Characterization of complete mitochondrial genome of Dezhou donkey (Equus asinus) and evolutionary analysis

被引：20

作者：

Sun, Yan ^{[1
]}

Jiang, Qiang ^{[1
]}

Yang, Chunhong ^{[1
]}

Wang, Xiuge ^{[1
]}

Tian, Fang ^{[2
]}

Wang, Yinchao ^{[2
]}

Ma, Yong ^{[3
]}

Ju, Zhihua ^{[1
]}

Huang, Jinming ^{[1
]}

Zhou, Xiangshan ^{[2
]}

Zhong, Jifeng ^{[1
]}

Wang, Changfa ^{[1
]}

机构：

[1] Shandong Acad Agr Sci, Dairy Cattle Res Ctr, 159 Ind North Rd, Jinan 250131, Shandong, Peoples R China

[2] Dong EE Jiao Co Ltd, Liaocheng 252201, Dong E County, Peoples R China

[3] BGI Shenzhen, Shenzhen 518083, Peoples R China

来源：

CURRENT GENETICS | 2016年 / 62卷 / 02期

关键词：

Dezhou donkey; Mitochondrial genome; Annotation; Phylogenetic analysis; SEQUENCE; HORSE;

D O I：

10.1007/s00294-015-0531-9

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

Mitochondrial DNA (mtDNA) has been widely used in species identification and genetic diversification. Comparisons among mtDNAs of closely related species are valuable for phylogenetic studies. However, only the partial mtDNA Cytb gene and the D-loop sequences were used to analysis the phylogenetic relationship between donkey breeds due to lack of complete mitochondrial genome. Dezhou donkey, as a bigger somatotype ass, is one of Chinese domestic donkey breeds, and used by many places as breeding stock. To further investigate the phylogenetic relationship of Dezhou donkey with other breeds, the complete mtDNA was firstly sequenced and de novo assembled using next generation sequence data from total genomic DNA. The genome was 16,813 bp in length (NCBI submission number: KT182635) and contained 13 protein coding genes, 2 ribosomal RNA genes, 25 transfer RNA genes, and 1 control region. Based on the novel complete mtDNA sequence, the sequences of 13 protein coding genes and 2 ribosomal RNA genes were amplifying in other 2 Dezhou donkeys and 3 Yunnan donkeys, respectively. The pattern of genetic variation in horse, wild ass and domestic donkeys among these 15 genes indicated the sequence polymorphisms. The more accurate phylogenetic relationships of donkey species (Dezhou donkey, Yunnan donkey and previously published donkeys) were first obtained using the combined sequences of 12S rRNA+16S rRNA+13 protein-coding genes. Molecular-based phylogeny supported the hypothesis that Chinese domestic donkey breeds may have originated from Somali wild ass, not from Asian wild ass by analyzing mitochondrial genomes.

引用

页码：383 / 390

页数：8

共 27 条

[1] Mitochondrial genomes from modern horses reveal the major haplogroups that underwent domestication [J].

Achilli, Alessandro ;

Olivieri, Anna ;

Soares, Pedro ;

Lancioni, Hovirag ;

Kashani, Baharak Hooshiar ;

Perego, Ugo A. ;

Nergadze, Solomon G. ;

Carossa, Valeria ;

Santagostino, Marco ;

Capomaccio, Stefano ;

Felicetti, Michela ;

Al-Achkar, Walid ;

Penedo, M. Cecilia T. ;

Verini-Supplizi, Andrea ;

Houshmand, Massoud ;

Woodward, Scott R. ;

Semino, Ornella ;

Silvestrelli, Maurizio ;

Giulotto, Elena ;

Pereira, Luisa ;

Bandelt, Hans-Juergen ;

Torroni, Antonio .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2012, 109 (07) :2449-2454

[2] Mitochondrial DNA variation and genetic relationships in Spanish donkey breeds (Equus asinus) [J].

Aranguren-Mendez, J ;

Beja-Pereira, A ;

Avellanet, R ;

Dzama, K ;

Jordana, J .

JOURNAL OF ANIMAL BREEDING AND GENETICS, 2004, 121 (05) :319-330

[3] African origins of the domestic donkey [J].

Beja-Pereira, A ;

England, PR ;

Ferrand, N ;

Jordan, S ;

Bakhiet, AO ;

Abdalla, MA ;

Mashkour, M ;

Jordana, J ;

Taberlet, P ;

Luikart, G .

SCIENCE, 2004, 304 (5678) :1781-1781

[4] Mitochondrial DNA diversity and population structure of four Chinese donkey breeds [J].

Chen, S. Y. ;

Zhou, F. ;

Xiao, H. ;

Sha, T. ;

Wu, S. F. ;

Zhang, Y. P. .

ANIMAL GENETICS, 2006, 37 (04) :427-429

[5] Mitochondrial genome of the basidiomycetous yeast Jaminaea angkorensis [J].

Hegedusova, Eva ;

Brejova, Brona ;

Tomaska, Lubomir ;

Sipiczki, Matthias ;

Nosek, Jozef .

CURRENT GENETICS, 2014, 60 (01) :49-59

[6] De novo assembly of the carrot mitochondrial genome using next generation sequencing of whole genomic DNA provides first evidence of DNA transfer into an angiosperm plastid genome [J].

Iorizzo, Massimo ;

Senalik, Douglas ;

Szklarczyk, Marek ;

Grzebelus, Dariusz ;

Spooner, David ;

Simon, Philipp .

BMC PLANT BIOLOGY, 2012, 12

[7] Speciation with gene flow in equids despite extensive chromosomal plasticity [J].

Jonsson, Hakon ;

Schubert, Mikkel ;

Seguin-Orlando, Andaine ;

Ginolhac, Aurelien ;

Petersen, Lillian ;

Fumagalli, Matteo ;

Albrechtsen, Anders ;

Petersen, Bent ;

Korneliussen, Thorfinn S. ;

Vilstrup, Julia T. ;

Lear, Teri ;

Myka, Jennifer Leigh ;

Lundquist, Judith ;

Miller, Donald C. ;

Alfarhan, Ahmed H. ;

Alquraishi, Saleh A. ;

Al-Rasheid, Khaled A. S. ;

Stagegaard, Julia ;

Strauss, Guenter ;

Bertelsen, Mads Frost ;

Sicheritz-Ponten, Thomas ;

Antczak, Douglas F. ;

Bailey, Ernest ;

Nielsen, Rasmus ;

Willerslev, Eske ;

Orlando, Ludovic .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2014, 111 (52) :18655-18660

[8] Species identification of Asini Corii Collas (donkey glue) by PCR amplification of cytochrome b gene [J].

Kumeta, Yukie ;

Maruyama, Takuro ;

Asama, Hiroshi ;

Yamamoto, Yutaka ;

Hakamatsuka, Takashi ;

Goda, Yukihiro .

JOURNAL OF NATURAL MEDICINES, 2014, 68 (01) :181-185

[9] De novo assembly of human genomes with massively parallel short read sequencing [J].

Li, Ruiqiang ;

Zhu, Hongmei ;

Ruan, Jue ;

Qian, Wubin ;

Fang, Xiaodong ;

Shi, Zhongbin ;

Li, Yingrui ;

Li, Shengting ;

Shan, Gao ;

Kristiansen, Karsten ;

Li, Songgang ;

Yang, Huanming ;

Wang, Jian ;

Wang, Jun .

GENOME RESEARCH, 2010, 20 (02) :265-272

[10] Whole mitochondrial genome sequencing of domestic horses reveals incorporation of extensive wild horse diversity during domestication [J].

Lippold, Sebastian ;

Matzke, Nicholas J. ;

Reissmann, Monika ;

Hofreiter, Michael .

BMC EVOLUTIONARY BIOLOGY, 2011, 11

← 1 2 3 →