Article ; Online: Genome-wide analysis on the maize genome reveals weak selection on synonymous mutations.
BMC genomics
2020 Volume 21, Issue 1, Page(s) 333
Abstract: ... of tAI.: Conclusion: The synonymous mutations in the maize genome are not strictly neutral. The tAI ... mutations which increase the tAI values are favored by natural selection.: Results: We use the maize ... Background: Synonymous mutations are able to change the tAI (tRNA adaptation index) of a codon and ...
| Abstract | Background: Synonymous mutations are able to change the tAI (tRNA adaptation index) of a codon and consequently affect the local translation rate. Intuitively, one may hypothesize that those synonymous mutations which increase the tAI values are favored by natural selection. Results: We use the maize (Zea mays) genome to test our assumption. The first supporting evidence is that the tAI-increasing synonymous mutations have higher fixed-to-polymorphic ratios than the tAI-decreasing ones. Next, the DAF (derived allele frequency) or MAF (minor allele frequency) of the former is significantly higher than the latter. Moreover, similar results are obtained when we investigate CAI (codon adaptation index) instead of tAI. Conclusion: The synonymous mutations in the maize genome are not strictly neutral. The tAI-increasing mutations are positively selected while those tAI-decreasing ones undergo purifying selection. This selection force might be weak but should not be automatically ignored. |
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| MeSH term(s) | Base Composition ; Codon/genetics ; Gene Frequency ; Genes, Plant ; Genetic Variation ; Genome, Plant ; Models, Genetic ; RNA Folding ; RNA, Transfer/genetics ; Selection, Genetic ; Silent Mutation ; Zea mays/genetics |
| Chemical Substances | Codon ; RNA, Transfer (9014-25-9) |
| Keywords | covid19 |
| Language | English |
| Publishing date | 2020-04-29 |
| Publishing country | England |
| Document type | Journal Article |
| ISSN | 1471-2164 |
| ISSN (online) | 1471-2164 |
| DOI | 10.1186/s12864-020-6745-3 |
| Database | MEDical Literature Analysis and Retrieval System OnLINE |
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