Analysis of codon usage bias of lumpy skin disease virus causing livestock infection
Lumpy skin disease virus (LSDV) causes lumpy skin disease (LSD) in livestock, which is a double-stranded DNA virus that belongs to the genus Capripoxvirus of the family Poxviridae. LSDV is an important poxvirus that has spread out far and wide to become distributed worldwide. It poses serious health...
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2022-12-01
|
| Series: | Frontiers in Veterinary Science |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fvets.2022.1071097/full |
| _version_ | 1811309314497839104 |
|---|---|
| author | Siddiq Ur Rahman Hassan Ur Rehman Inayat Ur Rahman Abdur Rauf Abdulrahman Alshammari Metab Alharbi Noor ul Haq Hafiz Ansar Rasul Suleria Sayed Haidar Abbas Raza Sayed Haidar Abbas Raza |
| author_facet | Siddiq Ur Rahman Hassan Ur Rehman Inayat Ur Rahman Abdur Rauf Abdulrahman Alshammari Metab Alharbi Noor ul Haq Hafiz Ansar Rasul Suleria Sayed Haidar Abbas Raza Sayed Haidar Abbas Raza |
| author_sort | Siddiq Ur Rahman |
| collection | DOAJ |
| description | Lumpy skin disease virus (LSDV) causes lumpy skin disease (LSD) in livestock, which is a double-stranded DNA virus that belongs to the genus Capripoxvirus of the family Poxviridae. LSDV is an important poxvirus that has spread out far and wide to become distributed worldwide. It poses serious health risks to the host and causes considerable negative socioeconomic impact on farmers financially and on cattle by causing ruminant-related diseases. Previous studies explained the population structure of the LSDV within the evolutionary time scale and adaptive evolution. However, it is still unknown and remains enigmatic as to how synonymous codons are used by the LSDV. Here, we used 53 LSDV strains and applied the codon usage bias (CUB) analysis to them. Both the base content and the relative synonymous codon usage (RSCU) analysis revealed that the AT-ended codons were more frequently used in the genome of LSDV. Further low codon usage bias was calculated from the effective number of codons (ENC) value. The neutrality plot analysis suggested that the dominant factor of natural selection played a role in the structuring of CUB in LSDV. Additionally, the results from a comparative analysis suggested that the LSDV has adapted host-specific codon usage patterns to sustain successful replication and transmission chains within hosts (Bos taurus and Homo sapiens). Both natural selection and mutational pressure have an impact on the codon usage patterns of the protein-coding genes in LSDV. This study is important because it has characterized the codon usage pattern in the LSDV genomes and has provided the necessary data for a basic evolutionary study on them. |
| first_indexed | 2024-04-13T09:40:08Z |
| format | Article |
| id | doaj.art-b172d488c5624d7c9667822fc14a9314 |
| institution | Directory Open Access Journal |
| issn | 2297-1769 |
| language | English |
| last_indexed | 2024-04-13T09:40:08Z |
| publishDate | 2022-12-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Veterinary Science |
| spelling | doaj.art-b172d488c5624d7c9667822fc14a93142022-12-22T02:51:56ZengFrontiers Media S.A.Frontiers in Veterinary Science2297-17692022-12-01910.3389/fvets.2022.10710971071097Analysis of codon usage bias of lumpy skin disease virus causing livestock infectionSiddiq Ur Rahman0Hassan Ur Rehman1Inayat Ur Rahman2Abdur Rauf3Abdulrahman Alshammari4Metab Alharbi5Noor ul Haq6Hafiz Ansar Rasul Suleria7Sayed Haidar Abbas Raza8Sayed Haidar Abbas Raza9Department of Computer Science and Bioinformatics, Khushal Khan Khattak University, Karak, PakistanDepartment of Computer Science and Bioinformatics, Khushal Khan Khattak University, Karak, PakistanDepartment of Botany, Khushal Khan Khattak University, Karak, PakistanDepartment of Chemistry, University of Swabi, Swabi, PakistanDepartment of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi ArabiaDepartment of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi ArabiaDepartment of Computer Science and Bioinformatics, Khushal Khan Khattak University, Karak, PakistanFaculty of Veterinary and Agricultural Sciences, School of Agriculture and Food, The University of Melbourne, Melbourne, VIC, AustraliaCollege of Animal Science and Technology, Northwest A&F University, Xianyang, ChinaSafety of Livestock and Poultry Products, College of Food Science, South China Agricultural University, Guangzhou, ChinaLumpy skin disease virus (LSDV) causes lumpy skin disease (LSD) in livestock, which is a double-stranded DNA virus that belongs to the genus Capripoxvirus of the family Poxviridae. LSDV is an important poxvirus that has spread out far and wide to become distributed worldwide. It poses serious health risks to the host and causes considerable negative socioeconomic impact on farmers financially and on cattle by causing ruminant-related diseases. Previous studies explained the population structure of the LSDV within the evolutionary time scale and adaptive evolution. However, it is still unknown and remains enigmatic as to how synonymous codons are used by the LSDV. Here, we used 53 LSDV strains and applied the codon usage bias (CUB) analysis to them. Both the base content and the relative synonymous codon usage (RSCU) analysis revealed that the AT-ended codons were more frequently used in the genome of LSDV. Further low codon usage bias was calculated from the effective number of codons (ENC) value. The neutrality plot analysis suggested that the dominant factor of natural selection played a role in the structuring of CUB in LSDV. Additionally, the results from a comparative analysis suggested that the LSDV has adapted host-specific codon usage patterns to sustain successful replication and transmission chains within hosts (Bos taurus and Homo sapiens). Both natural selection and mutational pressure have an impact on the codon usage patterns of the protein-coding genes in LSDV. This study is important because it has characterized the codon usage pattern in the LSDV genomes and has provided the necessary data for a basic evolutionary study on them.https://www.frontiersin.org/articles/10.3389/fvets.2022.1071097/fulllumpy skin disease viruscodon usage bias (CUB)effective number of codons (ENC)mutation pressurenatural selection |
| spellingShingle | Siddiq Ur Rahman Hassan Ur Rehman Inayat Ur Rahman Abdur Rauf Abdulrahman Alshammari Metab Alharbi Noor ul Haq Hafiz Ansar Rasul Suleria Sayed Haidar Abbas Raza Sayed Haidar Abbas Raza Analysis of codon usage bias of lumpy skin disease virus causing livestock infection Frontiers in Veterinary Science lumpy skin disease virus codon usage bias (CUB) effective number of codons (ENC) mutation pressure natural selection |
| title | Analysis of codon usage bias of lumpy skin disease virus causing livestock infection |
| title_full | Analysis of codon usage bias of lumpy skin disease virus causing livestock infection |
| title_fullStr | Analysis of codon usage bias of lumpy skin disease virus causing livestock infection |
| title_full_unstemmed | Analysis of codon usage bias of lumpy skin disease virus causing livestock infection |
| title_short | Analysis of codon usage bias of lumpy skin disease virus causing livestock infection |
| title_sort | analysis of codon usage bias of lumpy skin disease virus causing livestock infection |
| topic | lumpy skin disease virus codon usage bias (CUB) effective number of codons (ENC) mutation pressure natural selection |
| url | https://www.frontiersin.org/articles/10.3389/fvets.2022.1071097/full |
| work_keys_str_mv | AT siddiqurrahman analysisofcodonusagebiasoflumpyskindiseaseviruscausinglivestockinfection AT hassanurrehman analysisofcodonusagebiasoflumpyskindiseaseviruscausinglivestockinfection AT inayaturrahman analysisofcodonusagebiasoflumpyskindiseaseviruscausinglivestockinfection AT abdurrauf analysisofcodonusagebiasoflumpyskindiseaseviruscausinglivestockinfection AT abdulrahmanalshammari analysisofcodonusagebiasoflumpyskindiseaseviruscausinglivestockinfection AT metabalharbi analysisofcodonusagebiasoflumpyskindiseaseviruscausinglivestockinfection AT noorulhaq analysisofcodonusagebiasoflumpyskindiseaseviruscausinglivestockinfection AT hafizansarrasulsuleria analysisofcodonusagebiasoflumpyskindiseaseviruscausinglivestockinfection AT sayedhaidarabbasraza analysisofcodonusagebiasoflumpyskindiseaseviruscausinglivestockinfection AT sayedhaidarabbasraza analysisofcodonusagebiasoflumpyskindiseaseviruscausinglivestockinfection |