Hexagenia limbata early instar transcriptome assemblies & annotation

This data is part of a publication in process ("Characterizing Hox genes in mayflies (Ephemeroptera), with <em>Hexagenia limbata</em> as a new mayfly model"). The CLC contig data and original read sequencing methodology is also described in the masters thesis of coauthor Christopher Gonzalez (thesis title: "Evolutionary Developmental Biology in the Mayfly Hexagenia limbata, with a Focus on Hox Genes.") <strong>H_limbata_CLC_contigs.fa, H_limbata_ORP_contigs.fa</strong> The two contig assemblies were assembled from the same set of transcriptome reads (NCBI SRA accession SRX6489924), which were sequenced from a pooled sample of approximately 100 μl of whole-body nymphs, most 1st instar and some 2nd instar. The transcriptomes differ in their assembly methods, with CLC referring to assembly within CLC Genomics WorkBench v.6.0.4 (CLCBio, Boston, MA), while ORP refers to contig assembly via the Oyster River Protocol v2.2.6 (MacManes, 2018). <strong>Hexagenia_ORP_peps.fa</strong> Peptide sequences generated via TransDecoder v5.5.0 (https://github.com/TransDecoder/TransDecoder/wiki) from the ORP assembly were used to assess the phylogeny of Hox genes in H. limbata. Note that the generated header names do not match those of the contig or annotation files. <strong>H_limbata_ORP_annotation.tsv</strong> Protein homology annotations for the ORP assembly were done via Diamond v0.9.24.125 (Buchfink et. al., 2015). All headers refer to the generated contig names in H_limbata_ORP_contigs.fa.本数据集属于一篇待发表的研究论文《表征蜉蝣（Ephemeroptera，蜉蝣目）的Hox基因（Hox gene），以*Hexagenia limbata*（缘边六节蜉）作为新型蜉蝣研究模型》。CLC重叠群（contig）数据与原始读段（read）测序方法也在共同作者Christopher Gonzalez的硕士学位论文中进行了阐述，论文标题为《缘边六节蜉的进化发育生物学：以Hox基因为研究核心》。 **H_limbata_CLC_contigs.fa、H_limbata_ORP_contigs.fa**：上述两个重叠群组装数据集均来自同一套转录组（transcriptome）读段（NCBI SRA登录号SRX6489924），该读段测序样本为约100μL的混合全虫体若虫，其中绝大多数为1龄若虫，少量为2龄若虫。 两套转录组的组装方法存在差异：CLC组装指通过CLC Genomics WorkBench v.6.0.4（CLCBio，美国马萨诸塞州波士顿）完成的组装；ORP组装则指通过Oyster River Protocol v2.2.6（MacManes, 2018）完成的重叠群组装。 **Hexagenia_ORP_peps.fa**：从ORP组装结果中通过TransDecoder v5.5.0（https://github.com/TransDecoder/TransDecoder/wiki）预测得到的肽序列，被用于评估缘边六节蜉的Hox基因系统发育关系。需注意，本次生成的序列头名称与重叠群文件或注释文件中的名称并不一致。 **H_limbata_ORP_annotation.tsv**：ORP组装数据集的蛋白质同源注释通过Diamond v0.9.24.125（Buchfink et. al., 2015）完成。所有序列头均对应H_limbata_ORP_contigs.fa中生成的重叠群名称。