (i.e. control region) was located between ND5 and tRNAGln, with the A+T content of 67.47%. The length of the control region (830 bp), by contrast, is slightly longer than other presented Anodonta species (Soroka, 2010; Soroka & Burzynski, 2013).
2
X.-L. Song et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Characteristics of the maternal mitochondrial genome of A. lucida.
Mitochondrial DNA Downloaded from informahealthcare.com by Universitaet Zuerich on 06/02/14 For personal use only.
Gene COI COII ND3 tRNAHis tRNAAla tRNASer tRNASer tRNAGlu ND2 tRNAMet tRNATrp tRNAArg 12SrRNA tRNALys tRNAThr tRNATyr 16SrRNA tRNALeu tRNAAsn tRNAPro Cytb tRNAPhe ND5 CR tRNAGln tRNACys tRNAIle tRNAVal tRNALeu ND1 tRNAGly ND6 ND4 ND4L ATP8 tRNAAsp ATP6 COIII
Strand
From
To
Length
Amino-acids
H H H H L L L 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
1 1566 2259 2670 2840 2911 2977 3053 3441 4404 4515 4580 4644 5483 5545 5614 5677 6958 7035 7105 7171 8322 8424 10,161 10,991 11,065 11,140 11,207 11,271 11,337 12,237 12,319 12,857 14,196 14,493 14,682 14,768 15,489
1542 2246 2615 2733 2905 2974 3046 3120 4442 4472 4579 4643 5482 5544 5607 5676 6957 7023 7102 7170 8319 8389 10,160 10,990 11,060 11,134 11,204 11,270 11,335 12,236 12,298 12,810 14,203 14,492 14,681 14,745 15,469 16,268
1542 681 357 64 66 64 70 68 1002 69 65 64 839 62 63 63 281 66 68 66 1149 68 1737 830 70 70 70 64 65 900 62 492 1347 297 189 64 702 780
513 226 118
Declaration of interest This work is supported by grants from the National Natural Science Foundation of China (No. 31260515) and Leading talent training plan of the GanPo Outstanding Talents 555 Project (18000041), and the Youth Science Foundation of Jiangxi province education department (GJJ13025). The authors report no conflict of interest. The authors alone are responsible for the content and writing of this article.
References Brown WM. (1985). The mitochondrial genome of animals. New York: Plenum Press. Doucet-Beaupre´ H, Blier PU, Chapman EG, Helen P, France D, Bernard ES, Renee SM, et al. (2012). Pyganodon (Bivalvia: Unionoida: Unionidae) phylogenetics: A male- and female-transmitted mitochondrial DNA perspective. Mol Phylogenet Evol 63:430–44. Hu Z-Q. (2005). Geographical distribution of endemic species of Chinese freshwater bivalves. Chin J Zool 40:80–3.
Anti-codon
Start codon
Stop codon
Intergenic nucleotides
TTG ATG ATG
TAG TAA TAA
ATG
TAA
ATT
TAA
GTG
TAG
ATG
TAA
ATT ATT GTG ATG
TAG TAG TAG TAG
ATG ATG
TAA TAA
23 12 54 106 5 2 6 320 39 42 0 0 0 0 6 0 0 11 2 0 2 34 0 0 4 5 2 0 1 0 20 46 8 0 0 22 19 16
GUG UGC UGA UCU UUC 333 CAU UCA TUG UUU UGU GUA UAG GUU UGG 382 GAA 578 UUG UCA GAU UAC UAA 299 UCC 163 448 98 62 GTU 233 259
Huang X-C, Rong J, Liu Y, Zhang M-H, Wan Y, OuYang S, Wu X-P. (2013). The complete maternally and paternally inherited mitochondrial genomes of the endangered freshwater mussel Solenaia carinatus (Bivalvia: Unionidae) and implications for unionidae taxonomy. PLoS One 8:e84352. Huang X-C, Zhou C-H, OuYang S, Wu X-P. (2013). The complete F-type mitochondrial genome of threatened Chinese freshwater mussel Solenaia oleivora (Bivalvia: Unionidae: Gonideinae). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2013.823190. Simpson CT. (1900). Descriptive catalogue of the Naiades, or pearly freshwater mussel. Detroit, MI: The Ann Arbor Press. Soroka M. (2010). Characteristics of mitochondrial DNA of unionid bivalves (Mollusca: Bivalvia: Unionidae). II. Comparison of complete sequences of maternally inherited mitochondrial genomes of Sinanodonta woodiana and Unio pictorum. Folia Malacologica 18(4):189–209. Soroka M, Burzynski A. (2013). Complete female mitochondrial genome of Anodonta anatina (Mollusca: Unionidae): Confirmation of a novel protein-coding gene (F ORF). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2013.823176.
MITOGENOME ANNOUNCEMENT
Complete maternal mitochondrial genome of freshwater mussel Anodonta lucida (Bivalvia: Unionidae: Anodontinae) Xue-Lin Song1,2, Shan Ouyang2, Chun-Hua Zhou1,2, and Xiao-Ping Wu1,2 Center for Watershed Ecology, Institute of Life Science, Nanchang University, Nanchang, People’s Republic of China, and 2School of Life Sciences and Food Engineering, Nanchang University, Nanchang, People’s Republic of China
Mitochondrial DNA Downloaded from informahealthcare.com by Universitaet Zuerich on 06/02/14 For personal use only.
1
Abstract
Keywords
The taxonomy of genus Anodonta is rather ambiguous, as it has great variation on the shell shape. Anodonta lucida is an endemic species of freshwater mussel in China, characterized by shining epidermis. The complete maternal mitochondrial genome of freshwater mussel A. lucida was first determined (GenBank accession no. KF667529). The genome is 16,285 bp long with an AT content of 64.02%. All the 37 typical animal mitochondrial genes are found, including 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. The genome also contains 24 unassigned regions, ranking from 1 to 830 bp in length, the largest of which is the putative control region (CR). The base composition of the genome is A (36.32%), G (13.01%), T (27.70%) and C (22.98%). Gene order is identical to other species of Unionidae except Gonideinae.
Anodonta lucida, freshwater mussel, mitochondrial genome
Convergent evolution is pervasive in freshwater mussels, and its shell shape is easily influenced by environmental factors, causing some difficulties in species identification. With great conchological variance, genus Anodonta has much confusion in taxonomy and is treated as one of the thorniest group by mollusk taxonomists. Anodonta lucida (Heude, 1877) is an endemic species of China distributed only in Jiangxi and Hunan province (Hu, 2005). This species has stable genetic character and distinct shining, fuscous epidermis (Simpson, 1900). Doubly uniparental inheritance (DUI) of mitochondrial DNA existing in Unionoida, Mytiloida and Veneroida (Doucet-Beaupre´ et al., 2012) has been confirmed. In DUI, there are two divergent gender-associated mitogenomes: maternal and paternal genome. The complete mitochondrial genome would provide useful information to ascertain the taxonomy of genus Anodonta and contribute to the protection of imperiled species. The specimens were collected alive from Da Yuan reservoir (Jiangxi Province, China), and stored at 80 C. Microscopic examination of gonad tissue was used to determine the mussel gender. The total genomic DNA was extracted from the mantle tissue of female individual, using TIANGEN TIANamp Marine Animals DNA Kit (Tiangen Biotech, Beijing, China). The entire mitogenome was amplified in three overlapping segments according to our previous studies (Huang et al., 2013a). The PCR fragments were sequenced by Sangon Biotech (Shanghai, China) using the primer-walking strategy. The complete maternal mitochondrial genome of A. lucida is 16,285 bp in length, consisting of 13 protein-coding genes,
Correspondence: Xiao-Ping Wu and Chun-Hua Zhou, School of Life Sciences and Food Engineering, Nanchang University, Nanchang, People’s Republic of China. Tel: 86-791-83969531. Fax: 86-79183969531. E-mail: [email protected] (X.-P. Wu); zhouchunhuajx@ hotmail.com (C.-H. Zhou)
History Received 10 March 2014 Accepted 15 March 2014 Published online 4 April 2014
22 tRNA genes, 2 rRNA genes and 1 putative control region (Table 1). The sequence had been deposited in GenBank with an accession number KF667529. The arrangement of the 37 genes is identical to other female freshwater mussels, except for Gonideinae species (e.g. Solenaia oleivora (Huang et al., 2013b)). Two types of mitochondrial gene arrangement have been reported, difference mainly occurring among COII12SrRNA. Anodonta lucida presents the gene order of COIIND3-H-A-S2-S1-E-ND2-M-W-R-12SrRNA, while Gonideinae species presents COII-H-S1-ND2-M-ND3-A-S2-E-W-R12SrRNA. The base composition of the genome was A (36.32%), G (13.01%), T (27.70%) and C (22.98%). The AT content was 64.02%, showing a moderate AT-rich specialty, which conforms to A or T codon preference of invertebrate mitogenome (Brown, 1985). Among the 37 genes, COI, COII, COIII, ND3, tRNAHis, tRNAasp, ND5, ND4, ND4L, ATP6 and ATP8 are encoded on heavy strand, while the rest 26 genes are encoded on light strand (Table 1). There are two overlapping regions, one is 39 bp between ND2 and tRNAMet, the other is 8 bp between ND4 and ND4L. All protein-coding genes start with the orthodox ATG codon, except for COI (TTG), Cob (ATT), ND5 (GTG), ND6 (ATT), ND4 (ATT), ND4L (GTG). All 13 protein-coding genes have the complete stop codon TAA or TAG. The 22 tRNA genes, ranking from 62 to 70 bp in size, have the typical cloverleaf structure. The 12SrRNA is 839 bp long with an A+T content of 63.05%, and 16SrRNA is 1281 bp long with an A+T content of 66.20%. The largest unassigned region (i.e. control region) was located between ND5 and tRNAGln, with the A+T content of 67.47%. The length of the control region (830 bp), by contrast, is slightly longer than other presented Anodonta species (Soroka, 2010; Soroka & Burzynski, 2013).
2
X.-L. Song et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Characteristics of the maternal mitochondrial genome of A. lucida.
Mitochondrial DNA Downloaded from informahealthcare.com by Universitaet Zuerich on 06/02/14 For personal use only.
Gene COI COII ND3 tRNAHis tRNAAla tRNASer tRNASer tRNAGlu ND2 tRNAMet tRNATrp tRNAArg 12SrRNA tRNALys tRNAThr tRNATyr 16SrRNA tRNALeu tRNAAsn tRNAPro Cytb tRNAPhe ND5 CR tRNAGln tRNACys tRNAIle tRNAVal tRNALeu ND1 tRNAGly ND6 ND4 ND4L ATP8 tRNAAsp ATP6 COIII
Strand
From
To
Length
Amino-acids
H H H H L L L 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
1 1566 2259 2670 2840 2911 2977 3053 3441 4404 4515 4580 4644 5483 5545 5614 5677 6958 7035 7105 7171 8322 8424 10,161 10,991 11,065 11,140 11,207 11,271 11,337 12,237 12,319 12,857 14,196 14,493 14,682 14,768 15,489
1542 2246 2615 2733 2905 2974 3046 3120 4442 4472 4579 4643 5482 5544 5607 5676 6957 7023 7102 7170 8319 8389 10,160 10,990 11,060 11,134 11,204 11,270 11,335 12,236 12,298 12,810 14,203 14,492 14,681 14,745 15,469 16,268
1542 681 357 64 66 64 70 68 1002 69 65 64 839 62 63 63 281 66 68 66 1149 68 1737 830 70 70 70 64 65 900 62 492 1347 297 189 64 702 780
513 226 118
Declaration of interest This work is supported by grants from the National Natural Science Foundation of China (No. 31260515) and Leading talent training plan of the GanPo Outstanding Talents 555 Project (18000041), and the Youth Science Foundation of Jiangxi province education department (GJJ13025). The authors report no conflict of interest. The authors alone are responsible for the content and writing of this article.
References Brown WM. (1985). The mitochondrial genome of animals. New York: Plenum Press. Doucet-Beaupre´ H, Blier PU, Chapman EG, Helen P, France D, Bernard ES, Renee SM, et al. (2012). Pyganodon (Bivalvia: Unionoida: Unionidae) phylogenetics: A male- and female-transmitted mitochondrial DNA perspective. Mol Phylogenet Evol 63:430–44. Hu Z-Q. (2005). Geographical distribution of endemic species of Chinese freshwater bivalves. Chin J Zool 40:80–3.
Anti-codon
Start codon
Stop codon
Intergenic nucleotides
TTG ATG ATG
TAG TAA TAA
ATG
TAA
ATT
TAA
GTG
TAG
ATG
TAA
ATT ATT GTG ATG
TAG TAG TAG TAG
ATG ATG
TAA TAA
23 12 54 106 5 2 6 320 39 42 0 0 0 0 6 0 0 11 2 0 2 34 0 0 4 5 2 0 1 0 20 46 8 0 0 22 19 16
GUG UGC UGA UCU UUC 333 CAU UCA TUG UUU UGU GUA UAG GUU UGG 382 GAA 578 UUG UCA GAU UAC UAA 299 UCC 163 448 98 62 GTU 233 259
Huang X-C, Rong J, Liu Y, Zhang M-H, Wan Y, OuYang S, Wu X-P. (2013). The complete maternally and paternally inherited mitochondrial genomes of the endangered freshwater mussel Solenaia carinatus (Bivalvia: Unionidae) and implications for unionidae taxonomy. PLoS One 8:e84352. Huang X-C, Zhou C-H, OuYang S, Wu X-P. (2013). The complete F-type mitochondrial genome of threatened Chinese freshwater mussel Solenaia oleivora (Bivalvia: Unionidae: Gonideinae). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2013.823190. Simpson CT. (1900). Descriptive catalogue of the Naiades, or pearly freshwater mussel. Detroit, MI: The Ann Arbor Press. Soroka M. (2010). Characteristics of mitochondrial DNA of unionid bivalves (Mollusca: Bivalvia: Unionidae). II. Comparison of complete sequences of maternally inherited mitochondrial genomes of Sinanodonta woodiana and Unio pictorum. Folia Malacologica 18(4):189–209. Soroka M, Burzynski A. (2013). Complete female mitochondrial genome of Anodonta anatina (Mollusca: Unionidae): Confirmation of a novel protein-coding gene (F ORF). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2013.823176.
