A Comprehensive Plant microRNA Simple Sequence Repeat Marker Database to Accelerate Genetic Improvements in Crops
文献类型： 外文期刊
作者： Biswas, Manosh Kumar 1 ; Biswas, Dhiman 3 ; Bagchi, Mita 2 ; Yi, Ganjun 1 ; Deng, Guiming 1 ;
作者机构： 1.Guangdong Acad Agr Sci, Inst Fruit Tree Res, Guangzhou 510640, Peoples R China
2.Univ Leicester, Dept Genet & Genome Biol, Leicester LE1 7RH, Leics, England
3.Maulana Abul Kalam Azad Univ Technol, Dept Comp Sci & Engn, Kalyani 700064, W Bengal, India
关键词： microsatellite; microRNA; pre-miRNA; simple sequence repeat; marker database; legumes
期刊名称：AGRONOMY-BASEL （ 影响因子：3.417； 五年影响因子：3.64 ）
ISSN：
年卷期： 2021 年 11 卷 11 期
页码：
收录情况： SCI
摘要： Microsatellites, or simple sequences repeat (SSRs), are distributed in genes, intergenic regions and transposable elements in the genome. SSRs were identified for developing markers from draft genome assemblies, transcriptome sequences and genome survey sequences in plant and animals. The identification, distribution, and density of microsatellites in pre-microRNAs (miRNAs) are not well documented in plants. In this study, SSRs were identified in 16,892 pre-miRNA sequences from 292 plant species in six taxonomic groups (algae to dicots). Fifty-one percent of pre-miRNA sequences contained SSRs. Mononucleotide repeats were the most abundant, followed by di- and trinucleotide repeats. Tetra-, penta-, and hexarepeats were rare. A total of 9,498 (57.46%) microsatellite loci had potential as pre-miRNA SSR markers. Of the markers, 3,573 (37.62%) were non-redundant, and 2,341 (65.51%) primer pairs could be transferred to at least one of the plant taxonomic groups. All data and primer pairs were deposited in a user-friendly, freely accessible plant miRNA SSR marker database. The data presented in this study, accelerate the understanding of pre-miRNA evolution and serve as valuable genomic treasure for genetic improvements in a wide range of crops, including legumes, cereals, and cruciferous crops.
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