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->2015 Vol.34 No.1

Characteristics of Microsatellites in Arborophila rufipectus Genome Sequences Using 454 GS FLX
Author of the article:HUANG Jie1, ZHOU Yu1, LIU Yuzhi1, ZHU Dan1, SONG Xuhao1, CHEN Benping2, ZHANG Xiuyue1, YUE Bisong1*
Author's Workplace:1. Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610064, China;
2. Laojunshan National Nature Reserve Management Bureau, Pingshan, Sichuan Province 645350, China
Key Words:Arborophila rufipectus; genome; microsatellite; distribution
Abstract:The Sichuan hill partridge (Arborophila rufipectus) is a critically endangered species endemic to China. The entire genome of A. rufipectus was sequenced using Roche's 454 GS FLX platform. Microsatellites were identified by screening the genome sequences in silico mining and a large number of different kinds of repeat motif types of perfect microsatellite sequences were discovered. A total of 335 263 simple sequence repeats (SSRs) with 1~6 bp nucleotide motifs were identified. Moreover, A, AC, AAC, AAAC, AAACA, and AGGGTT were the most frequent repeat copy units of the six motif types, respectively. In the different repeat types of the microsatellites, mononucleotide (59.03%) was the most common repeat unit followed by the tetra (13.59%), tri (8.39%), hexa (7.55%), di (6.49%) and pentanucleotides (4.95%). In the A. rufipectus genome, A, AGGGTT, AAAC, AC, AAAT, AAC, C, AG, AAAG, AAACA, AAT, AGG, AT, AGC, AAGG, and CCG were the 16 predominant repeat types. This study provided significant genome information of A. rufipectus, which will contribute to further understanding of this species. The resources that we have developed will certainly facilitate the isolation of large numbers of high quality microsatellite markers for genetic diversity studies within species in the future.
2015,34(1): 8-14 收稿日期:2014-6-16
戴波, 陈本平, 岳碧松, 等. 2014. 四川山鹧鸪栖息地分析与预测[J]. 四川动物, 33(3): 329-336.
黄杰, 杜联明, 李玉芝, 等. 2012. 红原鸡全基因组中微卫星分布规律研究[J]. 四川动物, 31(3): 358-363.
李午佼, 李玉芝, 杜联明, 等. 2014. 大熊猫和北极熊基因组微卫星分布特征比较分析[J]. 四川动物, 33(6): 874-878.
廖文波, 胡锦矗. 2010. 四川山鹧鸪生态习性研究进展[J]. 绵阳师范学院学报, 29(2): 67-71.
马秋月, 戴晓港, 陈赢男, 等. 2013. 枣基因组的微卫星特征[J]. 林业科学, 49(12): 81-87.
戚文华, 蒋雪梅, 肖国生, 等. 2013. 牛和绵羊全基因组微卫星序列的搜索及其生物信息学分析[J]. 畜牧兽医学极, 44(11): 1724-1733.
汪自立, 黄杰, 杜联明, 等. 2013. 二斑叶螨和肩突硬蜱基因组微卫星分布规律研究[J]. 四川动物, 32(2): 481-486.
于颖, 杨孔, 王永, 等. 2009. 藏鸡微卫星文库的构建与微卫星标记筛选[J]. 四川动物, 28(3): 358-362.
Abdelkrim J, Robertson BC, Stanton JL, et al. 2009. Fast, cost-effective development of species-specific microsatellite markers by genomic sequencing[J]. Biotechniques, 46(3): 185-192.
Archie EA, Moss CJ, Alberts SC. 2003. Characterization of tetranucleotide microsatellite loci in the African Savannah Elephant (Loxodonta africana africana)[J]. Mol Ecol Notes, 3: 244-246.
Castagnone-Sereno P, Danchin EGJ, Deleury E, et al. 2010. Genome-wide survey and analysis of microsatellites in nematodes, with a focus on the plant-parasitic species Meloidogyne incognita[J]. BMC Genomics, 11: 598.
Collar NJ, Andreev AV, Chan S, et al. 2001. Threatened birds of Asia: The Bird Life International Red Data Book[M]. Cambridge, UK: Bird Life International: 836-843.
Dai B, Dowell SD, Garson PJ, et al. 2009. Habitat utilisation by the threatened Sichuan partridge, Arborophila rufipectus: consequences for managing newly protected areas in southern China[J]. Bird Conserv Int, 19(2): 187-198.
Du LM, Li YZ, Zhang XY, et al. 2013. MSDB: A user-friendly program for reporting distribution and building databases of microsatellites from genome sequences[J]. J Hered, 104(1): 154-157.
He LP, Wan QH, Fang SG, et al. 2006. Development of novel microsatellite loci and assessment of genetic diversity in the endangered Crested Ibis, Nipponia nippon[J]. Conserv Genetics, 7(1): 157-160.
He LW, Dai B, Zeng B, et al. 2009. The complete mitochondrial genome of the Sichuan Hill Partridge (Arborophila rufipectus) and a phylogenetic analysis with related species[J]. Gene, 435(1-2): 23-28.
Hong CP, Piao ZY, Kang TW, et al. 2007. Genomic distribution of simple sequence repeats in Brassica rapa[J]. Mol Cells, 23(3): 349-356.
Huang J, Li YZ, Li P, et al. 2013. Genetic quality of the Miyaluo captive forest musk deer (Moschus berezovskii) population as assessed by microsatellite loci[J]. Biochem Syst Ecol, 47: 25-30.
IUCN. 2014. The IUCN Red List of Threatened Species (Version 2014. 2)[EB/OL]. 2014.
Katti MV, Ranjekar PK, Gupta VS. 2001. Differential distribution of simple sequence repeats in eukaryotic genome sequences[J]. Mol Biol Evol, 18(7): 1161-1167.
Kayang BB, Inoue-Murayama M, Hoshi T, et al. 2002. Microsatellite loci in Japanese quail and cross-species amplification in chicken and guinea fowl[J]. Genet Sel Evol, 34(2): 233-253.
Kim TS, Booth JG., Gauch Jr HG, et al. 2008. Simple sequence repeats in Neurospora crassa: distribution, polymorphism and evolutionary inference[J]. BMC Genomics, 9: 31.
King B, Li GY. 1988. China's most endangered Galliformes[J]. Oryx, 22(4): 216-217.
Liao WB, Hu JC, Li C. 2007a. Habitat utilization during the pairing season by the common hill-partridge Arborophila torqueola in Baiposhan Natural Reserve, Sichuan, China[J]. Orn Sci, 6(2): 87-94.
Liao WB, Hu JC, Li C, et al. 2008. Roosting behaviour of the endangered Sichuan Hill-partridge Arborophila rufipectus during the breeding season[J]. Bird Conserv Internatn, 18(3): 260-266.
Liao WB, Li C, Hu JC, et al. 2007b. Habitat utilization of the Sichuan Hill-partridge (Arborophila rufipectus) in the non-breeding period in Laojunshan Nature Reserve[J]. Zool Res, 28(2): 172-178.
Liu ZF, He LW, Yuan HG, et al. 2012. CR1 retroposons provide a new insight into the phylogeny of Phasianidae species (Aves: Galliformes) [J]. Gene, 502(2): 125-132.
Page RB, Sankamethawee W, Pierce AJ, et al. 2014. High throughput sequencing enables discovery of microsatellites from the puff-throated bulbul (Alophoixus pallidus) and assessment of genetic diversity in Khao Yai National Park, Thailand[J]. Biochem Syst Ecol, 55: 176-183.
Reed KM, Roberts MC, Murtaugh J, et al. 2000. Eight new dinucleotide microsatellite loci in turkey (Meleagris gallopavo)[J]. Anim Genet, 31(2): 140.
Sambrook J, Russell DW. 2002. Molecular Cloning: a Laboratory Manual, 3rd ed[M]. Beijing: Science Press.
Schlotterer C, Tautz D. 1992. Slippage synthesis of simple sequence DNA[J]. Nucleic Acids Res, 20(2): 211-215.
Sharma PC, Grover A, Kahl G. 2007. Mining microsatellites in eukaryotic genomes[J]. Trends Biotechnol, 25(1): 490-498.
Subramanian S, Mishra RK, Singh L. 2003. Genome-wide analysis of microsatellite repeats in humans: their abundance and density in specific genomic regions[J]. Genome Biol, 4(2): R13.
Tóth G, Gaspari Z, Jurka J. 2000. Microsatellites in different eukaryotic genomes: survey and analysis[J]. Genome Res, 10(7): 967-981.
Wang SZ, Lorenzen MD, Beeman RW, et al. 2008. Analysis of repetitive DNA distribution patterns in the Tribolium castaneum genome[J]. Genome Biol, 9: R61.
Zhao XY, Tan ZY, Feng HP, et al. 2011. Microsatellites in different Potyvirus genomes: Survey and analysis[J]. Gene, 488(1-2): 52-56.
Zou HF, Dong HY, Kong WY, et al. 2010. Characterization of 18 polymorphic microsatellite loci in the red-crowned crane (Grus japonensis), an endangered bird[J]. Anim Sci J, 81(4): 519-522.
CopyRight©2022 Editorial Office of Sichuan Journal of Zoology 蜀ICP备08107403号-3