黑鳖（Nilssonia nigricans）完整线粒体基因组及其与其他鳖科的比较分析。,Scientific Reports

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黑鳖（Nilssonia nigricans）完整线粒体基因组及其与其他鳖科的比较分析。
Scientific Reports ( IF 3.8 ) Pub Date : 2018-Nov-26 , DOI: 10.1038/s41598-018-35822-5
Shantanu Kundu ₁ , Vikas Kumar ₁ , Kaomud Tyagi ₁ , Rajasree Chakraborty ₁ , Devkant Singha ₁ , Iftikar Rahaman ₁ , Avas Pakrashi ₁ , Kailash Chandra ₁

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线粒体基因组的表征已被证明是包括海龟在内的脊椎动物系统发育和进化分析的有效研究领域。本研究的目的是通过比较分析来区分鳖科物种线粒体基因组的结构和变异性。对濒临灭绝的淡水龟 Nilssonia nigricans 的完整线粒体基因组（16796 bp）进行了测序和注释。线粒体基因组编码 37 个基因和一个主要非编码控制区 (CR)。线粒体基因组呈 A + T 偏向 (62.16%)，包括 6 个重叠区域和 19 个基因间间隔区域。所有鳖科物种的相对同义密码子使用（RSCU）值是一致的；除了 N. nigricans、N. formosa 和 R. swinhoei 中丝氨酸 (TCG) 频率显着降低外。在 N. nigricans 中，除 trnS1 (GCT) 外，大多数转移 RNA (tRNA) 都通过 Watson-Crick 碱基配对折叠成经典的三叶草二级结构。比较分析表明，除了trnE（TTC）、trnQ（TTG）和trnM（CAT）外，大多数tRNA在结构上都不同。tRNA 的结构特征导致 12 个 tRNA 中有 ≥ 10 个错配或摆动碱基配对，这反映了 H 链和 L 链的核苷酸组成。N. nigricans 的线粒体基因组还揭示了CR 中两个独特的串联重复序列 (ATTAT) ₈和 (TATTA) _{20 。}此外，在所有鳖科物种的 CR 中都检测到了保守基序 5'-GACATA-3' 和稳定的茎环结构，它们在调节线粒体基因组的转录和复制中发挥着重要作用。此外，Ka/Ks 的比较分析表明大多数蛋白质编码基因（PCG）存在负选择。使用所有 PCG 构建的最大似然 (ML) 系统发育显示黑猪笼草与福莫萨猪笼草聚类。由此产生的系统发育说明了与先前描述的相似的拓扑结构并且与分类学分类一致。然而，为了更好地理解系统发育和进化关系，需要从不同的睾丸分类群中进行更多采样并对其有丝分裂基因组学进行研究。

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Complete mitochondrial genome of Black Soft-shell Turtle (Nilssonia nigricans) and comparative analysis with other Trionychidae.

The characterization of mitochondrial genome has been evidenced as an efficient field of study for phylogenetic and evolutionary analysis in vertebrates including turtles. The aim of this study was to distinguish the structure and variability of the Trionychidae species mitogenomes through comparative analysis. The complete mitogenome (16796 bp) of an endangered freshwater turtle, Nilssonia nigricans was sequenced and annotated. The mitogenome encoded for 37 genes and a major non-coding control region (CR). The mitogenome was A + T biased (62.16%) and included six overlapping and 19 intergenic spacer regions. The Relative synonymous codon usage (RSCU) value was consistent among all the Trionychidae species; with the exception of significant reduction of Serine (TCG) frequency in N. nigricans, N. formosa, and R. swinhoei. In N. nigricans, most of the transfer RNAs (tRNAs) were folded into classic clover-leaf secondary structures with Watson-Crick base pairing except for trnS1 (GCT). The comparative analysis revealed that most of the tRNAs were structurally different, except for trnE (TTC), trnQ (TTG), and trnM (CAT). The structural features of tRNAs resulted ≥ 10 mismatched or wobble base pairings in 12 tRNAs, which reflects the nucleotide composition in both H- and L-strands. The mitogenome of N. nigricans also revealed two unique tandem repeats (ATTAT)_8, and (TATTA)₂₀ in the CR. Further, the conserved motif 5'-GACATA-3' and stable stem-loop structure was detected in the CRs of all Trionychidae species, which play an significant role in regulating transcription and replication in the mitochondrial genome. Further, the comparative analysis of Ka/Ks indicated negative selection in most of the protein coding genes (PCGs). The constructed Maximum Likelihood (ML) phylogeny using all PCGs showed clustering of N. nigricans with N. formosa. The resulting phylogeny illustrated the similar topology as described previously and consistent with the taxonomic classification. However, more sampling from different taxonomic groups of Testudines and studies on their mitogenomics are desirable for better understanding of the phylogenetic and evolutionary relationships.

更新日期：2018-11-28

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