http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, 2015; 26(3): 483–484 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.880899
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Sus cebifrons (Sus, Suidae) Fang Liu1, Hong-Xia Tang2, Yong-Gang Liu3, Ming-Jie Bai4, and Yan-Xia Tang5 1
The Research Center of Life Sciences, Hebei North University, Zhangjiakou, Hebei, China, 2Department of Endocrinology, The First Hospital, Zhangjiakou, Hebei, China, 3Department of Surgical, The Maternal and Children Health Hospital, Zhangjiakou, Hebei, China, 4Operating Room, The Third Hospital, Zhangjiakou, Hebei, China, and 5Department of mathematics, College of Science, Hebei North University, Zhangjiakou, Hebei, China Abstract
Keywords
In this work, we report the complete mitochondrial genome sequence of Sus cebifrons (Visayan warty pig). The total length of the mitogenome was 16,475 bp, and its overall base composition was estimated to be 35.0% for A, 25.8% for T, 26.2% for C and 13.0% for G, indicating an A-T (60.8%)-rich feature in Sus cebifrons mitogenome. It contained the typical structure of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and a noncoding control region (D-loop region). The arrangement of these genes was the same as that found in other pigs. The complete mitochondrial genome sequence of the Sus cebifrons would provide new genetic resources for pig domestication study.
Mitochondrial genome, Sus cebifrons, Visayan warty pig
Many subspecies of wild boars have contributed to the breeding of the domestic pig, and there is a considerable species divergence between them (Giuffra et al., 2000; Kijas & Andersson, 2001). The domestication process has, to a large extent, been going on in parallel in Asia and Europe. The warty pig, represent one group of the Eurasian wild pigs. In this group, the Sus cebifrons (Visayan warty pig) is one of the endemic warty species that is already extinct or close to extinction on their original living islands/regions of the west Visayan region (Cox, 1987; Oliver, 1992; Oliver et al., 1993). Recent investigations suggest this species is also present in the South-East Asia (Lucchini et al., 2005). In this work, we reported the complete mitochondrial genome sequence of Sus cebifrons and deposited it in GenBank with the accession number: KF952600.
History Received 2 January 2014 Accepted 5 January 2014 Published online 4 February 2014
This mitochondrial genome was assembled from highthroughput sequencing data produced by Rubin et al. (2012). The total length of the mitogenome is 16,475 bp, with the base composition of 35.0% A, 25.8% T, 26.2% C, 13.0% G and an obvious A-T (60.8%)-rich feature (Table 1). It comprises 2 ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes and 1 non-coding control region (D-loop region), which is similar to other pigs (Xu et al., 2013). All the mitogenome genes were encoded on the H strand except for ND6 and eight tRNA genes. Except ND2, ND3 and ND5 using the start codon ATA and ND4L using GTG, other protein-coding genes use ATG as the start codon. These genes had four types of termination codon, six genes terminated with TAA, whereas ND1 and ND2 with TAG and CytB with AGA, and an incomplete termination
Table 1. List of genes encoded by Sus cebifrons mitochondrial genome. Position Gene D-loop tRNAPhe 12S rRNA tRNAVal 16S rRNA tRNALeu ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla
From 1 1045 1115 2073 2141 3712 3789 4744 4810 4884 4954 5996 6070
Base composition (%) To 1044 1114 2072 2140 3710 3786 4745 4812 4882 4953 5997 6063 6137
Size (bp)
A
C
G
T
1044 70 958 68 1570 75 957 69 73 70 1044 68 68
36.0 38.6 36.7 36.8 38.9 32.0 33.1 40.6 21.9 30.0 39.8 38.2 26.5
25.3 24.3 23.3 22.0 21.1 22.7 30.0 11.6 11.0 28.6 27.5 20.6 11.8
12.3 17.1 17.6 16.2 16.6 18.6 12.3 15.9 27.4 17.1 9.0 17.7 23.5
26.4 20.0 22.4 25.0 23.4 26.7 24.6 31.9 39.7 24.3 23.7 23.5 38.2
Start codon
Stop codon
Strand
ATG
TAG
ATA
TAG
H H H H H H H H L H H H L (continued )
Correspondence: Fang Liu. E-mail: [email protected]
484
F. Liu et al.
Mitochondrial DNA, 2015; 26(3): 483–484
Table 1. Continued
Position Gene Asn
tRNA tRNACys tRNATyr COX1 tRNASer tRNAAsp COX2 tRNALys ATP8 ATP6 COX3 tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer tRNALeu ND5 ND6 tRNAGlu Cyt b tRNAThr tRNAPro
Base composition (%)
From
To
Size (bp)
A
C
G
T
6139 6246 6312 6379 7927 8003 8071 8759 8827 8988 9668 10,452 10,521 10,868 10,937 11,227 12,599 12,668 12,727 12,797 14,601 15,129 15,202 16,342 16,409
6213 6311 6377 7923 7995 8070 8758 8825 9030 9668 10,451 10,520 10,866 10,936 11,233 12,598 12,667 12,726 12,796 14,617 15,128 15,197 16,341 16,409 16,473
75 66 66 1545 69 68 688 67 204 681 784 69 346 69 297 1372 69 59 70 1821 528 69 1140 68 65
28.0 25.7 33.3 29.1 24.6 35.3 34.3 29.8 40.7 34.5 29.1 37.7 34.7 42.0 32.7 34.5 42.0 32.2 38.6 35.1 20.6 27.5 32.1 33.8 18.5
14.7 18.2 18.2 24.9 16.0 13.2 24.6 22.4 23.0 29.1 27.7 18.8 29.5 13.1 26.3 29.5 10.2 23.7 17.1 28.5 8.0 13.1 29.4 25.0 13.8
24.0 25.8 22.7 16.8 29.0 16.2 13.1 20.9 7.4 9.8 15.2 13.1 10.7 8.7 11.4 9.9 11.6 15.3 18.6 10.4 27.3 21.7 12.5 19.1 30.8
33.3 30.3 25.8 29.2 30.4 35.3 28.0 26.9 28.9 26.6 28.0 30.4 25.1 36.2 29.6 26.1 36.2 28.8 25.7 26.0 44.1 37.7 26.0 22.1 36.9
codon T– – for COX2, COX3, ND3 and ND4. The 22 tRNA genes of Visayan warty pig ranged in size from 59 bp (tRNASer) to 75 bp (tRNALeu). The lengths of 12s rRNA and the 16s rRNA were 958 bp and 1570 bp. They were located between the tRNAPhe and tRNALeu genes and separated by the tRNAVal gene, and the result was the same as the other pigs. The control region of the Sus cebifrons mitochondrial DNA is located between the tRNAPhe and tRNAPro genes and measures 1044 bp. Since animal breeding became more organized in the eighteenth century, the selection goals in pigs have evolved in response to demand, and the genetic resources are quite valuable for breeding. The sequenced complete mitochondrial genome sequence of the Visayan warty pig would thus provide new resources for pig domestication (Rubin et al., 2012).
Acknowledgements We thank Rubin et al. for generating the sequence data of Sus cebifrons used in this study and the anonymous reviewers for providing valuable comments on the manuscript.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. This project was funded by the Cultivation of creative talents fund project, Hebei North University project (CXRC1306); Mandatory project
Start codon
Stop codon
ATG
TAA
ATG
T– –
ATG ATG ATG
TAA TAA T– –
ATA
T– –
GTG ATG
TAA T– –
ATA ATG
TAA TAA
ATG
AGA
Strand L L L H L H H H H H H H H H H H H H H H L L H H L
of Technology and Earthquakes local project (11110024D); and General Projects of Hebei North University (2013003).
References Cox R. (1987). The Philippine spotted deer and the Visayan warty pig. Oryx 21:37–42. ¨ , Jeon JT, Andersson L. Giuffra E, Kijas JMH, Amarger V, Carlborg O (2000). The origin of the domestic pig: Independent domestication and subsequent introgression. Genetics 154:1785–91. Kijas JMH, Andersson L. (2001). A phylogenetic study of the origin of the domestic pig estimated from the near-complete mtDNA genome. J Mol Evol 52:302–8. Lucchini V, Meijaard E, Diong CH, Groves CP, Randi E. (2005). New phylogenetic perspectives among species of South-east Asian wild pig (Sus sp.) based on mtDNA sequences and morphometric data. J Zool 266:25–35. Oliver WL. (1992). The taxonomy, distribution and status of Philippine wild pigs. Silliman J 36:55–64. Oliver WL, Cox CR, Groves CP. (1993). The Philippine warty pigs (Sus philippensis and S. cebifrons). In: Oliver WLR, editor. Status survey and conservation action plan: Pigs, peccaries and hippos. Gland, Switzerland: International Union for Conservation for Nature. p 145–54. Rubin CJ, Megens HJ, Barrio AM, Maqbool K, Sayyab S, Schwochow D, Wanga C, et al. (2012). Strong signatures of selection in the domestic pig genome. Proc Natl Acad Sci USA 109:19529–36. Xu D, Li QH, He CQ, Chai YL, Ma HM. (2013). The complete mitochondrial genome of the Ningxiang pig. Mitochondrial DNA 24:1–2. doi: 10.3109/19401736.2013.834433.
Copyright of Mitochondrial DNA: The Journal of DNA Mapping, Sequencing & Analysis is the property of Taylor & Francis Ltd and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use.
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Sus cebifrons (Sus, Suidae) Fang Liu1, Hong-Xia Tang2, Yong-Gang Liu3, Ming-Jie Bai4, and Yan-Xia Tang5 1
The Research Center of Life Sciences, Hebei North University, Zhangjiakou, Hebei, China, 2Department of Endocrinology, The First Hospital, Zhangjiakou, Hebei, China, 3Department of Surgical, The Maternal and Children Health Hospital, Zhangjiakou, Hebei, China, 4Operating Room, The Third Hospital, Zhangjiakou, Hebei, China, and 5Department of mathematics, College of Science, Hebei North University, Zhangjiakou, Hebei, China Abstract
Keywords
In this work, we report the complete mitochondrial genome sequence of Sus cebifrons (Visayan warty pig). The total length of the mitogenome was 16,475 bp, and its overall base composition was estimated to be 35.0% for A, 25.8% for T, 26.2% for C and 13.0% for G, indicating an A-T (60.8%)-rich feature in Sus cebifrons mitogenome. It contained the typical structure of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and a noncoding control region (D-loop region). The arrangement of these genes was the same as that found in other pigs. The complete mitochondrial genome sequence of the Sus cebifrons would provide new genetic resources for pig domestication study.
Mitochondrial genome, Sus cebifrons, Visayan warty pig
Many subspecies of wild boars have contributed to the breeding of the domestic pig, and there is a considerable species divergence between them (Giuffra et al., 2000; Kijas & Andersson, 2001). The domestication process has, to a large extent, been going on in parallel in Asia and Europe. The warty pig, represent one group of the Eurasian wild pigs. In this group, the Sus cebifrons (Visayan warty pig) is one of the endemic warty species that is already extinct or close to extinction on their original living islands/regions of the west Visayan region (Cox, 1987; Oliver, 1992; Oliver et al., 1993). Recent investigations suggest this species is also present in the South-East Asia (Lucchini et al., 2005). In this work, we reported the complete mitochondrial genome sequence of Sus cebifrons and deposited it in GenBank with the accession number: KF952600.
History Received 2 January 2014 Accepted 5 January 2014 Published online 4 February 2014
This mitochondrial genome was assembled from highthroughput sequencing data produced by Rubin et al. (2012). The total length of the mitogenome is 16,475 bp, with the base composition of 35.0% A, 25.8% T, 26.2% C, 13.0% G and an obvious A-T (60.8%)-rich feature (Table 1). It comprises 2 ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes and 1 non-coding control region (D-loop region), which is similar to other pigs (Xu et al., 2013). All the mitogenome genes were encoded on the H strand except for ND6 and eight tRNA genes. Except ND2, ND3 and ND5 using the start codon ATA and ND4L using GTG, other protein-coding genes use ATG as the start codon. These genes had four types of termination codon, six genes terminated with TAA, whereas ND1 and ND2 with TAG and CytB with AGA, and an incomplete termination
Table 1. List of genes encoded by Sus cebifrons mitochondrial genome. Position Gene D-loop tRNAPhe 12S rRNA tRNAVal 16S rRNA tRNALeu ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla
From 1 1045 1115 2073 2141 3712 3789 4744 4810 4884 4954 5996 6070
Base composition (%) To 1044 1114 2072 2140 3710 3786 4745 4812 4882 4953 5997 6063 6137
Size (bp)
A
C
G
T
1044 70 958 68 1570 75 957 69 73 70 1044 68 68
36.0 38.6 36.7 36.8 38.9 32.0 33.1 40.6 21.9 30.0 39.8 38.2 26.5
25.3 24.3 23.3 22.0 21.1 22.7 30.0 11.6 11.0 28.6 27.5 20.6 11.8
12.3 17.1 17.6 16.2 16.6 18.6 12.3 15.9 27.4 17.1 9.0 17.7 23.5
26.4 20.0 22.4 25.0 23.4 26.7 24.6 31.9 39.7 24.3 23.7 23.5 38.2
Start codon
Stop codon
Strand
ATG
TAG
ATA
TAG
H H H H H H H H L H H H L (continued )
Correspondence: Fang Liu. E-mail: [email protected]
484
F. Liu et al.
Mitochondrial DNA, 2015; 26(3): 483–484
Table 1. Continued
Position Gene Asn
tRNA tRNACys tRNATyr COX1 tRNASer tRNAAsp COX2 tRNALys ATP8 ATP6 COX3 tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer tRNALeu ND5 ND6 tRNAGlu Cyt b tRNAThr tRNAPro
Base composition (%)
From
To
Size (bp)
A
C
G
T
6139 6246 6312 6379 7927 8003 8071 8759 8827 8988 9668 10,452 10,521 10,868 10,937 11,227 12,599 12,668 12,727 12,797 14,601 15,129 15,202 16,342 16,409
6213 6311 6377 7923 7995 8070 8758 8825 9030 9668 10,451 10,520 10,866 10,936 11,233 12,598 12,667 12,726 12,796 14,617 15,128 15,197 16,341 16,409 16,473
75 66 66 1545 69 68 688 67 204 681 784 69 346 69 297 1372 69 59 70 1821 528 69 1140 68 65
28.0 25.7 33.3 29.1 24.6 35.3 34.3 29.8 40.7 34.5 29.1 37.7 34.7 42.0 32.7 34.5 42.0 32.2 38.6 35.1 20.6 27.5 32.1 33.8 18.5
14.7 18.2 18.2 24.9 16.0 13.2 24.6 22.4 23.0 29.1 27.7 18.8 29.5 13.1 26.3 29.5 10.2 23.7 17.1 28.5 8.0 13.1 29.4 25.0 13.8
24.0 25.8 22.7 16.8 29.0 16.2 13.1 20.9 7.4 9.8 15.2 13.1 10.7 8.7 11.4 9.9 11.6 15.3 18.6 10.4 27.3 21.7 12.5 19.1 30.8
33.3 30.3 25.8 29.2 30.4 35.3 28.0 26.9 28.9 26.6 28.0 30.4 25.1 36.2 29.6 26.1 36.2 28.8 25.7 26.0 44.1 37.7 26.0 22.1 36.9
codon T– – for COX2, COX3, ND3 and ND4. The 22 tRNA genes of Visayan warty pig ranged in size from 59 bp (tRNASer) to 75 bp (tRNALeu). The lengths of 12s rRNA and the 16s rRNA were 958 bp and 1570 bp. They were located between the tRNAPhe and tRNALeu genes and separated by the tRNAVal gene, and the result was the same as the other pigs. The control region of the Sus cebifrons mitochondrial DNA is located between the tRNAPhe and tRNAPro genes and measures 1044 bp. Since animal breeding became more organized in the eighteenth century, the selection goals in pigs have evolved in response to demand, and the genetic resources are quite valuable for breeding. The sequenced complete mitochondrial genome sequence of the Visayan warty pig would thus provide new resources for pig domestication (Rubin et al., 2012).
Acknowledgements We thank Rubin et al. for generating the sequence data of Sus cebifrons used in this study and the anonymous reviewers for providing valuable comments on the manuscript.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. This project was funded by the Cultivation of creative talents fund project, Hebei North University project (CXRC1306); Mandatory project
Start codon
Stop codon
ATG
TAA
ATG
T– –
ATG ATG ATG
TAA TAA T– –
ATA
T– –
GTG ATG
TAA T– –
ATA ATG
TAA TAA
ATG
AGA
Strand L L L H L H H H H H H H H H H H H H H H L L H H L
of Technology and Earthquakes local project (11110024D); and General Projects of Hebei North University (2013003).
References Cox R. (1987). The Philippine spotted deer and the Visayan warty pig. Oryx 21:37–42. ¨ , Jeon JT, Andersson L. Giuffra E, Kijas JMH, Amarger V, Carlborg O (2000). The origin of the domestic pig: Independent domestication and subsequent introgression. Genetics 154:1785–91. Kijas JMH, Andersson L. (2001). A phylogenetic study of the origin of the domestic pig estimated from the near-complete mtDNA genome. J Mol Evol 52:302–8. Lucchini V, Meijaard E, Diong CH, Groves CP, Randi E. (2005). New phylogenetic perspectives among species of South-east Asian wild pig (Sus sp.) based on mtDNA sequences and morphometric data. J Zool 266:25–35. Oliver WL. (1992). The taxonomy, distribution and status of Philippine wild pigs. Silliman J 36:55–64. Oliver WL, Cox CR, Groves CP. (1993). The Philippine warty pigs (Sus philippensis and S. cebifrons). In: Oliver WLR, editor. Status survey and conservation action plan: Pigs, peccaries and hippos. Gland, Switzerland: International Union for Conservation for Nature. p 145–54. Rubin CJ, Megens HJ, Barrio AM, Maqbool K, Sayyab S, Schwochow D, Wanga C, et al. (2012). Strong signatures of selection in the domestic pig genome. Proc Natl Acad Sci USA 109:19529–36. Xu D, Li QH, He CQ, Chai YL, Ma HM. (2013). The complete mitochondrial genome of the Ningxiang pig. Mitochondrial DNA 24:1–2. doi: 10.3109/19401736.2013.834433.
Copyright of Mitochondrial DNA: The Journal of DNA Mapping, Sequencing & Analysis is the property of Taylor & Francis Ltd and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use.
