http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–3 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.987249
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of the Wugangtong white goose Gui-Tao Jiang1*, Qian Lin1,2*, Ping He1, Xu Zhang1, Long Yun2, Xia Li2, Geng Liu2, Chuang Li1, Xi He2, and Qiu-Zhong Dai1,2 1
Department of Animal Nutrition and Feeding Technology, Hunan Institute of Animal Science and Veterinary Medicine, Changsha, P.R. China and College of Animal Science and Technology, Hunan Agricultural University, Changsha, P.R. China
Mitochondrial DNA Downloaded from informahealthcare.com by University of Washington on 03/23/15 For personal use only.
2
Abstract
Keywords
Wugangtong white goose is one of the famous native breed in Hunan province of China. In this study, the complete mitochondrial genome sequence of the Wugangtong white goose was reported in Hunan Province first, which was determined through PCR-based method. The total length of the mitogenome is 16,741 bp. It contains the typical structure, including 2 ribosomal RNA genes, 22 transfer RNA genes, 13 protein-coding genes and 1 non-coding control region (D-loop region) as that of most other vertebrates. The overall composition of the mitogenome was estimated to be 30.22% for A, 22.69% for T, 32.02% for C and 15.06% for G. All the protein initiation codons are ATG, except for COX1, COX2 and ND5 are GTG, ND6 is CTA. The complete mitochondrial genome sequence of the Wugangtong white goose will provide an important data set for the study in genetic mechanism of Wugangtong goose in Hunan province.
Genome, mitochondrial, PCR-based method, Wugangtong white goose
Wugangtong white goose (Anser cygnoides Linn. var domestica), popularly named as Wuganghuangtong goose, is one of the famous indigenous breeds of geese in Hunan Province of China, which has been bred in Wugang county. The features of Wugangtong white goose is fast growth and better quality of meat (Qu et al., 2013). In this study complete mitochondrial DNA (mtDNA) sequence of Wugangtong white goose has been determined, which has been registered in GenBank under accession number KP026178. The goose was farmed at the Wugangtong goose conservation farms (Shaoyang City, Hunan
History Received 3 November 2014 Accepted 10 November 2014 Published online 10 December 2014
Province, China). Mitochondrial DNA of Wugangtong white goose was extracted using the EasyPure Kit of Genomic DNA (Transgen Biotech, Beijing, China) according to its instruction manual. Polymerase chain reaction (PCR) was carried out to amplify the complete mitochondrial genome with 11 pairs of primers. PCR products of the Gel electrophoresis were purified by Gel AdvancedTM Gel Extraction (Rich Biotech, Taiwan, China) and sequenced by BioSune Biotech (Shanghai, China). DNA sequence was analyzed using DNAStar.Lasergene.v7.1 software (Madison, WI). The base composition and distribution of
Table 1. Organization of the mitochondrial genome of the Wugangtong white goose. Position Gene D-loop tRNAPhe 12S rRNA tRNAVal 16S rRNA tRNALeu ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp
Start 1 1178 1246 2234 2305 3915 3995 4971 5051 5121 5190 6229
Codon End
Size
1177 1245 2233 2304 3914 3988 4972 5043 5121 5189 6230 6301
1177 68 988 71 1610 74 978 73 71 69 1041 73
Start
Stop
Anti-codon
Strand
GAA
H H H H H H H L H H H
TAC TAA ATG
AGG GAT TTG CAT
ATG
TAG TCA
Space/overlap+
6 2 7 1 2 (continued )
*These two authors contributed equally to this study and share first authorship. Correspondence: Qiu-Zhong Dai, Department of Animal Nutrition and Feeding Technology, Hunan Institute of Animal Science and Veterinary Medicine, Changsha 410131, P.R. China. E-mail: [email protected]
2
G.-T. Jiang et al.
Mitochondrial DNA, Early Online: 1–3
Table 1. Continued.
Position Gene
Mitochondrial DNA Downloaded from informahealthcare.com by University of Washington on 03/23/15 For personal use only.
Ala
tRNA tRNAAsn tRNACys tRNATyr COX1 tRNASer tRNAAsp COX2 tRNALys ATPase8 ATPase6 COX3 tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer tRNALeu ND5 Cytb tRNAThr tRNAPro ND6 tRNAGlu
Codon
Start
End
Size
6307 6377 6453 6518 6590 8132 8207 8277 8965 9035 9193 9876 10,660 10,729 11,082 11,153 11,443 12,821 12,890 12,956 13,027 14,852 15,997 16,073 16,152 16,674
6375 6449 6518 6588 8140 8204 8275 8963 9033 9202 9876 10,659 10,728 11,080 11,152 11,449 12,820 12,889 12,956 13,026 14,844 15,994 16,072 16,141 16,673 16,741
69 73 66 71 1551 73 69 687 69 168 684 784 69 352 71 297 1378 69 67 71 1818 1143 76 69 522 68
Start
GTG
Stop
Anti-codon
Strand
TGC GTT GCA GTA
L L L L H L H H H H H H H H H H H H L H H H H L L L
AGG TGA GTC
GTG
TAA
ATG ATG ATG
TAA TAA T– –
ATG
TAG
ATG ATG
TAA T– –
TTT
TCC TCG GTG AGA TAG GTG ATG
AGA TAA TGT TGG
CTA
CAT TTC
Space/overlap+ 5 1 3 1 1 9 2 1 1 1 10 1 1 7 1 7 2 10
T– – means incomplete termination codon. +Negative numbers indicate overlapping nucleotides.
mitochondrial DNA sequence was analyzed using tRNA ScanSE1.21 software (http://lowelab.ucsc.edu/tRNAScan-SE/) (Lowe & Eddy, 1997) and DOGMA software (http://dogma.ccbb.utexas.edu/; Wyman et al., 2004). The total length of the mitogenome is 16,741 bp. It contains the typical structure, including 2 ribosomal RNA genes, 22 transfer RNA genes, 13 protein-coding genes and 1 non-coding control region (D-loop region) as that of most other vertebrates. The overall composition of the mitogenome was estimated to be 30.22% for A, 22.69% for T, 32.02% for C and 15.06% for G. And the percentage of A and T (52.91%) was higher than G and C (47.08%). All the protein initiation codons are ATG, except for COX1, COX2 and ND5 are GTG, ND6 is CTA (Table 1). All the mitogenome genes were encoded on the heavy (H) strand except for eight tRNA genes (tRNAGln, tRNAAla, tRNAAsn, tRNACys, tRNATyr, tRNASer, tRNAPro and tRNAGlu) and one protein-coding gene (ND6). Like other native goose breed in Hunan Province, all these genes had 9 overlaps and 14 spaces in the length of 1–10 bp (Lin et al., 2014a,b,c). These genes had six types of termination codon, including AGA for ND5, TAG for ND2 and ND3, TAA for COX2, ATPase8, ATPase6, ND4L and Cytb, CAT for ND6, AGG for ND1 and COX1, and an incomplete termination codon ‘‘T– – ’’ for COX3 and ND4, ‘‘T– –’’ is the 5’ terminal of the adjacent gene (Anderson et al., 1981). The lengths of 12s rRNA and the 16s rRNA were 988 bp and 1610 bp. They were located between the tRNAPhe and tRNALeu genes and separated by the tRNAVal gene, and the result was similar to other vertebrates. The total length of the 13 protein-coding genes is 11,403 bp, which represents 68.11% of the entire mitochondrial genome. Among 13 protein-coding genes, the longest one was ND5 gene (1818 bp), which was located between the tRNALeu and Cytb, and the shortest one was ATPase8 gene(168 bp), which was located between the tRNALys and ATPase6. And deduced 22 tRNA genes were distributed in rRNA and protein-coding genes,
ranging from 66 to 76 bp in size. And the longest tRNA is tRNAThr (76 bp), and the shortest is tRNACys (66 bp). The mitochondrial DNA D-loop region of the Wugangtong white goose was located between tRNAGlu and tRNAphe with a length of 1177 bp. The putative origin for light strand replication (OLR) had been identified in the tRNATrp-tRNAAla-tRNAAsn-tRNACystRNATyr region (WANCY) of most vertebrates (Lin et al., 2014; Wang et al., 2008; Zhang et al., 2012). However, Wugangtong white goose might be associated with the deletion of OLR. The length of 3 bp was located between tRNAAsn and tRNACys genes, which cannot be folded up into an OLR-like secondary structure (Table 1).
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 Modern Agricultural Technical System Foundation of China (CARS-43-39).
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. Lin Q, Cao R, Jiang GT, Qiu L, Hu GB, Dai QZ, Zhang SR, et al. (2014a). The complete mitochondrial genome of the Xupu goose. Mitochondrial DNA 18:1–2. [Epub ahead of print]. doi: 10.3109/19401736.2014. 926528. Lin Q, Cao R, Jiang GT, Liu G, Dai QZ, Zhang SR, Hou DX, He X. (2014b). Determination and analysis of the complete mitochondrial genome sequence of Yanling white goose. Mitochondrial DNA [Epub ahead of print]. doi: 10.3109/19401736.2014.926529. Lin Q, Jiang GT, Cao R, Yun L, Li GJ, Dai QZ, Zhang SR, et al. (2014c). Determination and analysis of the complete mitochondrial genome sequence of Wugangtong grey goose. Mitochondrial DNA [Epub ahead of print]. doi: 10.3109/19401736.2014.926527.
DOI: 10.3109/19401736.2014.987249
Mitochondrial DNA Downloaded from informahealthcare.com by University of Washington on 03/23/15 For personal use only.
Lowe TM, Eddy SR. (1997). tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–64. Qu XY, He J, He CQ, Jin H, Yang DD, Zhu LT, Fan ZY, et al. (2013). Comparison of meat quality characteristic between Wugang bronze geese and other three types of geese. Chin J Anim Nutr 25:2277–85. Wang CH, Chen Q, Lu GQ, Xu JW, Yang QL, Li SF. (2008). Complete mitochondrial genome of the grass carp (Ctenopharyngodon idella,
Complete mitogenome of the Wugangtong white goose
3
Teleostei): Insight into its phylogenic position within Cyprinidae. Gene 424:96–101. Wyman SK, Jansen RK, Boore JL. (2004). Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20: 3252–5. Zhang HH, Ren Y, Chen L, Sha WL. (2012). The complete mitochondrial genome of scimitar-horned oryx (Oryx dammah). Mitochondrial DNA 23:361–2.
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of the Wugangtong white goose Gui-Tao Jiang1*, Qian Lin1,2*, Ping He1, Xu Zhang1, Long Yun2, Xia Li2, Geng Liu2, Chuang Li1, Xi He2, and Qiu-Zhong Dai1,2 1
Department of Animal Nutrition and Feeding Technology, Hunan Institute of Animal Science and Veterinary Medicine, Changsha, P.R. China and College of Animal Science and Technology, Hunan Agricultural University, Changsha, P.R. China
Mitochondrial DNA Downloaded from informahealthcare.com by University of Washington on 03/23/15 For personal use only.
2
Abstract
Keywords
Wugangtong white goose is one of the famous native breed in Hunan province of China. In this study, the complete mitochondrial genome sequence of the Wugangtong white goose was reported in Hunan Province first, which was determined through PCR-based method. The total length of the mitogenome is 16,741 bp. It contains the typical structure, including 2 ribosomal RNA genes, 22 transfer RNA genes, 13 protein-coding genes and 1 non-coding control region (D-loop region) as that of most other vertebrates. The overall composition of the mitogenome was estimated to be 30.22% for A, 22.69% for T, 32.02% for C and 15.06% for G. All the protein initiation codons are ATG, except for COX1, COX2 and ND5 are GTG, ND6 is CTA. The complete mitochondrial genome sequence of the Wugangtong white goose will provide an important data set for the study in genetic mechanism of Wugangtong goose in Hunan province.
Genome, mitochondrial, PCR-based method, Wugangtong white goose
Wugangtong white goose (Anser cygnoides Linn. var domestica), popularly named as Wuganghuangtong goose, is one of the famous indigenous breeds of geese in Hunan Province of China, which has been bred in Wugang county. The features of Wugangtong white goose is fast growth and better quality of meat (Qu et al., 2013). In this study complete mitochondrial DNA (mtDNA) sequence of Wugangtong white goose has been determined, which has been registered in GenBank under accession number KP026178. The goose was farmed at the Wugangtong goose conservation farms (Shaoyang City, Hunan
History Received 3 November 2014 Accepted 10 November 2014 Published online 10 December 2014
Province, China). Mitochondrial DNA of Wugangtong white goose was extracted using the EasyPure Kit of Genomic DNA (Transgen Biotech, Beijing, China) according to its instruction manual. Polymerase chain reaction (PCR) was carried out to amplify the complete mitochondrial genome with 11 pairs of primers. PCR products of the Gel electrophoresis were purified by Gel AdvancedTM Gel Extraction (Rich Biotech, Taiwan, China) and sequenced by BioSune Biotech (Shanghai, China). DNA sequence was analyzed using DNAStar.Lasergene.v7.1 software (Madison, WI). The base composition and distribution of
Table 1. Organization of the mitochondrial genome of the Wugangtong white goose. Position Gene D-loop tRNAPhe 12S rRNA tRNAVal 16S rRNA tRNALeu ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp
Start 1 1178 1246 2234 2305 3915 3995 4971 5051 5121 5190 6229
Codon End
Size
1177 1245 2233 2304 3914 3988 4972 5043 5121 5189 6230 6301
1177 68 988 71 1610 74 978 73 71 69 1041 73
Start
Stop
Anti-codon
Strand
GAA
H H H H H H H L H H H
TAC TAA ATG
AGG GAT TTG CAT
ATG
TAG TCA
Space/overlap+
6 2 7 1 2 (continued )
*These two authors contributed equally to this study and share first authorship. Correspondence: Qiu-Zhong Dai, Department of Animal Nutrition and Feeding Technology, Hunan Institute of Animal Science and Veterinary Medicine, Changsha 410131, P.R. China. E-mail: [email protected]
2
G.-T. Jiang et al.
Mitochondrial DNA, Early Online: 1–3
Table 1. Continued.
Position Gene
Mitochondrial DNA Downloaded from informahealthcare.com by University of Washington on 03/23/15 For personal use only.
Ala
tRNA tRNAAsn tRNACys tRNATyr COX1 tRNASer tRNAAsp COX2 tRNALys ATPase8 ATPase6 COX3 tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer tRNALeu ND5 Cytb tRNAThr tRNAPro ND6 tRNAGlu
Codon
Start
End
Size
6307 6377 6453 6518 6590 8132 8207 8277 8965 9035 9193 9876 10,660 10,729 11,082 11,153 11,443 12,821 12,890 12,956 13,027 14,852 15,997 16,073 16,152 16,674
6375 6449 6518 6588 8140 8204 8275 8963 9033 9202 9876 10,659 10,728 11,080 11,152 11,449 12,820 12,889 12,956 13,026 14,844 15,994 16,072 16,141 16,673 16,741
69 73 66 71 1551 73 69 687 69 168 684 784 69 352 71 297 1378 69 67 71 1818 1143 76 69 522 68
Start
GTG
Stop
Anti-codon
Strand
TGC GTT GCA GTA
L L L L H L H H H H H H H H H H H H L H H H H L L L
AGG TGA GTC
GTG
TAA
ATG ATG ATG
TAA TAA T– –
ATG
TAG
ATG ATG
TAA T– –
TTT
TCC TCG GTG AGA TAG GTG ATG
AGA TAA TGT TGG
CTA
CAT TTC
Space/overlap+ 5 1 3 1 1 9 2 1 1 1 10 1 1 7 1 7 2 10
T– – means incomplete termination codon. +Negative numbers indicate overlapping nucleotides.
mitochondrial DNA sequence was analyzed using tRNA ScanSE1.21 software (http://lowelab.ucsc.edu/tRNAScan-SE/) (Lowe & Eddy, 1997) and DOGMA software (http://dogma.ccbb.utexas.edu/; Wyman et al., 2004). The total length of the mitogenome is 16,741 bp. It contains the typical structure, including 2 ribosomal RNA genes, 22 transfer RNA genes, 13 protein-coding genes and 1 non-coding control region (D-loop region) as that of most other vertebrates. The overall composition of the mitogenome was estimated to be 30.22% for A, 22.69% for T, 32.02% for C and 15.06% for G. And the percentage of A and T (52.91%) was higher than G and C (47.08%). All the protein initiation codons are ATG, except for COX1, COX2 and ND5 are GTG, ND6 is CTA (Table 1). All the mitogenome genes were encoded on the heavy (H) strand except for eight tRNA genes (tRNAGln, tRNAAla, tRNAAsn, tRNACys, tRNATyr, tRNASer, tRNAPro and tRNAGlu) and one protein-coding gene (ND6). Like other native goose breed in Hunan Province, all these genes had 9 overlaps and 14 spaces in the length of 1–10 bp (Lin et al., 2014a,b,c). These genes had six types of termination codon, including AGA for ND5, TAG for ND2 and ND3, TAA for COX2, ATPase8, ATPase6, ND4L and Cytb, CAT for ND6, AGG for ND1 and COX1, and an incomplete termination codon ‘‘T– – ’’ for COX3 and ND4, ‘‘T– –’’ is the 5’ terminal of the adjacent gene (Anderson et al., 1981). The lengths of 12s rRNA and the 16s rRNA were 988 bp and 1610 bp. They were located between the tRNAPhe and tRNALeu genes and separated by the tRNAVal gene, and the result was similar to other vertebrates. The total length of the 13 protein-coding genes is 11,403 bp, which represents 68.11% of the entire mitochondrial genome. Among 13 protein-coding genes, the longest one was ND5 gene (1818 bp), which was located between the tRNALeu and Cytb, and the shortest one was ATPase8 gene(168 bp), which was located between the tRNALys and ATPase6. And deduced 22 tRNA genes were distributed in rRNA and protein-coding genes,
ranging from 66 to 76 bp in size. And the longest tRNA is tRNAThr (76 bp), and the shortest is tRNACys (66 bp). The mitochondrial DNA D-loop region of the Wugangtong white goose was located between tRNAGlu and tRNAphe with a length of 1177 bp. The putative origin for light strand replication (OLR) had been identified in the tRNATrp-tRNAAla-tRNAAsn-tRNACystRNATyr region (WANCY) of most vertebrates (Lin et al., 2014; Wang et al., 2008; Zhang et al., 2012). However, Wugangtong white goose might be associated with the deletion of OLR. The length of 3 bp was located between tRNAAsn and tRNACys genes, which cannot be folded up into an OLR-like secondary structure (Table 1).
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 Modern Agricultural Technical System Foundation of China (CARS-43-39).
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. Lin Q, Cao R, Jiang GT, Qiu L, Hu GB, Dai QZ, Zhang SR, et al. (2014a). The complete mitochondrial genome of the Xupu goose. Mitochondrial DNA 18:1–2. [Epub ahead of print]. doi: 10.3109/19401736.2014. 926528. Lin Q, Cao R, Jiang GT, Liu G, Dai QZ, Zhang SR, Hou DX, He X. (2014b). Determination and analysis of the complete mitochondrial genome sequence of Yanling white goose. Mitochondrial DNA [Epub ahead of print]. doi: 10.3109/19401736.2014.926529. Lin Q, Jiang GT, Cao R, Yun L, Li GJ, Dai QZ, Zhang SR, et al. (2014c). Determination and analysis of the complete mitochondrial genome sequence of Wugangtong grey goose. Mitochondrial DNA [Epub ahead of print]. doi: 10.3109/19401736.2014.926527.
DOI: 10.3109/19401736.2014.987249
Mitochondrial DNA Downloaded from informahealthcare.com by University of Washington on 03/23/15 For personal use only.
Lowe TM, Eddy SR. (1997). tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–64. Qu XY, He J, He CQ, Jin H, Yang DD, Zhu LT, Fan ZY, et al. (2013). Comparison of meat quality characteristic between Wugang bronze geese and other three types of geese. Chin J Anim Nutr 25:2277–85. Wang CH, Chen Q, Lu GQ, Xu JW, Yang QL, Li SF. (2008). Complete mitochondrial genome of the grass carp (Ctenopharyngodon idella,
Complete mitogenome of the Wugangtong white goose
3
Teleostei): Insight into its phylogenic position within Cyprinidae. Gene 424:96–101. Wyman SK, Jansen RK, Boore JL. (2004). Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20: 3252–5. Zhang HH, Ren Y, Chen L, Sha WL. (2012). The complete mitochondrial genome of scimitar-horned oryx (Oryx dammah). Mitochondrial DNA 23:361–2.
