http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2015.1038802
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of the Trichogaster microlepis (Anabantoidei: Osphronemidae) Haiyan Yan, Xin Li, Lei Zhang, and Liu Jing
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 06/08/15 For personal use only.
Xijing Hospital, The Fourth Military Medical University, Xi’an, P.R. China
Abstract
Keywords
The complete mitochondrial genome of Trichogaster microlepis was determined in this study. It is 16,435 bp in size and consists of 2 rRNA genes, 13 protein-coding genes, 22 tRNA genes and a non-coding control region (D-loop). The overall base composition of the heavy strand of the T. microlepis mitochondrial genome is A: 29.50%, T: 28.38%, C: 26.62%, and G: 15.49%. The total length of the 13 protein-coding genes was 11,427 bp. This study provides an important data set for the phylogenetic and taxonomic analyses of the Trichogaster species.
Mitogenome, Osphronemidae, Trichogaster leeri
The Trichogaster microlepis belongs to the family Osphronemidae, which is mainly distributed in Taiwan and southeastern Asia. Trichogaster microlepis is an aquatic air-breathing fish, and inhabit freshwater and estuarine environments. The genus Trichogaster within the family Osphronemidae has eight species (Froese & Pauly, 2014). This genus is known to be very tolerant of wide ranges of environmental conditions which is a potential threat to natives (Geheber et al., 2010; Priest, 2002). We determined the mitochondrial genome for the Trichogaster species in this study.
History Received 1 April 2015 Accepted 5 April 2015 Published online 28 May 2015
The samples of T. microlepis were collected from the Panzhihua city, Sichuan Province, China. One individual was used to determine the mitochondrial genome and stored in Xijing hospital, Xi’an city, Shanxi Province, China. Standard phenolchloroform method (Sambrook & Russell, 2002) was used to extract genomic DNA from its tail fin clips. Eleven primer sets were used to amplify overlapping segments. The PCR procedures followed Peng et al. (2007). PCR products were purified and then directly sequenced.
Figure 1. Bayesian tree reconstructed based on the 12 protein-coding genes (with the exception of ND6) sequences of 16 species. The values beside the nodes are Bayesian posterior probabilities.
Correspondence: H. Yan, Xijing Hospital, The Fourth Military Medical University, Xi’an 710032, P.R. China. Tel: 029-84775507. E-mail: [email protected]
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 06/08/15 For personal use only.
2
H. Yan et al.
The overall base composition (16,435 bp, Accession no.: KP_342379) of the heavy strand of the T. microlepis mitochondrial genome is A: 29.50%, T: 28.38%, C: 26.62%, and G: 15.49%. It consists of two rRNA genes, 13 protein-coding genes, 22 tRNA genes and one non-coding control regions (D-loop). As reported in vertebrates (Peng et al., 2007), the overall characteristics, including its overall organization and the gene arrangement pattern, are identical to that of the typical vertebrate mitogenome. Nearly all the 21 tRNAs can fold into a typical cloverleaf secondary structure by tRNAscan-SE, except for tRNA-Ser (Lowe & Eddy, 1997). OriL was found within the WANCY cluster of five tRNA genes between tRNAAsn and tRNACys. All the proteincoding genes initiated with the traditional ATG start codon except for cox1. The cox1 gene started with GTG codon and was 1554 bp in length. The total length of 13 protein-coding genes was 11,427 bp, which corresponded to 69.53% of the whole mitochondrial genome. The 12 protein-coding genes (with the exception of ND6) of T. microlepis and other 15 species (Figure 1) downloaded from NCBI (National Center for Biotechnology Information) were aligned and analyzed using MEGA 5.0 (Tamura et al., 2011) and PAUP 4.0 (Swofford, 2002). Based on the 13 protein-coding genes, the Bayesian tree was reconstructed (Figure 1). The result showed that the species of Trichogaster (T. microlepis, T. trichopterus, T. lalius, T. fasciata and T. leeri) formed a monophyletic group and represented close relationship to other species in Anabantoidei. Phylogenetic analysis gives strong support to the basal position of T. microlepis in Percoidea. In addition, the Phylogenetic analysis showed that T. trichopterus has a very close relationship to T. microlepis (Figure 1). These results are in good agreement with the traditional fish taxonomy. This study provides an important data set for phylogenetic and taxonomic analyses of the Trichogaster species.
Mitochondrial DNA, Early Online: 1–2
Acknowledgements We would like to thank Pengfei Yan for his help in the experiment.
Declaration of interest The authors report no conflict of interest. The authors alone are responsible for the content and writing of the article.
References Froese R, Pauly D. (2014). FishBase. World Wide Web electronic publication. Available at: http://www.fishbase.org, version (02/2015). Geheber AD, McMahan CD, Piller KR. (2010). First record of the non-native three spot gourami, Trichogaster trichopterus (Pallas 1770) (Teleostei: Osphronemidae) in Jamaica. Aquatic Invasions 5:13–16. Lowe TM, Eddy SR. (1997). tRNAscan-SE: A program for improveddetection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–64. Peng R, Zeng B, Meng XX, Yue BS, Zhang ZH, Zou FD. (2007). The complete mitochondrial genome and phylogenetic analysis of the giant panda (Ailuropoda melanoleuca). Gene 397:76–83. Priest A. (2002). When two are three and gold is blue. Osphronemid 4:6–11. Sambrook J, Russell DW. (2002). Molecular cloning: A laboratory manual. 3rd ed. Beijing: Science Press. Swofford DL. (2002). PAUP*: Phylogenetic analysis using parsimony (*and other Methods). Version 4.0b10. Sunderland, MA: Sinauer Associates. 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.
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of the Trichogaster microlepis (Anabantoidei: Osphronemidae) Haiyan Yan, Xin Li, Lei Zhang, and Liu Jing
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 06/08/15 For personal use only.
Xijing Hospital, The Fourth Military Medical University, Xi’an, P.R. China
Abstract
Keywords
The complete mitochondrial genome of Trichogaster microlepis was determined in this study. It is 16,435 bp in size and consists of 2 rRNA genes, 13 protein-coding genes, 22 tRNA genes and a non-coding control region (D-loop). The overall base composition of the heavy strand of the T. microlepis mitochondrial genome is A: 29.50%, T: 28.38%, C: 26.62%, and G: 15.49%. The total length of the 13 protein-coding genes was 11,427 bp. This study provides an important data set for the phylogenetic and taxonomic analyses of the Trichogaster species.
Mitogenome, Osphronemidae, Trichogaster leeri
The Trichogaster microlepis belongs to the family Osphronemidae, which is mainly distributed in Taiwan and southeastern Asia. Trichogaster microlepis is an aquatic air-breathing fish, and inhabit freshwater and estuarine environments. The genus Trichogaster within the family Osphronemidae has eight species (Froese & Pauly, 2014). This genus is known to be very tolerant of wide ranges of environmental conditions which is a potential threat to natives (Geheber et al., 2010; Priest, 2002). We determined the mitochondrial genome for the Trichogaster species in this study.
History Received 1 April 2015 Accepted 5 April 2015 Published online 28 May 2015
The samples of T. microlepis were collected from the Panzhihua city, Sichuan Province, China. One individual was used to determine the mitochondrial genome and stored in Xijing hospital, Xi’an city, Shanxi Province, China. Standard phenolchloroform method (Sambrook & Russell, 2002) was used to extract genomic DNA from its tail fin clips. Eleven primer sets were used to amplify overlapping segments. The PCR procedures followed Peng et al. (2007). PCR products were purified and then directly sequenced.
Figure 1. Bayesian tree reconstructed based on the 12 protein-coding genes (with the exception of ND6) sequences of 16 species. The values beside the nodes are Bayesian posterior probabilities.
Correspondence: H. Yan, Xijing Hospital, The Fourth Military Medical University, Xi’an 710032, P.R. China. Tel: 029-84775507. E-mail: [email protected]
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 06/08/15 For personal use only.
2
H. Yan et al.
The overall base composition (16,435 bp, Accession no.: KP_342379) of the heavy strand of the T. microlepis mitochondrial genome is A: 29.50%, T: 28.38%, C: 26.62%, and G: 15.49%. It consists of two rRNA genes, 13 protein-coding genes, 22 tRNA genes and one non-coding control regions (D-loop). As reported in vertebrates (Peng et al., 2007), the overall characteristics, including its overall organization and the gene arrangement pattern, are identical to that of the typical vertebrate mitogenome. Nearly all the 21 tRNAs can fold into a typical cloverleaf secondary structure by tRNAscan-SE, except for tRNA-Ser (Lowe & Eddy, 1997). OriL was found within the WANCY cluster of five tRNA genes between tRNAAsn and tRNACys. All the proteincoding genes initiated with the traditional ATG start codon except for cox1. The cox1 gene started with GTG codon and was 1554 bp in length. The total length of 13 protein-coding genes was 11,427 bp, which corresponded to 69.53% of the whole mitochondrial genome. The 12 protein-coding genes (with the exception of ND6) of T. microlepis and other 15 species (Figure 1) downloaded from NCBI (National Center for Biotechnology Information) were aligned and analyzed using MEGA 5.0 (Tamura et al., 2011) and PAUP 4.0 (Swofford, 2002). Based on the 13 protein-coding genes, the Bayesian tree was reconstructed (Figure 1). The result showed that the species of Trichogaster (T. microlepis, T. trichopterus, T. lalius, T. fasciata and T. leeri) formed a monophyletic group and represented close relationship to other species in Anabantoidei. Phylogenetic analysis gives strong support to the basal position of T. microlepis in Percoidea. In addition, the Phylogenetic analysis showed that T. trichopterus has a very close relationship to T. microlepis (Figure 1). These results are in good agreement with the traditional fish taxonomy. This study provides an important data set for phylogenetic and taxonomic analyses of the Trichogaster species.
Mitochondrial DNA, Early Online: 1–2
Acknowledgements We would like to thank Pengfei Yan for his help in the experiment.
Declaration of interest The authors report no conflict of interest. The authors alone are responsible for the content and writing of the article.
References Froese R, Pauly D. (2014). FishBase. World Wide Web electronic publication. Available at: http://www.fishbase.org, version (02/2015). Geheber AD, McMahan CD, Piller KR. (2010). First record of the non-native three spot gourami, Trichogaster trichopterus (Pallas 1770) (Teleostei: Osphronemidae) in Jamaica. Aquatic Invasions 5:13–16. Lowe TM, Eddy SR. (1997). tRNAscan-SE: A program for improveddetection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–64. Peng R, Zeng B, Meng XX, Yue BS, Zhang ZH, Zou FD. (2007). The complete mitochondrial genome and phylogenetic analysis of the giant panda (Ailuropoda melanoleuca). Gene 397:76–83. Priest A. (2002). When two are three and gold is blue. Osphronemid 4:6–11. Sambrook J, Russell DW. (2002). Molecular cloning: A laboratory manual. 3rd ed. Beijing: Science Press. Swofford DL. (2002). PAUP*: Phylogenetic analysis using parsimony (*and other Methods). Version 4.0b10. Sunderland, MA: Sinauer Associates. 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.
