Mitochondrial DNA The Journal of DNA Mapping, Sequencing, and Analysis
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
Sequence analysis of the complete mitochondrial genome of Youxian sheldrake Shao-Ping He, Li-Li Liu, Qi-Fang Yu, Si Li & Jian-Hua He To cite this article: Shao-Ping He, Li-Li Liu, Qi-Fang Yu, Si Li & Jian-Hua He (2014): Sequence analysis of the complete mitochondrial genome of Youxian sheldrake, Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.945540
Published online: 04 Aug 2014.
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Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=imdn20 Download by: [Monash University Library]
Date: 21 September 2015, At: 04:42
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.945540
MITOGENOME ANNOUNCEMENT
Sequence analysis of the complete mitochondrial genome of Youxian sheldrake Shao-Ping He1, Li-Li Liu1,2, Qi-Fang Yu1, Si Li1, and Jian-Hua He1 College of Animal Science and Technology, Hunan Agricultural University, Changsha, P.R. China and 2College of Life Science, Hunan University of Science and Technology, Xiangtan, P.R. China
Downloaded by [Monash University Library] at 04:42 21 September 2015
1
Abstract
Keywords
Youxian sheldrake is excellent native breeds in Hunan province in China. The complete mitochondrial (mt) genome sequence plays an important role in the accurate determination of phylogenetic relationships among metazoans. This is the first study to determine the complete mitochondrial genome sequence of Youxian sheldrake using PCR-based amplification and Sanger sequencing. The characteristic of the entire mitochondrial genome was analyzed in detail, the total length of the mitogenome is 16,605 bp, with the base composition of 29.21% A, 22.18% T, 32.84% C, 15.77% G in the Youxian sheldrake. It contained 2 ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes and a major non-coding control region (D-loop region). The complete mitochondrial genome sequence of Youxian sheldrake provided an important data for further study of the phylogenetics of poultry, and available data for the genetics and breeding.
Genome, mitochondrial, PCR method, Youxian sheldrake
Youxian sheldrake is the native breed of Hunan province in China, which was recorded in Chinese famous livestock and poultry genetic resource list. This study determined complete mitochondrial DNA (mtDNA) sequence of Youxian sheldrake, which has been registered in GenBank under accession number KJ883269. The mitochondrial DNA was extracted by using the EasyPure Genomic DNA Kit (Transgen Biotech, Beijing, China) according to its instruction manual. Polymerase chain reaction (PCR) was carried out to amplify the complete mitochondrial genome with 19 pairs of primers designed according to the mtDNA sequence of Anas platyrhynchos (EU755253.1). PCR products of the Gel electrophoresis were purified by Gel AdvancedÔ Gel Extraction (Rich Biotech, Taiwan, China) and sequenced by Biosune Biotech Co. Ltd (Shanghai, China). DNA sequence was edited and assembled using the program DNAStar7.1 software (Madison, WI). The base composition and distribution of mtDNA sequence was analyzed using tRNA Scan-SE1.21 software (http://lowelab.ucsc.edu/tRNAScan-SE/) and DOGMA software (http://dogma.ccbb.utexas.edu/). The total length of the mitogenome was 16,605 bp, with the base composition of mtDNA was 29.21% A, 22.18% T, 32.84% C, 15.77% G. It contains the typical structure (Table 1), including 2
Correspondence: J-H He, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, P.R. China. E-mail: [email protected]
History Received 19 June 2014 Accepted 27 June 2014 Published online 4 August 2014
ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes, and a major non-coding control region (D-loop region). The mitochondrial genomic organization and gene order were consistent with that of Muscovy duck (Tu et al., 2014). Except for the COX1, COX2 and ND5 gene using GTG as the initiation codon, other 10 protein coding genes of the mtDNA in Youxian sheldrake started with the typical ATG codon. These genes had four types of termination codon, including TAA for COX2, ATPase8, ATPase6, ND3, ND4L, ND5, and Cytb, TAG for ND6, AGG for ND1 and COX1, and an incomplete termination codon ‘‘T– –’’ for ND2, ND4 and COX3, ‘‘T– –’’ is the 50 terminal of the adjacent gene (Anderson et al., 1981). The ND6 gene and eight tRNA genes, including tRNAGln, tRNAAla, tRNAAsn(AAY), tRNACys, tRNATyr, tRNASer(WSN), tRNAPro and tRNAGlu were encoded by the light (L) strand, whereas the other genes were encoded by the heavy (H) strand. The lengths of 12s rRNA and the 16s rRNA were 985 bp and 1602 bp. The two ribosomal RNA genes were located between the tRNALeu(CTM) and tRNAPhe genes and separated by the tRNAVal(GTM) gene, and the result was similar to other vertebrates. Among 13 protein-coding genes, the longest one was ND5 gene (1823 bp), which was located between the tRNALeu(CTM) and Cytb, and the shortest one was ATP8 gene (167 bp), which was located between the tRNALys and ATP6. The 22 tRNA genes were distributed in rRNA and protein-coding genes, ranging from 66–76 bp in length size. The D-loop region of the mtDNA is located between tRNAGlu and tRNAphe with a length of 1050 bp. The origin for light strand replication (OLR) has been identified in vertebrates and located in a cluster of the tRNATrp-tRNAAla-tRNAAsn(AAY)-tRNACys-tRNATyr (WANCY) region (Zhang et al., 2012). Youxian sheldrake might be associated with the absence of OLR between tRNAAsn and
2
S.-P. He et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Characteristics of the mitochondrial genome of Youxian sheldrake. Position
Downloaded by [Monash University Library] at 04:42 21 September 2015
Gene D-loop tRNAPhe 12S rRNA tRNAVal 16S rRNA tRNALeu(CTM) ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn(AAY) tRNACys tRNATyr COX1 tRNASer(WSN) tRNAAsp COX2 tRNALys ATPase8 ATPase6 COX3 tRNAGly ND3 tRNAArg(MGR) ND4L ND4 tRNAHis tRNASer(TCN) tRNALeu(CTM) ND5 Cytb tRNAThr(ACW) tRNAPro ND6 tRNAGlu
Codon
Start
End
Size
1 1051 1121 2106 2177 3779 3857 4833 4912 4982 5051 6090 6169 6240 6313 6378 6451 7993 8068 8138 8826 8896 9054 9737 10,521 10,590 10,943 11,013 11,303 12,681 12,750 12,815 12,886 14,709 15,854 15,931 16,014 16,535
1050 1120 2105 2176 3778 3852 4833 4904 4982 5050 6089 6165 6237 6312 6378 6449 8000 8065 8136 8823 8894 9062 9736 10,519 10,589 10,940 11,012 11,308 12,679 12,749 12,815 12,885 14,708 15,850 15,922 16,002 16,534 16,605
1050 70 985 71 1602 74 977 72 71 69 1039 76 69 73 66 72 1550 73 69 686 69 167 683 783 69 351 70 296 1377 69 66 71 1823 1142 69 72 521 71
Start
Stop
Anti-codon
Strand
Space/overlap+
GAA
H H H H H H H L H H H L L L L H L H H H H H H H H H H H H H H H H H L L L
/ 0 0 0 0 0 4 –1 7 –1 0 0 3 2 0 –1 1 –8 2 1 2 1 –9 0 1 0 2 0 –6 1 0 –1 0 0 3 8 11 0
TAC GAG ATG
AGG TAT TTG CAT
ATG
T– – TCA TGC ATT GCA GTA
GTG
AGG CGA GTC
GTG
TAA
ATG ATG ATG
TAA TAA T– –
ATG
TAA
ATG ATG
TAA T– –
CTT
ACC TCT ATG TGA TAG GTG ATG
TAA TAA AGT AGG
ATG
TAG TTC
+
*T– – means incomplete termination codon. Negative numbers indicate overlapping nucleotides.
tRNACys genes, which failed to be folded up into OLR-like secondary structure.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. This research was supported by Hunan Provincial Natural Science Foundation of China (No. 12JJ8014).
References Anderson S, Bankier AT, Barrell BG, de Bruijn MHL, Coulson AR, Drouin J, Eperon IC, et al. (1981). Sequence and organization of the human mitochondrial genome. Nature 290:457–64. Tu J, Si F, Wu Q, Cong B, Xing X, Yang FH. (2014). The complete mitochondrial genome of the Muscovy duck, Cairina moschata (Anseriformes, Anatidae, Cairina). Mitochondrial DNA 25:102–3. Zhang HH, Ren Y, Chen L, Sha WL. (2012). The complete mitochondrial genome of scimitar-horned oryx (Oryx dammah). Mitochondrial DNA 23:361–2.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
Sequence analysis of the complete mitochondrial genome of Youxian sheldrake Shao-Ping He, Li-Li Liu, Qi-Fang Yu, Si Li & Jian-Hua He To cite this article: Shao-Ping He, Li-Li Liu, Qi-Fang Yu, Si Li & Jian-Hua He (2014): Sequence analysis of the complete mitochondrial genome of Youxian sheldrake, Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.945540
Published online: 04 Aug 2014.
Submit your article to this journal
Article views: 19
View related articles
View Crossmark data
Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=imdn20 Download by: [Monash University Library]
Date: 21 September 2015, At: 04:42
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.945540
MITOGENOME ANNOUNCEMENT
Sequence analysis of the complete mitochondrial genome of Youxian sheldrake Shao-Ping He1, Li-Li Liu1,2, Qi-Fang Yu1, Si Li1, and Jian-Hua He1 College of Animal Science and Technology, Hunan Agricultural University, Changsha, P.R. China and 2College of Life Science, Hunan University of Science and Technology, Xiangtan, P.R. China
Downloaded by [Monash University Library] at 04:42 21 September 2015
1
Abstract
Keywords
Youxian sheldrake is excellent native breeds in Hunan province in China. The complete mitochondrial (mt) genome sequence plays an important role in the accurate determination of phylogenetic relationships among metazoans. This is the first study to determine the complete mitochondrial genome sequence of Youxian sheldrake using PCR-based amplification and Sanger sequencing. The characteristic of the entire mitochondrial genome was analyzed in detail, the total length of the mitogenome is 16,605 bp, with the base composition of 29.21% A, 22.18% T, 32.84% C, 15.77% G in the Youxian sheldrake. It contained 2 ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes and a major non-coding control region (D-loop region). The complete mitochondrial genome sequence of Youxian sheldrake provided an important data for further study of the phylogenetics of poultry, and available data for the genetics and breeding.
Genome, mitochondrial, PCR method, Youxian sheldrake
Youxian sheldrake is the native breed of Hunan province in China, which was recorded in Chinese famous livestock and poultry genetic resource list. This study determined complete mitochondrial DNA (mtDNA) sequence of Youxian sheldrake, which has been registered in GenBank under accession number KJ883269. The mitochondrial DNA was extracted by using the EasyPure Genomic DNA Kit (Transgen Biotech, Beijing, China) according to its instruction manual. Polymerase chain reaction (PCR) was carried out to amplify the complete mitochondrial genome with 19 pairs of primers designed according to the mtDNA sequence of Anas platyrhynchos (EU755253.1). PCR products of the Gel electrophoresis were purified by Gel AdvancedÔ Gel Extraction (Rich Biotech, Taiwan, China) and sequenced by Biosune Biotech Co. Ltd (Shanghai, China). DNA sequence was edited and assembled using the program DNAStar7.1 software (Madison, WI). The base composition and distribution of mtDNA sequence was analyzed using tRNA Scan-SE1.21 software (http://lowelab.ucsc.edu/tRNAScan-SE/) and DOGMA software (http://dogma.ccbb.utexas.edu/). The total length of the mitogenome was 16,605 bp, with the base composition of mtDNA was 29.21% A, 22.18% T, 32.84% C, 15.77% G. It contains the typical structure (Table 1), including 2
Correspondence: J-H He, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, P.R. China. E-mail: [email protected]
History Received 19 June 2014 Accepted 27 June 2014 Published online 4 August 2014
ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes, and a major non-coding control region (D-loop region). The mitochondrial genomic organization and gene order were consistent with that of Muscovy duck (Tu et al., 2014). Except for the COX1, COX2 and ND5 gene using GTG as the initiation codon, other 10 protein coding genes of the mtDNA in Youxian sheldrake started with the typical ATG codon. These genes had four types of termination codon, including TAA for COX2, ATPase8, ATPase6, ND3, ND4L, ND5, and Cytb, TAG for ND6, AGG for ND1 and COX1, and an incomplete termination codon ‘‘T– –’’ for ND2, ND4 and COX3, ‘‘T– –’’ is the 50 terminal of the adjacent gene (Anderson et al., 1981). The ND6 gene and eight tRNA genes, including tRNAGln, tRNAAla, tRNAAsn(AAY), tRNACys, tRNATyr, tRNASer(WSN), tRNAPro and tRNAGlu were encoded by the light (L) strand, whereas the other genes were encoded by the heavy (H) strand. The lengths of 12s rRNA and the 16s rRNA were 985 bp and 1602 bp. The two ribosomal RNA genes were located between the tRNALeu(CTM) and tRNAPhe genes and separated by the tRNAVal(GTM) gene, and the result was similar to other vertebrates. Among 13 protein-coding genes, the longest one was ND5 gene (1823 bp), which was located between the tRNALeu(CTM) and Cytb, and the shortest one was ATP8 gene (167 bp), which was located between the tRNALys and ATP6. The 22 tRNA genes were distributed in rRNA and protein-coding genes, ranging from 66–76 bp in length size. The D-loop region of the mtDNA is located between tRNAGlu and tRNAphe with a length of 1050 bp. The origin for light strand replication (OLR) has been identified in vertebrates and located in a cluster of the tRNATrp-tRNAAla-tRNAAsn(AAY)-tRNACys-tRNATyr (WANCY) region (Zhang et al., 2012). Youxian sheldrake might be associated with the absence of OLR between tRNAAsn and
2
S.-P. He et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Characteristics of the mitochondrial genome of Youxian sheldrake. Position
Downloaded by [Monash University Library] at 04:42 21 September 2015
Gene D-loop tRNAPhe 12S rRNA tRNAVal 16S rRNA tRNALeu(CTM) ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn(AAY) tRNACys tRNATyr COX1 tRNASer(WSN) tRNAAsp COX2 tRNALys ATPase8 ATPase6 COX3 tRNAGly ND3 tRNAArg(MGR) ND4L ND4 tRNAHis tRNASer(TCN) tRNALeu(CTM) ND5 Cytb tRNAThr(ACW) tRNAPro ND6 tRNAGlu
Codon
Start
End
Size
1 1051 1121 2106 2177 3779 3857 4833 4912 4982 5051 6090 6169 6240 6313 6378 6451 7993 8068 8138 8826 8896 9054 9737 10,521 10,590 10,943 11,013 11,303 12,681 12,750 12,815 12,886 14,709 15,854 15,931 16,014 16,535
1050 1120 2105 2176 3778 3852 4833 4904 4982 5050 6089 6165 6237 6312 6378 6449 8000 8065 8136 8823 8894 9062 9736 10,519 10,589 10,940 11,012 11,308 12,679 12,749 12,815 12,885 14,708 15,850 15,922 16,002 16,534 16,605
1050 70 985 71 1602 74 977 72 71 69 1039 76 69 73 66 72 1550 73 69 686 69 167 683 783 69 351 70 296 1377 69 66 71 1823 1142 69 72 521 71
Start
Stop
Anti-codon
Strand
Space/overlap+
GAA
H H H H H H H L H H H L L L L H L H H H H H H H H H H H H H H H H H L L L
/ 0 0 0 0 0 4 –1 7 –1 0 0 3 2 0 –1 1 –8 2 1 2 1 –9 0 1 0 2 0 –6 1 0 –1 0 0 3 8 11 0
TAC GAG ATG
AGG TAT TTG CAT
ATG
T– – TCA TGC ATT GCA GTA
GTG
AGG CGA GTC
GTG
TAA
ATG ATG ATG
TAA TAA T– –
ATG
TAA
ATG ATG
TAA T– –
CTT
ACC TCT ATG TGA TAG GTG ATG
TAA TAA AGT AGG
ATG
TAG TTC
+
*T– – means incomplete termination codon. Negative numbers indicate overlapping nucleotides.
tRNACys genes, which failed to be folded up into OLR-like secondary structure.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. This research was supported by Hunan Provincial Natural Science Foundation of China (No. 12JJ8014).
References Anderson S, Bankier AT, Barrell BG, de Bruijn MHL, Coulson AR, Drouin J, Eperon IC, et al. (1981). Sequence and organization of the human mitochondrial genome. Nature 290:457–64. Tu J, Si F, Wu Q, Cong B, Xing X, Yang FH. (2014). The complete mitochondrial genome of the Muscovy duck, Cairina moschata (Anseriformes, Anatidae, Cairina). Mitochondrial DNA 25:102–3. Zhang HH, Ren Y, Chen L, Sha WL. (2012). The complete mitochondrial genome of scimitar-horned oryx (Oryx dammah). Mitochondrial DNA 23:361–2.
