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Asian-Australas J Anim Sci > Accepted
doi: https://doi.org/10.5713/ajas.16.0608    [Accepted]
The complete mitochondrial genome sequence of the indigenous I pig (Sus scrofa) in Vietnam
Hieu Duc Nguyen, Tuan Anh Bui1, Phuong Thanh Nguyen, Oanh Thi Phuong Kim, Thuy Thi Bich Vo
Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Viet Nam
1Institute of Forensic Science, 99, Nguyen Tuan, Thanh Xuan, Hanoi (100000), Vietnam., Hanoi, Viet Nam
Received: August 11, 2016;  Accepted: December 13, 2016.  Published online December 27, 2016.

Objective The I pig is a long nurtured longstanding breed in Vietnam, and contains excellent indigenous genetic resources. However, after 1970s, I pig breeds have become a small population because of decreasing farming areas and increasing pressure from foreign breeds with a high growth rate. Thus, there is now the risk of the disappearance of the I pigs breed. The aim of this study was to focus on classifying and identifying the I pig genetic origin and supplying molecular makers for conservation activities. Methods This study sequenced the complete mitochondrial genome and used the sequencing result to analyze the phylogenetic relationship of I pig with Asian and European domestic pigs and wild boars. The full sequence was annotated and predicted the secondary tRNA. Results The total length of I pig mitochondrial genome (accession number KX094894) was 16,731 base pairs, comprised two rRNA (12S and 16S), 22 tRNA and 13 mRNA genes. The annotation structures were not different from other pig breeds. Some component indexes as AT content, GC and AT skew were counted, in which AT content (60.09%) was smaller than other pigs. We built the phylogenetic trees from full sequence and D loop sequence using Bayesian method. The result showed that I pig, Banna mini, Wild boar (WB) Vietnam and WB Hainan or WB Korea, WB Japan were a cluster. They were a group within the Asian clade distinct from Chinese pigs and other Asian breeds in both phylogenetic trees (0.0004 and 0.0057, respectively). Conclusion These results were similar to previous phylogenic study in Vietnamese pig and showed the genetic distinctness of I pig with other Asian domestic pigs.
Keywords: Complete mitochondrial genome; Genetic distance; I pig; Mitochondrial DNA; Phylogenetic relationships
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