Latest Cover

Online Office

Contact Us

Issue:ISSN 1000-7083
          CN 51-1193/Q
Director:Sichuan Association for Science and Technology
Sponsored by:Sichuan Society of Zoologists; Chengdu Giant Panda Breeding Research Foundation; Sichuan Association of Wildlife Conservation; Sichuan University
Address:College of Life Sciences, Sichuan University, No.29, Wangjiang Road, Chengdu, Sichuan Province, 610064, China
Fax:+86-28-85410485 &
Your Position :Home->Past Journals Catalog->2018 Vol.37 No.6

Sequencing and Analysis of the Mitochondrial Genome of Ixos mcclellandii
Author of the article:CHEN Yingzhu1, SONG Xuhao1, ZHOU Chuang1, ZHANG Wenbo1, CHEN Benping2, WU Shaobin3, YUE Bisong1*
Author's Workplace:1. Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China;
2. Sichuan Laojunshan National Nature Reserve, Pingshan, Sichuan Province 645350, China;
3. College of Life Science and Technology, Yangtze Normal University, Chongqing 408100, China
Key Words:Passeriformes; Ixos mcclellandii; mitochondrial genome; control region
Abstract:In this study, the complete mitochondrial genome of Ixos mcclellandii was determined. This circular genome of I. mcclellandii was 17 838 bp in length (GenBank accession: KX640824). The mitogenome harbored 2 overlapping protein regions, i.e., ATP6-ATP8 (10 bp) and ND4L-ND4 (7 bp), and there were also some overlapping regions positioned between the protein genes and their flanking tRNA genes. Conventional stop codons (i.e., TAA, AGA or AGG) could be assigned to most of the protein coding genes, while the rest ended with an incomplete stop codon T (COX Ⅲ and ND4) or TA (ND2 and ND4L). Among the 13 protein-coding genes, the most frequently used codons were CUA and ACC (217 times and 205 times, respectively), while the most infrequently used codons were GGU and GCG (only 24 times). The length of tRNA ranges from 64 bp to 75 bp, which loacated between rRNA genes and protein coding genes. Based on the new data and the publicly accessible mitochondrial genomes in Passeriformes, 3 types of mitochondrial control regions were found: 1) Only one control region; 2) Two control regions with high similarity (control region 1+control region 2); 3) Two highly heterogeneous control regions (control region+non-coding region). The mitochondrial genome of I. mcclellandii contained 2 control regions, which were determined to be 1 116 bp and 1 144 bp in length, respectively. Furthermore, the intra-genomic similarity between the 2 noncoding regions was detected (91.6%).
2018,37(6): 646-652 收稿日期:2018-04-16
白洁. 2012.大山雀和绿背山雀线粒体基因组序列测定和系统发生分析[D]. 西安: 陕西师范大学.
陈娟. 2015. 鹰形目和雀形目七种鸟类的线粒体全基因组序列的测序与分析[D]. 芜湖: 安徽师范大学.
陈四海, 区又君, 李加儿. 2011. 鱼类线粒体DNA及其研究进展[J]. 生物技术通报, 3: 13-20.
邓青珊, 朱琼琼, 鲁长虎. 2008. 南方红豆杉的天然更新格局及食果鸟类对其种子的传播[J]. 生态学杂志, 27: 712-717.
丁虎林. 2013. 浙江天童三种鹎科鸟类栖息地选择的季节变化[D]. 上海: 华东师范大学.
高瑞瑞. 2013. 三种雀形目鸟类线粒体基因组测定及雀形目鸟类系统发生研究[D]. 西安: 陕西师范大学.
林立亮. 2011. 四种山雀线粒体基因组测序与雀形目线粒体谱系基因组学分析[D]. 西安: 陕西师范大学.
钱朝菊. 2013. 雀形目13种鸟类线粒体全基因组序列的测定与分析[D]. 芜湖: 安徽师范大学.
孙利元, 杨天燕, 孟玮, 等. 2017. 8种石首鱼类线粒体基因组特征及分子系统进化分析[J]. 海洋科学, 41: 48-54.
章明, 贾晓旭, 陆俊贤, 等. 2016. 文昌鸡线粒体控制区遗传多态性及系统进化分析[J]. 安徽农业大学学报, 43: 690-693.
郑光美. 2017. 中国鸟类分类与分布名录(第三版)[M]. 北京: 科学出版社.
Bess AS, Crocker TL, Ryde IT, et al. 2012. Mitochondrial dynamics and autophagy aid in removal of persistent mitochondrial DNA damage in Caenorhabditis elegans[J]. Nucleic Acids Research, 40: 7916-7931.
Chen DS, Qian CJ, Ren QQ, et al. 2015. Complete mitochondrial genome of the Chinese hwamei Garrulax canorus (Aves: Passeriformes): the first representative of the Leiothrichidae family with a duplicated control region[J]. Genetics and Molecular Research, 14: 8964-8976.
Choudhury MN, Uddin A, Chakraborty S. 2017. Gene expression, nucleotide composition and codon usage bias of genes associated with human y chromosome[J]. Genetica, 145: 295-305.
Cleland MM, Youle RJ. 2011. Mitochondrial dynamics and apoptosis[J]. Genes & Development, 22: 1577.
Curole JP, Kocher TD. 1999. Mitogenomics: digging deeper with complete mitochondrial genomes[J]. Trends in Ecology & Evolution, 14(10): 394-398.
Eberhard JR, Wright TF, Bermingham E. 2001. Duplication and concerted evolution of the mitochondrial control region in the parrot genus Amazona[J]. Molecular Biology and Evolution, 18(7): 1330-1342.
Elodie B, Fanny R, Thierry A. 2011. Microdialect and group signature in the song of the skylark Alauda arvensis[J]. Bioacoustics, 20: 219-233.
Keith BF, Benesh MK, Vandergon AJ, et al. 2012. Contrasting evolutionary dynamics and information content of the avian mitochondrial control region and ND2 gene[J]. PLoS ONE, 7: e46403. DOI: 10.1371/journal.pone.0046403.
Kumar CS, Hazarika NM, Kumar S. 2015. Analysis of synonymous codon usage in the vp2 protein gene of infectious bursal disease virus[J]. Archives of Virology, 160: 2359-2366.
Li WX, Zhang D, Boyce K, et al. 2017. The complete mitochondrial DNA of three monozoic tapeworms in the Caryophyllidea: a mitogenomic perspective on the phylogeny of eucestodes[J]. Parasite Vector, 10: 314.
Lowe TM, Chan PP. 2016. tRNAscan-SE on-line: integrating search and context for analysis of transfer RNA genes[J]. Nucleic Acids Research, 44: W54-W57.
Marshall HD, Baker AJ, Grant AR. 2013. Complete mitochondrial genomes from four subspecies of common chaffinch (Fringilla coelebs): new inferences about mitochondrial rate heterogeneity, neutral theory, and phylogenetic relationships within the order Passeriformes[J]. Gene, 517: 37-45.
Mikami E, Fuku N, Takahashi H, et al. 2013. Polymorphisms in the control region of mitochondrial DNA associated with elite Japanese athlete status[J]. Scandinavian Journal of Medicine & Science in Sports, 23: 593-599.
Min W, Kalyanasundaram A, Jie Z. 2013. Structural and biomechanical basis of mitochondrial movement in eukaryotic cells[J]. International Journal of Nanomedicine, 8: 4033-4042.
Mindell DP, Sorenson MD, Dimcheff DE. 1998. Multiple independent origins of mitochondrial gene order in birds[J]. Proceedings of the National Academy of Sciences of the USA, 95: 10693-10697.
Mjelle KA, Karlsen BO, Jorgensen TE, et al. 2008. Halibut mitochondrial genomes contain extensive heteroplasmic tandem repeat arrays involved in DNA recombination[J]. BMC Genomics, 9(1): 1-11.
Moyle RG, Marks BD. 2006. Phylogenetic relationships of the bulbuls (Aves: Pycnonotidae) based on mitochondrial and nuclear DNA sequence data[J]. Molecular Phylogenetics and Evolution, 40: 687-695.
Parmakelis A, Spanos E, Papagiannakis G, et al. 2015. Mitochondrial DNA phylogeny and morphological diversity in the genus Mastus (Beck, 1837): a study in a recent (Holocene) island group (Koufonisi, south-east Crete)[J]. Biological Journal of the Linnean Society, 78: 383-399.
Qian C, Wang Y, Guo Z, et al. 2013. Complete mitochondrial genome of skylark, Alauda arvensis (Aves: Passeriformes): the first representative of the family Alaudidae with two extensive heteroplasmic control regions[J]. Mitochondrial DNA, 24: 246-248.
Schirtzinger EE, Tavare ES, Gonzales LA, et al. 2012. Multiple independent origins of mitochondrial control region duplications in the order Psittaciformes[J]. Molecular Phylogenetics and Evolution, 64: 342-356.
Song XH, Huang J, Yan C, et al. 2014. The complete mitochondrial genome of Accipiter virgatus, and evolutionary history of the pseudo-control regions in Falconiformes[J]. Biochemical Systematics and Ecology, 58: 75-84.
Tzur S, Rosset S. 2015. Strictly conserved tri-nucleotide motif "CAT" is associated with TAS DNA protein-binding sites in human mitochondrial DNA control region[J]. Mitochondrial DNA, 28: 250-253.
Wang X, Yuan H, Liu N, et al. 2015. Seven complete mitochondrial genome sequences of bushtits (Passeriformes, Aegithalidae, Aegithalos): the evolution pattern in duplicated control regions[J]. Mitochondrial DNA, 26(3): 350-356.
Wen L, Liao F. 2016. Complete mitochondrial genome of Pycnonotus xanthorrhous (Passeriformes, Pycnonotidae) and phylogenetic consideration[J]. Biochemical Systematics and Ecology, 69: 83-90.
Zhang H, Bai Y, Shi X, et al. 2018. The complete mitochondrial genomes of Tarsiger cyanurus, and phoenicurus auroreus: a phylogenetic analysis of Passeriformes[J]. Genes & Genomics, 40: 151-165.
Zheng BY, Cao LJ, Tang P, et al. 2018. Gene arrangement and sequence of mitochondrial genomes yield insights into the phylogeny and evolution of bees and sphecid wasps (Hymenoptera: Apoidea)[J]. Molecular Phylogenetics and Evolution,124: 1-9.
Zhuang X, Qu M, Zhang X, et al. 2013. A comprehensive description and evolutionary analysis of 22 grouper (Perciformes, Epinephelidae) mitochondrial genomes with emphasis on two novel genome organizations[J]. PLoS ONE, 8: e73561. DOI: 10.1371/journal.pone.0073561.
CopyRight©2020 Editorial Office of Sichuan Journal of Zoology