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
| Autor: | Supriyo Chakraborty, Sophiarani Yengkhom, Arif Uddin |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2019 |
| Předmět: |
0106 biological sciences
Agriculture (General) codon usage bias Plant Science Biology medicine.disease_cause 01 natural sciences Biochemistry Genome S1-972 Food Animals chloroplast genes medicine Camellia sinensis Gene Chinese tea Genetics Mutation Ecology food and beverages 04 agricultural and veterinary sciences Camellia sinensis var. sinensis Camellia pubicosta Codon usage bias Camellia 040103 agronomy & agriculture 0401 agriculture forestry and fisheries Animal Science and Zoology Camellia sinensis var. assamica mutation Agronomy and Crop Science GC-content 010606 plant biology & botany Food Science |
| Zdroj: | Journal of Integrative Agriculture, Vol 18, Iss 12, Pp 2771-2785 (2019) |
| ISSN: | 2095-3119 |
| Popis: | 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 |
| Databáze: | OpenAIRE |
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