Deciphering codon usage patterns and evolutionary forces in chloroplast genes of Camellia sinensis var. assamica and Camellia sinensis var. sinensis in comparison to Camellia pubicosta
Codon usage bias (CUB) is a unique property of genome which refers to non-random usage of synonymous codons in coding sequences. The present study makes an attempt to find out the pattern of CUB in chloroplast (cp) genes among three tea species, i.e., Camellia sinensis var. assamica (Assam tea), Cam...
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KeAi Communications Co., Ltd.
2019-12-01
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| Series: | Journal of Integrative Agriculture |
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| author | Sophiarani Yengkhom Arif Uddin Supriyo Chakraborty |
| author_facet | Sophiarani Yengkhom Arif Uddin Supriyo Chakraborty |
| author_sort | Sophiarani Yengkhom |
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| description | Codon usage bias (CUB) is a unique property of genome which refers to non-random usage of synonymous codons in coding sequences. The present study makes an attempt to find out the pattern of CUB in chloroplast (cp) genes among three tea species, i.e., Camellia sinensis var. assamica (Assam tea), Camellia sinensis var. sinensis (Chinese tea) and Camellia pubicosta (wild tea species) as no work on CUB was reported earlier. To understand the patterns of codon usage among the cp genes of three tea groups, we used bioinformatic tools to investigate the protein coding sequences of cp genes. In our present study, the mean nucleobase T was the highest whereas C was the lowest in all the three tea groups. The overall AT content was more than GC content, i.e., genes were AT rich. The scaled chi-square (SCS) value indicated that the CUB of cp genes was low. The codon CGT (Arg) was over-represented in C. sinensis var. sinensis whereas GGA (Pro) was over-represented in C. pubicosta species. Heatmap study revealed that most of the GC ending codons showed positive correlations between codon usage and GC3 while AT ending codons exhibited negative correlations. From neutrality plot analysis, it was evident that natural selection had played a major role, while mutation pressure exerted a minor effect in the CUB of cp genes in three tea groups. Highly significant (P<0.01) positive correlation was found between SCS and synonymous codon usage order (SCUO) of cp genes which suggested that high expression of cp genes was associated with high degree of CUB. |
| format | Article |
| id | doaj-art-d98782e248ab4ee09bb8601cc2f797f8 |
| institution | Kabale University |
| issn | 2095-3119 |
| language | English |
| publishDate | 2019-12-01 |
| publisher | KeAi Communications Co., Ltd. |
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| series | Journal of Integrative Agriculture |
| spelling | doaj-art-d98782e248ab4ee09bb8601cc2f797f82025-08-20T03:58:54ZengKeAi Communications Co., Ltd.Journal of Integrative Agriculture2095-31192019-12-0118122771278510.1016/S2095-3119(19)62716-4Deciphering codon usage patterns and evolutionary forces in chloroplast genes of Camellia sinensis var. assamica and Camellia sinensis var. sinensis in comparison to Camellia pubicostaSophiarani Yengkhom0Arif Uddin1Supriyo Chakraborty2Department of Biotechnology, Assam University, Silchar 788011, Assam, IndiaDepartment of Zoology, Moinul Hoque Choudhury Memorial Science College, Algapur, Hailakandi 788150, Assam, IndiaDepartment of Biotechnology, Assam University, Silchar 788011, Assam, India; Correspondence Supriyo ChakrabortyCodon usage bias (CUB) is a unique property of genome which refers to non-random usage of synonymous codons in coding sequences. The present study makes an attempt to find out the pattern of CUB in chloroplast (cp) genes among three tea species, i.e., Camellia sinensis var. assamica (Assam tea), Camellia sinensis var. sinensis (Chinese tea) and Camellia pubicosta (wild tea species) as no work on CUB was reported earlier. To understand the patterns of codon usage among the cp genes of three tea groups, we used bioinformatic tools to investigate the protein coding sequences of cp genes. In our present study, the mean nucleobase T was the highest whereas C was the lowest in all the three tea groups. The overall AT content was more than GC content, i.e., genes were AT rich. The scaled chi-square (SCS) value indicated that the CUB of cp genes was low. The codon CGT (Arg) was over-represented in C. sinensis var. sinensis whereas GGA (Pro) was over-represented in C. pubicosta species. Heatmap study revealed that most of the GC ending codons showed positive correlations between codon usage and GC3 while AT ending codons exhibited negative correlations. From neutrality plot analysis, it was evident that natural selection had played a major role, while mutation pressure exerted a minor effect in the CUB of cp genes in three tea groups. Highly significant (P<0.01) positive correlation was found between SCS and synonymous codon usage order (SCUO) of cp genes which suggested that high expression of cp genes was associated with high degree of CUB.http://www.sciencedirect.com/science/article/pii/S2095311919627164Camellia sinensis var. assamicaCamellia sinensis var. sinensisCamellia pubicostachloroplast genescodon usage biasmutation |
| spellingShingle | Sophiarani Yengkhom Arif Uddin Supriyo Chakraborty Deciphering codon usage patterns and evolutionary forces in chloroplast genes of Camellia sinensis var. assamica and Camellia sinensis var. sinensis in comparison to Camellia pubicosta Journal of Integrative Agriculture Camellia sinensis var. assamica Camellia sinensis var. sinensis Camellia pubicosta chloroplast genes codon usage bias mutation |
| title | Deciphering codon usage patterns and evolutionary forces in chloroplast genes of Camellia sinensis var. assamica and Camellia sinensis var. sinensis in comparison to Camellia pubicosta |
| title_full | Deciphering codon usage patterns and evolutionary forces in chloroplast genes of Camellia sinensis var. assamica and Camellia sinensis var. sinensis in comparison to Camellia pubicosta |
| title_fullStr | Deciphering codon usage patterns and evolutionary forces in chloroplast genes of Camellia sinensis var. assamica and Camellia sinensis var. sinensis in comparison to Camellia pubicosta |
| title_full_unstemmed | Deciphering codon usage patterns and evolutionary forces in chloroplast genes of Camellia sinensis var. assamica and Camellia sinensis var. sinensis in comparison to Camellia pubicosta |
| title_short | Deciphering codon usage patterns and evolutionary forces in chloroplast genes of Camellia sinensis var. assamica and Camellia sinensis var. sinensis in comparison to Camellia pubicosta |
| title_sort | deciphering codon usage patterns and evolutionary forces in chloroplast genes of camellia sinensis var assamica and camellia sinensis var sinensis in comparison to camellia pubicosta |
| topic | Camellia sinensis var. assamica Camellia sinensis var. sinensis Camellia pubicosta chloroplast genes codon usage bias mutation |
| url | http://www.sciencedirect.com/science/article/pii/S2095311919627164 |
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