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), 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.

Plant Remains from an Archaeological Site as Indicators of Vegetation and Agricultural Practice Between(3 320±400) and(2 080±80) yr BP in Gangetic West Bengal,India

多样的植物遗体在 Pakhanna 的 Bhairabdanga 区域从一个考古学的地点恢复了 ofChalcolithic 早历史性的年龄(纬度 23 ° 2 5''N， longitude87 ° 2 3''E ) ，位于 Damodar 河的西岸， Bankura 区域，韦斯特孟加拉，印度，包括食物谷物，木头炭，和 palynomorphs。恢复生物遗体标明日期的放射性碳是揭示这个地点的年龄(3 320 ± 400 ) 到(2 080 ± 80 ) 年 BP。食用粮食作为 Oryza sativa L 被识别。并且 Brassica cf 的 Vigna mungoL，和种子。campestris L.were 也发现了；这些显示从 Chalcolithic 生活在 Pakhanna 到早历史性的时期的古老的人的农业实践和食性。包括植物遗体的沉积广泛地被划分了成二个地区，就标明日期的考古学的调查结果和放射性碳而言。植物的分析留下(即木头炭和 palynomorphs )除了栽培食物，谷物表明了一个富有的植被封面在这个区域存在，与占优势热带并且湿润气候，包括产出木材的植物 Shorea sp ， Terminaliasp ，和 Tamarindus sp ，与多样的灌木和植物的下层林丛在 Chalcolithicperiod 期间(地区我)过时( 3 320 ± 400 )植物遗体的 BP.Comparatively 更穷的表示和频率在早历史性的时期(地区 II )期间显示更干燥的气候的年是标明日期( 2 110 ±3 40 )到( 2 080 ± 80 )年 BP 。 archaeobotanical 数据的比较从 theChalcolithic 和早历史性的时期并且也恢复了一个原则部件分析在区域的气候显示一个变化从在热带、潮湿( 3 320 ± 400 )年 BP 到热带、更干燥的条件在( 2 110 ± 340 )到( 2 080 ± 80 )年 BP 。present-daytropical，区域的干燥脱落植被建议自从同时期的过去，那个气候变化发生在区域。植物遗体数据库被利用了重建在这个地点在之间的社区生活的解决模式(3 320 ± 400 ) 并且(2 080 ± 80 ) 年 BP。Thecommunity 在河岸附近安定，练习耕作。