De novo assembly, gene annotation, and marker discovery in stored-product pest Liposcelis entomophila (Enderlein) using transcriptome sequences.
BACKGROUND
As 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.


RESULTS
We 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
We 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.
Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, P. R. China.
Dan-Dan
DD
Wei
Er-Hu
EH
Chen
Tian-Bo
TB
Ding
Shi-Chun
SC
Chen
Wei
W
Dou
Jin-Jun
JJ
Wang
D000818:Animals; D002802:Cholinesterases / Q000145:classification / Q000235:genetics; D003577:Cytochrome P-450 Enzyme System / Q000145:classification / Q000235:genetics; D030541:Databases, Genetic; D002523:Edible Grain / Q000469:parasitology; D020224:Expressed Sequence Tags; D015870:Gene Expression; D020869:Gene Expression Profiling; D005819:Genetic Markers; D005982:Glutathione Transferase / Q000145:classification / Q000235:genetics; D006360:Heat-Shock Proteins / Q000145:classification / Q000235:genetics; D019476:Insect Proteins / Q000145:classification / Q000235:genetics*; D007313:Insecta / Q000235:genetics*; D007305:Insecticide Resistance / Q000235:genetics*; D018895:Microsatellite Repeats; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D059467:Transcriptome
D005819:Genetic Markers; D006360:Heat-Shock Proteins; D019476:Insect Proteins; D003577:Cytochrome P-450 Enzyme System; D005982:Glutathione Transferase; D002802:Cholinesterases