Characteristics of microsatellite distributions in genomes of Hipposideros armiger (Chiroptera)
Received date: 2022-08-13
Accepted date: 2022-11-07
Online published: 2023-03-23
The vertebrate genome is rich in microsatellite information. In this study, the distribution of microsatellite (SSRs) in the complete genome and its genes of Hipposideros armiger (Chiroptera) was analyzed, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) containing microsatellite coding sequence (CDS) were explored. The results showed that the total genome size of H. armiger was 2.24 Gb and contained 497 883 microsatellites. Mononucleotide (173 953 microsatellites) and dinucleotide repeats (222 591 microsatellites) were the most diverse in the genome of H. armiger accounting for 34.94% and 44.71% of whole genome size, with their relative abundance of 77.78 loci/Mb and 99.52 loci/Mb, respectively. The most microsatellite types from mononucleotide repeat to hexanucleotide repeat were (A)n, (AC)n, (TAT)n, (TTTA)n, (AACAA)n and (TATATA)n, with their frequency of 95.14%, 55.25%, 38.41%, 22.17%, 48.68% and 20.30% respectively. The number and abundance of microsatellites were different in both gene regions and intergenic regions. The diversity of microsatellites was highest in intergenic region with 322 666 microsatellites, and its abundance was 2 541.57 loci/Mb, whereas lowest in coding region with 1 461 microsatellites, and its abundance was 461.98 loci/Mb. The distribution characteristics of microsatellites in intergenic region and total genome were similar. Trinucleotide repeat were the most common types of microsatellites in the coding region, while mono-, di- and tri-nucleotide repeat were the most common types of microsatellites in the exons. The positional specificity of microsatellites abundance distributions in 500 bp upstream, exon, intron and 500 bp downstream were 16 400.94 loci/Mb, 972.12 loci/Mb, 2 180.66 loci/Mb and 3 899.89 loci/Mb, respectively. A total of 1 461 microsatellite coding sequences (CDS) were found in the genome of H. armiger, and 1 226 genes were annotated. GO was mainly annotated into 63 functional genes and assigned to 26 439 GO items. The most significant KEGG enrichment was in the signal transduction pathway, which contained 146 genes. The results of this study not only provide a reference for the screening of high-quality microsatellites in H. armiger, it will also provide a reference for genome-wide analysis of microsatellite distribution in other Chiroptera species and the study of their biological functions in the whole genome.
Key words： Chiroptera; Hipposideros armiger; Genome; Microsatellite; GO analysis; KEGG enrichment
Weiwei SHAO , Fen QIAO , Wei CAI , Zhihua LIN , Li WEI . Characteristics of microsatellite distributions in genomes of Hipposideros armiger (Chiroptera)[J]. ACTA THERIOLOGICA SINICA, 2023 , 43(2) : 182 -192 . DOI: 10.16829/j.slxb.150724
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