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Genome Survey and Large-scale Isolation of Microsatellites through Illumina Sequencing from the Red Swamp Crayfish Procambarus clarkii

文献类型： 外文期刊

作者： Zhang, Xiao 1 ; Shen, Guoqing 1 ; Wang, Yang 1 ; Huang, Pengdan 1 ; Shui, Yan 2 ; Xu, Zenghong 2 ; Shen, Huaishun 1 ;

作者机构： 1.Nanjing Agr Univ, Wuxi Fisheries Coll, Nanjing 210095, Peoples R China

2.Chinese Acad Fishery Sci, Minist Agr, Freshwater Fisheries Res Ctr, Key Lab Freshwater Fisheries & Germplasm Resources, 9 Shanshui East Rd, Wuxi 214081, Peoples R China

关键词： Microsatellite marker; Procambarus clarkia; Genome survey; Solexa sequencing; Polymorphic loci

期刊名称：PAKISTAN JOURNAL OF ZOOLOGY （ 影响因子：0.6； 五年影响因子：0.7 ）

ISSN： 0030-9923

年卷期： 2023 年 55 卷 2 期

页码：

收录情况： SCI

摘要： Microsatellites, also known as simple sequence repeats (SSRs), are a type of DNA marker that are highly polymorphic in the genome. However, the microsatellite markers available for the red swamp crayfish Procambarus clarkii are limited. In this study, a sizeable number of microsatellites were identified using the data of the P. clarkii genome survey generated from Illumina Hi-Seq PE sequencing. A total length of 1,625 Mb genomic sequences of P. clarkii were assembled based on 124 Gb raw sequencing data. Based on a Kmer analysis, the P. clarkii genome size was projected as approximately 3.6 Gb. A total of 336,275 SSRs (simple sequence repeats) identified motifs were identified. There were 167,999 the most common type di-nucleotide repeat motifs (49.94%). The second most common repeats were the tri-nucleotide ones (131,405, 39.09%). A total of 312,454 microsatellite loci had flanking sequences. A subset of 56 primer pairs was randomly selected for the PCR experiments to validate the SSRs that had been identified. Forty-six primer pairs (80%) had PCR products that matched the sizes expected, and the products from 40 primer pairs (71%) exhibited polymorphism. Thirty-nine P. clarkii individuals were analyzed for their primer sets, and 22 were identified. The average allelic number in the 22 polymorphic loci was 3.6. The 22 microsatellite loci all had good polymorphisms. Among them, the polymorphism information content of the 12 loci is greater than 0.5, which is highly polymorphic.

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