Limits...
Global transcriptome profiling of the pine shoot beetle, Tomicus yunnanensis (Coleoptera: Scolytinae).

Zhu JY, Zhao N, Yang B - PLoS ONE (2012)

Bottom Line: In total, 80,932 unigenes were classified into GO, 13,599 unigenes were assigned to COG, and 33,875 unigenes were found in KO categories.In depth analysis of the data revealed a large number of genes related to insecticides resistance and heat shock protein genes associated with environmental stress.The results facilitate the investigations of molecular resistance mechanisms to insecticides and environmental stress.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, College of Forestry, Southwest Forestry University, Kunming, China. jyzhu001@gmail.com

ABSTRACT

Background: The pine shoot beetle Tomicus yunnanensis (Coleoptera: Scolytinae) is an economically important pest of Pinus yunnanensis in southwestern China. Developed resistance to insecticides due to chemical pesticides being used for a long time is a factor involved in its serious damage, which poses a challenge for management. In addition, highly efficient adaptation to divergent environmental ecologies results in this pest posing great potential threat to pine forests. However, the molecular mechanisms remain unknown as only limited nucleotide sequence data for this species is available.

Methodology/principal findings: In this study, we applied next generation sequencing (Illumina sequencing) to sequence the adult transcriptome of T. yunnanensis. A total of 51,822,230 reads were obtained. They were assembled into 140,702 scaffolds, and 60,031 unigenes. The unigenes were further functionally annotated with gene descriptions, Gene Ontology (GO), Clusters of Orthologous Groups (COG), and Kyoto Encyclopedia of Genes and Genome (KEGG). In total, 80,932 unigenes were classified into GO, 13,599 unigenes were assigned to COG, and 33,875 unigenes were found in KO categories. A biochemical pathway database containing 219 predicted pathways was also created based on the annotations. In depth analysis of the data revealed a large number of genes related to insecticides resistance and heat shock protein genes associated with environmental stress.

Conclusions/significance: The results facilitate the investigations of molecular resistance mechanisms to insecticides and environmental stress. This study lays the foundation for future functional genomics studies of important biological questions of this pest.

Show MeSH

Related in: MedlinePlus

Alignment of the partial amino acid sequence of Tomicus yunnanensis HSP60 with that of other insects.(A) the ATP-binding motif. (B) The classical mt-HSP60 signature (underlined) motif. Identical amino acids are shaded black, and conserved residues are shaded grey. Tca, Tribolium castaneum (XP_971630), Ame, Apis mellifera (XP_392899), Csu, Chilo suppressalis (ACT52824); Lsa, Liriomyza sativae (AAW49251).
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3285671&req=5

pone-0032291-g008: Alignment of the partial amino acid sequence of Tomicus yunnanensis HSP60 with that of other insects.(A) the ATP-binding motif. (B) The classical mt-HSP60 signature (underlined) motif. Identical amino acids are shaded black, and conserved residues are shaded grey. Tca, Tribolium castaneum (XP_971630), Ame, Apis mellifera (XP_392899), Csu, Chilo suppressalis (ACT52824); Lsa, Liriomyza sativae (AAW49251).

Mentions: HSP60, a major group of the heat shock proteins, includes stress inducible and constitutively expressed members. It is believed to be predominately mitochondrial, although some are also reported in cytosol and in extracellular compartments [50]. Eighteen unigenes coding for putative HSP60 were identified in the database (Table S5). Compared with orthologues from other organisms, the percentage identity of the deduced amino acid sequence of these unnigenes is high, between 45–93%, confirming the remarkable conservation of this family. Among them, only Unigene59944 was with the length above 1 kb, the others were shorter than 600 bp. Alignment of the predicted amino acid sequence of Unigene59944 with that of other insects revealed it contained the signature peptide known as conserved ATP-binding motif [51] (Figure 8). The classical mitochondrial HSP60 signature motif was found in the deduced amino acid sequence [52], suggesting the HSP60 coded by Unigene59944 presented here is a member of the mitochondrial HSP60 chaperone family. As Unigene59944 was 3′ and 5′-truncted, a fragment of about 30 amino acids at the N terminus required for import into the mitochondriaa and a typical GGM repeat motif for HSP60 at the C terminus were not observed.


Global transcriptome profiling of the pine shoot beetle, Tomicus yunnanensis (Coleoptera: Scolytinae).

Zhu JY, Zhao N, Yang B - PLoS ONE (2012)

Alignment of the partial amino acid sequence of Tomicus yunnanensis HSP60 with that of other insects.(A) the ATP-binding motif. (B) The classical mt-HSP60 signature (underlined) motif. Identical amino acids are shaded black, and conserved residues are shaded grey. Tca, Tribolium castaneum (XP_971630), Ame, Apis mellifera (XP_392899), Csu, Chilo suppressalis (ACT52824); Lsa, Liriomyza sativae (AAW49251).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3285671&req=5

pone-0032291-g008: Alignment of the partial amino acid sequence of Tomicus yunnanensis HSP60 with that of other insects.(A) the ATP-binding motif. (B) The classical mt-HSP60 signature (underlined) motif. Identical amino acids are shaded black, and conserved residues are shaded grey. Tca, Tribolium castaneum (XP_971630), Ame, Apis mellifera (XP_392899), Csu, Chilo suppressalis (ACT52824); Lsa, Liriomyza sativae (AAW49251).
Mentions: HSP60, a major group of the heat shock proteins, includes stress inducible and constitutively expressed members. It is believed to be predominately mitochondrial, although some are also reported in cytosol and in extracellular compartments [50]. Eighteen unigenes coding for putative HSP60 were identified in the database (Table S5). Compared with orthologues from other organisms, the percentage identity of the deduced amino acid sequence of these unnigenes is high, between 45–93%, confirming the remarkable conservation of this family. Among them, only Unigene59944 was with the length above 1 kb, the others were shorter than 600 bp. Alignment of the predicted amino acid sequence of Unigene59944 with that of other insects revealed it contained the signature peptide known as conserved ATP-binding motif [51] (Figure 8). The classical mitochondrial HSP60 signature motif was found in the deduced amino acid sequence [52], suggesting the HSP60 coded by Unigene59944 presented here is a member of the mitochondrial HSP60 chaperone family. As Unigene59944 was 3′ and 5′-truncted, a fragment of about 30 amino acids at the N terminus required for import into the mitochondriaa and a typical GGM repeat motif for HSP60 at the C terminus were not observed.

Bottom Line: In total, 80,932 unigenes were classified into GO, 13,599 unigenes were assigned to COG, and 33,875 unigenes were found in KO categories.In depth analysis of the data revealed a large number of genes related to insecticides resistance and heat shock protein genes associated with environmental stress.The results facilitate the investigations of molecular resistance mechanisms to insecticides and environmental stress.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, College of Forestry, Southwest Forestry University, Kunming, China. jyzhu001@gmail.com

ABSTRACT

Background: The pine shoot beetle Tomicus yunnanensis (Coleoptera: Scolytinae) is an economically important pest of Pinus yunnanensis in southwestern China. Developed resistance to insecticides due to chemical pesticides being used for a long time is a factor involved in its serious damage, which poses a challenge for management. In addition, highly efficient adaptation to divergent environmental ecologies results in this pest posing great potential threat to pine forests. However, the molecular mechanisms remain unknown as only limited nucleotide sequence data for this species is available.

Methodology/principal findings: In this study, we applied next generation sequencing (Illumina sequencing) to sequence the adult transcriptome of T. yunnanensis. A total of 51,822,230 reads were obtained. They were assembled into 140,702 scaffolds, and 60,031 unigenes. The unigenes were further functionally annotated with gene descriptions, Gene Ontology (GO), Clusters of Orthologous Groups (COG), and Kyoto Encyclopedia of Genes and Genome (KEGG). In total, 80,932 unigenes were classified into GO, 13,599 unigenes were assigned to COG, and 33,875 unigenes were found in KO categories. A biochemical pathway database containing 219 predicted pathways was also created based on the annotations. In depth analysis of the data revealed a large number of genes related to insecticides resistance and heat shock protein genes associated with environmental stress.

Conclusions/significance: The results facilitate the investigations of molecular resistance mechanisms to insecticides and environmental stress. This study lays the foundation for future functional genomics studies of important biological questions of this pest.

Show MeSH
Related in: MedlinePlus