School of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China.
Jiangsu Open University (The City Vocational College of Jiangsu), College of Environment and Ecology, Nanjing, Jiangsu, China.
PeerJ. 2022 Apr 18;10:e13268. doi: 10.7717/peerj.13268. eCollection 2022.
The genus (Charadriiformes, Scolopacidae) includes shorebirds known as dunlin, knots, and sanderlings. The relationships between species nested within , including , and , are not well-resolved.
Samples were collected from Xiaoyangkou, Rudong County, Jiangsu Province, China. Mitogenomes were sequenced using the Illumina Novaseq 6000 platform for PE 2 × 150 bp sequencing, and then checked for PCR products. Protein-coding genes were determined using an Open Reading Frame Finder. tRNAscan-SE, MITOS, and ARWEN were used to confirm tRNA and rRNA annotations. Bioinformatic analyses were conducted using DnaSP 5.1 and MEGA X. Phylogenic trees were constructed using maximum likelihood and Bayesian analyses.
We sequenced and annotated the mitogenome of five species and obtained four complete mitogenomes and one nearly complete mitogenome. Circular mitogenomes displayed moderate size variation, with a mean length of 16,747 bp, ranging from 16,642 to 16,791 bp. The mitogenome encoded a control region and a typical set of 37 genes containing two rRNA genes, 13 protein-coding genes, and 22 tRNA genes. There were four start codons, four stop codons, and one incomplete stop codon (T-). The nucleotide composition was consistently AT-biased. The average uncorrected pairwise distances revealed heterogeneity in the evolutionary rate for each gene; the COIII had a slow evolutionary rate, whereas the ATP8 gene had a fast rate. dN/dS analysis indicated that the protein-coding genes were under purifying selection. The genetic distances between species showed that the greatest genetic distance was between and (22.5%), and the shortest was between and (12.8%). Phylogenetic trees revealed that is not a monophyletic genus, as species from the genera and were nested within . The molecular data obtained in this study are valuable for research on the taxonomy, population genetics, and evolution of birds in the genus .
属（Charadriiformes，Scolopacidae）包括被称为黑腹滨鹬、斑尾塍鹬和红腹滨鹬的滨鸟。物种之间的关系嵌套在 属内，包括 、 和 ，尚未得到很好的解决。
样本采集自中国江苏省如东县小洋口。使用 Illumina Novaseq 6000 平台进行 PE 2×150 bp 测序对线粒体基因组进行测序，并检查 PCR 产物。使用开放阅读框查找器确定蛋白质编码基因。使用 tRNAscan-SE、MITOS 和 ARWEN 确认 tRNA 和 rRNA 注释。使用 DnaSP 5.1 和 MEGA X 进行生物信息学分析。使用最大似然法和贝叶斯分析法构建系统发育树。
我们对 5 个物种的线粒体基因组进行了测序和注释，获得了 4 个完整的线粒体基因组和 1 个近乎完整的线粒体基因组。圆形线粒体基因组显示出中等大小的变化，平均长度为 16747bp，范围为 16642-16791bp。线粒体基因组编码了一个控制区和一个典型的 37 个基因组成的集合，其中包含两个 rRNA 基因、13 个蛋白质编码基因和 22 个 tRNA 基因。有四个起始密码子、四个终止密码子和一个不完全终止密码子（T-）。核苷酸组成一致地偏向 AT。未校正的成对差异显示出每个基因进化率的异质性；COIII 具有缓慢的进化率，而 ATP8 基因具有快速的进化率。dN/dS 分析表明，蛋白质编码基因受到纯化选择的影响。物种之间的遗传距离表明，最大的遗传距离是 和 （22.5%）之间，最短的是 和 （12.8%）之间。系统发育树表明， 不是一个单系属，因为来自 和 属的物种嵌套在 属内。本研究获得的分子数据对鸟类属的分类学、群体遗传学和进化研究具有重要价值。
