Assessment of simple sequence repeats signature in hepatitis E virus (HEV) genomes
Abstract Background Hepatitis E virus (HEV) is small (27–34 nm diameter) non-enveloped with positive sense ssRNA genome. Microsatellites or simple sequence repeats (SSR) are short tandem repeat sequences present across coding and non-coding regions of both prokaryotes and eukaryotes. They are involv...
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| Format: | Article |
| Language: | English |
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Elsevier
2022-05-01
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| Series: | Journal of Genetic Engineering and Biotechnology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s43141-022-00365-w |
| _version_ | 1797203544269389824 |
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| author | Md Gulam Jilani Safdar Ali |
| author_facet | Md Gulam Jilani Safdar Ali |
| author_sort | Md Gulam Jilani |
| collection | DOAJ |
| description | Abstract Background Hepatitis E virus (HEV) is small (27–34 nm diameter) non-enveloped with positive sense ssRNA genome. Microsatellites or simple sequence repeats (SSR) are short tandem repeat sequences present across coding and non-coding regions of both prokaryotes and eukaryotes. They are involved with genome function and evolution at multiple levels. Results The complete genome sequences of 22 HEV genomes of the family Hepeviridae and genus Orthohepevirus (21 species) and Piscihepevirus (1 species) were extracted from NCBI database ( http://www.ncbi.nlm.nih.gov/ ). The extraction of microsatellites was done using Imperfect Microsatellite Extractor (IMEx) in ‘Advance-Mode’. The average genome size of the studied HEV genomes was 7003nt and it ranged from 6649nt (HEV11) to 7310nt (HEV22). The average GC content of the genomes was ~ 55%. A total of 519 SSRs and 21 cSSRS were extracted from the HEV genomes with an average incidence of 24 per genome ranging from 14 (HEV13) to 34 (HEV19). The cSSR incidence ranged from 0 (eight species) to 4 (HEV19). The genomes with no cSSR incidence had an SSR incidence range from 14 to 28. There were just four hexa-nucleotide repeat motifs and 5 penta-nucleotide repeat motifs observed. The most prevalent mono-, di-, and tri-nucleotide repeat motifs were “C”, “GT/TG”, and “GAC/CTG” respectively. The studied genomes had a minimum of ~ 90% incident SSRs present in the coding regions. Viruses with same or similar hosts are placed together on the phylogenetic tree implicating viral host being one of the driving forces for evolution. Conclusions Host range in viruses is being decided by multiple factors aided by the unique genome SSR signature and genomes of varied compositions need to be analyzed to forge a widely acceptable rule for predicting the same. |
| first_indexed | 2024-04-24T08:21:01Z |
| format | Article |
| id | doaj.art-01e37b4a98494e70b1306892d09029ba |
| institution | Directory Open Access Journal |
| issn | 2090-5920 |
| language | English |
| last_indexed | 2024-04-24T08:21:01Z |
| publishDate | 2022-05-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Genetic Engineering and Biotechnology |
| spelling | doaj.art-01e37b4a98494e70b1306892d09029ba2024-04-17T00:42:46ZengElsevierJournal of Genetic Engineering and Biotechnology2090-59202022-05-012011810.1186/s43141-022-00365-wAssessment of simple sequence repeats signature in hepatitis E virus (HEV) genomesMd Gulam Jilani0Safdar Ali1Clinical and Applied Genomics (CAG) Laboratory, Department of Biological Sciences, Aliah UniversityClinical and Applied Genomics (CAG) Laboratory, Department of Biological Sciences, Aliah UniversityAbstract Background Hepatitis E virus (HEV) is small (27–34 nm diameter) non-enveloped with positive sense ssRNA genome. Microsatellites or simple sequence repeats (SSR) are short tandem repeat sequences present across coding and non-coding regions of both prokaryotes and eukaryotes. They are involved with genome function and evolution at multiple levels. Results The complete genome sequences of 22 HEV genomes of the family Hepeviridae and genus Orthohepevirus (21 species) and Piscihepevirus (1 species) were extracted from NCBI database ( http://www.ncbi.nlm.nih.gov/ ). The extraction of microsatellites was done using Imperfect Microsatellite Extractor (IMEx) in ‘Advance-Mode’. The average genome size of the studied HEV genomes was 7003nt and it ranged from 6649nt (HEV11) to 7310nt (HEV22). The average GC content of the genomes was ~ 55%. A total of 519 SSRs and 21 cSSRS were extracted from the HEV genomes with an average incidence of 24 per genome ranging from 14 (HEV13) to 34 (HEV19). The cSSR incidence ranged from 0 (eight species) to 4 (HEV19). The genomes with no cSSR incidence had an SSR incidence range from 14 to 28. There were just four hexa-nucleotide repeat motifs and 5 penta-nucleotide repeat motifs observed. The most prevalent mono-, di-, and tri-nucleotide repeat motifs were “C”, “GT/TG”, and “GAC/CTG” respectively. The studied genomes had a minimum of ~ 90% incident SSRs present in the coding regions. Viruses with same or similar hosts are placed together on the phylogenetic tree implicating viral host being one of the driving forces for evolution. Conclusions Host range in viruses is being decided by multiple factors aided by the unique genome SSR signature and genomes of varied compositions need to be analyzed to forge a widely acceptable rule for predicting the same.https://doi.org/10.1186/s43141-022-00365-wHepatitis E virusSimple sequence repeatsImperfect microsatellite extractor (IMEx)IncidencePrevalencePhylogenetic |
| spellingShingle | Md Gulam Jilani Safdar Ali Assessment of simple sequence repeats signature in hepatitis E virus (HEV) genomes Journal of Genetic Engineering and Biotechnology Hepatitis E virus Simple sequence repeats Imperfect microsatellite extractor (IMEx) Incidence Prevalence Phylogenetic |
| title | Assessment of simple sequence repeats signature in hepatitis E virus (HEV) genomes |
| title_full | Assessment of simple sequence repeats signature in hepatitis E virus (HEV) genomes |
| title_fullStr | Assessment of simple sequence repeats signature in hepatitis E virus (HEV) genomes |
| title_full_unstemmed | Assessment of simple sequence repeats signature in hepatitis E virus (HEV) genomes |
| title_short | Assessment of simple sequence repeats signature in hepatitis E virus (HEV) genomes |
| title_sort | assessment of simple sequence repeats signature in hepatitis e virus hev genomes |
| topic | Hepatitis E virus Simple sequence repeats Imperfect microsatellite extractor (IMEx) Incidence Prevalence Phylogenetic |
| url | https://doi.org/10.1186/s43141-022-00365-w |
| work_keys_str_mv | AT mdgulamjilani assessmentofsimplesequencerepeatssignatureinhepatitisevirushevgenomes AT safdarali assessmentofsimplesequencerepeatssignatureinhepatitisevirushevgenomes |