黑尾地鸦线粒体基因组序列测定与分析

doi:10.3724/SP.J.1005.2010.00951

[an error occurred while processing this directive]

HEREDITAS ›› 2010, Vol. 32 ›› Issue (9): 951-960.doi: 10.3724/SP.J.1005.2010.00951

• en • Previous Articles Next Articles

Sequencing and analysis of the complete mitochondrial genome of Podoces hendersoni (Ave, Corvidae)

KE Yang¹, HUANG Yuan¹, LEI Fu-Min²

1. School of Life Sciences, Shaanxi Normal University, Xi’an 710062, China; 2. Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China

Received:2010-01-07 Revised:2010-02-10 Online:2010-09-20 Published:2010-09-20
Contact: LEI Fu-Min E-mail:leifm@ioz.ac.cn

Abstract

Abstract: The complete mitochondrial genome of a China endemic bird, Podoces hendersoni, was sequenced using La-PCR and conserved primer walking approaches. The mtDNA seqnence is 16 867 bp in length and deposited in GenBank with accession number GU592504. The mitochondrial genomic organization of P. hendersoni is the same with that in chicken, which contains 13 protein coding genes (PCGs), 22 tRNA, 2 rRNA, and a control region. Except for COI gene, which uses GTG as the initiation codon, all other 12 PCGs of the P. hendersoni mtDNA start with the typical ATG codon. Codons TAA, AGG, and AGA were used in 11 PCGs as usual termination codons; however, the COIII and ND4 had incomplete termination codon T. The secondary structures of 20 tRNAs formed typical cloverleaf, except for tRNA^Ser(AGY) that had an absence of the DHU arm and tRNA^Leu(CUN) in which anticodon-loop consisted of 9 bases, rather than the standard 7 bases. The secondary structures of rRNA were predicted. There are 4 domains, 43 helices structures in 12S rRNA, and 6 domains, 55 helices structures in 16S rRNA. Besides, F-box, D-box, C-box, B-box, Bird similarity-box and CSB1-box, which were found in the control region of other birds, also existed in the P. hendersoni.

Key words: Podoces hendersoni, mitochondrial DNA, rRNA secondary structure, control region

KE Yang, HUANG Yuan, LEI Fu-Min. Sequencing and analysis of the complete mitochondrial genome of Podoces hendersoni (Ave, Corvidae)[J]. HEREDITAS, 2010, 32(9): 951-960.

References

[1] Russo CA, Takezaki N, Nei M. Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny. Mol Biol Evol, 1996, 13(3): 525–536. [2] Pollock DD, Eisen JA, Doggett NA, Cummings MP. A case for evolutionary genomics and the comprehensive examination of sequence biodiversity. Mol Biol Evol, 2000, 17(12): 1776–1788. [3] Roques S, Fox CJ, Villasana MI, Rico C. The complete mitochondrial genome of the whiting, Merlangius mer-langus and the haddock, Melanogrammus aeglefinus: a detailed genomic comparison among closely related spe-cies of the Gadidae family. Gene, 2006, 383: 12–23. [4] Desjardins P, Morais R. Sequence and gene organization of the chicken mitochondrial genome. A novel gene order in higher vertebrates. J Mol Biol, 1990, 212(4): 599–634. [5] Mindell DP, Sorenson MD, Dimcheff DE, Hasegawa M, Ast JC, Yuri T. Interordinal relationships of birds and other reptiles based on whole mitochondrial genomes. Syst Biol, 1999, 48(1): 138–152. [6] Slack KE, Delsuc F, McLenachan PA, Arnason U, Penny D. Resolving the root of the avian mitogenomic tree by breaking up long branches. Mol Phylogenet Evol, 2007, 42(1): 1–13. [7] Singh TR, Shneor O, Huchon D. Bird mitochondrial gene order: insight from 3 warbler mitochondrial genomes. Mol Biol Evol, 2008, 25(3): 475–477. [8] Härlid A, Arnason U. Analyses of mitochondrial DNA nest ratite birds within the Neognathae: supporting a neotenous origin of ratite morphological characters. Royal Society of London. Biol Sci, 1999, 266(1416): 305–309. [9] 雷富民, 卢汰春. 中国鸟类特有种. 北京: 科学出版社, 2005, 391–394. [10] 马鸣, 殷守敬, 徐峰, Dixon A, Ragyov D. 新疆黑尾地鸦初步调查. 动物学杂志, 2006, 41(2): 135. [11] 汪松, 谢焱. 中国物种红色名录(第一卷). 北京: 高等教育出版社, 2004, 248. [12] Mlíkovsky J. Brain size and foramen magnum area in crows and allies (Aves: Corvidae). Acta Soc Zool Bohem, 2003, 67(1–4): 203–211. [13] Ericson PGP, Jansén AL, Johansson US, Ekman J. In-ter-generic relationships of the crows, jays, magpies and allied groups (Aves: Corvidae) based on nucleotide se-quence data. J Avian Biol, 2005, 36(3): 222–234. [14] Kerr KC, Birks SM, Kalyakin MV, Red'kin YA, Koblik EA, Hebert PD. Filling the gap-COI barcode resolution in eastern Palearctic birds. Front Zool, 2009, 6(1): 29–42. [15] Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. Clustal W and Clustal X version 2.0. Bioinformatics, 2007, 23(21): 2947–2948. [16] Sorenson MD, Ast JC, Dimcheff DE, Yuri T, Mindell DP. Primers for a PCR-based approach to mitochondrial ge-nome sequencing in birds and other vertebrates. Mol Phylogenet Evol, 1999, 12(2): 105–114. [17] Bonfield JK, Smith K, Staden R. A new DNA sequence assembly program. Nucleic Acids Res, 1995, 23(24): 4992–4999. [18] Lowe TM, Eddy SR. tRNAscan-SE: a program for im-proved detection of transfer RNA genes in genomic se-quence. Nucleic Acids Res, 1997, 25(5): 955–964. [19] Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecu-lar Evolutionary Genetics Analysis (MEGA) software ver-sion 4.0. Mol Biol Evol, 2007, 24(8): 1596–1599. [20] Espinosa de los Monteros A. Models of the primary and sec-ondary structure for the 12S rRNA of birds: a guideline for sequence alignment. DNA Seq, 2003, 14(4): 241–256. [21] Cannone JJ, Subramanian S, Schnare MN, Collett JR, D'Souza LM, Du Y, Feng B, Lin N, Madabusi LV, Müller KM, Pande N, Shang Z, Yu N, Gutell RR. The compara-tive RNA web (CRW) site: an online database of com-parative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics, 2002, 3(2): 1–31. [22] Burk A, Douzery EJP, Springer M. The secondary struc-

Metrics

Comments

www.chinagene.cn
备案号：京ICP备09063187号

Sequencing and analysis of the complete mitochondrial genome of Podoces hendersoni (Ave, Corvidae)

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	Ruijia Song, Lu Han, Haifeng Sun, Bin Shen. Advances in mitochondrial DNA base editing technology [J]. Hereditas(Beijing), 2023, 45(8): 632-642.
[2]	Jiaoyang Tian, Yuchun Li, Qingpeng Kong, Yaping Zhang. The origin and evolution history of East Asian populations from genetic perspectives [J]. Hereditas(Beijing), 2018, 40(10): 814-824.
[3]	Meifen Xu, Yiqun He, Junwei Geng, Yanzi Meng, Han Yu, Zhi Lin, Suxue Shi, Ling Xue, Zhongqiu Lu, Minxin Guan. The mitochondrial tRNAMet/tRNAGlnA4401G and tRNACysG5821A mutations may be associated with hypertension in two Han Chinese families [J]. HEREDITAS, 2014, 36(2): 127-134.
[4]	Li Liu, Yuquan Shao, Baorong Zhang, Pingping Jiang, Ailian Du, Minxin Guan. Mitochondrial genome analysis in the probands of six Chinese families with MELAS [J]. HEREDITAS(Beijing), 2014, 36(11): 1159-1167.
[5]	Haysa Ayelhan, Yan Guo, Wei Meng, Tianyan Yang, Yanwu Ma. Phylogeny and divergence time estimation of Schizothoracinae fishes in Xinjiang [J]. HEREDITAS(Beijing), 2014, 36(10): 1013-1020.
[6]	MA Zhi-Jie ZHONG Jin-Cheng HAN Jian-Lin XU Jing-Tao LIU Zhong-Na BAI Wen-Lin. Research progress on molecular genetic diversity of the yak (Bos grunniens) [J]. HEREDITAS, 2013, 35(2): 151-160.
[7]	WANG Jin-Feng, ZHANG Ya-Ping, YU Li. Summary of phylogeny in family Felidae of Carnivora [J]. HEREDITAS, 2012, 34(11): 1365-1378.
[8]	YANG Chao WANG Qing-Xiong HUANG Yuan XIAO Hong. Analysis of the complete mitochondrial genome sequence of Larus brunnicephalus (Aves, Laridae) [J]. HEREDITAS, 2012, 34(11): 1434-1446.
[9]	SONG Yan-Rui, LIU Zhong, GU Chu-Lian, JIAN Li-Juan, YAN Qiang-Feng. Advances in the molecular pathogenesis of hypertrophic cardiomyopathy [J]. HEREDITAS, 2011, 33(6): 549-557.
[10]	JI Yan-Chun, LIU Xiao-Ling, ZHAO Fu-Xin, ZHANG Juan-Juan, ZHANG Yu, ZHOU Xiang-Tian, QU Jia, GUAN Min-Xin. The mitochondrial ND5 T12338C mutation may be associated with Leber’s hereditary optic neuropathy in two Chinese families [J]. HEREDITAS, 2011, 33(4): 322-328.
[11]	WEI Jin-Pu, BO Hua-Feng, LI Gong-Quan, DUAN Fei. Distribution and evolution of simple repeats in the mtDNA D-loop in mammalian [J]. HEREDITAS, 2011, 33(1): 67-74.
[12]	DIAO Li-Xia, DIAO Gao-Beng, ZHOU Huan-Min. Review on the genomic imprinting at the mammalian DLK1-DIO3 cluster [J]. HEREDITAS, 2010, 32(8): 769-778.
[13]	ZHANG Yong-Mei, JI Yan-Chun, LIU Xiao-Ling, ZHOU Xiang-Tian, DIAO Fu-Xin, SUN Yan-Gong, HUI Qi-Beng, ZHANG Juan-Juan, LIU Yan, JI Jia, GUAN Min-Xin. Leber’s hereditary optic neuropathy may be associated with the mi-tochondrial tRNA A14693G mutation in three Chinese families [J]. HEREDITAS, 2010, 32(4): 353-359.
[14]	LIU Yan, PENG Chu-Liu, TONG Shi, JI Jia, ZHOU Xiang-Tian, DIAO Fu-Xin, ZHANG Juan-Juan, ZHANG Yong-Mei, ZHANG Shu. Leber's hereditary optic neuropathy and limbs abnormity claudication may be associated with the mitochondrial ND1 T3866C mutation [J]. HEREDITAS, 2010, 32(2): 141-147.
[15]	CHEN Fang-Jian, YU Hong, FAN Fan, LU Jian-Xin. Mitochondrial D-Loop gene polymorphisms in the patients with type 2 diabetes mellitus [J]. HEREDITAS, 2009, 31(3): 265-272.