4种DNA条形码在黄毛鼠种类鉴定中的比较

doi:10.11853/j.issn.1003.4692.2015.03.017

中国媒介生物学及控制杂志 ›› 2015, Vol. 26 ›› Issue (3): 286-289.DOI: 10.11853/j.issn.1003.4692.2015.03.017

4种DNA条形码在黄毛鼠种类鉴定中的比较

胡群¹, 马思杰¹, 裘炯良²

1 大榭出入境检验检疫局鼠传疾病检测实验室, 浙江宁波315812;
2 宁波出入境检验检疫局

收稿日期:2014-12-10 出版日期:2015-06-20 发布日期:2015-06-20
作者简介:胡群,男,硕士,高级工程师,主要从事口岸医学媒介鉴定与病原体检测研究,Email: nbhuqun@sina.com
基金资助:
宁波市自然科学基金(2013A610240)

Comparison of four DNA barcoding in Rattus losea identification

HU Qun¹, MA Si-jie¹, QIU Jiong-liang²

1 Daxie Entry-Exit Inspection and Quarantine Bureau, Ningbo 315812, Zhejiang Province, China;
2 Ningbo Entry-Exit Inspection and Quarantine Bureau

Received:2014-12-10 Online:2015-06-20 Published:2015-06-20
Supported by:
Supported by the Ningbo Natural Science Fund(No. 2013A610240)

摘要/Abstract

摘要：

目的比较COⅠ、Cytb、16S rRNA、D-loop四个DNA条形码对黄毛鼠鼠种的鉴定效果。方法将大榭港区捕获的1只黄毛鼠样本HX41,提取基因组DNA,使用特异性引物对线粒体COⅠ、Cytb、16S rRNA、D-loop基因进行扩增并对扩增产物进行测序。将测序结果与GenBank中的相似鼠种DNA构建分子进化树进行同源性分析。结果以COⅠ、Cytb、D-loop基因所构建分子进化树中,黄毛鼠均能独立形成分支,且HX41均处于黄毛鼠分支上。HX41的COⅠ基因序列与黄毛鼠HN158 株遗传距离最为接近,值为0.0034;Cytb基因序列与黄胸鼠HN99株遗传距离最为接近,值为0.0355,但HN99鼠种数据存在错误;D-loop基因序列与黄毛鼠HN105株遗传距离最为接近,值为0.0439。由于现有GenBank中缺少黄毛鼠16S rRNA基因序列,无法构建进化树。结论对鼠种进行分子鉴定时,有必要根据GenBank数据库的完整性和准确性选择合适的DNA条形码。

关键词: 黄毛鼠, 种类鉴定, DNA条形码

Abstract:

Objective To evaluate CO Ⅰ, Cytb, 16S rRNA, D-loop genes as DNA barcodes for Rattus losea species identification. Methods Genome DNA was extracted from a R. losea sample HX41 captured in Daxie port. The mitochondrial COⅠ, Cytb, 16S rRNA, D-loop genes were amplified using the specific primers and sequenced. The phylogenetic trees was constructed based on the nucleotide sequences of HX41 with Rattus published in GenBank and the homology was analyzed. Results HX41 was located in the branch of the R. losea on phylogenetic tree based on COⅠ, Cytb, and D-loop genes, which form a single branch. The genetic distance analysis showed that the COⅠ gene distance of HX41 to R. losea HN158 is nearest, the value is 0.0034. The Cytb gene distance of HX41 to R. tanezumi HN99 is nearest, the value is 0.0355, but the species database of HN99 in GenBank was incorrect. The D-loop gene of HX41 to R. losea HN105 is nearest, the value is 0.0439. Because of lacking the data of R. losea 16S rRNA gene in the GenBank, the phylogenetic tree cannot be constructed. Conclusion Using molecular identification method for rat species identification, it is necessary to choose suitable DNA barcode according to the integrity and accuracy of the GenBank database.

Key words: Rattus losea, Species identification, DNA barcoding

中图分类号:

S443

胡群, 马思杰, 裘炯良. 4种DNA条形码在黄毛鼠种类鉴定中的比较[J]. 中国媒介生物学及控制杂志, 2015, 26(3): 286-289.

HU Qun, MA Si-jie, QIU Jiong-liang. Comparison of four DNA barcoding in Rattus losea identification[J]. Chines Journal of Vector Biology and Control, 2015, 26(3): 286-289.

参考文献

[1] Hebert PDN, Cywinska A, Ball SL, et al. Biological identifications through DNA barcodes[J]. Proc Biol Sci,2003,270(1512): 313-321.
[2] Hebert PD,Ratnasingham S,de-Waard JR. Barcoding animal life:cytochrome c oxidase subunit 1 divergences among closely related species[J]. Proc Biol Sci,2003,270 Suppl 1:S96-99.
[3] Robins JH,Hingston M,Matisoo-Smith E,et al. Identifying Rattus species using mitochondrial DNA[J]. Mol Ecol Notes,2007,7 (5):717-729.
[4] Tamrin NAM,Abdullah-Analysis MT. Molecular phylogenetics and systematics of five genera of Malaysian murine rodents (Maxomys,Sundamys,Leopoldamys,Niviventer and Rattus) inferred from partial mitochondrial cytochrome c oxidase subunitⅠ(COⅠ)gene[J]. Anal(Mega),2011,4:36.
[5] Harris D,Rogers DS,Sullivan J. Phylogeography of Peromyscus furvus (Rodentia:Muridae) based on cytochrome b sequence data[J]. Mol Ecol,2000,9(12):2129-2135.
[6] Nicolas V,Schaeffer B,Missoup AD,et al. Assessment of three mitochondrial genes(16S,Cytb,COⅠ)for identifying species in the Praomyini Tribe(Rodentia:Muridae)[J]. PLoS One, 2012,7(5):e36586.
[7] Safieh AR,Jalal R,Darvish J,et al. Identification of three Iranian species of the genus Rattus(Rodentia:Muridae)using a PCR-RFLP technique on mitochondrial DNA[J]. Hys-trix It J Mamm,2009,20(1):69-77.
[8] 何锴,王文智,李权,等. DNA 条形码技术在小型兽类物种鉴定中的探索:以甘肃莲花山为例[J]. 生物多样性,2013,21 (2):197-205.
[9] 李长龙,卢领群,郭红刚,等. 长爪沙鼠线粒体DNA 控制区全序列测定及分析[J]. 中国比较医学杂志,2010,20(4): 40-45.
[10] 谢建云,冯洁,柏熊,等. 四种群东方田鼠线粒体DNA D-loop 多态性研究[J]. 实验动物与比较医学,2008,28(5): 299-303.
[11] Ivanova NV,Zemlak TS,Hanner RH,et al. Universal primer cocktails for fish DNA barcoding[J]. Mol Ecol Notes,2007,7 (4):544-548.
[12] Nicolas V, Quérouil S, Verheyen E, et al. Mitochondrial phylogeny of African wood mice,genus Hylomyscus(Rodentia: Muridae):implications for their taxonomy and biogeography[J]. Mol Phy Evo,2006,38(3):779-793.
[13] Liu J, Liu DY, Chen W, et al. Genetic analysis of hantaviruses and their rodent hosts in central - south China[J]. Virus Res, 2012,163(2):439-447.
[14] Ceballos G,Ehrlich PR. Discoveries of new mammal species and their implications for conservation and ecosystem services[J]. Proc Natl Acad Sci,2009,106(10):3841-3846.
[15] 韦健红,吴文如,喻良文,等. DNA 条形码技术在生物分类中的应用[J]. 广东药学院学报,2010,26(4):430-433.
[16] Lu L,Chesters D,Zhang W,et al. Small mammal investigation in spotted fever focus with DNA - barcoding and taxonomic implications on rodents species from Hainan of China[J]. PLoS One,2012,7(8):e43479.

4种DNA条形码在黄毛鼠种类鉴定中的比较

Comparison of four DNA barcoding in Rattus losea identification

PDF

可视化

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 15

编辑推荐

Metrics

本文评价

[1]	姜洪雪, 姚丹丹, 林思亮, 冯志勇. 基于4种线粒体基因序列的广东省南雄市农区小型兽类DNA条形码分析[J]. 中国媒介生物学及控制杂志, 2022, 33(1): 48-53.
[2]	徐颖, 刘海江, 庞英杰, 陈晓光, 张娟, 张瑾, 徐翮飞, 滕新栋. 青岛口岸入境货物中截获输入性东亚异蚤蝇[J]. 中国媒介生物学及控制杂志, 2022, 33(1): 133-136.
[3]	姚丹丹, 姜洪雪, 隋晶晶, 冯志勇. 抗凝血杀鼠剂选择压力下黄毛鼠抗药性相关解毒酶的研究[J]. 中国媒介生物学及控制杂志, 2020, 31(6): 657-661.
[4]	兰晓宇, 鲁亮, 候芝林, 杜国义, 史献明, 崔耀仁, 刘冠纯, 陈永明, 康东梅, 郑楠, 任兴宇, 闫东. DNA条形码技术在河北省鼠疫疫源地常见蚤种鉴定中的应用[J]. 中国媒介生物学及控制杂志, 2020, 31(6): 662-666.
[5]	姚丹丹, 姜洪雪, 隋晶晶, 冯志勇. 广东省江门市捕获鼠类的DNA条形码分析[J]. 中国媒介生物学及控制杂志, 2020, 31(3): 305-309.
[6]	刘维俊, 徐国英, 肖方震, 林代华, 刘菁, 韩腾伟. DNA条形码技术在福建省鼠种鉴定中的应用[J]. 中国媒介生物学及控制杂志, 2020, 31(2): 175-179.
[7]	姚丹丹, 姜洪雪, 刘福佳, 冯志勇. 广东省江门市黄毛鼠对第一代抗凝血杀鼠剂的抗药性及其与VKORC1基因的相关性研究[J]. 中国媒介生物学及控制杂志, 2019, 30(6): 613-617.
[8]	尹小平, 刘戈, 王安东, 颜彬, 白岑, 田延河, 张兆冠, 赵姗姗, 王远志. DNA条形码技术在蚤类鉴定中的应用[J]. 中国媒介生物学及控制杂志, 2019, 30(5): 561-563.
[9]	郭丽民, 席进孝, 盖永志, 吴斌, 王世明, 苗克军, 穆洮霞, 徐大琴. 甘肃省鼠疫疫源地啮齿动物DNA条形码分析[J]. 中国媒介生物学及控制杂志, 2019, 30(2): 176-179.
[10]	郑凌霄, 尹灿灿, 王逸枭, 李梦楠, 邵黄芳, 方惟希, 杨曼, 赵金红, 孙恩涛. 基于DNA条形码技术的粉螨种类鉴定研究[J]. 中国媒介生物学及控制杂志, 2019, 30(2): 180-184.
[11]	王逸枭, 郑凌霄, 管国宇, 尹灿灿, 刘啸, 汪书然, 温子昂, 陈樱玮, 程序, 孙恩涛. 居室内检获的羽美绥螨形态和DNA条形码鉴定[J]. 中国媒介生物学及控制杂志, 2018, 29(6): 582-585.
[12]	姚丹丹, 冯志勇, 姜洪雪. 广东省青毛鼠的DNA条形码鉴定[J]. 中国媒介生物学及控制杂志, 2018, 29(2): 143-146.
[13]	魏晓雅, 刘德星, 邱德义, 岳巧云. 中山口岸截获国内未见分布染色硬翅蠊的鉴定[J]. 中国媒介生物学及控制杂志, 2018, 29(1): 23-26.
[14]	李基旭, 宋振海, 朴光明. 吉林省延边地区图们江流域按蚊形态学及基因特征分析[J]. 中国媒介生物学及控制杂志, 2018, 29(1): 42-46.
[15]	邱德义, 廖俊蕾, 魏晓雅, 岳巧云. 基于DNA条形码丽蝇科49种常见种的分类鉴定[J]. 中国媒介生物学及控制杂志, 2017, 28(4): 322-331.