Deep, Staged Transcriptomic Resources for the Novel Coleopteran Models Atrachya menetriesi and Callosobruchus maculatus

Abstract

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, staged transcriptomic data for two coleopteran species, Atrachya menetriesi (Faldermann 1835) and Callosobruchus maculatus (Fabricius 1775). Our sampling covered key stages in ovary and early embryonic development in each species. We utilized this data to build combined assemblies for each species which were then analysed 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 these assemblies, 34.6% and 32.4% of contigs were identified using Blast2GO, and 97% and 98.3% of the BUSCO set of metazoan orthologs were present, respectively. We also carried out manual annotation of developmental signalling pathways and found that nearly all expected genes were present in each transcriptome. Our analyses show that both transcriptomes are of high quality. Lastly, we performed read mapping utilising our timed, stage specific RNA samples to identify differentially expressed contigs. The resources presented here will provide a firm basis for a variety of experimentation, both in developmental biology and in comparative genomic studies.

The evolution of insect germline specification strategies

“…2). A transcriptomic analysis of the beetle Callosobruchus maculatus , which has clear germ plasm and early pole cells [10], has identified an osk ortholog [11], further supporting the correlation between the presence of an osk gene and the presence of maternal provision of germ plasm.…”

“…Blue boxes indicate osk ortholog in the genome [5,7,9,11,12], a box with a question mark indicates that no large scale genomic or transcriptomic data has been published to help determine whether osk is present, those without indications appear to lack osk based on its absence in large scale sequencing projects [8,39,51–53]. Genus names in blue are those in which maternal provision mode is used [3,7,9,58,63], while those in red use zygotic induction [13,31,40,41,56,57,64].…”

Bacterial contribution to genesis of the novel germ line determinantoskar

“…It is unclear why Dipteran Osk LOTUS domains cluster separately from those of other insect Osk proteins. We speculate that the evolution of the Long Oskar domain 3,4 , which appears to be a novelty within Diptera (Supplementary Files: Alignments>OSKAR_FINAL.fasta), may have influenced the evolution of the Osk LOTUS domain in at least some of these insects. Consistent with this hypothesis, of the 17 Dipteran oskar genes we examined, the seven oskar genes possessing a Long Osk domain clustered into two clades based on the sequences of their LOTUS domain.…”

RNase reverses segment sequence in the anterior of a beetle egg (Callosobruchus maculatus, Coleoptera)

“…Maternal effect AP segmentation genes in Tribolium include axin (Fu et al., ), zen (personal communication from S. Brown and L. Farzana to van der Zee; unpublished data from van der Zee and S. R. reported by van der Zee, Berns, & Roth, ), cad (Copf, Schröder, & Averof, ; Schoppmeier, Fischer, Schmitt‐Engel, Löhr, & Klingler, ), hb (Wolff, Sommer, Schröder, Glaser, & Tautz, ; Marquez‐Souza, Randa, & Tautz, ), and otd (Kotkamp, Klingler, & Schoppmeier, ). They occur also in Callosobruchus (Benton, Kenny, Conrads, Roth, & Lynch, ), but their function is unknown. The suggestion is to test for effects on AP segmentation by puncture of the anterior of Callosobruchus eggs submerged in dsRNA for these Tribolium genes.…”