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.

Novel seminal fluid proteins in the seed beetle Callosobruchus maculatus identified by a proteomic and transcriptomic approach

“… Transcript ID corresponds with the de novo transcriptome used for identification (Sayadi et al ., ).…”

“…The protein sequences identified here in the seed beetle were compared against sequences previously identified by proteomic analysis of honeybee (Apis mellifera; Baer et al, 2009) and Drosophila melanogaster (Findlay & Swanson, 2010) ejaculates. Additionally, predicted SFPs Transcript ID corresponds with the de novo transcriptome used for identification (Sayadi et al, 2016).…”

“…The in-house de novo transcriptome was prepared as described in Sayadi et al (2016). Briefly, RNA was extracted from our isogenic C. maculatus reference population (SI4), reared on mung beans at 298C, 60% RH and a 12 h L: 12 h D light cycle, at various developmental and physiological stages.…”

Combining Experimental Evolution and Genomics to Understand How Seed Beetles Adapt to a Marginal Host Plant

“…It has long served as a model system for investigating the evolution of insect-plant interactions [58][59][60], and has been used more recently to examine a variety of questions in evolutionary biology, especially those involving sexual selection and sexual conflict (e.g., [61][62][63][64][65]). Because of current advances in genomic resources, this system is poised as an emerging model system for evolutionary genomics as well [38,66,67].…”

Genomic studies of biochemical compounds determining arabica coffee (Coffea arabica L.) quality

“…However, Lee et al (2016) proved that this links to genome duplication or recent hybridisation between seagrass species which is also the case of arabica (Lashermes et al, 1999;Tesfaye et al, 2007). Sayadi et al (2016) also stated that this may represent allelic variation (heterozygosity) in the sample used to construct the assembly, gene duplication and/or mechanisms such as alternative splicing. Using different approaches of genome completion assessment indicted the completion of the genome assembly.…”