TY - JOUR T1 - Deep, Staged Transcriptomic Resources for the Novel Coleopteran Models <em>Atrachya menetriesi</em> and <em>Callosobruchus maculatus</em> JF - bioRxiv DO - 10.1101/035998 SP - 035998 AU - Matthew A. Benton AU - Nathan J. Kenny AU - Kai H. Conrads AU - Siegfried Roth AU - Jeremy A. Lynch Y1 - 2016/01/01 UR - http://biorxiv.org/content/early/2016/01/05/035998.abstract N2 - Background: Despite recent efforts to sample broadly across metazoan and insect diversity, current sequence resources in the Coleoptera do not adequately describe the diversity of the clade. Here we present deep transcriptomic data generated with Illumina platform sequencing of a number of key stages in the development of two coleopteran species, the false melon beetle Atrachya menetriesi (Faldermann 1835) and the cowpea weevil Callosobruchus maculatus (Fabricius 1775). These species are both agricultural pests and are of great interest to developmental biology, as well as providing additional coleopteran datapoints for comparative genomic analysis.Results: By sampling at a range of timepoints covering ovary development and several crucial phases of embryonic development we assembled five and three timed transcriptomes for A. menetriesi and C. maculatus, respectively. We utilized this sequence data to build a transcriptomic resource combining all reads into a single, combined assembly for each species, and we analysed each of these resources in detail. The combined A. menetriesi assembly consists of 228,096 contigs with an N50 of 1,598 bp, while the combined C. maculatus assembly consists of 128,837 contigs with an N50 of 2,263 bp. For each of these assemblies, we identified 78,879 (34.6%) and 41,744 (32.4%) of contigs by BLASTx against the nr database using Blast2GO, and we found that 97% and 98.3% of the BUSCO set of metazoan orthologs were present in these assemblies. We also carried out manual analysis of 38 key developmental genes, and found that nearly all expected genes were present in our transcriptomes. Each of these analyses showed that these transcriptomes are of very high quality. Lastly, we performed read mapping using the individual timed RNA samples, allowing us to identify up- and down-regulated contigs at key stages in the development of these beetles for further analysis.Conclusions: The data presented here represent a significant increase in the publicly available transcriptomic resources in the Coleoptera. They have also allowed us to note significant changes in expression at important embryonic stages, and will provide a firm basis for a variety of experimentation, both in developmental biology and in wider exploration of the genomic basis of growth and differentiation. ER -