http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2015.1028032
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Nyctalus noctula (Chiroptera: Vespertilionidae) Kenan Qian1,2, Danna Yu2, Hongyi Cheng2, Kenneth B. Storey3, and Jiayong Zhang1,2 Institute of Ecology, Zhejiang Normal University, Jinhua, Zhejiang Province, China, 2College of Life Science and Chemistry, Zhejiang Normal University, Jinhua, Zhejiang Province, China, and 3Department of Biology, Carleton University, Ottawa, Ontario, Canada
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 05/30/15 For personal use only.
1
Abstract
Keywords
The mitochondrial genome of Nyctalus noctula is a circular molecule of 17,478 bp in length, containing 22 transfer RNA genes, 13 protein-coding genes, 2 ribosomal RNAs and a D-loop region. The overall A + T content of the H-strand is 61.4% (A 32.0%, T 29.4%, C 24.1% and G 14.5%). Among the 13 protein-coding genes, most of them begin with ATG as the start codon except for ND5 with ATA and ND2 and ND3 with ATT. ND1 and ND2 genes terminate with TAG as the stop codon, Cyt b ends with AGA, COIII, ND3 and ND4 genes end with an incomplete stop codon (T– –) and the other protein-coding genes end with TAA. In Bayesian inference (BI) and Maximum likelihood (ML) trees, we found that N. noctula is a sister clade to Pipistrellus abramus, and (Nyctalus + Pipistrellus) is a sister clade to (Chalinolobus + (Eptesicus + Vespertilio)) (1.00 in BI and 100% in ML).
Chiroptera, mitogenome, Nyctalus noctula, phylogenetic relationship, Vespertilionidae
The eight species of the bat genus Nyctalus are members of the family Vespertilionidae (Wilson & Reeder, 2005). The noctule bat, N. noctula, is widely distributed across temperate and subtropical areas of Europe, Asia and North Africa. Although partial sequences of selected mitochondrially-encoded genes from N. noctula are available in Genbank, the complete mitochondrial genome has not yet been reported for any species of the genus Nyctalus. Hence, the present study sequenced the mt genome of N. noctula and analyzed the complete mt nucleotide sequence of the species providing information for future studies of the biology and biogeography of N. noctula populations. Samples of N. noctula liver were extracted from bats that were wild collected in Jinhua, Zhejiang province, China. Previously published mitochondrial genomes of genus Myotis (Jiang et al., 2014; Kim et al., 2011; Nam et al., 2013; Wang et al., 2014; Yoon et al., 2013) were used to design universal primers for polymerase chain reaction (PCR) amplification, and the specific primers were designed by primer premier 5.0 (PRIMER Biosoft International, Palo Alto, CA). All PCRs were carried out using a MyCycler Thermal Cycler (Bio-Rad, Hercules, CA). Products were sent to Sangon Biotech Company (Shanghai, China) for sequencing on automatic DNA sequencer (ABI 3730) with both strands.
Correspondence: Hongyi Cheng, Institute of Ecology, Zhejiang Normal University, Jinhua 321004, Zhejiang Province, China. Tel: 086 0579 82281811. Fax: 086 0579 82281811. E-mail: [email protected]
History Received 1 February 2015 Accepted 8 March 2015 Published online 22 May 2015
The complete mtDNA is 17,478 bp in length. The overall base composition of the H-strand is as follows: T 29.4%, C 24.1%, A 32.0% and G 14.5%. The A + T content of complete mtDNA is 61.4%. The complete mtDNA contains 22 transfer RNA genes, 13 protein-coding genes, 2 ribosomal RNAs and non-coding regions. Most tRNA genes are encoded by the H strand, whereas tRNAGln, tRNAAla, tRNAAsn, tRNACys, tRNATyr, tRNASer, tRNAGlu and tRNAPro are encoded by the L strand. Protein-coding genes are encoded by the H strand, with the exception of the ND6 gene that is encoded by the L strand. Most protein-coding genes begin with ATG as the start codon, except ND2 and ND3 genes have ATT and ND5 starts with ATA. ND1 and ND2 genes are terminated with TAG as the stop codon, Cyt b ends with AGA, COIII, ND3 and ND4 genes end with an incomplete stop codon (T– –) and the other protein-coding genes end with TAA. The Bayesian inference (BI) and Maximum likelihood (ML) trees were constructed using 13 protein-coding genes of 18 species, including Rhinolophus formosae and Pteronotus rubiginosus as outgroups to confirm the phylogenetic position of N. noctula in Vespertilionidae (Figure 1). To select conserved regions of the putative nucleotide, each alignment was analyzed with the program Gblocks 0.91 b (Castresana, 2000) using default settings. BI analysis and ML analysis was performed by MrBayes 3.1.2 (Huelsenbeck & Ronquist, 2001) and PAUP* 4.0b10 (Swofford, 2002), respectively. In BI and ML trees, we found that N. noctula is a sister clade to Pipistrellus abramus, and (Nyctalus + Pipistrellus) is a sister clade to (Chalinolobus + (Eptesicus + Vespertilio)) (1.00 in BI and 100% in ML). The monophyly of Myotis, Murina and Plecotus was well supported (1.00 in BI and 100% in ML).
2
K. Qian et al.
Mitochondrial DNA, Early Online: 1–2
Pteronotus rubiginosus HG003312
Declaration of interest
Rhinolophus formosae EU166918
This research was supported by grants from the Natural Sciences and Engineering Research Council of Canada (No. 6793). The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
Chalinolobus tuberculatus AF321051
1.00 96 1.00 100
Vespertilio sinensis KM092493
1.00 100
1.00 100 1.00 100
1.00
Eptesicus serotinus KF111725
Vespertilio sinensis KJ081440 Pipistrellus abramus AB061528 Nyctalus noctula KP273590 Lasiurus borealis JN209842
1.00 100
Plecotus auritus HM164052
0.56 _ 1.00 99
Plecotus rafinesquii JN209841 1.00 100
Murina ussuriensis JX872285
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 05/30/15 For personal use only.
Murina leucogaster KM893454 1.00 99
Myotis brandtii KM199849
1.00 100 1.00 100
BI ML 0.1
1.00 77 1.00 100
Myotis formosus HQ184048 Myotis ikonnikovi KF111724 Myotis macrodactylus KF440685 Myotis davidii KM233172
Figure 1. Phylogenetic tree of the relationships among 18 species of Vespertilionidae, including N. noctula based on the nucleotide dataset of the 13 mitochondrial protein-coding genes of 11,547 nucleotides. Branch lengths and topology are from the BI analysis. Numbers above branches specify posterior probabilities from BI and bootstrap percentages from ML (ML, 1000 replications) analyses. The GenBank numbers of all species are shown in the figure.
Nucleotide sequence accession number The complete mitochondrial genome of N. noctula has been assigned with GenBank accession number KP273590.
References Castresana J. (2000). Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17: 540–52. Huelsenbeck JP, Ronquist F. (2001). MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754–5. Jiang JJ, Wang SQ, Li YJ, Zhang W, Yin AG, Hu M. (2014). The complete mitochondrial genome of insect-eating brandt’s bat, Myotis brandtii (Myotis, Vespertilionidae). Mitochondrial DNA. doi: 10.3109/ 19401736.2014.947601. Kim YM, Choi EH, Kim SK, Jan KH, Ryu SH, Hwang UW. (2011). Complete mitochondrial genome of the Hodgson’s bat Myotis formosus (Mammalia, Chiroptera, Vespertilionidae). Mitochondrial DNA 22: 71–3. Nam TW, Kim HR, Cho JY, Park YC. (2013). Complete mitochondrial genome of a large-footed bat, Myotis macrodactylus (Vespertilionidae). Mitochondrial DNA. doi: 10.3109/19401736.2013.840. Swofford, DL. (2002). PAUP*: Phylogenetic analysis using parsimony (* and other methods). Version 4.0b10. Sunderland, MA: Sinauer Associates. Wang SQ, Li YJ, Yin AG, Zhang W, Jiang JJ, Wang WL, Hu M. (2014). The complete mitochondrial genome of David’s myotis, Myotis davidii (Myotis, Vespertilionidae). Mitochondrial DNA. doi:10.3109/ 19401736.2014.958681. Wilson DE, Reeder DM. (2005). Mammal species of the world: A taxonomic and geographic reference. 3rd edition. Baltimore, MD: The Johns Hopkins University Press. Yoon, KB, Cho JY, Park YC. (2013). Complete mitochondrial genome of the Korean ikonnikov’s bat Myotis ikonnikovi (Chiroptera: Vespertilionidae). Mitochondrial DNA. doi:10.3109/19401736.2013. 823179.
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Nyctalus noctula (Chiroptera: Vespertilionidae) Kenan Qian1,2, Danna Yu2, Hongyi Cheng2, Kenneth B. Storey3, and Jiayong Zhang1,2 Institute of Ecology, Zhejiang Normal University, Jinhua, Zhejiang Province, China, 2College of Life Science and Chemistry, Zhejiang Normal University, Jinhua, Zhejiang Province, China, and 3Department of Biology, Carleton University, Ottawa, Ontario, Canada
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 05/30/15 For personal use only.
1
Abstract
Keywords
The mitochondrial genome of Nyctalus noctula is a circular molecule of 17,478 bp in length, containing 22 transfer RNA genes, 13 protein-coding genes, 2 ribosomal RNAs and a D-loop region. The overall A + T content of the H-strand is 61.4% (A 32.0%, T 29.4%, C 24.1% and G 14.5%). Among the 13 protein-coding genes, most of them begin with ATG as the start codon except for ND5 with ATA and ND2 and ND3 with ATT. ND1 and ND2 genes terminate with TAG as the stop codon, Cyt b ends with AGA, COIII, ND3 and ND4 genes end with an incomplete stop codon (T– –) and the other protein-coding genes end with TAA. In Bayesian inference (BI) and Maximum likelihood (ML) trees, we found that N. noctula is a sister clade to Pipistrellus abramus, and (Nyctalus + Pipistrellus) is a sister clade to (Chalinolobus + (Eptesicus + Vespertilio)) (1.00 in BI and 100% in ML).
Chiroptera, mitogenome, Nyctalus noctula, phylogenetic relationship, Vespertilionidae
The eight species of the bat genus Nyctalus are members of the family Vespertilionidae (Wilson & Reeder, 2005). The noctule bat, N. noctula, is widely distributed across temperate and subtropical areas of Europe, Asia and North Africa. Although partial sequences of selected mitochondrially-encoded genes from N. noctula are available in Genbank, the complete mitochondrial genome has not yet been reported for any species of the genus Nyctalus. Hence, the present study sequenced the mt genome of N. noctula and analyzed the complete mt nucleotide sequence of the species providing information for future studies of the biology and biogeography of N. noctula populations. Samples of N. noctula liver were extracted from bats that were wild collected in Jinhua, Zhejiang province, China. Previously published mitochondrial genomes of genus Myotis (Jiang et al., 2014; Kim et al., 2011; Nam et al., 2013; Wang et al., 2014; Yoon et al., 2013) were used to design universal primers for polymerase chain reaction (PCR) amplification, and the specific primers were designed by primer premier 5.0 (PRIMER Biosoft International, Palo Alto, CA). All PCRs were carried out using a MyCycler Thermal Cycler (Bio-Rad, Hercules, CA). Products were sent to Sangon Biotech Company (Shanghai, China) for sequencing on automatic DNA sequencer (ABI 3730) with both strands.
Correspondence: Hongyi Cheng, Institute of Ecology, Zhejiang Normal University, Jinhua 321004, Zhejiang Province, China. Tel: 086 0579 82281811. Fax: 086 0579 82281811. E-mail: [email protected]
History Received 1 February 2015 Accepted 8 March 2015 Published online 22 May 2015
The complete mtDNA is 17,478 bp in length. The overall base composition of the H-strand is as follows: T 29.4%, C 24.1%, A 32.0% and G 14.5%. The A + T content of complete mtDNA is 61.4%. The complete mtDNA contains 22 transfer RNA genes, 13 protein-coding genes, 2 ribosomal RNAs and non-coding regions. Most tRNA genes are encoded by the H strand, whereas tRNAGln, tRNAAla, tRNAAsn, tRNACys, tRNATyr, tRNASer, tRNAGlu and tRNAPro are encoded by the L strand. Protein-coding genes are encoded by the H strand, with the exception of the ND6 gene that is encoded by the L strand. Most protein-coding genes begin with ATG as the start codon, except ND2 and ND3 genes have ATT and ND5 starts with ATA. ND1 and ND2 genes are terminated with TAG as the stop codon, Cyt b ends with AGA, COIII, ND3 and ND4 genes end with an incomplete stop codon (T– –) and the other protein-coding genes end with TAA. The Bayesian inference (BI) and Maximum likelihood (ML) trees were constructed using 13 protein-coding genes of 18 species, including Rhinolophus formosae and Pteronotus rubiginosus as outgroups to confirm the phylogenetic position of N. noctula in Vespertilionidae (Figure 1). To select conserved regions of the putative nucleotide, each alignment was analyzed with the program Gblocks 0.91 b (Castresana, 2000) using default settings. BI analysis and ML analysis was performed by MrBayes 3.1.2 (Huelsenbeck & Ronquist, 2001) and PAUP* 4.0b10 (Swofford, 2002), respectively. In BI and ML trees, we found that N. noctula is a sister clade to Pipistrellus abramus, and (Nyctalus + Pipistrellus) is a sister clade to (Chalinolobus + (Eptesicus + Vespertilio)) (1.00 in BI and 100% in ML). The monophyly of Myotis, Murina and Plecotus was well supported (1.00 in BI and 100% in ML).
2
K. Qian et al.
Mitochondrial DNA, Early Online: 1–2
Pteronotus rubiginosus HG003312
Declaration of interest
Rhinolophus formosae EU166918
This research was supported by grants from the Natural Sciences and Engineering Research Council of Canada (No. 6793). The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
Chalinolobus tuberculatus AF321051
1.00 96 1.00 100
Vespertilio sinensis KM092493
1.00 100
1.00 100 1.00 100
1.00
Eptesicus serotinus KF111725
Vespertilio sinensis KJ081440 Pipistrellus abramus AB061528 Nyctalus noctula KP273590 Lasiurus borealis JN209842
1.00 100
Plecotus auritus HM164052
0.56 _ 1.00 99
Plecotus rafinesquii JN209841 1.00 100
Murina ussuriensis JX872285
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 05/30/15 For personal use only.
Murina leucogaster KM893454 1.00 99
Myotis brandtii KM199849
1.00 100 1.00 100
BI ML 0.1
1.00 77 1.00 100
Myotis formosus HQ184048 Myotis ikonnikovi KF111724 Myotis macrodactylus KF440685 Myotis davidii KM233172
Figure 1. Phylogenetic tree of the relationships among 18 species of Vespertilionidae, including N. noctula based on the nucleotide dataset of the 13 mitochondrial protein-coding genes of 11,547 nucleotides. Branch lengths and topology are from the BI analysis. Numbers above branches specify posterior probabilities from BI and bootstrap percentages from ML (ML, 1000 replications) analyses. The GenBank numbers of all species are shown in the figure.
Nucleotide sequence accession number The complete mitochondrial genome of N. noctula has been assigned with GenBank accession number KP273590.
References Castresana J. (2000). Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17: 540–52. Huelsenbeck JP, Ronquist F. (2001). MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754–5. Jiang JJ, Wang SQ, Li YJ, Zhang W, Yin AG, Hu M. (2014). The complete mitochondrial genome of insect-eating brandt’s bat, Myotis brandtii (Myotis, Vespertilionidae). Mitochondrial DNA. doi: 10.3109/ 19401736.2014.947601. Kim YM, Choi EH, Kim SK, Jan KH, Ryu SH, Hwang UW. (2011). Complete mitochondrial genome of the Hodgson’s bat Myotis formosus (Mammalia, Chiroptera, Vespertilionidae). Mitochondrial DNA 22: 71–3. Nam TW, Kim HR, Cho JY, Park YC. (2013). Complete mitochondrial genome of a large-footed bat, Myotis macrodactylus (Vespertilionidae). Mitochondrial DNA. doi: 10.3109/19401736.2013.840. Swofford, DL. (2002). PAUP*: Phylogenetic analysis using parsimony (* and other methods). Version 4.0b10. Sunderland, MA: Sinauer Associates. Wang SQ, Li YJ, Yin AG, Zhang W, Jiang JJ, Wang WL, Hu M. (2014). The complete mitochondrial genome of David’s myotis, Myotis davidii (Myotis, Vespertilionidae). Mitochondrial DNA. doi:10.3109/ 19401736.2014.958681. Wilson DE, Reeder DM. (2005). Mammal species of the world: A taxonomic and geographic reference. 3rd edition. Baltimore, MD: The Johns Hopkins University Press. Yoon, KB, Cho JY, Park YC. (2013). Complete mitochondrial genome of the Korean ikonnikov’s bat Myotis ikonnikovi (Chiroptera: Vespertilionidae). Mitochondrial DNA. doi:10.3109/19401736.2013. 823179.
