Karumathil Sudeesh, Dirisala Vijaya R, Srinadh Uthpala, Nikhil Valaboju, Kumar N Satya Sampath, Nair Rahul R
Aushmath Biosciences, Administrative office, Devaraj Corner, Vadavalli Post, Coimbatore, Tamil Nadu, India.
Department of Biotechnology, Vignan's University (Vignan's Foundation for Science, Technology and Research University), Guntur, Andhra Pradesh, India.
Bioinform Biol Insights. 2016 Sep 22;10:167-84. doi: 10.4137/BBI.S38192. eCollection 2016.
Chaetognatha is a minor phylum, comprising transparent marine invertebrates varying in size from 0.5 to 12 cm. The exact phylogenetic position of Chaetognatha in Metazoa has not been deciphered as some embryological characteristics place chaetognaths among deuterostomes and some morphological characteristics place these among protostomes. In this study, the major factors that drive synonymous codon usage bias (SCUB) in the mitogenomes of representative species of Chaetognatha and chosen species of other closely related phyla were analyzed. Spearman's rank correlation analyses of nucleotide contents suggested that mutational pressure and selection were acting in all examined mitogenomes but with varying intensities. The quantification of SCUB using effective number of codons vs. GC composition at the third codon position (GC3) plot suggested that mutational pressure due to GC compositional constraints might be one of the major influencing forces driving the SCUB in all chaetognaths except Sagitta enflata. However, neutrality plots revealed no significant correlation between GC3 and cumulative GC content at first and second codon positions (GC12) in all other species, except in Daphnia pulex. The parity rule 2 bias plot showed that significant compositional differences existed between C and G, as well as between A and T, contents in most of the protein-coding genes (PCGs) and, comparatively, A and T contents were used more proportionally than C and G contents in all chosen mitogenomes. Chi-square analysis revealed the presence of putative optimal codons in all species, except in S. enflata. The correspondence analysis identified that mutational pressure and selection act on the mitogenomes of the selected chaetognaths and other phyla with varying intensities. The cluster analysis based on relative synonymous codon usage (RSCU) values revealed that RSCU variations in the PCGs of mitogenomes of chaetognaths are more comparable with those of protostomes. Apart from mutational pressure and selection, certain unknown selective forces might be acting on the PCGs in the analyzed mitogenomes as the phenomenon of SCUB could not be explained by mutational pressure, by selection, or by both.
毛颚动物门是一个小门类，由体长0.5至12厘米不等的透明海洋无脊椎动物组成。毛颚动物在后生动物中的准确系统发育位置尚未确定，因为一些胚胎学特征将毛颚动物置于后口动物之中，而一些形态学特征又将它们置于原口动物之中。在本研究中，分析了毛颚动物代表性物种及其他相近门类选定物种的线粒体基因组中驱动同义密码子使用偏好（SCUB）的主要因素。核苷酸含量的斯皮尔曼等级相关分析表明，突变压力和选择作用于所有检测的线粒体基因组，但强度各异。使用有效密码子数与第三密码子位置的GC组成（GC3）作图对SCUB进行量化分析表明，除肥胖箭虫外，GC组成限制导致的突变压力可能是驱动所有毛颚动物SCUB的主要影响因素之一。然而，中性绘图显示，除蚤状溞外，所有其他物种的GC3与第一和第二密码子位置的累积GC含量（GC12）之间均无显著相关性。奇偶规则2偏差绘图显示，大多数蛋白质编码基因（PCG）的C和G含量以及A和T含量之间存在显著的组成差异，并且在所有选定的线粒体基因组中相比之下，A和T含量的使用比例高于C和G含量。卡方分析表明，除肥胖箭虫外，所有物种中均存在推定的最优密码子。对应分析确定，突变压力和选择以不同强度作用于选定的毛颚动物和其他门类的线粒体基因组。基于相对同义密码子使用（RSCU）值的聚类分析表明，毛颚动物线粒体基因组PCG中的RSCU变异与原口动物的更具可比性。除了突变压力和选择外，某些未知的选择力量可能作用于分析的线粒体基因组中的PCG，因为SCUB现象无法用突变压力、选择或两者来解释。
