四川麻鸭mtDNA 全序列的克隆和生物信息学分析

doi:10.11843/j.issn.0366-6964.2017.03.006

Abstract

Abstract:

The objective of this study was to obtain the complete mitochondrial DNA (mtDNA) sequence of Sichuan Sheldrake duck, and to provide reference data for protection and utilization of this genetic resources of duck. Sixteen pairs of primers were designed by Primer 6.0 according to the mitochondrial genome sequences of duck homologous species. The genomic sequence of Sichuan Sheldrake duck’s mtDNA were then amplified by PCR and sequencing technology. The results showed that the length of Sichuan Sheldrake duck’s mtDNA genome was 16 604 bp, which composed of A (29.19%), C (32.82%), G (15.79%) and T (22.20%). The whole genome contained 22 tRNA genes, 2 rRNA genes, 13 protein-encoding genes and a non-encoding control area (D-loop area). The analysis by online software of tRNAscan-SE 1.21 and RNA structure 5.6 found that 22 tRNA genes were the standard secondary structures with 4 constant arms which like a clover. The D-loop region of Sichuan Sheldrake duck’s mtDNA genome contained Poly (c), TAS, E-box, F-box, D-box, Bird-similarity box and CXB1 conserved box. The neighbor joint (NJ) phylogenetic tree was established by MEGA6.0 basing on the D-loop region and the complete mtDNA sequence, respectively, and the results showed that the Longsheng duck was more closer to Sichuan Sheldrake duck.

CLC Number:

S834.83
S813

XIE Ai-xuan,WU Qi-chao, LI Si-de, LUO Jun, ZHANG Tao, LIU He-he, ZHANG Jun, HE Hua. Complete Sequence Cloning and Bioinformatics Analysis of Sichuan Sheldrake Duck Mitochondrial Genome[J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2017, 48(3): 436-445.

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References

［1］DONNE-GOUSSÉ C, LAUDET V, HÄNNI C. A molecular phylogeny of anseriformes based on mitochondrial DNA analysis［J］. Mol Phylogenet Evol, 2002, 23(3): 339-356.
［2］STONEKING M, SOODYALL H. Human evolution and the mitochondrial genome［J］. Curr Opin Genet Dev, 1996, 6(6): 731-736.
［3］BROWN W M, GEORGE M Jr, WILSON A C. Rapid evolution of animal mitochondrial DNA［J］. Proc Natl Acad Sci U S A, 1979, 76(4): 1967-1971.
［4］何大乾. 中国主要地方鸭种线粒体DNA部分序列的遗传多样性及其起源进化研究［D］. 雅安：四川农业大学, 2007.
HE D Q.Study on the genetic diversity of the mtDNA partial sequences and its evolution for the main Chinese domestic duck［D］. Ya’an: Sichuan Agricultural University,2007.(in Chinese)
［5］涂剑锋，黄银花，刘三凤，等. 北京鸭线粒体基因组全序列测定和分析［J］. 动物学杂志, 2009, 44(2): 28-33.
TU J F,HUANG Y H,LIU S F,et al. Complete sequence determination and analysis of Beijing duck mitochondrial genome［J］.Chinese Journal of Zoology, 2009, 44(2): 28-33. (in Chinese)
［6］涂剑锋，黄银花，刘三凤，等. 绿头鸭线粒体基因组全序列分析及河鸭类系统发育［J］. 农业生物技术学报, 2009, 17(6): 995-1000.
TU J F,HUANG Y H,LIU S F,et al.Complete mitochondrial genome sequence analysis of Mallard and phylogeny of Anatini［J］.Journal of Agricultural Biotechnology, 2009, 17(6): 995-1000. (in Chinese)
［7］涂剑锋，司方方，邢秀梅，等. 绍兴鸭线粒体基因组全序列测定与分析［J］. 浙江农业学报, 2011, 23(2): 268-272.
TU J F,SI F F,XING X M,et al. Complete sequence determination and analysis of mitochondrial genome of Shaoxing duck［J］. Acta Agriculturae Zhejiangensis, 2011, 23(2): 268-272. (in Chinese)
［8］涂剑锋，黄银花，刘三凤，等. 建昌鸭线粒体基因组全序列分析［J］. 西南大学学报：自然科学版, 2010, 32(2): 38-43.
TU J F,HUANG Y H,LIU S F,et al. Complete mitochondrial genome sequence analysis of Jianchang duck［J］. Journal of Southwest University: Natural Science Edition, 2010, 32(2): 38-43. (in Chinese)
［9］穆春宇，黄正洋，陈阳，等. 斑嘴鸭线粒体全基因组序列测定及分析［J］. 中国兽医学报, 2015, 35(2): 257-263.
MU C Y,HUNG Z Y,CHEN Y,et al. Complete sequence and gene organization of Anas poecilorhyncha mitochondrial genome［J］. Chinese Journal of Veterinary Science, 2015, 35(2): 257-263. (in Chinese)
［10］国家畜禽遗传资源委员会. 中国畜禽遗传资源志:家禽志［M］. 北京：中国农业出版社, 2011.
National livestock and Poultry Genetic Resources Committee. Animal genetic resources in China: poultry［M］.Beijing: China Agricultural Press, 2011. (in Chinese)
［11］张军，吕佳，叶建超，等. 四川麻鸭体尺性状和生产性能观测［J］. 中国家禽, 2016, 38(5): 56-57.
ZHANG J,LV J,YE J C,et al.Observation of Sichuan Sheldrake Duck Body Traits and production performance［J］.China Poultry, 2016, 38(5): 56-57. (in Chinese)
［12］李慧芳，李碧春，陈宽维，等. 中国地方鸭品种资源的分子遗传多样性［J］. 畜牧兽医学报, 2006, 37(11): 1107-1113.
LI H F,LI B C,CHEN K W,et al.Study on molecular genetic diversity of native duck breeds in China［J］. Acta Veterinaria et Zootechnica Sinica, 2006, 37(11): 1107-1113. (in Chinese)
［13］LALITHA S. Primer Premier 5［J］. Biotech Softw Int Rep, 2000, 1(6): 270-272.
［14］BURLAND T G. DNASTAR's Lasergene sequence analysis software.［J］. Methods Mol Biol, 2000, 132: 71-91.
［15］LOWE T M, EDDY S R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence［J］. Nucleic Acids Res, 1997, 25(5): 955-964.
［16］REUTER J S, MATHEWS D H. RNAstructure: software for RNA secondary structure prediction and analysis［J］. BMC Bioinformatics, 2010, 11:129.
［17］AIYAR A. The use of CLUSTAL W and CLUSTAL X for multiple sequence alignment［J］. Methods Mol Biol, 2000, 132(132): 221-241.
［18］TAMURA K, STECHER G, PETERSON D, et al. MEGA6: Molecular evolutionary genetics analysis version 6.0［J］. Mol Biol Evol, 2013, 30(12): 2725-2729.
［19］SCHATTNER P, BROOKS A N, LOWE T M. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs［J］. Nucleic Acids Res, 2005, 33(S2): W686-W689.
［20］THOMPSON J D, GIBSON T J, HIGGINS D G. Multiple sequence alignment using clustalW and ClustalX［M］. Current Protocols in Bioinformatics, 2002:2-3.
［21］WEI X Q, KONG Q P, ZHANG Y, et al. A case of Leigh syndrome associated with respiratory chain complex I deficiency due to mitochondrial gene 13513G>A mutation［J］. Chin J Contemp Pediatr, 2009, 11(5): 333-336.
［22］CARROLL J, FEARNLEY I M, SKEHEL J M, et al. Bovine complex I is a complex of 45 different subunits［J］. J Biol Chem, 2006, 281(43): 32724-32727.
［23］STOTHARD P, WISHART D S. Circular genome visualization and exploration using CGView［J］. Bioinformatics, 2005, 21(4): 537-539.
［24］张汤杰，李慧芳，陈宽维，等.利用线粒体D-loop区分析家鸭品种遗传多态性与系统进化［J］. 畜牧兽医学报, 2007, 38(11): 1168-1175.
ZHANG T J,LI H F,CHEN K W,et al.Analysis on the genetic polymorphism and systematic evolution in domestic ducks by mitochondrial DNA D-loop region［J］.Acta Veterinaria et Zootechnica Sinica, 2007,38(11):1168-1175.(in Chinese)
［25］于萍，曹婷，施力光，等. 五指山猪线粒体控制区序列分析及遗传多样性研究［J］. 中国畜牧兽医, 2015, 42(5): 1222-1231.
YU P,CAO T,SHI L G,et al.Complete mitochondrial DNA D-loop sequence and genetic diversity of Wuzhishan pig［J］. China Animal Husbandry & Veterinary Medicine, 2015, 42(5): 1222-1231. (in Chinese)
［26］于萍, 曹婷, 赵春萍,等. 五指山猪线粒体基因组全序列测定与分析［J］. 西北农业学报, 2015, 24(7):16-22.
YU P, CAO T, ZHAO C P,et al.Complete mitochondrial genome sequence and analysis of Wuzhishan pig［J］. Acta Agriculturae Boreali-occidentalis Sinica, 2015, 24(7):16-22. (in Chinese)

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Complete Sequence Cloning and Bioinformatics Analysis of Sichuan Sheldrake Duck Mitochondrial Genome

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