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

Rarefaction analysis of the gene representation.Randomly sampled reads from the combined seven sequenced libraries were aligned against the T. castaneum official gene dataset. The number of genes that were hit by reads at least 1, 10, 50, 100 and 200 times was recorded.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0134824.g001: Rarefaction analysis of the gene representation.Randomly sampled reads from the combined seven sequenced libraries were aligned against the T. castaneum official gene dataset. The number of genes that were hit by reads at least 1, 10, 50, 100 and 200 times was recorded.

Mentions: To evaluate whether sufficient sequencing depth was achieved to cover EAB genes, the relationship between sequencing depth and the number of gene discoveries was examined by a rarefaction analysis. Because the complete genomic sequence of EAB is not available, we adopted a random re-sampling method and compared these reads with the closely related species T. castaneum. Increments of random sampled reads from 0.1 to 100 million pairs of reads were aligned to the T. castaneum official genes dataset. As shown in Fig 1, 9,292 genes can be detected with at least one pair of reads using the random dataset of 75 million paired reads, while 6,695 genes are represented by at least 50 pairs of reads. Increasing the dataset to 100 million pairs of reads, resulted in the detection of 9,373 while 6,976 genes are represented by at least 50 pairs of reads. These results indicate that the gene discovery rate is saturated above 75 million pairs of reads. Since the total numbers of pre-filtered reads exceeds 332.3 million pairs, the dataset is considered sufficient to detect most of the genes in the samples.


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)

Rarefaction analysis of the gene representation.Randomly sampled reads from the combined seven sequenced libraries were aligned against the T. castaneum official gene dataset. The number of genes that were hit by reads at least 1, 10, 50, 100 and 200 times was recorded.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0134824.g001: Rarefaction analysis of the gene representation.Randomly sampled reads from the combined seven sequenced libraries were aligned against the T. castaneum official gene dataset. The number of genes that were hit by reads at least 1, 10, 50, 100 and 200 times was recorded.
Mentions: To evaluate whether sufficient sequencing depth was achieved to cover EAB genes, the relationship between sequencing depth and the number of gene discoveries was examined by a rarefaction analysis. Because the complete genomic sequence of EAB is not available, we adopted a random re-sampling method and compared these reads with the closely related species T. castaneum. Increments of random sampled reads from 0.1 to 100 million pairs of reads were aligned to the T. castaneum official genes dataset. As shown in Fig 1, 9,292 genes can be detected with at least one pair of reads using the random dataset of 75 million paired reads, while 6,695 genes are represented by at least 50 pairs of reads. Increasing the dataset to 100 million pairs of reads, resulted in the detection of 9,373 while 6,976 genes are represented by at least 50 pairs of reads. These results indicate that the gene discovery rate is saturated above 75 million pairs of reads. Since the total numbers of pre-filtered reads exceeds 332.3 million pairs, the dataset is considered sufficient to detect most of the genes in the samples.

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