Vieira Gabriel A, Prosdocimi Francisco
Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil.
PeerJ. 2019 Jan 24;7:e6271. doi: 10.7717/peerj.6271. eCollection 2019.
The advent of Next Generation Sequencing has reduced sequencing costs and increased genomic projects from a huge amount of organismal taxa, generating an unprecedented amount of genomic datasets publicly available. Often, only a tiny fraction of outstanding relevance of the genomic data produced by researchers is used in their works. This fact allows the data generated to be recycled in further projects worldwide. The assembly of complete mitogenomes is frequently overlooked though it is useful to understand evolutionary relationships among taxa, especially those presenting poor mtDNA sampling at the level of genera and families. This is exactly the case for ants (Hymenoptera:Formicidae) and more specifically for the subfamily Pseudomyrmecinae, a group of arboreal ants with several cases of convergent coevolution without any complete mitochondrial sequence available. In this work, we assembled, annotated and performed comparative genomics analyses of 14 new complete mitochondria from Pseudomyrmecinae species relying solely on public datasets available from the Sequence Read Archive (SRA). We used all complete mitogenomes available for ants to study the gene order conservation and also to generate two phylogenetic trees using both (i) concatenated set of 13 mitochondrial genes and (ii) the whole mitochondrial sequences. Even though the tree topologies diverged subtly from each other (and from previous studies), our results confirm several known relationships and generate new evidences for sister clade classification inside Pseudomyrmecinae clade. We also performed a synteny analysis for Formicidae and identified possible sites in which nucleotidic insertions happened in mitogenomes of pseudomyrmecine ants. Using a data mining/bioinformatics approach, the current work increased the number of complete mitochondrial genomes available for ants from 15 to 29, demonstrating the unique potential of public databases for mitogenomics studies. The wide applications of mitogenomes in research and presence of mitochondrial data in different public dataset types makes the "no budget mitogenomics" approach ideal for comprehensive molecular studies, especially for subsampled taxa.
新一代测序技术的出现降低了测序成本，并增加了来自大量生物分类群的基因组项目，产生了前所未有的大量公开可用的基因组数据集。通常，研究人员生成的基因组数据中只有极小一部分具有突出相关性的内容被用于他们的研究工作。这一事实使得所生成的数据能够在全球范围内的进一步项目中被循环利用。尽管完整线粒体基因组的组装对于理解分类群之间的进化关系很有用，尤其是对于那些在属和科水平上线粒体DNA采样不足的分类群，但它经常被忽视。蚂蚁（膜翅目：蚁科）的情况正是如此，更具体地说是伪切叶蚁亚科，这是一群树栖蚂蚁，有几例趋同共进化的情况，但没有任何完整的线粒体序列。在这项工作中，我们仅依靠序列读取存档（SRA）中可用的公共数据集，对14个来自伪切叶蚁亚科物种的新的完整线粒体进行了组装、注释和比较基因组学分析。我们使用了所有可获得的蚂蚁完整线粒体基因组来研究基因顺序的保守性，并使用（i）13个线粒体基因的串联集和（ii）整个线粒体序列生成了两棵系统发育树。尽管这两棵树的拓扑结构彼此之间（以及与先前的研究）略有不同，但我们的结果证实了几个已知的关系，并为伪切叶蚁亚科分支内的姐妹分支分类产生了新的证据。我们还对蚁科进行了共线性分析，并确定了伪切叶蚁线粒体基因组中发生核苷酸插入的可能位点。通过数据挖掘/生物信息学方法，当前的工作将可获得的蚂蚁完整线粒体基因组数量从15个增加到了29个，证明了公共数据库在线粒体基因组学研究中的独特潜力。线粒体基因组在研究中的广泛应用以及不同公共数据集类型中线粒体数据的存在，使得“无预算线粒体基因组学”方法成为全面分子研究的理想选择，特别是对于抽样不足的分类群。
