Data from: Identification and qualification of 500 nuclear, single-copy, orthologous genes for the Eupulmonata (Gastropoda) using transcriptome sequencing and exon-capture

The qualification of orthology is a significant challenge when developing large, multi-loci phylogenetic datasets from assembled transcripts. Transcriptome assemblies have various attributes, such as fragmentation, frameshifts, and mis-indexing, which pose problems to automated methods of orthology assessment. Here, we identify a set of orthologous single-copy genes from transcriptome assemblies for the land snails and slugs (Eupulmonata) using a thorough approach to orthology determination involving manual alignment curation, gene tree assessment and sequencing from genomic DNA. We qualified the orthology of 500 nuclear, protein coding genes from the transcriptome assemblies of 21 eupulmonate species to produce the most complete gene data matrix for a major molluscan lineage to date, both in terms of taxon and character completeness. Exon-capture of the 500 genes for 22 species of Australian Camaenidae successfully captured sequences of 2,825 exons, with only a 3.7% reduction in the data matrix due to the presence of putative paralogs or pseudogenes. The automated pipeline Agalma retrieved the majority of the manually qualified 500 single-copy gene set and identified a further 375 putative single-copy genes, although it failed to account for fragmented transcripts resulting in lower data matrix completeness. This could potentially explain the minor inconsistencies we observed in the supported topologies for the 21 eupulmonate species between the manually curated and Agalma-equivalent dataset (sharing 458 genes). Overall, our study confirms the utility of the 500 gene set to resolve phylogenetic relationships at a broad range of evolutionary depths, and highlights the importance of addressing fragmentation at the homolog alignment stage.

基于组装转录本构建大型多位点系统发育数据集时，直系同源（orthology）鉴定是一项重大挑战。转录组组装存在片段化、移码突变与索引错误等多种问题，会对直系同源评估的自动化方法造成阻碍。本研究针对真肺目（Eupulmonata，涵盖陆生蜗牛与蛞蝓）类群，采用涵盖手动比对校正、基因树评估与基因组DNA测序的严谨直系同源鉴定策略，从其转录组组装结果中筛选出一套直系同源单拷贝基因。我们对21个真肺目物种转录组组装结果中的500个核蛋白编码基因的直系同源性进行了确证，最终构建了截至目前分类群覆盖度与特征覆盖度均最为完整的大型软体动物支系基因数据矩阵。针对22种澳大利亚蜗牛科（Camaenidae）物种开展的500个基因外显子捕获（exon-capture）实验，成功获取了2825个外显子的序列，仅因推定旁系同源基因与假基因的存在导致数据矩阵缩减3.7%。自动化分析流程Agalma成功检索到本研究手动鉴定的500个单拷贝基因集中的绝大多数，并额外筛选出375个推定单拷贝基因；但该流程未考虑转录本片段化问题，导致数据矩阵完整性有所下降。这或可解释本研究在手动校正数据集与基于Agalma的等效数据集（共享458个基因）中，21个真肺目物种的支持系统发育拓扑结构存在的细微不一致。综上，本研究证实了该500个基因集可有效解析广泛进化层级下的系统发育关系，并强调了在同源序列比对阶段处理转录本片段化问题的重要性。