title: The De Novo Transcriptome and Its Functional Annotation in the Seed Beetle Callosobruchus maculatus.
abstract: Despite their unparalleled biodiversity, the genomic resources available for beetles (Coleoptera) remain relatively scarce. We present an integrative and high quality annotated transcriptome of the beetle Callosobruchus maculatus, an important and cosmopolitan agricultural pest as well as an emerging model species in ecology and evolutionary biology. Using Illumina sequencing technology, we sequenced 492 million read pairs generated from 51 samples of different developmental stages (larvae, pupae and adults) of C. maculatus. Reads were de novo assembled using the Trinity software, into a single combined assembly as well as into three separate assemblies based on data from the different developmental stages. The combined assembly generated 218,192 transcripts and 145,883 putative genes. Putative genes were annotated with the Blast2GO software and the Trinotate pipeline. In total, 33,216 putative genes were successfully annotated using Blastx against the Nr (non-redundant) database and 13,382 were assigned to 34,100 Gene Ontology (GO) terms. We classified 5,475 putative genes into Clusters of Orthologous Groups (COG) and 116 metabolic pathways maps were predicted based on the annotation. Our analyses suggested that the transcriptional specificity increases with ontogeny. For example, out of 33,216 annotated putative genes, 51 were only expressed in larvae, 63 only in pupae and 171 only in adults. Our study illustrates the importance of including samples from several developmental stages when the aim is to provide an integrative and high quality annotated transcriptome. Our results will represent an invaluable resource for those working with the ecology, evolution and pest control of C. maculatus, as well for comparative studies of the transcriptomics and genomics of beetles more generally.
authors.affiliation: Animal Ecology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.
authors.forename: Ahmed
authors.initials: A
authors.lastname: Sayadi
authors.affiliation: Animal Ecology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.
authors.forename: Elina
authors.initials: E
authors.lastname: Immonen
authors.affiliation: Animal Ecology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.
authors.forename: Helen
authors.initials: H
authors.lastname: Bayram
authors.affiliation: Animal Ecology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.
authors.forename: Göran
authors.identifier: http://orcid.org/0000-0002-3501-3376
authors.initials: G
authors.lastname: Arnqvist
mesh_terms: D000818:Animals; D001517:Coleoptera / Q000235:genetics*; D063990:Gene Ontology; D017344:Genes, Insect; D007814:Larva / Q000235:genetics; D058977:Molecular Sequence Annotation; D011679:Pupa / Q000235:genetics; D012639:Seeds / Q000469:parasitology*; D017423:Sequence Analysis, RNA; D013223:Statistics as Topic; D059467:Transcriptome / Q000235:genetics*