Mitochondrial phylogenomics and genetic relationships of closely related pine moth (Lasiocampidae: Dendrolimus) species in China, using whole mitochondrial genomes.
Mitochondrial phylogenomics and genetic relationships of closely related pine moth (Lasiocampidae: Dendrolimus) species in China, using whole mitochondrial genomes.
复制标题
使用全线粒体基因组研究中国近缘松蛾（Lasiocampidae：Dendrolimus）物种的线粒体系统发育学和遗传关系
DOI：
10.1186/s12864-015-1566-5
复制
发表时间：
2015-06-04
期刊：
影响因子：
4.4
通讯作者：
Zhang AB
中科院分区：
文献类型：
--
作者：
Qin J;Zhang Y;Zhou X;Kong X;Wei S;Ward RD;Zhang AB
松毛虫(鳞翅目；蚕总科；松毛虫科：松毛虫属)是最严重的森林害虫之一，特别是在中国南部。虽然COI条形码(线粒体细胞色素C氧化酶亚基I基因的标准化部分)可以区分该属的一些成员，但马尾松毛虫、油松毛虫和斯氏松毛虫这三个形态种之间的进化关系在很大程度上仍未解决。我们测定了包括文山马尾藻在内的8个标本的线粒体全基因组序列。这是一明确的马尾藻亚种，并且被用作推断马尾藻复合体的另外两个形态种的亲缘关系的参考。结果3个形态种的8个全序列线粒体基因组在基因含量、碱基组成、总AT偏倚水平和密码子使用等方面与其他家蚕总科物种具有相似的基因组结构。然而，松毛虫基因组在大的核糖体16S RNA亚基(RrnL)中具有独特的特征，它比超家族的其他成员长60多个碱基，并且具有更高的AC比例。松毛虫的8个线粒体基因组在许多方面高度保守，例如具有相同的终止密码子和重叠的区域。基于线粒体基因组的系统发育树、遗传距离、物种划分和基因组特征(如基因间隔区等)，我们的结果表明，油松毛虫与文山毛点毛虫的亲缘关系和遗传距离是一样的，而小斑毛虫则是从油松毛虫和斑点毛虫独立进化而来的。完整的线粒体DNA系统发育分析表明，D.spectabilis形成了一个有良好支持的单系支系，与这里研究的其他同类物种有明确的物种边界。然而，油松毛虫经常与马尾松毛虫和文山毛点毛虫亚种聚在一起。遗传距离分析表明，油松毛虫与马尾松毛虫的遗传距离一般小于马尾松毛虫及其亚种文山毛虫的种内距离。在泊松树过程(PTP)的物种划分分析中，油松毛虫、马尾松毛虫和文山毛点毛虫聚为一个推定种，与斑点毛虫分离。在基因间隔区特征方面，油松毛虫和斑点毛虫也表现出相似的结构。这些不同类型的证据表明，油松毛虫与文山毛点毛虫及其亚种非常接近，很可能是毛点毛虫的另一个亚种。结论与传统的单基因或多基因的系统发育研究相比，油松毛虫线粒体全基因组具有相对丰富的遗传信息。它们可以用来更好地推断分类学群体的系统发育关系和亲缘程度，至少从母系谱系的角度来看：由于该基因组只有母系遗传，应谨慎行事。我们的结果表明，镜纹盘藻是一个独立的谱系，而油菜盘藻与斑纹盘藻有极近的亲缘关系。
BackgroundPine moths (Lepidoptera; Bombycoidea; Lasiocampidae: Dendrolimus spp.) are among the most serious insect pests of forests, especially in southern China. Although COI barcodes (a standardized portion of the mitochondrial cytochrome c oxidase subunit I gene) can distinguish some members of this genus, the evolutionary relationships of the three morphospecies Dendrolimus punctatus, D. tabulaeformis and D. spectabilis have remained largely unresolved. We sequenced whole mitochondrial genomes of eight specimens, including D. punctatuswenshanensis. This is an unambiguous subspecies of D. punctatus, and was used as a reference for inferring the relationships of the other two morphospecies of the D. punctatus complex. We constructed phylogenetic trees from this data, including twelve published mitochondrial genomes of other Bombycoidea species, and examined the relationships of the Dendrolimus taxa using these trees and the genomic features of the mitochondrial genome.ResultsThe eight fully sequenced mitochondrial genomes from the three morphospecies displayed similar genome structures as other Bombycoidea species in terms of gene content, base composition, level of overall AT-bias and codon usage. However, the Dendrolimus genomes possess a unique feature in the large ribosomal 16S RNA subunits (rrnL), which are more than 60 bp longer than other members of the superfamily and have a higher AC proportion. The eight mitochondrial genomes of Dendrolimus were highly conservative in many aspects, for example with identical stop codons and overlapping regions. But there were many differences in start codons, intergenic spacers, and numbers of mismatched base pairs of tRNA (transfer RNA genes).Our results, based on phylogenetic trees, genetic distances, species delimitation and genomic features (such as intergenic spacers) of the mitochondrial genome, indicated that D. tabulaeformis is as close to D. punctatus as is D. punctatus wenshanensis, whereas D. spectabilis evolved independently from D. tabulaeformis and D. punctatus. Whole mitochondrial DNA phylogenies showed that D. spectabilis formed a well-supported monophyletic clade, with a clear species boundary separating it from the other congeners examined here. However, D. tabulaeformis often clustered with D. punctatus and with the subspecies D. punctatus wenshanensis. Genetic distance analyses showed that the distance between D. tabulaeformis and D. punctatus is generally less than the intraspecific distance of D. punctatus and its subspecies D. punctatus wenshanensis. In the species delimitation analysis of Poisson Tree Processes (PTP), D. tabulaeformis, D. punctatus and D. punctatus wenshanensis clustered into a putative species separated from D. spectabilis. In comparison with D. spectabilis, D. tabulaeformis and D. punctatus also exhibit a similar structure in intergenic spacer characterization. These different types of evidence suggest that D. tabulaeformis is very close to D. punctatus and its subspecies D. punctatus wenshanensis, and is likely to be another subspecies of D. punctatus.ConclusionsWhole mitochondrial genomes possess relatively rich genetic information compared with the traditional use of single or multiple genes for phylogenetic purposes. They can be used to better infer phylogenetic relationships and degrees of relatedness of taxonomic groups, at least from the aspect of maternal lineage: caution should be taken due to the maternal-only inheritance of this genome. Our results indicate that D. spectabilis is an independent lineage, while D. tabulaeformis shows an extremely close relationship to D. punctatus.
登录
查看更多内容
DOI：
10.1098/rsbl.2003.0025
发表时间：
2003-08-07
影响因子：
4.7
作者：
Hebert, PDN;Ratnasingham, S;deWaard, JR
通讯作者：
deWaard, JR
仁智丝翅蛾和云南丝翅蛾两种鬼蛾的完整线粒体基因组：鳞翅目祖先基因排列
影响因子：
4.4
作者：
Cao YQ;Ma C;Chen JY;Yang DR
通讯作者：
Yang DR
影响因子：
3.7
作者：
Bazinet AL;Cummings MP;Mitter KT;Mitter CW
通讯作者：
Mitter CW
影响因子：
4.1
作者：
Dowton, Mark;Cameron, Stephen L.;Whiting, Michael F.
通讯作者：
Whiting, Michael F.
DOI：
10.1098/rspb.2002.2218
发表时间：
2003-02-07
影响因子：
4.7
作者：
Hebert, PDN;Cywinska, A;DeWaard, JR
通讯作者：
DeWaard, JR