Department of Biological, Geological and Environmental Sciences - University of Bologna, via Selmi 3, 40126, Bologna, Italy.
Okinawa Institute of Science & Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan.
Sci Rep. 2019 Oct 15;9(1):14806. doi: 10.1038/s41598-019-51313-7.
Thousands of eukaryotes transcriptomes have been generated, mainly to investigate nuclear genes expression, and the amount of available data is constantly increasing. A neglected but promising use of this large amount of data is to assemble organelle genomes. To assess the reliability of this approach, we attempted to reconstruct complete mitochondrial genomes from RNA-Seq experiments of Reticulitermes termite species, for which transcriptomes and conspecific mitogenomes are available. We successfully assembled complete molecules, although a few gaps corresponding to tRNAs had to be filled manually. We also reconstructed, for the first time, the mitogenome of Reticulitermes banyulensis. The accuracy and completeness of mitogenomes reconstruction appeared independent from transcriptome size, read length and sequencing design (single/paired end), and using reference genomes from congeneric or intra-familial taxa did not significantly affect the assembly. Transcriptome-derived mitogenomes were found highly similar to the conspecific ones obtained from genome sequencing (nucleotide divergence ranging from 0% to 3.5%) and yielded a congruent phylogenetic tree. Reads from contaminants and nuclear transcripts, although slowing down the process, did not result in chimeric sequence reconstruction. We suggest that the described approach has the potential to increase the number of available mitogenomes by exploiting the rapidly increasing number of transcriptomes.
已经生成了数千个真核生物转录组，主要用于研究核基因表达，并且可用数据的数量还在不断增加。利用这些大量数据的一个被忽视但有前途的用途是组装细胞器基因组。为了评估这种方法的可靠性，我们尝试从白蚁物种的 RNA-Seq 实验中重建完整的线粒体基因组，这些转录组和同种的线粒体基因组都是可用的。我们成功地组装了完整的分子，尽管必须手动填充几个对应 tRNA 的缺口。我们还首次重建了 Reticulitermes banyulensis 的线粒体基因组。线粒体基因组重建的准确性和完整性似乎与转录组大小、读长和测序设计（单端/双端）无关，并且使用来自同属或同科的参考基因组并不显著影响组装。从转录组中获得的线粒体基因组与从基因组测序中获得的同种基因组高度相似（核苷酸差异范围为 0%至 3.5%），并产生了一致的系统发育树。尽管会减缓进程，但来自污染物和核转录物的reads 并没有导致嵌合序列的重建。我们建议，通过利用快速增加的转录组数量，该方法有潜力增加可用的线粒体基因组数量。
