Separating homeologs by phasing in the tetraploid wheat transcriptome

Fil: Krasileva, Ksenia V. University of California. Dept. Plant Sciences. Davis, CA 9561, USA.

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Detalles Bibliográficos
Autores principales:	Krasileva, Ksenia V., Buffalo, Vince, Bailey, Paul, Pearce, Stephen, Ayling, Sarah, Tabbita, Facundo, Soria, Marcelo Abel, Wang, Shichen, Akhunov, Eduard, Uauy, Cristobal, Dubcovsky, Jorge
Formato:	Artículo publishedVersion
Lenguaje:	Inglés
Publicado:	2013
Materias:	GENE PREDICTION PHASING POLYPLOID PSEUDOGENES TRANSCRIPTOME ASSEMBLY TRITICUM TURGIDUM TRITICUM URARTU WHEAT CONTIG PROTEOME TRANSCRIPTOME CONTROLLED STUDY DIPLOIDY GENE SEQUENCE GENOME GENOMICS HETEROZYGOTE HOMEOLOG NONHUMAN OPEN READING FRAME PLANT GENOME SINGLE NUCLEOTIDE POLYMORPHISM TETRAPLOIDY TRITICUM AESTIVUM MULTIPLE K-MER ASSEMBLY COMPLEMENTARY DNA
Acceso en línea:	http://ri.agro.uba.ar/greenstone3/library/collection/arti/document/2013krasileva
Aporte de:	FAUBA Digital - Facultad de Agronomía (UBA) de Universidad de Buenos Aires

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institution	Universidad de Buenos Aires
institution_str	I-28
repository_str	R-140
collection	FAUBA Digital - Facultad de Agronomía (UBA)
language	Inglés
orig_language_str_mv	eng
topic	GENE PREDICTION PHASING POLYPLOID PSEUDOGENES TRANSCRIPTOME ASSEMBLY TRITICUM TURGIDUM TRITICUM URARTU WHEAT CONTIG PROTEOME TRANSCRIPTOME CONTROLLED STUDY DIPLOIDY GENE SEQUENCE GENOME GENOMICS HETEROZYGOTE HOMEOLOG NONHUMAN OPEN READING FRAME PLANT GENOME SINGLE NUCLEOTIDE POLYMORPHISM TETRAPLOIDY TRITICUM AESTIVUM MULTIPLE K-MER ASSEMBLY PHASING COMPLEMENTARY DNA
spellingShingle	GENE PREDICTION PHASING POLYPLOID PSEUDOGENES TRANSCRIPTOME ASSEMBLY TRITICUM TURGIDUM TRITICUM URARTU WHEAT CONTIG PROTEOME TRANSCRIPTOME CONTROLLED STUDY DIPLOIDY GENE SEQUENCE GENOME GENOMICS HETEROZYGOTE HOMEOLOG NONHUMAN OPEN READING FRAME PLANT GENOME SINGLE NUCLEOTIDE POLYMORPHISM TETRAPLOIDY TRITICUM AESTIVUM MULTIPLE K-MER ASSEMBLY PHASING COMPLEMENTARY DNA Krasileva, Ksenia V. Buffalo, Vince Bailey, Paul Pearce, Stephen Ayling, Sarah Tabbita, Facundo Soria, Marcelo Abel Wang, Shichen Akhunov, Eduard Uauy, Cristobal Dubcovsky, Jorge Separating homeologs by phasing in the tetraploid wheat transcriptome
topic_facet	GENE PREDICTION PHASING POLYPLOID PSEUDOGENES TRANSCRIPTOME ASSEMBLY TRITICUM TURGIDUM TRITICUM URARTU WHEAT CONTIG PROTEOME TRANSCRIPTOME CONTROLLED STUDY DIPLOIDY GENE SEQUENCE GENOME GENOMICS HETEROZYGOTE HOMEOLOG NONHUMAN OPEN READING FRAME PLANT GENOME SINGLE NUCLEOTIDE POLYMORPHISM TETRAPLOIDY TRITICUM AESTIVUM MULTIPLE K-MER ASSEMBLY PHASING COMPLEMENTARY DNA
description	Fil: Krasileva, Ksenia V. University of California. Dept. Plant Sciences. Davis, CA 9561, USA.
format	Artículo Artículo publishedVersion publishedVersion
author	Krasileva, Ksenia V. Buffalo, Vince Bailey, Paul Pearce, Stephen Ayling, Sarah Tabbita, Facundo Soria, Marcelo Abel Wang, Shichen Akhunov, Eduard Uauy, Cristobal Dubcovsky, Jorge
author_facet	Krasileva, Ksenia V. Buffalo, Vince Bailey, Paul Pearce, Stephen Ayling, Sarah Tabbita, Facundo Soria, Marcelo Abel Wang, Shichen Akhunov, Eduard Uauy, Cristobal Dubcovsky, Jorge
author_sort	Krasileva, Ksenia V.
title	Separating homeologs by phasing in the tetraploid wheat transcriptome
title_short	Separating homeologs by phasing in the tetraploid wheat transcriptome
title_full	Separating homeologs by phasing in the tetraploid wheat transcriptome
title_fullStr	Separating homeologs by phasing in the tetraploid wheat transcriptome
title_full_unstemmed	Separating homeologs by phasing in the tetraploid wheat transcriptome
title_sort	separating homeologs by phasing in the tetraploid wheat transcriptome
publishDate	2013
url	http://ri.agro.uba.ar/greenstone3/library/collection/arti/document/2013krasileva
work_keys_str_mv	AT krasilevakseniav separatinghomeologsbyphasinginthetetraploidwheattranscriptome AT buffalovince separatinghomeologsbyphasinginthetetraploidwheattranscriptome AT baileypaul separatinghomeologsbyphasinginthetetraploidwheattranscriptome AT pearcestephen separatinghomeologsbyphasinginthetetraploidwheattranscriptome AT aylingsarah separatinghomeologsbyphasinginthetetraploidwheattranscriptome AT tabbitafacundo separatinghomeologsbyphasinginthetetraploidwheattranscriptome AT soriamarceloabel separatinghomeologsbyphasinginthetetraploidwheattranscriptome AT wangshichen separatinghomeologsbyphasinginthetetraploidwheattranscriptome AT akhunoveduard separatinghomeologsbyphasinginthetetraploidwheattranscriptome AT uauycristobal separatinghomeologsbyphasinginthetetraploidwheattranscriptome AT dubcovskyjorge separatinghomeologsbyphasinginthetetraploidwheattranscriptome
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spelling	snrd:2013krasileva2021-10-15T16:56:07Z Krasileva, Ksenia V. Buffalo, Vince Bailey, Paul Pearce, Stephen Ayling, Sarah Tabbita, Facundo Soria, Marcelo Abel Wang, Shichen Akhunov, Eduard Uauy, Cristobal Dubcovsky, Jorge 2013 Fil: Krasileva, Ksenia V. University of California. Dept. Plant Sciences. Davis, CA 9561, USA. Fil: Buffalo, Vince. University of California. Dept. Plant Sciences. Davis, CA 9561, USA. Fil: Bailey, Paul. The Genome Analysis Centre. Norwich Research Park. Norwich NR4 7UH, UK. Fil: Pearce, Stephen. University of California. Dept. Plant Sciences. Davis, CA 9561, USA. Fil: Ayling, Sarah. The Genome Analysis Centre. Norwich Research Park. Norwich NR4 7UH, UK. Fil: Tabbita, Facundo. University of California. Dept. Plant Sciences. Davis, CA 9561, USA. Fil: Soria, Marcelo Abel. University of California. Dept. Plant Sciences. Davis, CA 9561, USA. Fil: Soria, Marcelo Abel. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Biología Aplicada y Alimentos. Cátedra de Microbiología Agrícola. Buenos Aires, Argentina. Fil: Soria, Marcelo Abel. Universidad de Buenos Aires. Facultad de Agronomía. Instituto de Investigaciones en Biociencias Agrícolas y Ambientales (INBA). Buenos Aires, Argentina. Fil: Soria, Marcelo Abel. CONICET – Universidad de Buenos Aires. Instituto de Investigaciones en Biociencias Agrícolas y Ambientales (INBA). Buenos Aires, Argentina. Fil: Wang, Shichen. Kansas State University. Department of Plant Pathology. Manhattan, KS 66506, USA. Fil: Akhunov, Eduard. Kansas State University. Department of Plant Pathology. Manhattan, KS 66506, USA. Fil: Uauy, Cristobal. John Innes Centre. Norwich Research Park. Norwich NR4 7UH, UK. Fil: Dubcovsky, Jorge. University of California. Dept. Plant Sciences. Davis, CA 9561, USA. Fil: Dubcovsky, Jorge. Howard Hughes Medical Institute. Chevy Chase, MD 20815, USA. Background: The high level of identity among duplicated homoeologous genomes in tetraploid pasta wheat presents substantial challenges for de novo transcriptome assembly. To solve this problem, we develop a specialized bioinformatics workflow that optimizes transcriptome assembly and separation of merged homoeologs. To evaluate our strategy, we sequence and assemble the transcriptome of one of the diploid ancestors of pasta wheat, and compare both assemblies with a benchmark set of 13,472 full-length, non-redundant bread wheat cDNAs. Results: A total of 489 million 100 bp paired-end reads from tetraploid wheat assemble in 140,118 contigs, including 96 percent of the benchmark cDNAs. We used a comparative genomics approach to annotate 66,633 open reading frames. The multiple k-mer assembly strategy increases the proportion of cDNAs assembled full-length in a single contig by 22 percent relative to the best single k-mer size. Homoeologs are separated using a post-assembly pipeline that includes polymorphism identification, phasing of SNPs, read sorting, and re-assembly of phased reads. Using a reference set of genes, we determine that 98.7 percent of SNPs analyzed are correctly separated by phasing. Conclusions: Our study shows that de novo transcriptome assembly of tetraploid wheat benefit from multiple k-mer assembly strategies more than diploid wheat. Our results also demonstrate that phasing approaches originally designed for heterozygous diploid organisms can be used to separate the close homoeologous genomes of tetraploid wheat. The predicted tetraploid wheat proteome and gene models provide a valuable tool for the wheat research community and for those interested in comparative genomic studies. application/pdf doi:10.1186/gb-2013-14-6-r66 issn:1474-760X http://ri.agro.uba.ar/greenstone3/library/collection/arti/document/2013krasileva eng info:eu-repo/semantics/openAccess openAccess http://ri.agro.uba.ar/greenstone3/library/page/biblioteca#section4 Genome Biology Vol.14, no.6 14:R66 http://genomebiology.com/ GENE PREDICTION PHASING POLYPLOID PSEUDOGENES TRANSCRIPTOME ASSEMBLY TRITICUM TURGIDUM TRITICUM URARTU WHEAT CONTIG PROTEOME TRANSCRIPTOME CONTROLLED STUDY DIPLOIDY GENE SEQUENCE GENOME GENOMICS HETEROZYGOTE HOMEOLOG NONHUMAN OPEN READING FRAME PLANT GENOME SINGLE NUCLEOTIDE POLYMORPHISM TETRAPLOIDY TRITICUM AESTIVUM MULTIPLE K-MER ASSEMBLY PHASING COMPLEMENTARY DNA Separating homeologs by phasing in the tetraploid wheat transcriptome info:eu-repo/semantics/article info:ar-repo/semantics/artículo publishedVersion info:eu-repo/semantics/publishedVersion

Separating homeologs by phasing in the tetraploid wheat transcriptome

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