Microsatellite diversity and complexity in the viral genomes of the family Caliciviridae

Md Gulam Jilani; Mehboob Hoque; Safdar Ali

doi:10.1186/s43141-023-00582-x

Microsatellite diversity and complexity in the viral genomes of the family Caliciviridae

J Genet Eng Biotechnol. 2023 Nov 24;21(1):140. doi: 10.1186/s43141-023-00582-x.

Authors

Md Gulam Jilani¹, Mehboob Hoque², Safdar Ali³

Affiliations

¹ Department of Biological Sciences, Clinical and Applied Genomics (CAG) Laboratory, Aliah University, IIA/27, Newtown, Kolkata, 700160, India.
² Department of Biological Sciences, Applied Bio-Chemistry (ABC) Lab, Aliah University, Kolkata, India.
³ Department of Biological Sciences, Clinical and Applied Genomics (CAG) Laboratory, Aliah University, IIA/27, Newtown, Kolkata, 700160, India. safdar_mgl@live.in.

Abstract

Background: Microsatellites or simple sequence repeats (SSR) consist of 1-6 nucleotide motifs of DNA or RNA which are ubiquitously present in tandem repeated sequences across genome in viruses: prokaryotes and eukaryotes. They may be localized to both the coding and non-coding regions. SSRs play an important role in replication, gene regulation, transcription, and protein function. The Caliciviridae (CLV) family of viruses have ss-RNA, non-enveloped, icosahedral symmetry 27-35 nm in diameter in size. The size of the genome lies between 6.4 and 8.6 kb.

Results: The incidence, composition, diversity, complexity, and host range of different microsatellites in 62 representatives of the family of Caliciviridae were systematically analyzed. The full-length genome sequences were assessed from NCBI ( https://www.ncbi.nlm.nih.gov ), and microsatellites were extracted through MISA software. The average genome size is about 7538 bp ranging from 6273 (CLV61) to 8798 (CLV47) bp. The average GC content of the genomes was ~ 51%. There are a total of 1317 SSRs and 53 cSSRs in the studied genomes. CLV 41 and CLV 49 contain the highest and lowest value of SSRs with 32 and 10 respectively, while CLV16 had maximum cSSR incidence of 4. There were 29 species which do not contain any cSSR. The incidence of mono-, di-, and tri-nucleotide SSRs was 219, 884, and 206, respectively. The most prevalent mono-, di-, and tri-nucleotide repeat motifs were "C" (126 SSRs), AC/CA (240 SSRs), and TGA/ACT (23 SSRs), respectively. Most of the SSRs and cSSRs are biased toward the coding region with a minimum of ~ 90% incident SSRs in the genomes' coding region. Viruses with similar host are found close to each other on the phylogenetic tree suggesting virus host being one of the driving forces for their evolution.

Conclusions: The Caliciviridae genomes does not conform to any pattern of SSR signature in terms of incidence, composition, and localization. This unique property of SSR plays an important role in viral evolution. Clustering of similar host in the phylogenetic tree is the evidence of the uniqueness of SSR signature.

Keywords: Caliciviridae; Incidence; MISA; Phylogenetics; Prevalence; Simple sequence repeats.