Cargando…
The Shift in Synonymous Codon Usage Reveals Similar Genomic Variation during Domestication of Asian and African Rice
The domestication of wild rice occurred together with genomic variation, including the synonymous nucleotide substitutions that result in synonymous codon usage bias (SCUB). SCUB mirrors the evolutionary specialization of plants, but its characteristics during domestication were not yet addressed. H...
Autores principales: | , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2022
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9656316/ https://www.ncbi.nlm.nih.gov/pubmed/36361651 http://dx.doi.org/10.3390/ijms232112860 |
_version_ | 1784829403557003264 |
---|---|
author | Xiao, Guilian Zhou, Junzhi Huo, Zhiheng Wu, Tong Li, Yingchun Li, Yajing Wang, Yanxia Wang, Mengcheng |
author_facet | Xiao, Guilian Zhou, Junzhi Huo, Zhiheng Wu, Tong Li, Yingchun Li, Yajing Wang, Yanxia Wang, Mengcheng |
author_sort | Xiao, Guilian |
collection | PubMed |
description | The domestication of wild rice occurred together with genomic variation, including the synonymous nucleotide substitutions that result in synonymous codon usage bias (SCUB). SCUB mirrors the evolutionary specialization of plants, but its characteristics during domestication were not yet addressed. Here, we found cytosine- and guanidine-ending (NNC and NNG) synonymous codons (SCs) were more pronounced than adenosine- and thymine-ending SCs (NNA and NNT) in both wild and cultivated species of Asian and African rice. The ratios of NNC/G to NNA/T codons gradually decreased following the rise in the number of introns, and the preference for NNA/T codons became more obvious in genes with more introns in cultivated rice when compared with those in wild rice. SCUB frequencies were heterogeneous across the exons, with a higher preference for NNA/T in internal exons than in terminal exons. The preference for NNA/T in internal but not terminal exons was more predominant in cultivated rice than in wild rice, with the difference between wild and cultivated rice becoming more remarkable with the rise in exon numbers. The difference in the ratios of codon combinations representing DNA methylation-mediated conversion from cytosine to thymine between wild and cultivated rice coincided with their difference in SCUB frequencies, suggesting that SCUB reveals the possible association between genetic and epigenetic variation during the domestication of rice. Similar patterns of SCUB shift in Asian and African rice indicate that genomic variation occurs in the same non-random manner. SCUB representing non-neutral synonymous mutations can provide insight into the mechanism of genomic variation in domestication and can be used for the genetic dissection of agricultural traits in rice and other crops. |
format | Online Article Text |
id | pubmed-9656316 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-96563162022-11-15 The Shift in Synonymous Codon Usage Reveals Similar Genomic Variation during Domestication of Asian and African Rice Xiao, Guilian Zhou, Junzhi Huo, Zhiheng Wu, Tong Li, Yingchun Li, Yajing Wang, Yanxia Wang, Mengcheng Int J Mol Sci Article The domestication of wild rice occurred together with genomic variation, including the synonymous nucleotide substitutions that result in synonymous codon usage bias (SCUB). SCUB mirrors the evolutionary specialization of plants, but its characteristics during domestication were not yet addressed. Here, we found cytosine- and guanidine-ending (NNC and NNG) synonymous codons (SCs) were more pronounced than adenosine- and thymine-ending SCs (NNA and NNT) in both wild and cultivated species of Asian and African rice. The ratios of NNC/G to NNA/T codons gradually decreased following the rise in the number of introns, and the preference for NNA/T codons became more obvious in genes with more introns in cultivated rice when compared with those in wild rice. SCUB frequencies were heterogeneous across the exons, with a higher preference for NNA/T in internal exons than in terminal exons. The preference for NNA/T in internal but not terminal exons was more predominant in cultivated rice than in wild rice, with the difference between wild and cultivated rice becoming more remarkable with the rise in exon numbers. The difference in the ratios of codon combinations representing DNA methylation-mediated conversion from cytosine to thymine between wild and cultivated rice coincided with their difference in SCUB frequencies, suggesting that SCUB reveals the possible association between genetic and epigenetic variation during the domestication of rice. Similar patterns of SCUB shift in Asian and African rice indicate that genomic variation occurs in the same non-random manner. SCUB representing non-neutral synonymous mutations can provide insight into the mechanism of genomic variation in domestication and can be used for the genetic dissection of agricultural traits in rice and other crops. MDPI 2022-10-25 /pmc/articles/PMC9656316/ /pubmed/36361651 http://dx.doi.org/10.3390/ijms232112860 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Xiao, Guilian Zhou, Junzhi Huo, Zhiheng Wu, Tong Li, Yingchun Li, Yajing Wang, Yanxia Wang, Mengcheng The Shift in Synonymous Codon Usage Reveals Similar Genomic Variation during Domestication of Asian and African Rice |
title | The Shift in Synonymous Codon Usage Reveals Similar Genomic Variation during Domestication of Asian and African Rice |
title_full | The Shift in Synonymous Codon Usage Reveals Similar Genomic Variation during Domestication of Asian and African Rice |
title_fullStr | The Shift in Synonymous Codon Usage Reveals Similar Genomic Variation during Domestication of Asian and African Rice |
title_full_unstemmed | The Shift in Synonymous Codon Usage Reveals Similar Genomic Variation during Domestication of Asian and African Rice |
title_short | The Shift in Synonymous Codon Usage Reveals Similar Genomic Variation during Domestication of Asian and African Rice |
title_sort | shift in synonymous codon usage reveals similar genomic variation during domestication of asian and african rice |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9656316/ https://www.ncbi.nlm.nih.gov/pubmed/36361651 http://dx.doi.org/10.3390/ijms232112860 |
work_keys_str_mv | AT xiaoguilian theshiftinsynonymouscodonusagerevealssimilargenomicvariationduringdomesticationofasianandafricanrice AT zhoujunzhi theshiftinsynonymouscodonusagerevealssimilargenomicvariationduringdomesticationofasianandafricanrice AT huozhiheng theshiftinsynonymouscodonusagerevealssimilargenomicvariationduringdomesticationofasianandafricanrice AT wutong theshiftinsynonymouscodonusagerevealssimilargenomicvariationduringdomesticationofasianandafricanrice AT liyingchun theshiftinsynonymouscodonusagerevealssimilargenomicvariationduringdomesticationofasianandafricanrice AT liyajing theshiftinsynonymouscodonusagerevealssimilargenomicvariationduringdomesticationofasianandafricanrice AT wangyanxia theshiftinsynonymouscodonusagerevealssimilargenomicvariationduringdomesticationofasianandafricanrice AT wangmengcheng theshiftinsynonymouscodonusagerevealssimilargenomicvariationduringdomesticationofasianandafricanrice AT xiaoguilian shiftinsynonymouscodonusagerevealssimilargenomicvariationduringdomesticationofasianandafricanrice AT zhoujunzhi shiftinsynonymouscodonusagerevealssimilargenomicvariationduringdomesticationofasianandafricanrice AT huozhiheng shiftinsynonymouscodonusagerevealssimilargenomicvariationduringdomesticationofasianandafricanrice AT wutong shiftinsynonymouscodonusagerevealssimilargenomicvariationduringdomesticationofasianandafricanrice AT liyingchun shiftinsynonymouscodonusagerevealssimilargenomicvariationduringdomesticationofasianandafricanrice AT liyajing shiftinsynonymouscodonusagerevealssimilargenomicvariationduringdomesticationofasianandafricanrice AT wangyanxia shiftinsynonymouscodonusagerevealssimilargenomicvariationduringdomesticationofasianandafricanrice AT wangmengcheng shiftinsynonymouscodonusagerevealssimilargenomicvariationduringdomesticationofasianandafricanrice |