Optimisation of next generation sequencing transcriptome annotation for species lacking sequenced genomes

Next generation sequencing methods, such as RNA-seq, have permitted the exploration of gene expression in a range of organisms which have been studied in ecological contexts but lack a sequenced genome. However, the efficacy and accuracy of RNA-seq annotation methods using reference genomes from related species have yet to be robustly characterised. Here we conduct a comprehensive power analysis employing RNA-seq data from Drosophila melanogaster in conjunction with 11 additional genomes from related Drosophila species to compare annotation methods and quantify the impact of evolutionary divergence between transcriptome and the reference genome. Our analyses demonstrate that, regardless of the level of sequence divergence, direct genome mapping, where transcript short reads are aligned directly to the reference genome, significantly outperforms the widely used de novo and guided assembly-based methods in both the quantity and accuracy of gene detection. Our analysis also reveals that di...

以RNA-seq（RNA测序）为代表的下一代测序技术，已为研究者探索多种在生态学研究中被关注但尚未完成基因组测序的生物的基因表达提供了可行路径。然而，利用近缘物种参考基因组开展分析的RNA-seq注释方法，其实际效能与分析准确性仍未得到充分且严谨的系统表征。本研究以黑腹果蝇（Drosophila melanogaster）的RNA-seq数据为基础，结合11份近缘果蝇物种的基因组数据，开展了全面的效能分析，用以对比不同注释方法的表现，并量化转录组与参考基因组之间的进化分化程度对分析结果的影响。本研究的分析结果表明，无论序列分化程度高低，直接基因组映射法——即直接将转录组短读长序列比对至参考基因组的方法——在基因检出的数量与准确性两方面，均显著优于当前广泛使用的从头组装（de novo）与引导组装法。本研究的分析还揭示了，di……