Hu Chaochao, Zhang Chenling, Sun Lei, Zhang Yi, Xie Wenli, Zhang Baowei, Chang Qing
Analytical and Testing Center, Nanjing Normal University, Nanjing, Jiangsu, People's Republic of China.
Faculty of Life Science and Chemical Engineering, Jiangsu Second Normal University, Nanjing, Jiangsu, People's Republic of China.
PLoS One. 2017 Apr 6;12(4):e0175244. doi: 10.1371/journal.pone.0175244. eCollection 2017.
The Charadriiformes, among the most diverse orders of bird, is a good source to research on evolution. The mitochondrial genome sequencing database has rapidly increased in recent years, while Charadriiformes mitogenome has not been well studied. In this research, we determined the complete mitogenome sequence of Gallinago stenura, and comparatively analysed 20 mitogenomes of Charadriiformes. The mitogenomes display moderate size variation, and most of variation due to mutations in the control region. In 13 protein-coding genes, we found: 1. The GC skews are always negative, while the negative AT skews are found in 5 genes, 2. The average uncorrected pairwise distances reveal heterogeneity of evolutionary rate for each gene, 3. The ATG and TAA, respectively, are observed the most commonly start and stop codon. The highest dN/dS is detected for ATP8 (0.16) among Charadriiformes, while the lowest for COI (0.01), indicating that 13 protein-coding genes are evolving under the purifying selection. Predicted secondary structures of tRNAs indicate that the sequences and structures of anticodon, amino acceptor, and TψC arms are highly conserved, and most nucleotide variation is restricted to dihydrouridine arms with obvious indel polymorphisms. A total of 15 conserved sequence boxes were recognized in the control regions, and the 4 bp (5'-AAAC-3') and 7 bp (5'- AAACAAC -3') repeat sequences occurred frequently. Phylogenomic analysis based on the nearly complete mitochondrial genomes strongly supported the monophyly of the order, and the suborder Charadrii is at the basal of Charadriiformes. Moreover, our results well resolved the complexity family-level relationships and clearly depicted the evolutionary processes of Charadriiformes, based on 12 mitochondrial protein-coding genes from 18 families. This study improves our understanding of mitogenomic structure and evolution, which can provide further insights into our understanding of phylogeny and taxonomy in Charadriiformes.
鸻形目是鸟类中最多样化的目之一，是研究进化的良好来源。近年来线粒体基因组测序数据库迅速增加，而鸻形目线粒体基因组尚未得到充分研究。在本研究中，我们测定了细嘴沙锥的完整线粒体基因组序列，并对20种鸻形目线粒体基因组进行了比较分析。线粒体基因组显示出适度的大小变异，且大部分变异是由控制区的突变引起的。在13个蛋白质编码基因中，我们发现：1. GC偏斜总是负的，而在5个基因中发现了负的AT偏斜；2. 平均未校正的成对距离揭示了每个基因进化速率的异质性；3. 最常见的起始密码子和终止密码子分别是ATG和TAA。在鸻形目中，ATP8的dN/dS最高（0.16），而COI的最低（0.01），这表明13个蛋白质编码基因在纯化选择下进化。预测的tRNA二级结构表明，反密码子、氨基受体和TψC臂的序列和结构高度保守，大多数核苷酸变异仅限于具有明显插入缺失多态性的二氢尿嘧啶臂。在控制区共识别出15个保守序列框，4 bp（5'-AAAC-3'）和7 bp（5'-AAACAAC-3'）重复序列频繁出现。基于近乎完整的线粒体基因组的系统基因组分析有力地支持了该目的单系性，且鸻亚目位于鸻形目的基部。此外，我们的结果很好地解决了科级水平关系的复杂性，并基于18个科的12个线粒体蛋白质编码基因清晰地描绘了鸻形目的进化过程。这项研究增进了我们对线粒体基因组结构和进化的理解，可为我们进一步了解鸻形目的系统发育和分类学提供见解。
