Analysis of transcriptome data in the red flour beetle, Tribolium castaneum
ABSTRACT The whole genome sequence of Tribolium castaneum, a worldwide coleopteran pest of stored products, has recently been determined. In order to facilitate accurate annotation and detailed functional analysis of this genome, we have compiled and analyzed all available expressed sequence tag (EST) data. The raw data consist of 61,228 ESTs, including 10,704 obtained from NCBI and an additional 50,524 derived from 32,544 clones generated in our laboratories. These sequences were amassed from cDNA libraries representing six different tissues or stages, namely: whole embryos, whole larvae, larval hindguts and Malpighian tubules, larval fat bodies and carcasses, adult ovaries, and adult heads. Assembly of the 61,228 sequences collapsed into 12,269 clusters (groups of overlapping ESTs representing single genes), of which 10,134 mapped onto 6,463 (39%) of the 16,422 GLEAN gene models (i.e. official Tribolium gene list). Approximately 1,600 clusters (13% of the total) lack corresponding GLEAN models, despite high matches to the genome, suggesting that a considerable number of transcribed sequences were missed by the gene prediction programs or were removed by GLEAN. We conservatively estimate that the current EST set represents more than 7,500 transcription units.
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ABSTRACT: Chemosensory proteins (CSPs) are small scavenger proteins that are mainly known as transporters of pheromone/odor molecules at the periphery of sensory neurons in the insect antennae and in the producing cells from the moth female pheromone gland. Sequencing cDNAs of RNA encoding CSPs in the antennae, legs, head, pheromone gland and wings from five single individual adult females of the silkworm moth Bombyx mori showed that they differed from genomic sequences by subtle nucleotide replacement (RDD). Both intronless and intronic CSP genes expressed RDDs, although in different rates. Most interestingly, in our study the degree of RDDs in CSP genes were found to be tissue-specific. The proportion of CSP-RDDs was found to be significantly much higher in the pheromone gland. In addition, Western blot analysis of proteins in different tissues showed existence of multiple CSP protein variant chains particularly found in the pheromone gland. Peptide sequencing demonstrated the occurrence of a pleiad of protein variants for most of all BmorCSPs from the pheromone gland. Our findings show that RNA editing is an important feature in the expression of CSPs and that a high variety of RDDs is found to expand drastically thus altering the repertoire of CSP proteins in a tissue-specific manner.PLoS ONE 02/2014; 9(2):e86932. DOI:10.1371/journal.pone.0086932 · 3.53 Impact Factor
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ABSTRACT: Diuresis, the removal of excess metabolic waste through production of primary urine while maintaining homeostasis, is an important biological process that is tightly regulated by endocrine factors. Several hormonal components that act as diuretic or antidiuretic factors in insects have been identified in the last few decades. Physiological mechanisms responsible for ion and water transport across biological membranes have been intensively studied. The large amount of data rapidly accumulating in the genomics era has led to an increased dependence on reverse genetic and physiological approaches, first identifying candidate genes and subsequently deriving functions. In many cases, the reverse approaches have been highly successful, especially in studies of the receptors for diuretic factors, which are mainly G-protein-coupled receptors. This review summarizes research on insect diuretic and antidiuretic endocrine factors, and their receptors. Emphases of the review are given to the genomics of ligands and their receptors, as well as to their implications for evolution and function.Canadian Journal of Zoology 04/2012; 90(4):507-520. DOI:10.1139/z2012-013 · 1.35 Impact Factor
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ABSTRACT: Despite the recent sequencing of seven ant genomes, no genomic data are available for the genus Formica, an important group for the study of eusocial traits. We sequenced the transcriptome of the ant Formica exsecta with the 454 FLX Titanium technology from a pooled sample of workers from 70 Finnish colonies. About 1,000,000 reads were obtained from a normalised cDNA library. We compared the assemblers MIRA3.0 and Newbler2.6 and showed that the latter performed better on this dataset due to a new option which is dedicated to improve contig formation in low depth portions of the assemblies. The 29,579 contigs represent 27 Mb. 50% showed similarity with known proteins and 25% could be assigned a category of gene ontology. We found more than 13,000 high-quality single nucleotide polymorphisms. The Δ9 desaturase gene family is an important multigene family involved in chemical communication in insects. We found six Δ9 desaturases in this Formica exsecta transcriptome dataset that were used to reconstruct a maximum-likelihood phylogeny of insect desaturases and to test for signatures of positive selection in this multigene family in ant lineages. We found differences with previous phylogenies of this gene family in ants, and found two clades potentially under positive selection. This first transcriptome reference sequence of Formica exsecta provided sequence and polymorphism data that will allow researchers working on Formica ants to develop studies to tackle the genetic basis of eusocial phenotypes. In addition, this study provided some general guidelines for de novo transcriptome assembly that should be useful for future transcriptome sequencing projects. Finally, we found potential signatures of positive selection in some clades of the Δ9 desaturase gene family in ants, which suggest the potential role of sequence divergence and adaptive evolution in shaping the large diversity of chemical cues in social insects.PLoS ONE 07/2013; 8(7):e68200. DOI:10.1371/journal.pone.0068200 · 3.53 Impact Factor