De Novo Assembly, Gene Annotation, and Marker Discovery in Stored-Product Pest Liposcelis entomophila (Enderlein) Using Transcriptome Sequences

Abstract

BackgroundAs a major stored-product pest insect, Liposcelis entomophila has developed high levels of resistance to various insecticides in grain storage systems. However, the molecular mechanisms underlying resistance and environmental stress have not been characterized. To date, there is a lack of genomic information for this species. Therefore, studies aimed at profiling the L. entomophila transcriptome would provide a better understanding of the biological functions at the molecular levels.Methodology/Principal FindingsWe applied Illumina sequencing technology to sequence the transcriptome of L. entomophila. A total of 54,406,328 clean reads were obtained and that de novo assembled into 54,220 unigenes, with an average length of 571 bp. Through a similarity search, 33,404 (61.61%) unigenes were matched to known proteins in the NCBI non-redundant (Nr) protein database. These unigenes were further functionally annotated with gene ontology (GO), cluster of orthologous groups of proteins (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. A large number of genes potentially involved in insecticide resistance were manually curated, including 68 putative cytochrome P450 genes, 37 putative glutathione S-transferase (GST) genes, 19 putative carboxyl/cholinesterase (CCE) genes, and other 126 transcripts to contain target site sequences or encoding detoxification genes representing eight types of resistance enzymes. Furthermore, to gain insight into the molecular basis of the L. entomophila toward thermal stresses, 25 heat shock protein (Hsp) genes were identified. In addition, 1,100 SSRs and 57,757 SNPs were detected and 231 pairs of SSR primes were designed for investigating the genetic diversity in future.Conclusions/SignificanceWe developed a comprehensive transcriptomic database for L. entomophila. These sequences and putative molecular markers would further promote our understanding of the molecular mechanisms underlying insecticide resistance or environmental stress, and will facilitate studies on population genetics for psocids, as well as providing useful information for functional genomic research in the future.

RNA sequencing, de novo assembly, and functional annotation of an endangered Nymphalid butterfly, Fabriciana nerippe Felder, 1862

“…The different selection criteria for SSRs may explain the relatively lower abundance of SSRs discovered from other insect transcriptomes (Wei et al . ; Bu et al . ).…”

“…In the identified SSRs from other insect transcriptomes, ATs accounted for a greater proportion of dinucleotide repeats while the predominant tri‐ and tetranucleotide repeats were variable (Wei et al . ; Tian et al . ).…”

Transcriptome profiling of the testis reveals genes involved in spermatogenesis and marker discovery in the oriental fruit fly, Bactrocera dorsalis

“…The inferred functions of 28.5% of the unigenes were not resolved. There were differences compared with the transcriptomes of B. dorsalis (Shen et al ., ; Zheng et al ., ), and other insects (Dou et al ., ; Wei et al ., ; Chen et al ., ); however, the results were similar to those of the transcriptome of the midgut of B. dorsalis (Shen et al ., ).…”

“…A total of 20 107 distinct sequences (65.89% of all the unigenes) matched known genes that encoded functional proteins, suggesting that the assembly quality was high. The percentage of unigenes matching known proteins was much higher than those reported in the whole body transcriptome of B. dorsalis (55.1%; Shen et al ., ), Bemisia tabaci (16.2%; Wang et al ., ), Nilaparvata lugens (40.0%; Bao et al ., ), Plutella xylostella (22.3%; He et al ., ), L. entomophila (61.6%; Wei et al ., ) and D. citri (44.8%; Chen et al ., ), as well as for the tissue transcriptome of testis and male accessory glands in D. variabilis (30.9%; Sonenshine et al ., ). Amongst the 30 516 unigenes, almost a third shared no significant similarities to known genes and may be novel/or fast‐evolving sequences.…”

“…Transcriptome sequencing yields the subset of genes from the genome that are functionally active in selected species or tissues of interest. Many insect transcriptomes have been sequenced recently, such as Maruca vitrata (Margam et al ., ), Anopheles gambiae (Harker et al ., ), Liposcelis entomophila (Wei et al ., ), L. bostrychophila (Dou et al ., ) and Dialeurodes citri (Chen et al ., ). These high‐throughput sequence databases represent a valuable resource for tephritid fruit flies, whose genome sequences have not been determined or released, unlike model insects whose genomes have been sequenced, such as Drosophila melanogaster (Adams et al ., ), An.…”