Comprehensive Analysis of Codon Usage in <i>Quercus</i> Chloroplast Genome and Focus on <i>psbA</i> Gene
<i>Quercus</i> (oak) is an important economic and ecological tree species in the world, and it is the necessary feed for oak silkworm feeding. Chloroplasts play an important role in green plants but the codon usage of oak chloroplast genomes is not fully studied. We examined the codon us...
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| Format: | Article |
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MDPI AG
2022-11-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/13/11/2156 |
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| author | Sheng-Lin Shi Yan-Qun Liu Run-Xi Xia Li Qin |
| author_facet | Sheng-Lin Shi Yan-Qun Liu Run-Xi Xia Li Qin |
| author_sort | Sheng-Lin Shi |
| collection | DOAJ |
| description | <i>Quercus</i> (oak) is an important economic and ecological tree species in the world, and it is the necessary feed for oak silkworm feeding. Chloroplasts play an important role in green plants but the codon usage of oak chloroplast genomes is not fully studied. We examined the codon usage of the oak chloroplast genomes in detail to facilitate the understanding of their biology and evolution. We downloaded all the protein coding genes of 26 non-redundant chloroplast reference genomes, removed short ones and those containing internal stop codons, and finally retained 50 genes shared by all genomes for comparative analyses. The base composition, codon bias, and codon preference are not significantly different between genomes but are significantly different among genes within these genomes. Oak chloroplast genomes prefer T/A-ending codons and avoid C/G-ending codons, and the <i>psbA</i> gene has the same preference except for the codons encoding amino acid Phe. Complex factors such as context-dependent mutations are the major factors affecting codon usage in these genomes, while selection plays an important role on the <i>psbA</i> gene. Our study provided an important understanding of codon usage in the oak chloroplast genomes and found that the <i>psbA</i> gene has nearly the same codon usage preference as other genes in the oak chloroplasts. |
| first_indexed | 2024-03-09T18:19:07Z |
| format | Article |
| id | doaj.art-e885ab6a39a34ef1aec2344ea864b739 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-09T18:19:07Z |
| publishDate | 2022-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-e885ab6a39a34ef1aec2344ea864b7392023-11-24T08:27:10ZengMDPI AGGenes2073-44252022-11-011311215610.3390/genes13112156Comprehensive Analysis of Codon Usage in <i>Quercus</i> Chloroplast Genome and Focus on <i>psbA</i> GeneSheng-Lin Shi0Yan-Qun Liu1Run-Xi Xia2Li Qin3College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, ChinaCollege of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, ChinaCollege of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, ChinaCollege of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China<i>Quercus</i> (oak) is an important economic and ecological tree species in the world, and it is the necessary feed for oak silkworm feeding. Chloroplasts play an important role in green plants but the codon usage of oak chloroplast genomes is not fully studied. We examined the codon usage of the oak chloroplast genomes in detail to facilitate the understanding of their biology and evolution. We downloaded all the protein coding genes of 26 non-redundant chloroplast reference genomes, removed short ones and those containing internal stop codons, and finally retained 50 genes shared by all genomes for comparative analyses. The base composition, codon bias, and codon preference are not significantly different between genomes but are significantly different among genes within these genomes. Oak chloroplast genomes prefer T/A-ending codons and avoid C/G-ending codons, and the <i>psbA</i> gene has the same preference except for the codons encoding amino acid Phe. Complex factors such as context-dependent mutations are the major factors affecting codon usage in these genomes, while selection plays an important role on the <i>psbA</i> gene. Our study provided an important understanding of codon usage in the oak chloroplast genomes and found that the <i>psbA</i> gene has nearly the same codon usage preference as other genes in the oak chloroplasts.https://www.mdpi.com/2073-4425/13/11/2156<i>Quercus</i> specieschloroplast genomecodon usagecontext-dependent mutationtranslational selection<i>psbA</i> gene |
| spellingShingle | Sheng-Lin Shi Yan-Qun Liu Run-Xi Xia Li Qin Comprehensive Analysis of Codon Usage in <i>Quercus</i> Chloroplast Genome and Focus on <i>psbA</i> Gene Genes <i>Quercus</i> species chloroplast genome codon usage context-dependent mutation translational selection <i>psbA</i> gene |
| title | Comprehensive Analysis of Codon Usage in <i>Quercus</i> Chloroplast Genome and Focus on <i>psbA</i> Gene |
| title_full | Comprehensive Analysis of Codon Usage in <i>Quercus</i> Chloroplast Genome and Focus on <i>psbA</i> Gene |
| title_fullStr | Comprehensive Analysis of Codon Usage in <i>Quercus</i> Chloroplast Genome and Focus on <i>psbA</i> Gene |
| title_full_unstemmed | Comprehensive Analysis of Codon Usage in <i>Quercus</i> Chloroplast Genome and Focus on <i>psbA</i> Gene |
| title_short | Comprehensive Analysis of Codon Usage in <i>Quercus</i> Chloroplast Genome and Focus on <i>psbA</i> Gene |
| title_sort | comprehensive analysis of codon usage in i quercus i chloroplast genome and focus on i psba i gene |
| topic | <i>Quercus</i> species chloroplast genome codon usage context-dependent mutation translational selection <i>psbA</i> gene |
| url | https://www.mdpi.com/2073-4425/13/11/2156 |
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