http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.905835
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of Red-rumped Swallow, Cecropis daurica (Passeriformes: Hirundinidae) Shuo Liu, Yang Chen, Jing-Dong Liu, Yi-Hui Wu, Jian-Hui Xie, and Yi-Wen Shen
Mitochondrial DNA Downloaded from informahealthcare.com by Rutgers University on 06/09/14 For personal use only.
Department of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai, China
Abstract
Keywords
The complete mitochondrial genome of the Cecropis daurica was determined by using a PCRbased method. The complete mitochondrial DNA of this swallow was 17,949 bp in length, including 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and 2 control regions. All genes were encoded on the heavy strain except for ND6 and eight tRNA genes. The gene arrangement of the Cecropis daurica was similar to that found in other passerines. Base composition of the heavy strain was A (30.5%), T (23.0%), C (32.1%) and G (14.3%) with the A + T bias of 53.5%.
Cecropis daurica, Hirundinidae, mitochondrial genome, Passeriformes
Cecropis daurica (Red-rumped Swallow) is a small passerine bird in the Hirundinidae family. It breeds across southern Europe and eastern Asia to southern Siberia and Japan. These populations are migratory, wintering in sub-Saharan Africa or south Asia. There are resident races in Africa, and most Indian and Sri Lanka breeders are also year-round residents. This species is a regular vagrant outside its breeding range (Turner & Rose, 1989). In this study we sequenced the complete mitochondrial genome (mitogenome) of the C. daurica. The sampled specimen of C. daurica was collected from Jiangxi Province, China. Total genomic DNA was extracted from a piece of muscle tissue using QIAamp DNA Mini Kit (Qiagen, Hilden, Germany). Eighteen pairs of primers that were designed on the basis of the conserved regions of the mitogenome of Tachycineta albilinea (JQ071619),
History Received 2 March 2014 Accepted 15 March 2014 Published online 4 April 2014
Tachycineta albiventer (JQ071620), Tachycineta bicolor (JQ071614), Tachycineta cyaneoviridis (JQ071617), Tachycineta euchrysea (JQ071616), Tachycineta leucorrhoa (JQ071621), Tachycineta meyeni (JQ071622), Tachycineta stolzmanni (JQ071618) and Tachycineta thalassina (JQ071615) were used to amplify contiguous, overlapping segments of C. daurica mitogenome by polymerase chain reaction (PCR) (Cerasale et al., 2012). The mitogenome data of C. daurica has been deposited in GenBank with the accession number KJ499911. The complete mitogenome of C. daurica was 17,949 bp in length, including 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and 2 control regions (Table 1). This gene arrangement is similar to that found in other passerines (Mindell et al., 1998; Shao & Barker, 2003;
Table 1. Characteristics of the mitochondrial genome of C. daurica. Position Genes 12S rRNA tRNAVal 16S rRNA tRNALeu ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn tRNACys
From 1 975 1046 2647 2739 3723 3802 3872 3941 4981 5053 5132 5204
Codon To 973 1045 2646 2721 3716 3794 3872 3940 4981 5051 5121 5202 5269
Length (bp) 973 71 1601 75 978 72 71 69 1041 71 69 71 66
Start
Stop
ATG
AGG
ATG
TAA
Intergenic nucleotides*
Strandy
1 0 0 17 6 7 –1 0 –1 1 10 1 –1
H H H H H H L H H H L L L (continued )
Correspondence: Jian-Hui Xie and Yi-Wen Shen, Department of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai 200032, China. Tel: +86 2154237569 (J.-H. Xie); +86 2154237402 (Y.-W. Shen). Fax: +862154237668. E-mail: [email protected] (J.-H. Xie); [email protected] (Y.-W. Shen).
2
S. Liu et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Position Genes
Mitochondrial DNA Downloaded from informahealthcare.com by Rutgers University on 06/09/14 For personal use only.
Tyr
tRNA COI tRNASer tRNAAsp COII tRNALys ATPase8 ATPase6 COIII tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer(AGY) tRNALeu ND5 Cytb tRNAThr control region 1 tRNAPro ND6 tRNAGlu control region 2 tRNAPhe
Codon
From
To
Length (bp)
5269 5341 6883 6962 7041 7726 7798 7956 8646 9430 9499 9852 9923 10,213 11,591 11,660 11,725 11,796 13,622 14,780 14,849 15,943 16,021 16,541 16,613 17,881
5339 6891 6957 7030 7724 7796 7965 8639 9429 9498 9849 9921 10,219 11,590 11,659 11,725 11,795 13,613 14,764 14,848 15,942 16,012 16,539 16,612 17,880 17,949
71 1551 75 69 684 71 168 684 784 69 351 70 297 1378 69 66 71 1818 1143 69 1094 70 519 72 1268 69
Start
Stop
GTG
AGG
ATG
TAA
ATG ATG ATG
TAA TAA T– –
ATT
TAG
ATG ATG
TAA T– –
ATG ATG
AGA TAA
ATG
TAG
Intergenic nucleotides*
Strandy
1 –9 4 10 1 1 –10 6 0 0 2 1 –7 0 0 –1 0 8 15 0 0 8 1 0 0 0
L H L H H H H H H H H H H H H H H H H H H L L L H H
*Numbers correspond to the nucleotides separating different genes. Positive numbers indicate the number of nucleotides found in intergenic spaces, negative numbers indicate overlapping nucleotides between adjacent genes. yH and L indicate heavy and light strands, respectively.
Singh et al., 2008). The base composition of the heavy strain was 30.5% for A, 32.1% for C, 23.0% for T and 14.3% for G, with the A + T bias of 53.5%. All genes were encoded on the heavy strain except for ND6 and eight tRNA genes. Among the mitochondrial protein-coding genes, the ND5 was the longest (1818 bp), while the ATPase8 was the shortest (168 bp). The usage of the start codon was mainly ATG in the most of mitochondrial proteincoding genes besides the COI gene employing the GTG and the ND3 gene employing the ATT; the usage of the stop one was either complete (TAA, TAG, AGA, AGG) or incomplete (T– –). Among 13 protein-coding genes, there were partial gene overlaps found in seven pairs of adjacent genes, tRNAGln-tRNAMet, ND2tRNATrp, tRNACys-tRNATyr, COI-tRNASer, ATP8-ATP6, ND4LND4 and tRNASer(AGY)-tRNALeu with the overlapped size of 1, 1, 1, 9, 10, 7 and 1 bp, respectively. The 22 tRNA genes showed variable length from 66 to 75 bp. The 12 S rRNA (973 bp) and 16 S rRNA (1601 bp) genes were located between tRNAPhe and tRNALeu. The two control regions (CR) were 1094 bp and 1268 bp long, and they had a continuous region (1055 bp) of near identical sequence (499% sequence identity). The CR1 had no repeat units detected, while the CR2 had a microsatellite consisting of a series of complex cytosine-adenine repeats. The tRNAPro, ND6 and tRNAGlu genes occurred between the two CRs. This gene order was termed the duplicate CR gene order (Macey et al., 1997; Moritz & Brown, 1986; Gibb et al., 2007).
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. This work was
supported by National Natural Science Foundation of China (31270862) and National Science Foundation for Fostering Talents in Basic Research of China (J1210041).
References Cerasale DJ, Dor R, Winkler DW, Lovette IJ. (2012). Phylogeny of the Tachycineta genus of New World swallows: Insights from complete mitochondrial genomes. Mol Phylogenet Evol 63:64–71. Gibb GC, Kardailsky O, Kimball RT, Braun EL, Penny D. (2007). Mitochondrial genomes and avian phylogeny: Complex characters and resolvability without explosive radiations. Mol Biol Evol 24: 269–80. Macey JR, Larson A, Ananjeva NB, Fang Z, Papenfuss TJ. (1997). Two novel gene orders and the role of light-strand replication in rearrangement of the vertebrate mitochondrial genome. Mol Biol Evol 14:91–104. Mindell DP, Sorenson MD, Dimcheff DE. (1998). Multiple independent origins of mitochondrial gene order in birds. PNAS 95:10693–7. Moritz C, Brown WM. (1986). Tandem duplication of D-loop and ribosomal RNA sequences in lizard mitochondrial DNA. Science 233: 1425–7. Shao R, Barker SC. (2003). The highly rearranged mitochondrial genome of the plague thrips, Thrips imaginis (Insecta: Thysanoptera): Convergence of two novel gene boundaries and an extraordinary arrangement of rRNA genes. Mol Biol Evol 20:362–70. Singh TR, Shneor O, Huchon D. (2008). Bird mitochondrial gene order: Insight from 3 warbler mitochondrial genomes. Mol Biol Evol 25: 475–77. Turner AK, Rose C. (1989). Swallows & Martins: An identification guide and handbook. Boston: Houghton Mifflin.
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of Red-rumped Swallow, Cecropis daurica (Passeriformes: Hirundinidae) Shuo Liu, Yang Chen, Jing-Dong Liu, Yi-Hui Wu, Jian-Hui Xie, and Yi-Wen Shen
Mitochondrial DNA Downloaded from informahealthcare.com by Rutgers University on 06/09/14 For personal use only.
Department of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai, China
Abstract
Keywords
The complete mitochondrial genome of the Cecropis daurica was determined by using a PCRbased method. The complete mitochondrial DNA of this swallow was 17,949 bp in length, including 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and 2 control regions. All genes were encoded on the heavy strain except for ND6 and eight tRNA genes. The gene arrangement of the Cecropis daurica was similar to that found in other passerines. Base composition of the heavy strain was A (30.5%), T (23.0%), C (32.1%) and G (14.3%) with the A + T bias of 53.5%.
Cecropis daurica, Hirundinidae, mitochondrial genome, Passeriformes
Cecropis daurica (Red-rumped Swallow) is a small passerine bird in the Hirundinidae family. It breeds across southern Europe and eastern Asia to southern Siberia and Japan. These populations are migratory, wintering in sub-Saharan Africa or south Asia. There are resident races in Africa, and most Indian and Sri Lanka breeders are also year-round residents. This species is a regular vagrant outside its breeding range (Turner & Rose, 1989). In this study we sequenced the complete mitochondrial genome (mitogenome) of the C. daurica. The sampled specimen of C. daurica was collected from Jiangxi Province, China. Total genomic DNA was extracted from a piece of muscle tissue using QIAamp DNA Mini Kit (Qiagen, Hilden, Germany). Eighteen pairs of primers that were designed on the basis of the conserved regions of the mitogenome of Tachycineta albilinea (JQ071619),
History Received 2 March 2014 Accepted 15 March 2014 Published online 4 April 2014
Tachycineta albiventer (JQ071620), Tachycineta bicolor (JQ071614), Tachycineta cyaneoviridis (JQ071617), Tachycineta euchrysea (JQ071616), Tachycineta leucorrhoa (JQ071621), Tachycineta meyeni (JQ071622), Tachycineta stolzmanni (JQ071618) and Tachycineta thalassina (JQ071615) were used to amplify contiguous, overlapping segments of C. daurica mitogenome by polymerase chain reaction (PCR) (Cerasale et al., 2012). The mitogenome data of C. daurica has been deposited in GenBank with the accession number KJ499911. The complete mitogenome of C. daurica was 17,949 bp in length, including 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and 2 control regions (Table 1). This gene arrangement is similar to that found in other passerines (Mindell et al., 1998; Shao & Barker, 2003;
Table 1. Characteristics of the mitochondrial genome of C. daurica. Position Genes 12S rRNA tRNAVal 16S rRNA tRNALeu ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn tRNACys
From 1 975 1046 2647 2739 3723 3802 3872 3941 4981 5053 5132 5204
Codon To 973 1045 2646 2721 3716 3794 3872 3940 4981 5051 5121 5202 5269
Length (bp) 973 71 1601 75 978 72 71 69 1041 71 69 71 66
Start
Stop
ATG
AGG
ATG
TAA
Intergenic nucleotides*
Strandy
1 0 0 17 6 7 –1 0 –1 1 10 1 –1
H H H H H H L H H H L L L (continued )
Correspondence: Jian-Hui Xie and Yi-Wen Shen, Department of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai 200032, China. Tel: +86 2154237569 (J.-H. Xie); +86 2154237402 (Y.-W. Shen). Fax: +862154237668. E-mail: [email protected] (J.-H. Xie); [email protected] (Y.-W. Shen).
2
S. Liu et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Position Genes
Mitochondrial DNA Downloaded from informahealthcare.com by Rutgers University on 06/09/14 For personal use only.
Tyr
tRNA COI tRNASer tRNAAsp COII tRNALys ATPase8 ATPase6 COIII tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer(AGY) tRNALeu ND5 Cytb tRNAThr control region 1 tRNAPro ND6 tRNAGlu control region 2 tRNAPhe
Codon
From
To
Length (bp)
5269 5341 6883 6962 7041 7726 7798 7956 8646 9430 9499 9852 9923 10,213 11,591 11,660 11,725 11,796 13,622 14,780 14,849 15,943 16,021 16,541 16,613 17,881
5339 6891 6957 7030 7724 7796 7965 8639 9429 9498 9849 9921 10,219 11,590 11,659 11,725 11,795 13,613 14,764 14,848 15,942 16,012 16,539 16,612 17,880 17,949
71 1551 75 69 684 71 168 684 784 69 351 70 297 1378 69 66 71 1818 1143 69 1094 70 519 72 1268 69
Start
Stop
GTG
AGG
ATG
TAA
ATG ATG ATG
TAA TAA T– –
ATT
TAG
ATG ATG
TAA T– –
ATG ATG
AGA TAA
ATG
TAG
Intergenic nucleotides*
Strandy
1 –9 4 10 1 1 –10 6 0 0 2 1 –7 0 0 –1 0 8 15 0 0 8 1 0 0 0
L H L H H H H H H H H H H H H H H H H H H L L L H H
*Numbers correspond to the nucleotides separating different genes. Positive numbers indicate the number of nucleotides found in intergenic spaces, negative numbers indicate overlapping nucleotides between adjacent genes. yH and L indicate heavy and light strands, respectively.
Singh et al., 2008). The base composition of the heavy strain was 30.5% for A, 32.1% for C, 23.0% for T and 14.3% for G, with the A + T bias of 53.5%. All genes were encoded on the heavy strain except for ND6 and eight tRNA genes. Among the mitochondrial protein-coding genes, the ND5 was the longest (1818 bp), while the ATPase8 was the shortest (168 bp). The usage of the start codon was mainly ATG in the most of mitochondrial proteincoding genes besides the COI gene employing the GTG and the ND3 gene employing the ATT; the usage of the stop one was either complete (TAA, TAG, AGA, AGG) or incomplete (T– –). Among 13 protein-coding genes, there were partial gene overlaps found in seven pairs of adjacent genes, tRNAGln-tRNAMet, ND2tRNATrp, tRNACys-tRNATyr, COI-tRNASer, ATP8-ATP6, ND4LND4 and tRNASer(AGY)-tRNALeu with the overlapped size of 1, 1, 1, 9, 10, 7 and 1 bp, respectively. The 22 tRNA genes showed variable length from 66 to 75 bp. The 12 S rRNA (973 bp) and 16 S rRNA (1601 bp) genes were located between tRNAPhe and tRNALeu. The two control regions (CR) were 1094 bp and 1268 bp long, and they had a continuous region (1055 bp) of near identical sequence (499% sequence identity). The CR1 had no repeat units detected, while the CR2 had a microsatellite consisting of a series of complex cytosine-adenine repeats. The tRNAPro, ND6 and tRNAGlu genes occurred between the two CRs. This gene order was termed the duplicate CR gene order (Macey et al., 1997; Moritz & Brown, 1986; Gibb et al., 2007).
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. This work was
supported by National Natural Science Foundation of China (31270862) and National Science Foundation for Fostering Talents in Basic Research of China (J1210041).
References Cerasale DJ, Dor R, Winkler DW, Lovette IJ. (2012). Phylogeny of the Tachycineta genus of New World swallows: Insights from complete mitochondrial genomes. Mol Phylogenet Evol 63:64–71. Gibb GC, Kardailsky O, Kimball RT, Braun EL, Penny D. (2007). Mitochondrial genomes and avian phylogeny: Complex characters and resolvability without explosive radiations. Mol Biol Evol 24: 269–80. Macey JR, Larson A, Ananjeva NB, Fang Z, Papenfuss TJ. (1997). Two novel gene orders and the role of light-strand replication in rearrangement of the vertebrate mitochondrial genome. Mol Biol Evol 14:91–104. Mindell DP, Sorenson MD, Dimcheff DE. (1998). Multiple independent origins of mitochondrial gene order in birds. PNAS 95:10693–7. Moritz C, Brown WM. (1986). Tandem duplication of D-loop and ribosomal RNA sequences in lizard mitochondrial DNA. Science 233: 1425–7. Shao R, Barker SC. (2003). The highly rearranged mitochondrial genome of the plague thrips, Thrips imaginis (Insecta: Thysanoptera): Convergence of two novel gene boundaries and an extraordinary arrangement of rRNA genes. Mol Biol Evol 20:362–70. Singh TR, Shneor O, Huchon D. (2008). Bird mitochondrial gene order: Insight from 3 warbler mitochondrial genomes. Mol Biol Evol 25: 475–77. Turner AK, Rose C. (1989). Swallows & Martins: An identification guide and handbook. Boston: Houghton Mifflin.
