Expressed Sequence Tags (ESTs) analysis of Tenebrio molitor larvae

Abstract

Tenebrio molitor has been seriously investigated as a model insect in elucidating Toll signaling pathway and related regulators of innate immunity. However, little is known with regards to the genomic information in T. molitor. In an attempt towards exploiting the rich transcriptomics data that would offer further insights into the study on insect immunity through potential screening of immune‐related genes in the model insect, we constructed a cDNA library (library titer = 5.0 × 105pfu/ml) of T. molitor larvae and analyzed expressed sequence tag (EST) sequences from 1056 clones. The base calling and quality check of obtained chromatogram files were performed by using the Phred program (trim_alt 0.05 (P‐score > 20). After removal of vector and 100 bp and less sequences, 1023 sequences were generated having an average insert size of 792 bp, including 160 clusters, 164 contigs and 387 singletons through clustering and assembling process using the TGI Clustering Tools (TGICL) package. The unique EST sequences were searched against the NCBI nr database by local BLAST (blastx, E < e−5) with 940 sequences showing significant hits. Subsequently, KOG (clusters of orthologous groups for eukaryotic complete genomes) analysis was conducted (blastx, E < e−10) towards prediction of transcriptomal functions, leading to the categorization of 638 genes. The majority of genes belonged to Z category (cytoskeleton‐related genes), R category (general function prediction), and C category (energy production and conversion related genes). These basic EST datasets and their bioinformatics analysis will be helpful in investigating the biological mechanism and molecular pathway related genes involved in innate immunity mechanisms of T. molitor.

Molecular Cloning, Sequence Characterization and Expression Analysis of a CD63 Homologue from the Coleopteran Beetle, Tenebrio molitor

“…Initially, the partial sequence of the putative CD63 gene was identified by conducting a comprehensive expressed sequence tag (EST) analysis of T. molitor larvae towards identification of immune-related genes [41]. …”

Construction of PANM Database (Protostome DB) for rapid annotation of NGS data in Mollusks

“…From the NGS sequencing and assembly processes to the annotation analysis, many datasets in different file formats are shared within researchers that warrants an expansion in hard disk storage (Baker, 2010 we constructed a local stand-alone BLAST server for the mollusk by translating the downloaded DNA and amino acid sequences from NCBI using the formatdb program (Lee et al, 2004). The BLAST server was convenient for quick and contamination-free annotation of large-scale EST data generated through first-generation Sanger sequencers (Jeong et al, 2013;Jeong et al, 2015). Subsequently, we developed mollusks sequence database (an updated version of stand-alone BLAST server for the mollusk) (http://www.malacol.or.kr/blast) that suggested a modification of the server to improve the significant hits percentage during the annotation of molluscan genes (Kang et al, 2014).…”

Cloning, expression analysis, and RNA interference study of a HORMA domain containing autophagy-related gene 13 (ATG13) from the coleopteran beetle, Tenebrio molitor

“…We have screened and characterized immune genes from this insect using expressed sequence tag (EST) and RNA sequence (RNAseq) analysis (Jeong et al, 2013; Patnaik et al, 2013, 2014; Tindwa et al, 2013; Noh et al, 2014). We have also screened and identified the autophagy genes from T. molitor using the RNA-seq approach.…”