Volume 18 Issue 1
Feb.  2022
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PENG Ye, LI Jie, WANG Tao, ZHANG Kai, NING Xianhui, JI Jie, YIN Shaowu. Preliminary study on distribution characteristics and positioning of microsatellites in whole genome of Pelteobagrus vachelli[J]. South China Fisheries Science, 2022, 18(1): 90-98. DOI: 10.12131/20210168
Citation: PENG Ye, LI Jie, WANG Tao, ZHANG Kai, NING Xianhui, JI Jie, YIN Shaowu. Preliminary study on distribution characteristics and positioning of microsatellites in whole genome of Pelteobagrus vachelli[J]. South China Fisheries Science, 2022, 18(1): 90-98. DOI: 10.12131/20210168
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Preliminary study on distribution characteristics and positioning of microsatellites in whole genome of Pelteobagrus vachelli

  • College of Marine Science and Engineering, Nanjing Normal University/Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, Nanjing 210023, China

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  • Received Date: June 03, 2021
  • Revised Date: June 29, 2021
  • Accepted Date: July 22, 2021
  • Available Online: August 03, 2021
    Graphical Abstract
    • Abstract
  • In this study, MISA (MIcroSAtellite identification tool) was used to screen and analyze the distribution characteristics of microsatellites in the whole genome of Pelteobagrus vachelli, aiming to provide a basis for the selection of functional microsatellite markers. The genes containing microsatellites in the exon regions were subjected to GO annotation and KEGG enrichment. In the whole genome of P. vachelli (Approximately 663.53 Mb), 417 724 perfect microsatellites were identified, accounting for 1.48% of the total length. The relative abundance of microsatellites in P. vachelli was 630 pcs·Mb−1. Among the six repeat types, dinucleotides were the most frequent, accounting for 43.36% of the total microsatellites, followed by mononucleotides (39.02%), tetranucleotides (9.05%), trinucleotides (7.34%), pentanucleotides (1.12%) and hexanucleotides (0.12%). By investigating the locations of microsatellites in the genome, we found that 10 924 microsatellites which belonged to 5 788 genes were located in the exons. The GO annotation shows that the number of genes annotated to biological process was the largest, mainly associated with binding activity and cellular macromolecular metabolism. KEGG enrichment analysis shows that these genes were enriched in 273 pathways, among which, flavonoids and flavonol biosynthesis (P=0) were the most significantly enriched pathways. Integrated analysis indicates that the microsatellites located in the exons of genes in P. vachelli were closely related to the biological metabolism processes.
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