DNA barcoding analysis of small mammals in the agricultural area in Nanxiong of Guangdong province based on four mitochondrial gene sequences

doi:10.11853/j.issn.1003.8280.2022.01.009

Abstract

Abstract: Objective To investigate the reliability of different DNA barcoding genes in identifying small mammals by using four mitochondrial genes to identify the species of farmland rodent pests in Nanxiong city of Guangdong province, China. Methods A total of 110 samples of mouse-like rodents were captured in the farmland of Zhuji town in Nanxiong city in 2019. Genomic DNA extraction was performed for some of these samples, and universal primers were used for the amplification and sequencing of cytochrome c oxidase subunit Ⅰ (COⅠ), cytochrome B (Cytb), 16S rRNA, and mitochondrial DNA control region (D-loop) gene fragments. Rodent species was identified based on homology alignment, genetic distance analysis, and phylogenetic tree construction, and the identification results were compared with the results of conventional morphological identification. Results The DNA barcoding analysis of the four gene sequences showed that the samples belonged to 6 species in 4 genera, 2 families, and 2 orders. The D-loop gene bands of Suncus murinus were not amplified, and the Cytb gene sequence of S. murinus and the 16S rRNA gene sequence of Rattus losea were not correctly identified by BLAST. Intraspecific genetic distance was smaller than interspecific genetic distance for different rodent species and genes. The phylogenetic tree showed that individuals of the same rodent species were clustered into one branch, with a support rate of >99%. Genetic identification results were different from morphological identification results for the 6 samples. Conclusion The DNA barcoding technique is a powerful supplement to conventional morphological identification. In practical application, suitable DNA barcode genes should be selected according to the integrity and accuracy of database, and multi-gene mutual validation should be used to ensure the accuracy of identification results.

Key words: DNA barcoding, Small mammal, Species identification, Mitochondrial gene

摘要： 目的利用4种线粒体基因对广东省南雄市农田害鼠进行鉴定，探讨不同条形码基因应用于小型兽类鉴定的可靠性。方法 2019年在南雄市珠玑镇农田捕获110只鼠形动物样本，对部分样本通过提取基因组DNA、通用引物扩增线粒体细胞色素C氧化酶亚基Ⅰ（COⅠ）、线粒体细胞色素B（Cytb）、16S rRNA和线粒体DNA控制区（D-loop）基因片段及测序，经同源性比对、遗传距离分析和系统发育树构建鉴定鼠种，并与传统形态学鉴定结果进行比较。结果经过4种基因序列条形码分析，样本隶属于2目2科4属6种。其中臭鼩鼱D-loop不能扩增出条带，臭鼩鼱Cytb、黄毛鼠16S rRNA序列不能正确比对。不同鼠种及不同基因种内遗传距离均小于种间遗传距离。系统发育树显示，同一鼠种均聚为一支，支持率在99%以上，6个样本遗传学鉴定结果与形态学鉴定结果不同。结论 DNA条形码技术是传统形态学鉴定的有力补充，实际应用时，可依据数据库的完整性和准确性合理选择不同的条形码基因，并利用多基因相互验证，以保证鉴定结果准确。

关键词: DNA条形码, 小型兽类, 种类鉴定, 线粒体基因

CLC Number:

S443
Q38

JIANG Hong-xue, YAO Dan-dan, LIN Si-liang, FENG Zhi-yong. DNA barcoding analysis of small mammals in the agricultural area in Nanxiong of Guangdong province based on four mitochondrial gene sequences[J]. Chinese Journal of Vector Biology and Control, 2022, 33(1): 48-53.

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.

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