SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing

The western black cottonwood (Populus trichocarpa) was the first tree to have its genome fully sequenced and has emerged as the model species for the study of secondary growth and wood formation. It is also a good candidate species for the production of lignocellulosic biofuels. Here, we present and...

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Published in	Molecular ecology resources Vol. 11; no. s1; pp. 81 - 92
Main Authors	GERALDES, ARMANDO, PANG, JOHNSON, THIESSEN, NINA, CEZARD, TIMOTHEE, MOORE, RICHARD, ZHAO, YONGJUN, TAM, ANGELA, WANG, SHUCAI, FRIEDMANN, MICHAEL, BIROL, INANC, JONES, STEVEN J.M, CRONK, QUENTIN C.B, DOUGLAS, CARL J
Format	Journal Article
Language	English
Published	Oxford, UK Blackwell Publishing Ltd 01.03.2011 Wiley Subscription Services, Inc
Subjects	alternative splicing Biofuels Candidate species Chromosome Mapping evolution Evolution & development exons Gene Expression Profiling Genes Genetics Genome, Plant Genomes Genomics high-throughput nucleotide sequencing introns lignocellulose mRNA next generation sequencing Polymorphism, Single Nucleotide Populus Populus - genetics Populus trichocarpa secondary xylem Sequence Analysis, DNA single nucleotide polymorphism transcriptome transcriptomics trees wood Xylem Xylem - genetics
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ISSN	1755-0998 1755-098X 1755-0998
DOI	10.1111/j.1755-0998.2010.02960.x

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Abstract	The western black cottonwood (Populus trichocarpa) was the first tree to have its genome fully sequenced and has emerged as the model species for the study of secondary growth and wood formation. It is also a good candidate species for the production of lignocellulosic biofuels. Here, we present and make available to the research community the results of the sequencing of the transcriptome of developing xylem in 20 accessions with high-throughput next generation sequencing technology. We found over 0.5 million putative single nucleotide polymorphisms (SNPs) in 26 595 genes that are expressed in developing secondary xylem. More than two-thirds of all SNPs were found in annotated exons, with 18% and 14% in regions of the genome annotated as introns and intergenic, respectively, where only 3% and 4% of sequence reads mapped. This suggests that the current annotation of the poplar genome is remarkably incomplete and that there are many transcripts and novel genes waiting to be annotated. We hope that this resource will stimulate further research in expression profiling, detection of alternative splicing and adaptive evolution in poplar.
AbstractList	The western black cottonwood (Populus trichocarpa) was the first tree to have its genome fully sequenced and has emerged as the model species for the study of secondary growth and wood formation. It is also a good candidate species for the production of lignocellulosic biofuels. Here, we present and make available to the research community the results of the sequencing of the transcriptome of developing xylem in 20 accessions with high-throughput next generation sequencing technology. We found over 0.5 million putative single nucleotide polymorphisms (SNPs) in 26,595 genes that are expressed in developing secondary xylem. More than two-thirds of all SNPs were found in annotated exons, with 18% and 14% in regions of the genome annotated as introns and intergenic, respectively, where only 3% and 4% of sequence reads mapped. This suggests that the current annotation of the poplar genome is remarkably incomplete and that there are many transcripts and novel genes waiting to be annotated. We hope that this resource will stimulate further research in expression profiling, detection of alternative splicing and adaptive evolution in poplar. The western black cottonwood ( Populus trichocarpa ) was the first tree to have its genome fully sequenced and has emerged as the model species for the study of secondary growth and wood formation. It is also a good candidate species for the production of lignocellulosic biofuels. Here, we present and make available to the research community the results of the sequencing of the transcriptome of developing xylem in 20 accessions with high‐throughput next generation sequencing technology. We found over 0.5 million putative single nucleotide polymorphisms (SNPs) in 26 595 genes that are expressed in developing secondary xylem. More than two‐thirds of all SNPs were found in annotated exons, with 18% and 14% in regions of the genome annotated as introns and intergenic, respectively, where only 3% and 4% of sequence reads mapped. This suggests that the current annotation of the poplar genome is remarkably incomplete and that there are many transcripts and novel genes waiting to be annotated. We hope that this resource will stimulate further research in expression profiling, detection of alternative splicing and adaptive evolution in poplar. The western black cottonwood (Populus trichocarpa) was the first tree to have its genome fully sequenced and has emerged as the model species for the study of secondary growth and wood formation. It is also a good candidate species for the production of lignocellulosic biofuels. Here, we present and make available to the research community the results of the sequencing of the transcriptome of developing xylem in 20 accessions with high-throughput next generation sequencing technology. We found over 0.5 million putative single nucleotide polymorphisms (SNPs) in 26595 genes that are expressed in developing secondary xylem. More than two-thirds of all SNPs were found in annotated exons, with 18% and 14% in regions of the genome annotated as introns and intergenic, respectively, where only 3% and 4% of sequence reads mapped. This suggests that the current annotation of the poplar genome is remarkably incomplete and that there are many transcripts and novel genes waiting to be annotated. We hope that this resource will stimulate further research in expression profiling, detection of alternative splicing and adaptive evolution in poplar. [PUBLICATION ABSTRACT] The western black cottonwood (Populus trichocarpa) was the first tree to have its genome fully sequenced and has emerged as the model species for the study of secondary growth and wood formation. It is also a good candidate species for the production of lignocellulosic biofuels. Here, we present and make available to the research community the results of the sequencing of the transcriptome of developing xylem in 20 accessions with high-throughput next generation sequencing technology. We found over 0.5 million putative single nucleotide polymorphisms (SNPs) in 26,595 genes that are expressed in developing secondary xylem. More than two-thirds of all SNPs were found in annotated exons, with 18% and 14% in regions of the genome annotated as introns and intergenic, respectively, where only 3% and 4% of sequence reads mapped. This suggests that the current annotation of the poplar genome is remarkably incomplete and that there are many transcripts and novel genes waiting to be annotated. We hope that this resource will stimulate further research in expression profiling, detection of alternative splicing and adaptive evolution in poplar.The western black cottonwood (Populus trichocarpa) was the first tree to have its genome fully sequenced and has emerged as the model species for the study of secondary growth and wood formation. It is also a good candidate species for the production of lignocellulosic biofuels. Here, we present and make available to the research community the results of the sequencing of the transcriptome of developing xylem in 20 accessions with high-throughput next generation sequencing technology. We found over 0.5 million putative single nucleotide polymorphisms (SNPs) in 26,595 genes that are expressed in developing secondary xylem. More than two-thirds of all SNPs were found in annotated exons, with 18% and 14% in regions of the genome annotated as introns and intergenic, respectively, where only 3% and 4% of sequence reads mapped. This suggests that the current annotation of the poplar genome is remarkably incomplete and that there are many transcripts and novel genes waiting to be annotated. We hope that this resource will stimulate further research in expression profiling, detection of alternative splicing and adaptive evolution in poplar. The western black cottonwood (Populus trichocarpa) was the first tree to have its genome fully sequenced and has emerged as the model species for the study of secondary growth and wood formation. It is also a good candidate species for the production of lignocellulosic biofuels. Here, we present and make available to the research community the results of the sequencing of the transcriptome of developing xylem in 20 accessions with high-throughput next generation sequencing technology. We found over 0.5 million putative single nucleotide polymorphisms (SNPs) in 26595 genes that are expressed in developing secondary xylem. More than two-thirds of all SNPs were found in annotated exons, with 18% and 14% in regions of the genome annotated as introns and intergenic, respectively, where only 3% and 4% of sequence reads mapped. This suggests that the current annotation of the poplar genome is remarkably incomplete and that there are many transcripts and novel genes waiting to be annotated. We hope that this resource will stimulate further research in expression profiling, detection of alternative splicing and adaptive evolution in poplar.
Author	BIROL, INANC JONES, STEVEN J. M. THIESSEN, NINA WANG, SHUCAI CEZARD, TIMOTHEE TAM, ANGELA MOORE, RICHARD PANG, JOHNSON FRIEDMANN, MICHAEL ZHAO, YONGJUN CRONK, QUENTIN C. B. GERALDES, ARMANDO DOUGLAS, CARL J.
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Snippet	The western black cottonwood (Populus trichocarpa) was the first tree to have its genome fully sequenced and has emerged as the model species for the study of... The western black cottonwood ( Populus trichocarpa ) was the first tree to have its genome fully sequenced and has emerged as the model species for the study...
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SubjectTerms	alternative splicing Biofuels Candidate species Chromosome Mapping evolution Evolution & development exons Gene Expression Profiling Genes Genetics Genome, Plant Genomes Genomics high-throughput nucleotide sequencing introns lignocellulose mRNA next generation sequencing Polymorphism, Single Nucleotide Populus Populus - genetics Populus trichocarpa secondary xylem Sequence Analysis, DNA single nucleotide polymorphism transcriptome transcriptomics trees wood Xylem Xylem - genetics
Title	SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing
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