Liu Wei, Hu Chaochao, Xie Wenli, Chen Peng, Zhang Yi, Yao Ran, Li Kexin, Chang Qing
Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1# Wenyuan Road, Nanjing, 210023, Jiangsu, People's Republic of China.
Analytical and Testing Center, Nanjing Normal University, Nanjing, Jiangsu, People's Republic of China.
Genes Genomics. 2018 May;40(5):455-463. doi: 10.1007/s13258-017-0632-6. Epub 2018 Jan 12.
The red-necked phalarope is a wonderful species with specific morphological characters and lifestyles. Mitochondrial genomes, encoding necessary proteins involved in the system of energy metabolism, are important for the evolution and adaption of species. In this study, we determined the complete mitogenome sequence of Phalaropus lobatus (Charadriiformes: Scolopacidae). The circular genome is 16714 bp in size, containing 13 PCGs, two ribosomal RNAs and 22 tRNAs and a high AT-rich control region. The AT skew and GC skew of major strand is positive and negative respectively. Most of PCGs are biased towards A-rich except ND1. A codon usage analysis shows that 3 start codons (ATG, GTG and ATA), 4 stop codons (TAA, TAG, AGG, AGA) and two incomplete terminate codons (T-). Twenty two transfer RNAs have the typical cloverleaf structure, and a total of ten base pairs are mismatched throughout the nine tRNA genes. The phylogenetic tree based on 13 PCGs and 2 rRNA genes indicates that monophyly of the family and genus Phalaropus is close to genus Xenus plus Tringa. The analysis of selective pressure shows 13 protein-coding genes are evolving under the purifying selection and P. lobatus is different from other Scolopacidae species on the selective pressure of gene ND4. This study helps us know the inherent mechanism of mitochondrial structure and natural selection.
红颈瓣蹼鹬是一种具有独特形态特征和生活方式的奇妙物种。线粒体基因组编码能量代谢系统中必需的蛋白质，对物种的进化和适应至关重要。在本研究中，我们测定了红颈瓣蹼鹬（鸻形目：鹬科）的完整线粒体基因组序列。该环状基因组大小为16714 bp，包含13个蛋白质编码基因、两个核糖体RNA、22个转运RNA和一个富含AT的控制区。重链的AT偏斜和GC偏斜分别为正和负。除ND1外，大多数蛋白质编码基因偏向于富含A。密码子使用分析表明有3个起始密码子（ATG、GTG和ATA）、4个终止密码子（TAA、TAG、AGG、AGA）和两个不完全终止密码子（T-）。22个转运RNA具有典型的三叶草结构，在9个tRNA基因中共有10个碱基对错配。基于13个蛋白质编码基因和2个rRNA基因构建的系统发育树表明，瓣蹼鹬科和瓣蹼鹬属的单系性与半蹼鹬属和鹬属相近。选择压力分析表明，13个蛋白质编码基因在纯化选择下进化，红颈瓣蹼鹬在基因ND4的选择压力上与其他鹬科物种不同。本研究有助于我们了解线粒体结构和自然选择的内在机制。
