http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2015.1046129
MITOGENOME ANNOUNCEMENT
The complete F-type mitochondrial genome of Chinese freshwater mussel Anodonta euscaphys Ting Xue1,2, Meiling Chen1,2, Guiling Wang1,2, Zhenyong Han1,2, and Jiale Li1,2 1
Key Laboratory of Freshwater Aquatic Genetic Resources Certificated by Ministry of Agriculture, Shanghai Ocean University, Shanghai, China and Shanghai Engineering Research Center of Aquaculture, Shanghai, China
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 07/01/15 For personal use only.
2
Abstract
Keywords
Anodonta euscaphys is the endemic species of freshwater mussel in China. The complete F-type mitochondrial genome of the A. euscaphys is amplified and analyzed in this study. It is 15,741 bp in length. The base composition of the genome with A + T bias is 64.78%. There are 24 noncoding regions found throughout the mitogenome of A. euscaphys, ranging in size from 3 to 302 bp, the largest of which was between ND2 and tRNAGlu. The phylogenetic tree based on 22 mitogenome, including 16 F-type freshwater mussels, 2 M-type freshwater mussels and 4 marine mussels were analyzed in our study, the results showed that the F-type and the M-type of the freshwater mussels were clustered respectively, the A. euscaphys was clustered with Anodonta family species firstly, and it was the closest to the Anodonta arcaeformis in our analysis.
Anodonta euscaphys, F-type mitogenome, noncoding region, phylogenetic tree
In animals, mitochondrial DNA is typically transmitted to offspring by the mother alone. The discovery of doubly uniparental inheritance (DUI) of mtDNA in some bivalves challenged the rules of strict maternal inheritance (SMI) (Breton et al., 2007). In species with DUI, two kinds of mitochondrial genomes that came to be known as F-type (Female inherited) and M-type (Male inherited) co-occur in the mtDNA heritance (Zouros, 2013). Anodonta euscaphys is the endemic freshwater mussel species of China, which is only distributed in Heilongjiang, Hebei, Jiangsu and Hunan Provinces in China. In this study, the complete F-type mitochondrial genome of A. euscaphys is firstly determined. The samples were collected from Dianshan Lake, Shanghai, China. The fresh tissues were extracted from the gonad of female adult. Partial sequences of the COI and 16S rRNA genes of A. euscaphys were amplified via PCR using universal primers, and then we designed two primer pairs to amplify fragments with the length of approximately 5 and 10 kb, respectively. The PCR products were sequenced using Shot Gun Sequencing. The sequences obtained were analyzed and combined using BioEdit (Hall, 1999). The location of tRNAs were determined using tRNA scan-SE 1.21 (Schattner et al., 2005).
Correspondence: G.L. Wang, Key Laboratory of Freshwater Aquatic Genetic Resources Certificated by Ministry of Agriculture, College of Fisheries and Life Science, Shanghai Ocean University, No.999, Huchenghuan Road, Nanhui New City, Shanghai 201306, P. R. China. Tel: 86-021-61900436. Fax: 86-021-61900436. E-mail: [email protected]
History Received 23 March 2015 Accepted 26 April 2015 Published online 22 May 2015
The complete F-type mitochondrial genome of A. euscaphys is deposited in GenBank database, with the accession number KP187851. The length of the complete F-type mitochondrial genome of A. euscaphys is 15,741 bp, which consists 13 proteincoding genes, 2 rRNA genes, 22 tRNA genes and 24 noncoding regions. The mitogenome base composition of A + T bias is 64.78%, which was similar to other freshwater mussels. The COICOIII, ND3-ND5, ND4L, ATP6, ATP8, tRNAAsp and tRNAHis of F-type mitogenome were encoded on the heavy strand, whereas the remaining genes were encoded on the light strand. Except for ND4, ND6, ND1 with ATA start codon, the remaining proteincoding genes initiated with the ATG. Two complete stop codons (TAA and TAG) were used in the protein-coding genes. There were 24 noncoding regions found throughout the F-type mitogenome of A. euscaphys, ranged in length from 3 to 302 bp, the largest of which was between ND2 and tRNAGlu, it was similar to freshwater mussel Lamprotula tortuosa (Wang et al., 2013). The phylogenetic trees were constructed using MEGA5.1 software (Tamura et al., 2011) with Maximum Parsimony, Neighbor Joining and Maximum Likelihood methods to analyze the phylogenetic relationship of A. euscaphys, and the results of the three methods were concordant. Maximum Likelihood tree of amino acid sequences for all protein-coding genes in bivalves is shown in Figure 1. The F-type and M-type of the freshwater mussels were clustered respectively, it was consistent with European Mytilus family (San´ko & Burzyn´ski, 2014). The A. euscaphys relative was the closest to the A. arcaeformis, and Anodonta family species clustered firstly, finally clustered together with marine mussels. Compared with the freshwater mussels, the marine mussels did not have ATP8 genes, which might be related to the balance of osmotic pressure in the
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 07/01/15 For personal use only.
2
T. Xue et al.
Mitochondrial DNA, Early Online: 1–2
Figure 1. Maximum likelihood tree of the amino acid sequences of all protein-coding genes in bivalves. The numbers on the nodes show the maximum likelihood bootstrap percentages.
cytoplasm (Helfenbein et al., 2001). This study would provide basic data for genetic and DUI analyses.
Declaration of interest This study was supported by the National Natural Science Foundation of China (31101939), Innovation Program of Shanghai Municipal Education Commission (13ZZ128), and Shanghai Collaborative Innovation Center for Aquatic Animal Genetics and Breeding (ZF1206). The authors report no conflict of interest. The authors alone are responsible for the content and writing of the paper.
References Breton S, Beaupre´ HD, Stewart DT, Hoeh WR, Blier PU. (2007). The unusual system of doubly uniparental inheritance of mtDNA: isn’t one enough? Trends Genetics 23:65–74. Hall TA. (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucl Acids Symp Series 41:95–8.
Helfenbein KG, Brown WM, Boore JL. (2001). The complete mitochondrial genome of the articulate brachiopod Terebratalia transversa. Mol Biol Evol 18:1734–44. San´ko TJ, Burzyn´ski A. (2014). Co-expressed mitochondrial genomes: Recently masculinized, recombinant mitochondrial genome is co-expressed with the female – transmitted mtDNA genome in a male Mytilus trossulus mussel from the Baltic Sea. Bio Med Central Genetics 15:1–10. Schattner P, Brooks AN, Lowe TM. (2005). The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucl Acids Res 33:W686–9. 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. Wang GL, Cao XR, Li JL. (2013). Complete F-type mitochondrial genome of Chinese freshwater mussel Lamprotula tortuosa. Mitochondrial DNA 24:513–15. Zouros E. (2013). Biparental inheritance through uniparental transmission: The doubly uniparental inheritance (DUI) of mitochondrial DNA. Evol Biol 40:1–31.
MITOGENOME ANNOUNCEMENT
The complete F-type mitochondrial genome of Chinese freshwater mussel Anodonta euscaphys Ting Xue1,2, Meiling Chen1,2, Guiling Wang1,2, Zhenyong Han1,2, and Jiale Li1,2 1
Key Laboratory of Freshwater Aquatic Genetic Resources Certificated by Ministry of Agriculture, Shanghai Ocean University, Shanghai, China and Shanghai Engineering Research Center of Aquaculture, Shanghai, China
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 07/01/15 For personal use only.
2
Abstract
Keywords
Anodonta euscaphys is the endemic species of freshwater mussel in China. The complete F-type mitochondrial genome of the A. euscaphys is amplified and analyzed in this study. It is 15,741 bp in length. The base composition of the genome with A + T bias is 64.78%. There are 24 noncoding regions found throughout the mitogenome of A. euscaphys, ranging in size from 3 to 302 bp, the largest of which was between ND2 and tRNAGlu. The phylogenetic tree based on 22 mitogenome, including 16 F-type freshwater mussels, 2 M-type freshwater mussels and 4 marine mussels were analyzed in our study, the results showed that the F-type and the M-type of the freshwater mussels were clustered respectively, the A. euscaphys was clustered with Anodonta family species firstly, and it was the closest to the Anodonta arcaeformis in our analysis.
Anodonta euscaphys, F-type mitogenome, noncoding region, phylogenetic tree
In animals, mitochondrial DNA is typically transmitted to offspring by the mother alone. The discovery of doubly uniparental inheritance (DUI) of mtDNA in some bivalves challenged the rules of strict maternal inheritance (SMI) (Breton et al., 2007). In species with DUI, two kinds of mitochondrial genomes that came to be known as F-type (Female inherited) and M-type (Male inherited) co-occur in the mtDNA heritance (Zouros, 2013). Anodonta euscaphys is the endemic freshwater mussel species of China, which is only distributed in Heilongjiang, Hebei, Jiangsu and Hunan Provinces in China. In this study, the complete F-type mitochondrial genome of A. euscaphys is firstly determined. The samples were collected from Dianshan Lake, Shanghai, China. The fresh tissues were extracted from the gonad of female adult. Partial sequences of the COI and 16S rRNA genes of A. euscaphys were amplified via PCR using universal primers, and then we designed two primer pairs to amplify fragments with the length of approximately 5 and 10 kb, respectively. The PCR products were sequenced using Shot Gun Sequencing. The sequences obtained were analyzed and combined using BioEdit (Hall, 1999). The location of tRNAs were determined using tRNA scan-SE 1.21 (Schattner et al., 2005).
Correspondence: G.L. Wang, Key Laboratory of Freshwater Aquatic Genetic Resources Certificated by Ministry of Agriculture, College of Fisheries and Life Science, Shanghai Ocean University, No.999, Huchenghuan Road, Nanhui New City, Shanghai 201306, P. R. China. Tel: 86-021-61900436. Fax: 86-021-61900436. E-mail: [email protected]
History Received 23 March 2015 Accepted 26 April 2015 Published online 22 May 2015
The complete F-type mitochondrial genome of A. euscaphys is deposited in GenBank database, with the accession number KP187851. The length of the complete F-type mitochondrial genome of A. euscaphys is 15,741 bp, which consists 13 proteincoding genes, 2 rRNA genes, 22 tRNA genes and 24 noncoding regions. The mitogenome base composition of A + T bias is 64.78%, which was similar to other freshwater mussels. The COICOIII, ND3-ND5, ND4L, ATP6, ATP8, tRNAAsp and tRNAHis of F-type mitogenome were encoded on the heavy strand, whereas the remaining genes were encoded on the light strand. Except for ND4, ND6, ND1 with ATA start codon, the remaining proteincoding genes initiated with the ATG. Two complete stop codons (TAA and TAG) were used in the protein-coding genes. There were 24 noncoding regions found throughout the F-type mitogenome of A. euscaphys, ranged in length from 3 to 302 bp, the largest of which was between ND2 and tRNAGlu, it was similar to freshwater mussel Lamprotula tortuosa (Wang et al., 2013). The phylogenetic trees were constructed using MEGA5.1 software (Tamura et al., 2011) with Maximum Parsimony, Neighbor Joining and Maximum Likelihood methods to analyze the phylogenetic relationship of A. euscaphys, and the results of the three methods were concordant. Maximum Likelihood tree of amino acid sequences for all protein-coding genes in bivalves is shown in Figure 1. The F-type and M-type of the freshwater mussels were clustered respectively, it was consistent with European Mytilus family (San´ko & Burzyn´ski, 2014). The A. euscaphys relative was the closest to the A. arcaeformis, and Anodonta family species clustered firstly, finally clustered together with marine mussels. Compared with the freshwater mussels, the marine mussels did not have ATP8 genes, which might be related to the balance of osmotic pressure in the
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 07/01/15 For personal use only.
2
T. Xue et al.
Mitochondrial DNA, Early Online: 1–2
Figure 1. Maximum likelihood tree of the amino acid sequences of all protein-coding genes in bivalves. The numbers on the nodes show the maximum likelihood bootstrap percentages.
cytoplasm (Helfenbein et al., 2001). This study would provide basic data for genetic and DUI analyses.
Declaration of interest This study was supported by the National Natural Science Foundation of China (31101939), Innovation Program of Shanghai Municipal Education Commission (13ZZ128), and Shanghai Collaborative Innovation Center for Aquatic Animal Genetics and Breeding (ZF1206). The authors report no conflict of interest. The authors alone are responsible for the content and writing of the paper.
References Breton S, Beaupre´ HD, Stewart DT, Hoeh WR, Blier PU. (2007). The unusual system of doubly uniparental inheritance of mtDNA: isn’t one enough? Trends Genetics 23:65–74. Hall TA. (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucl Acids Symp Series 41:95–8.
Helfenbein KG, Brown WM, Boore JL. (2001). The complete mitochondrial genome of the articulate brachiopod Terebratalia transversa. Mol Biol Evol 18:1734–44. San´ko TJ, Burzyn´ski A. (2014). Co-expressed mitochondrial genomes: Recently masculinized, recombinant mitochondrial genome is co-expressed with the female – transmitted mtDNA genome in a male Mytilus trossulus mussel from the Baltic Sea. Bio Med Central Genetics 15:1–10. Schattner P, Brooks AN, Lowe TM. (2005). The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucl Acids Res 33:W686–9. 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. Wang GL, Cao XR, Li JL. (2013). Complete F-type mitochondrial genome of Chinese freshwater mussel Lamprotula tortuosa. Mitochondrial DNA 24:513–15. Zouros E. (2013). Biparental inheritance through uniparental transmission: The doubly uniparental inheritance (DUI) of mitochondrial DNA. Evol Biol 40:1–31.
