Canadian Forest Service Publications

Transcriptome analysis of the emerald ash borer (EAB), agrilus planipennis: de novo assembly, functional annotation and comparative analysis. 2015. Duan, J.; Ladd, T.; Doucet, D.; Cusson, M. van Frankenhuyzen, K.; Mittapalli, O.; Krell, Quan, G. PlosOne DOI: 10.1371/journal.pone.0134824.

Year: 2015

Available from: Great Lakes Forestry Centre

Catalog ID: 36455

Language: English

CFS Availability: PDF (request by e-mail)

Available from the Journal's Web site.
DOI: 10.1371/journal.pone.0134824.

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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.

Plain Language Summary

: Emerald ash borer (EAB) is an invasive phloem-feeding 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. In this study, we adopted the high-throughput low cost RNA-sequencing technology called RNA-seq to deeply sequence entire transcriptomes including larvae, pupae, adults and midguts from larval and adult. A reference transcriptome was reconstructed by de novo assembly all the transcriptomes followed by gene annotation. 11, 229 unigenes were annotated by searching against the public data base. The EAB transcriptome assembly was compared with 13 other sequenced insect species, resulting in the prediction of 536 unigenes that are Coleoptera-specific. In addition, 1,167 differentially expressed unigenes were identified from larval and adult midguts. This study provides one of the most fundamental and comprehensive transcriptome resources available to date. Identification of the tissue- stage- or species- specific unigenes will benefit the further study of gene functions and development of pest management reagents in EAB and other pest insects.

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