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Chestnut resistance to the blight disease: insights from transcriptome analysis.

Barakat A, Staton M, Cheng CH, Park J, Yassin NB, Ficklin S, Yeh CC, Hebard F, Baier K, Powell W, Schuster SC, Wheeler N, Abbott A, Carlson JE, Sederoff R - BMC Plant Biol. (2012)

Bottom Line: A significant number of additional DTA genes involved in the defense-response not reported in a previous study were identified here.The similar set of GDTAs in American chestnut and Chinese chestnut suggests that the variation in sensitivity to this pathogen between these species may be the result of different timing and amplitude of the response of the two to the pathogen infection.Resources developed in this study are useful for functional genomics, comparative genomics, resistance breeding and phylogenetics in the Fagaceae.

View Article: PubMed Central - HTML - PubMed

Affiliation: The School of Forest Resources, and The Huck Institutes of the Life Sciences, Pennsylvania State University, 326 Forest Resources Building, University Park, PA 16802, USA. abaraka@clemson.edu

ABSTRACT

Background: A century ago, Chestnut Blight Disease (CBD) devastated the American chestnut. Backcross breeding has been underway to introgress resistance from Chinese chestnut into surviving American chestnut genotypes. Development of genomic resources for the family Fagaceae, has focused in this project on Castanea mollissima Blume (Chinese chestnut) and Castanea dentata (Marsh.) Borkh (American chestnut) to aid in the backcross breeding effort and in the eventual identification of blight resistance genes through genomic sequencing and map based cloning. A previous study reported partial characterization of the transcriptomes from these two species. Here, further analyses of a larger dataset and assemblies including both 454 and capillary sequences were performed and defense related genes with differential transcript abundance (GDTA) in canker versus healthy stem tissues were identified.

Results: Over one and a half million cDNA reads were assembled into 34,800 transcript contigs from American chestnut and 48,335 transcript contigs from Chinese chestnut. Chestnut cDNA showed higher coding sequence similarity to genes in other woody plants than in herbaceous species. The number of genes tagged, the length of coding sequences, and the numbers of tagged members within gene families showed that the cDNA dataset provides a good resource for studying the American and Chinese chestnut transcriptomes. In silico analysis of transcript abundance identified hundreds of GDTA in canker versus healthy stem tissues. A significant number of additional DTA genes involved in the defense-response not reported in a previous study were identified here. These DTA genes belong to various pathways involving cell wall biosynthesis, reactive oxygen species (ROS), salicylic acid (SA), ethylene, jasmonic acid (JA), abscissic acid (ABA), and hormone signalling. DTA genes were also identified in the hypersensitive response and programmed cell death (PCD) pathways. These DTA genes are candidates for host resistance to the chestnut blight fungus, Cryphonectria parasitica.

Conclusions: Our data allowed the identification of many genes and gene network candidates for host resistance to the chestnut blight fungus, Cryphonectria parasitica. The similar set of GDTAs in American chestnut and Chinese chestnut suggests that the variation in sensitivity to this pathogen between these species may be the result of different timing and amplitude of the response of the two to the pathogen infection. Resources developed in this study are useful for functional genomics, comparative genomics, resistance breeding and phylogenetics in the Fagaceae.

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Histogram presentation of Gene Ontology classification of putative biological processes of contigs from American chestnut (AC), and Chinese chestnut (CC). The Y axis indicates the annotation count corresponding to each biological process indicated on the X axis.
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Figure 2: Histogram presentation of Gene Ontology classification of putative biological processes of contigs from American chestnut (AC), and Chinese chestnut (CC). The Y axis indicates the annotation count corresponding to each biological process indicated on the X axis.

Mentions: For the two Fagaceae species in this study, over one and half million sequencing reads were generated and yielded a total of 93,018 contigs in total for the separate assemblies of the cDNA libraries for the 10 tissues sampled. A small fraction of contigs matched mitochondrial (1.3%) and chloroplast (3%) genes. Similarly, ~2.5% of American and Chinese chestnut sequences obtained from canker tissues had best BLASTX alignments to the Cryphonectria parasitica proteome. Transcriptome assembly, version 2 (using all of the reads combined across all tissues), led to the identification of 34,800 and 48,501 contigs from American and Chinese chestnut respectively, from pyrosequencing alone, and 34,800 and 48,335 contigs, with the addition of the Sanger sequences for American chestnut and Chinese chestnut, respectively (Table 2). GO annotation using the Arabidopsis thaliana proteome as reference showed that the transcriptome of these species covers a wide range of biological processes (Figure 2) suggesting that the cDNA libraries were unbiased and well-suited for studies of development and physiology. The distribution of biological processes of the identified contigs from American and Chinese chestnut (Figure 2) did not show any statistically significant differences (p-value > 0.05) [17]. BLASTX alignments to model system proteomes showed that ~ 60% of the transcript contig sequences from the chestnut species studied have strong similarity to predicted proteins in Arabidopsis thaliana or Populus trichocarpa. Of the contig sequences that did not have any significant matches to Arabidopsis thaliana genes, 5 to 6% had a match to Populus trichocarpa genes. The remaining contigs (~30%) did not match any sequence in either the Arabidopsis thaliana or Populus trichocarpa proteomes. We observed a bias toward longer sequences in the contigs with BLASTX alignments to the model proteomes. The distribution of contig length showed that ~85% of sequences without BLASTX alignments to the proteomes of the two model species were short (< 250 nt). In contrast, only about 50% of contigs with good BLASTX hits on the model species proteomes were shorter than 250 nt.


Chestnut resistance to the blight disease: insights from transcriptome analysis.

Barakat A, Staton M, Cheng CH, Park J, Yassin NB, Ficklin S, Yeh CC, Hebard F, Baier K, Powell W, Schuster SC, Wheeler N, Abbott A, Carlson JE, Sederoff R - BMC Plant Biol. (2012)

Histogram presentation of Gene Ontology classification of putative biological processes of contigs from American chestnut (AC), and Chinese chestnut (CC). The Y axis indicates the annotation count corresponding to each biological process indicated on the X axis.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3376029&req=5

Figure 2: Histogram presentation of Gene Ontology classification of putative biological processes of contigs from American chestnut (AC), and Chinese chestnut (CC). The Y axis indicates the annotation count corresponding to each biological process indicated on the X axis.
Mentions: For the two Fagaceae species in this study, over one and half million sequencing reads were generated and yielded a total of 93,018 contigs in total for the separate assemblies of the cDNA libraries for the 10 tissues sampled. A small fraction of contigs matched mitochondrial (1.3%) and chloroplast (3%) genes. Similarly, ~2.5% of American and Chinese chestnut sequences obtained from canker tissues had best BLASTX alignments to the Cryphonectria parasitica proteome. Transcriptome assembly, version 2 (using all of the reads combined across all tissues), led to the identification of 34,800 and 48,501 contigs from American and Chinese chestnut respectively, from pyrosequencing alone, and 34,800 and 48,335 contigs, with the addition of the Sanger sequences for American chestnut and Chinese chestnut, respectively (Table 2). GO annotation using the Arabidopsis thaliana proteome as reference showed that the transcriptome of these species covers a wide range of biological processes (Figure 2) suggesting that the cDNA libraries were unbiased and well-suited for studies of development and physiology. The distribution of biological processes of the identified contigs from American and Chinese chestnut (Figure 2) did not show any statistically significant differences (p-value > 0.05) [17]. BLASTX alignments to model system proteomes showed that ~ 60% of the transcript contig sequences from the chestnut species studied have strong similarity to predicted proteins in Arabidopsis thaliana or Populus trichocarpa. Of the contig sequences that did not have any significant matches to Arabidopsis thaliana genes, 5 to 6% had a match to Populus trichocarpa genes. The remaining contigs (~30%) did not match any sequence in either the Arabidopsis thaliana or Populus trichocarpa proteomes. We observed a bias toward longer sequences in the contigs with BLASTX alignments to the model proteomes. The distribution of contig length showed that ~85% of sequences without BLASTX alignments to the proteomes of the two model species were short (< 250 nt). In contrast, only about 50% of contigs with good BLASTX hits on the model species proteomes were shorter than 250 nt.

Bottom Line: A significant number of additional DTA genes involved in the defense-response not reported in a previous study were identified here.The similar set of GDTAs in American chestnut and Chinese chestnut suggests that the variation in sensitivity to this pathogen between these species may be the result of different timing and amplitude of the response of the two to the pathogen infection.Resources developed in this study are useful for functional genomics, comparative genomics, resistance breeding and phylogenetics in the Fagaceae.

View Article: PubMed Central - HTML - PubMed

Affiliation: The School of Forest Resources, and The Huck Institutes of the Life Sciences, Pennsylvania State University, 326 Forest Resources Building, University Park, PA 16802, USA. abaraka@clemson.edu

ABSTRACT

Background: A century ago, Chestnut Blight Disease (CBD) devastated the American chestnut. Backcross breeding has been underway to introgress resistance from Chinese chestnut into surviving American chestnut genotypes. Development of genomic resources for the family Fagaceae, has focused in this project on Castanea mollissima Blume (Chinese chestnut) and Castanea dentata (Marsh.) Borkh (American chestnut) to aid in the backcross breeding effort and in the eventual identification of blight resistance genes through genomic sequencing and map based cloning. A previous study reported partial characterization of the transcriptomes from these two species. Here, further analyses of a larger dataset and assemblies including both 454 and capillary sequences were performed and defense related genes with differential transcript abundance (GDTA) in canker versus healthy stem tissues were identified.

Results: Over one and a half million cDNA reads were assembled into 34,800 transcript contigs from American chestnut and 48,335 transcript contigs from Chinese chestnut. Chestnut cDNA showed higher coding sequence similarity to genes in other woody plants than in herbaceous species. The number of genes tagged, the length of coding sequences, and the numbers of tagged members within gene families showed that the cDNA dataset provides a good resource for studying the American and Chinese chestnut transcriptomes. In silico analysis of transcript abundance identified hundreds of GDTA in canker versus healthy stem tissues. A significant number of additional DTA genes involved in the defense-response not reported in a previous study were identified here. These DTA genes belong to various pathways involving cell wall biosynthesis, reactive oxygen species (ROS), salicylic acid (SA), ethylene, jasmonic acid (JA), abscissic acid (ABA), and hormone signalling. DTA genes were also identified in the hypersensitive response and programmed cell death (PCD) pathways. These DTA genes are candidates for host resistance to the chestnut blight fungus, Cryphonectria parasitica.

Conclusions: Our data allowed the identification of many genes and gene network candidates for host resistance to the chestnut blight fungus, Cryphonectria parasitica. The similar set of GDTAs in American chestnut and Chinese chestnut suggests that the variation in sensitivity to this pathogen between these species may be the result of different timing and amplitude of the response of the two to the pathogen infection. Resources developed in this study are useful for functional genomics, comparative genomics, resistance breeding and phylogenetics in the Fagaceae.

Show MeSH
Related in: MedlinePlus