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为探明鳞翅目昆虫全基因组SSR分布规律,本研究利用MSDB v2.4软件和生物信息学方法搜索和提取了家蚕(Bombyx mori)、小菜蛾(Plutella xylostella)、菜粉蝶(Pieris rapae)、烟草天蛾(Manduca sexta)、棉铃虫(Helicoverpa armigera)和帝王蝶(Danaus plexippus)共6种鳞翅目昆虫全基因组完整型SSRs序列,对其分布规律进行比较分析。结果表明,基因组最大的昆虫是烟草天蛾,达到419.42 MB,但SSR总数最多的是家蚕,其SSR标记相对丰富,有141 311个,占基因组的0.61%,SSRs总数与基因组大小不成正比。纯微卫星(pure microsatellites, P-SSRs)在调查的6种昆虫的SSR类型中最丰富,均占总SSR的97%以上;家蚕和棉铃虫中单碱基-SSRs最为丰富,分别占全部碱基类型的51%和33%,帝王蝶中二碱基-SSRs最为丰富,占43%,小菜蛾、菜粉蝶、烟草天蛾中四碱基-SSR最为丰富,分别占31.56%、31.74%和28.72%,五、六碱基在所有昆虫SSR中含量都非常低;6种昆虫SSR重复类型碱基A-T总含量均比G-C含量高,A-T含量最高的物种为菜粉蝶,最低的是小菜蛾。各物种的优势碱基基序不同,6种昆虫一至四碱基重复类型的优势碱基序列较一致,五、六碱基的优势序列差异较大,说明碱基重复次数越高,稳定性及多态性越低。每种昆虫显示了物种特有的碱基类型丰度及优势碱基序列,这与物种的遗传特性、SSR的检索和分析条件及序列大小等因素有关。研究结果为鳞翅目昆虫的SSRs分子标记筛选和遗传分析提供参考数据。
Abstract：In order to ascertain the distribution regularities of whole genome SSR of lepidopteran insects, simple sequence repeats(SSRs) were searched and extracted by using the Microsatellite Search and Building Database and bioinformatics method in the complete genomes of Bombyx mori, Plutella xylostella, Pieris rapae, Manduca sexta, Helicoverpa armigera, and Danaus plexippus. The results showed that the largest insect in the genome was the M. sexta, reaching 419.42 MB, but the largest number of SSRs was B. mori with 141 311, accounting for 0.61% of the genome. The total number of SSRs was not proportional to the genome size. Pure microsatel lites(P-SSRs) were the most abundant among the six SSR types investigated, accounting for more than 97% of the total SSR. The Mono-SSRs were the most abundant in B. mori and H. armigera, accounting for 51% and 33%, respectively. What's more, Di-SSRs were the most abundant in D. plexippus, accounting for 43%. Tetra-SSR was the most abundant in P. xylostella, P. rapae and M. sexta, accounting for 31.56%, 31.74% and 28.72%, respectively. The content of Penta-and Hexa-bases in all insect SSRs was very low. The total content of base A-T in six insect SSR repeat types was higher than that in G-C. The species with the highest A-T content was P. rapae,and the lowest was P. xylostella. The dominant base sequence of each species was different. The dominant base sequences of Mono-SSR to Tetra-SSR of six insects were relatively consistent, and the dominant base sequences of Penta-bases and Hexa-bases were quite different, indicating that the higher the number of SSR base repeats,the lower the stability and polymorphism of SSR. Each insect shows the species-specific base type abundance and dominant base sequence, which is related to the genetic characteristics of the species, SSR retrieval and analysis conditions and sequence size. The results provide reference data for screening SSRS molecular markers and genetic analysis of Lepidoptera insects.
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基本信息:
DOI：10.13417/j.gab.040.001022
中图分类号:Q963
引用信息:
[1]甘丽萍,田辉,唐恒,等.6种鳞翅目昆虫全基因组SSR分布规律[J].基因组学与应用生物学,2021,40(03):1022-1030.DOI:10.13417/j.gab.040.001022.
基金信息:
重庆市教委项目(KJ1710246)资助
2019-09-09
2019-09-09
2019-09-09