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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

Differential gene expression analysis between larval midguts and adult midguts.The volcano plot shows the magnitude of differential expression of transcripts between larval and adult midguts. Each dot represents a transcript that had detectable expression. The horizontal line marks the threshold (FDR < 0.01) for defining a transcript as up-regulated in larval midguts (blue) or adult midguts (red), with a combined change > 4-fold.
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pone.0134824.g006: Differential gene expression analysis between larval midguts and adult midguts.The volcano plot shows the magnitude of differential expression of transcripts between larval and adult midguts. Each dot represents a transcript that had detectable expression. The horizontal line marks the threshold (FDR < 0.01) for defining a transcript as up-regulated in larval midguts (blue) or adult midguts (red), with a combined change > 4-fold.

Mentions: Both the EAB larvae and adults feed, but they consume different parts of the ash tree. The larvae feed exclusively on phloem and cambial tissues, while the adults feed exclusively on foliage. To explore potential factors contributing to EAB diet selection, we compared the midgut transcriptomes of larvae and adults. An overall view of the expression pattern is depicted in Fig 6. A total of 1,167 unigenes were detected as being differentially expressed (S4 Table). Of these, 732 unigenes were up-regulated in adult midgut, and 435 unigenes were up-regulated in larval midgut (Log2FC>2; FDR <0.01). Functional annotation of these unigenes showed that many genes were associated with digestive physiology and related metabolic processes, including serine protease, trypsin, glucose dehydrogenase, sugar transporter, endoglucanase. The laccase transcript was 22-fold higher in adult midgut than in larval midgut. Transcripts corresponding to alcohol dehydrogenases, aldehyde dehydrogenases, cytochrome P450s were also highly expressed in the adult midgut.


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)

Differential gene expression analysis between larval midguts and adult midguts.The volcano plot shows the magnitude of differential expression of transcripts between larval and adult midguts. Each dot represents a transcript that had detectable expression. The horizontal line marks the threshold (FDR < 0.01) for defining a transcript as up-regulated in larval midguts (blue) or adult midguts (red), with a combined change > 4-fold.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0134824.g006: Differential gene expression analysis between larval midguts and adult midguts.The volcano plot shows the magnitude of differential expression of transcripts between larval and adult midguts. Each dot represents a transcript that had detectable expression. The horizontal line marks the threshold (FDR < 0.01) for defining a transcript as up-regulated in larval midguts (blue) or adult midguts (red), with a combined change > 4-fold.
Mentions: Both the EAB larvae and adults feed, but they consume different parts of the ash tree. The larvae feed exclusively on phloem and cambial tissues, while the adults feed exclusively on foliage. To explore potential factors contributing to EAB diet selection, we compared the midgut transcriptomes of larvae and adults. An overall view of the expression pattern is depicted in Fig 6. A total of 1,167 unigenes were detected as being differentially expressed (S4 Table). Of these, 732 unigenes were up-regulated in adult midgut, and 435 unigenes were up-regulated in larval midgut (Log2FC>2; FDR <0.01). Functional annotation of these unigenes showed that many genes were associated with digestive physiology and related metabolic processes, including serine protease, trypsin, glucose dehydrogenase, sugar transporter, endoglucanase. The laccase transcript was 22-fold higher in adult midgut than in larval midgut. Transcripts corresponding to alcohol dehydrogenases, aldehyde dehydrogenases, cytochrome P450s were also highly expressed in the adult midgut.

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