Genome-wide analysis on the maize genome reveals weak selection on synonymous mutations
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 t...
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| Format: | Article |
| Language: | English |
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BMC
2020-04-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-020-6745-3 |
| _version_ | 1818303825781456896 |
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| author | Duan Chu Lai Wei |
| author_facet | Duan Chu Lai Wei |
| author_sort | Duan Chu |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-13T06:00:58Z |
| format | Article |
| id | doaj.art-53c819deb1b54373a018984b56e3fc95 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-13T06:00:58Z |
| publishDate | 2020-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-53c819deb1b54373a018984b56e3fc952022-12-21T23:57:21ZengBMCBMC Genomics1471-21642020-04-0121111110.1186/s12864-020-6745-3Genome-wide analysis on the maize genome reveals weak selection on synonymous mutationsDuan Chu0Lai Wei1College of Life Sciences, Beijing Normal UniversityCollege of Life Sciences, Beijing Normal UniversityAbstract 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.http://link.springer.com/article/10.1186/s12864-020-6745-3Synonymous mutationstRNA adaptation index (tAI)Maize (Zea mays)Derived allele frequency (DAF)Minor allele frequency (MAF)Natural selection |
| spellingShingle | Duan Chu Lai Wei Genome-wide analysis on the maize genome reveals weak selection on synonymous mutations BMC Genomics Synonymous mutations tRNA adaptation index (tAI) Maize (Zea mays) Derived allele frequency (DAF) Minor allele frequency (MAF) Natural selection |
| title | Genome-wide analysis on the maize genome reveals weak selection on synonymous mutations |
| title_full | Genome-wide analysis on the maize genome reveals weak selection on synonymous mutations |
| title_fullStr | Genome-wide analysis on the maize genome reveals weak selection on synonymous mutations |
| title_full_unstemmed | Genome-wide analysis on the maize genome reveals weak selection on synonymous mutations |
| title_short | Genome-wide analysis on the maize genome reveals weak selection on synonymous mutations |
| title_sort | genome wide analysis on the maize genome reveals weak selection on synonymous mutations |
| topic | Synonymous mutations tRNA adaptation index (tAI) Maize (Zea mays) Derived allele frequency (DAF) Minor allele frequency (MAF) Natural selection |
| url | http://link.springer.com/article/10.1186/s12864-020-6745-3 |
| work_keys_str_mv | AT duanchu genomewideanalysisonthemaizegenomerevealsweakselectiononsynonymousmutations AT laiwei genomewideanalysisonthemaizegenomerevealsweakselectiononsynonymousmutations |