Limits...
Transcriptome Analysis of the Emerald Ash Borer (EAB), Agrilus planipennis: De Novo Assembly, Functional Annotation and Comparative Analysis.

Duan J, Ladd T, Doucet D, Cusson M, vanFrankenhuyzen K, Mittapalli O, Krell PJ, Quan G - PLoS ONE (2015)

Bottom Line: The EAB transcriptome assembly was compared with 13 other sequenced insect species, resulting in the prediction of 536 unigenes that are Coleoptera-specific.This study provides one of the most fundamental and comprehensive transcriptome resources available for EAB to date.Identification of the tissue- stage- or species- specific unigenes will benefit the further study of gene functions during growth and metamorphosis processes in EAB and other pest insects.

View Article: PubMed Central - PubMed

Affiliation: Great Lakes Forestry Centre, Canadian Forest Service, Natural Resources Canada, Sault Ste. Marie, Ontario, Canada; Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.

ABSTRACT

Background: The Emerald ash borer (EAB), Agrilus planipennis, is an invasive phloem-feeding insect pest of ash trees. Since its initial discovery near the Detroit, US- Windsor, Canada area in 2002, the spread of EAB has had strong negative economic, social and environmental impacts in both countries. Several transcriptomes from specific tissues including midgut, fat body and antenna have recently been generated. However, the relatively low sequence depth, gene coverage and completeness limited the usefulness of these EAB databases.

Methodology and principal findings: High-throughput deep RNA-Sequencing (RNA-Seq) was used to obtain 473.9 million pairs of 100 bp length paired-end reads from various life stages and tissues. These reads were assembled into 88,907 contigs using the Trinity strategy and integrated into 38,160 unigenes after redundant sequences were removed. We annotated 11,229 unigenes by searching against the public nr, Swiss-Prot and COG. The EAB transcriptome assembly was compared with 13 other sequenced insect species, resulting in the prediction of 536 unigenes that are Coleoptera-specific. Differential gene expression revealed that 290 unigenes are expressed during larval molting and 3,911 unigenes during metamorphosis from larvae to pupae, respectively (FDR< 0.01 and log2 FC>2). In addition, 1,167 differentially expressed unigenes were identified from larval and adult midguts, 435 unigenes were up-regulated in larval midgut and 732 unigenes were up-regulated in adult midgut. Most of the genes involved in RNA interference (RNAi) pathways were identified, which implies the existence of a system RNAi in EAB.

Conclusions and significance: This study provides one of the most fundamental and comprehensive transcriptome resources available for EAB to date. Identification of the tissue- stage- or species- specific unigenes will benefit the further study of gene functions during growth and metamorphosis processes in EAB and other pest insects.

No MeSH data available.


Related in: MedlinePlus

COG function classification of the EAB transcriptome.The EAB unigenes were also aligned to the Clusters of Orthologous Groups (COG) database to predict and classify potential functions. A total of 7,080 unigenes were classified in 25 categories. The categories are shown in the order of increasing numbers of genes/category.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4526369&req=5

pone.0134824.g004: COG function classification of the EAB transcriptome.The EAB unigenes were also aligned to the Clusters of Orthologous Groups (COG) database to predict and classify potential functions. A total of 7,080 unigenes were classified in 25 categories. The categories are shown in the order of increasing numbers of genes/category.

Mentions: To annotate the EAB unigenes, a homology search was performed by BLASTing them against the Swiss-Port public protein database. Significant hits were obtained for 8,446 (22.1%) unigenes that displayed an E-value of 10−6. 10,975 unigenes (28.8%) had corresponding homologs identified by searching against the NCBI nr database, of which, 6,893 exhibited significant similarity to T. castaneum genes (S2 Fig), indicating the close relationship between EAB and T. castaneum. The EAB unigenes were also aligned to the Clusters of Orthologous Groups (COG) database to predict and classify potential functions (Fig 4). A total of 7,080 unigenes were COG classified. Among the 24 COG categories, the cluster for ‘general function prediction’ represented the largest group (1,798 unigenes, 25.4%) followed by ‘signal transduction mechanisms’ (780 unigenes, 11.0%) and ‘posttranslational modification, protein turnover and chaperones’ (528 unigenes, 7.5%). Cell motility (36 unigenes, 0.5%) and nuclear structure (16 unigenes, 0.2%) represented the smallest groups. Gene Ontology assignments were also used to classify the functions of the unigenes. In total, 5,325 EAB unigenes were categorized into GO functional groups. The terms “cellular process”, “biological regulation”, “metabolic process” were the most represented in the main category of biological process. In summary, 11,229 unigenes were annotated using nr, Swiss-Prot, COG, and KEGG databases.


Transcriptome Analysis of the Emerald Ash Borer (EAB), Agrilus planipennis: De Novo Assembly, Functional Annotation and Comparative Analysis.

Duan J, Ladd T, Doucet D, Cusson M, vanFrankenhuyzen K, Mittapalli O, Krell PJ, Quan G - PLoS ONE (2015)

COG function classification of the EAB transcriptome.The EAB unigenes were also aligned to the Clusters of Orthologous Groups (COG) database to predict and classify potential functions. A total of 7,080 unigenes were classified in 25 categories. The categories are shown in the order of increasing numbers of genes/category.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4526369&req=5

pone.0134824.g004: COG function classification of the EAB transcriptome.The EAB unigenes were also aligned to the Clusters of Orthologous Groups (COG) database to predict and classify potential functions. A total of 7,080 unigenes were classified in 25 categories. The categories are shown in the order of increasing numbers of genes/category.
Mentions: To annotate the EAB unigenes, a homology search was performed by BLASTing them against the Swiss-Port public protein database. Significant hits were obtained for 8,446 (22.1%) unigenes that displayed an E-value of 10−6. 10,975 unigenes (28.8%) had corresponding homologs identified by searching against the NCBI nr database, of which, 6,893 exhibited significant similarity to T. castaneum genes (S2 Fig), indicating the close relationship between EAB and T. castaneum. The EAB unigenes were also aligned to the Clusters of Orthologous Groups (COG) database to predict and classify potential functions (Fig 4). A total of 7,080 unigenes were COG classified. Among the 24 COG categories, the cluster for ‘general function prediction’ represented the largest group (1,798 unigenes, 25.4%) followed by ‘signal transduction mechanisms’ (780 unigenes, 11.0%) and ‘posttranslational modification, protein turnover and chaperones’ (528 unigenes, 7.5%). Cell motility (36 unigenes, 0.5%) and nuclear structure (16 unigenes, 0.2%) represented the smallest groups. Gene Ontology assignments were also used to classify the functions of the unigenes. In total, 5,325 EAB unigenes were categorized into GO functional groups. The terms “cellular process”, “biological regulation”, “metabolic process” were the most represented in the main category of biological process. In summary, 11,229 unigenes were annotated using nr, Swiss-Prot, COG, and KEGG databases.

Bottom Line: The EAB transcriptome assembly was compared with 13 other sequenced insect species, resulting in the prediction of 536 unigenes that are Coleoptera-specific.This study provides one of the most fundamental and comprehensive transcriptome resources available for EAB to date.Identification of the tissue- stage- or species- specific unigenes will benefit the further study of gene functions during growth and metamorphosis processes in EAB and other pest insects.

View Article: PubMed Central - PubMed

Affiliation: Great Lakes Forestry Centre, Canadian Forest Service, Natural Resources Canada, Sault Ste. Marie, Ontario, Canada; Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.

ABSTRACT

Background: The Emerald ash borer (EAB), Agrilus planipennis, is an invasive phloem-feeding insect pest of ash trees. Since its initial discovery near the Detroit, US- Windsor, Canada area in 2002, the spread of EAB has had strong negative economic, social and environmental impacts in both countries. Several transcriptomes from specific tissues including midgut, fat body and antenna have recently been generated. However, the relatively low sequence depth, gene coverage and completeness limited the usefulness of these EAB databases.

Methodology and principal findings: High-throughput deep RNA-Sequencing (RNA-Seq) was used to obtain 473.9 million pairs of 100 bp length paired-end reads from various life stages and tissues. These reads were assembled into 88,907 contigs using the Trinity strategy and integrated into 38,160 unigenes after redundant sequences were removed. We annotated 11,229 unigenes by searching against the public nr, Swiss-Prot and COG. The EAB transcriptome assembly was compared with 13 other sequenced insect species, resulting in the prediction of 536 unigenes that are Coleoptera-specific. Differential gene expression revealed that 290 unigenes are expressed during larval molting and 3,911 unigenes during metamorphosis from larvae to pupae, respectively (FDR< 0.01 and log2 FC>2). In addition, 1,167 differentially expressed unigenes were identified from larval and adult midguts, 435 unigenes were up-regulated in larval midgut and 732 unigenes were up-regulated in adult midgut. Most of the genes involved in RNA interference (RNAi) pathways were identified, which implies the existence of a system RNAi in EAB.

Conclusions and significance: This study provides one of the most fundamental and comprehensive transcriptome resources available for EAB to date. Identification of the tissue- stage- or species- specific unigenes will benefit the further study of gene functions during growth and metamorphosis processes in EAB and other pest insects.

No MeSH data available.


Related in: MedlinePlus