Study on the Characteristic Codon Usage Pattern in Porcine Epidemic Diarrhea Virus Genomes and Its Host Adaptation Phenotype
Porcine epidemic diarrhea virus (PEDV), which classified in the genus Alphacoronavirus, family Coronaviridae, is one of the most important pathogens that cause heavy economic losses in pig industry. Although intensive mutation and recombination analysis of PEDV strains were provided, systematic geno...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2021-10-01
|
| Series: | Frontiers in Microbiology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2021.738082/full |
| _version_ | 1818581123969581056 |
|---|---|
| author | Fusheng Si Li Jiang Ruisong Yu Wenqiang Wei Zhen Li |
| author_facet | Fusheng Si Li Jiang Ruisong Yu Wenqiang Wei Zhen Li |
| author_sort | Fusheng Si |
| collection | DOAJ |
| description | Porcine epidemic diarrhea virus (PEDV), which classified in the genus Alphacoronavirus, family Coronaviridae, is one of the most important pathogens that cause heavy economic losses in pig industry. Although intensive mutation and recombination analysis of PEDV strains were provided, systematic genome analysis were needed to elucidate the evolution mechanism and codon usage adaptation profiles of the pathogen. Here, a comprehensive investigation was carried out to reveal the systematic evolutionary processes of synonymous codon usage and host-adapted evolution phenotype of PEDV genome. We found a low codon usage bias (CUB) in PEDV genome and that nucleotide compositions, natural selection, mutation pressure and geographical diversity shapes the codon usage patterns of PEDV, with natural selection dominated the overall codon usage bias in PEDV than the others. By using the relative codon deoptimization index (RCDI) and similarity index (SiD) analysis, we observed that genotype II PEDV strains showed the highest level of adaptation phenotype to Sus scrofa than another divergent clade. To the best of our knowledge, this is the first comprehensive report elaborating the codon usage and host adaptation of PEDV. The findings offer an insight into our understanding of factors involved in PEDV evolution, adaptation and fitness toward their hosts. |
| first_indexed | 2024-12-16T07:28:30Z |
| format | Article |
| id | doaj.art-f3dbd1a961d4407cbbe78cd71e035c2a |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-16T07:28:30Z |
| publishDate | 2021-10-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-f3dbd1a961d4407cbbe78cd71e035c2a2022-12-21T22:39:27ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2021-10-011210.3389/fmicb.2021.738082738082Study on the Characteristic Codon Usage Pattern in Porcine Epidemic Diarrhea Virus Genomes and Its Host Adaptation PhenotypeFusheng Si0Li Jiang1Ruisong Yu2Wenqiang Wei3Zhen Li4Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Engineering Research Center of Breeding Pig, Institute of Animal Science and Veterinary Medicine, Shanghai Academy of Agricultural Sciences, Shanghai, ChinaSouth China Botanical Garden, Chinese Academy of Sciences, Guangzhou, ChinaShanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Engineering Research Center of Breeding Pig, Institute of Animal Science and Veterinary Medicine, Shanghai Academy of Agricultural Sciences, Shanghai, ChinaDepartment of Microbiology, School of Basic Medical Sciences, Henan University, Kaifeng, ChinaShanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Engineering Research Center of Breeding Pig, Institute of Animal Science and Veterinary Medicine, Shanghai Academy of Agricultural Sciences, Shanghai, ChinaPorcine epidemic diarrhea virus (PEDV), which classified in the genus Alphacoronavirus, family Coronaviridae, is one of the most important pathogens that cause heavy economic losses in pig industry. Although intensive mutation and recombination analysis of PEDV strains were provided, systematic genome analysis were needed to elucidate the evolution mechanism and codon usage adaptation profiles of the pathogen. Here, a comprehensive investigation was carried out to reveal the systematic evolutionary processes of synonymous codon usage and host-adapted evolution phenotype of PEDV genome. We found a low codon usage bias (CUB) in PEDV genome and that nucleotide compositions, natural selection, mutation pressure and geographical diversity shapes the codon usage patterns of PEDV, with natural selection dominated the overall codon usage bias in PEDV than the others. By using the relative codon deoptimization index (RCDI) and similarity index (SiD) analysis, we observed that genotype II PEDV strains showed the highest level of adaptation phenotype to Sus scrofa than another divergent clade. To the best of our knowledge, this is the first comprehensive report elaborating the codon usage and host adaptation of PEDV. The findings offer an insight into our understanding of factors involved in PEDV evolution, adaptation and fitness toward their hosts.https://www.frontiersin.org/articles/10.3389/fmicb.2021.738082/fullcoronavirusPEDVcodon usageselection pressurehost adaptationviral evolution |
| spellingShingle | Fusheng Si Li Jiang Ruisong Yu Wenqiang Wei Zhen Li Study on the Characteristic Codon Usage Pattern in Porcine Epidemic Diarrhea Virus Genomes and Its Host Adaptation Phenotype Frontiers in Microbiology coronavirus PEDV codon usage selection pressure host adaptation viral evolution |
| title | Study on the Characteristic Codon Usage Pattern in Porcine Epidemic Diarrhea Virus Genomes and Its Host Adaptation Phenotype |
| title_full | Study on the Characteristic Codon Usage Pattern in Porcine Epidemic Diarrhea Virus Genomes and Its Host Adaptation Phenotype |
| title_fullStr | Study on the Characteristic Codon Usage Pattern in Porcine Epidemic Diarrhea Virus Genomes and Its Host Adaptation Phenotype |
| title_full_unstemmed | Study on the Characteristic Codon Usage Pattern in Porcine Epidemic Diarrhea Virus Genomes and Its Host Adaptation Phenotype |
| title_short | Study on the Characteristic Codon Usage Pattern in Porcine Epidemic Diarrhea Virus Genomes and Its Host Adaptation Phenotype |
| title_sort | study on the characteristic codon usage pattern in porcine epidemic diarrhea virus genomes and its host adaptation phenotype |
| topic | coronavirus PEDV codon usage selection pressure host adaptation viral evolution |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2021.738082/full |
| work_keys_str_mv | AT fushengsi studyonthecharacteristiccodonusagepatterninporcineepidemicdiarrheavirusgenomesanditshostadaptationphenotype AT lijiang studyonthecharacteristiccodonusagepatterninporcineepidemicdiarrheavirusgenomesanditshostadaptationphenotype AT ruisongyu studyonthecharacteristiccodonusagepatterninporcineepidemicdiarrheavirusgenomesanditshostadaptationphenotype AT wenqiangwei studyonthecharacteristiccodonusagepatterninporcineepidemicdiarrheavirusgenomesanditshostadaptationphenotype AT zhenli studyonthecharacteristiccodonusagepatterninporcineepidemicdiarrheavirusgenomesanditshostadaptationphenotype |