Cargando…
Separating homeologs by phasing in the tetraploid wheat transcriptome
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 m...
Autores principales: | , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2013
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053977/ https://www.ncbi.nlm.nih.gov/pubmed/23800085 http://dx.doi.org/10.1186/gb-2013-14-6-r66 |
_version_ | 1782320480745684992 |
---|---|
author | Krasileva, Ksenia V Buffalo, Vince Bailey, Paul Pearce, Stephen Ayling, Sarah Tabbita, Facundo Soria, Marcelo 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 Wang, Shichen Akhunov, Eduard Uauy, Cristobal Dubcovsky, Jorge |
author_sort | Krasileva, Ksenia V |
collection | PubMed |
description | 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% 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% 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% 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. |
format | Online Article Text |
id | pubmed-4053977 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-40539772014-06-13 Separating homeologs by phasing in the tetraploid wheat transcriptome Krasileva, Ksenia V Buffalo, Vince Bailey, Paul Pearce, Stephen Ayling, Sarah Tabbita, Facundo Soria, Marcelo Wang, Shichen Akhunov, Eduard Uauy, Cristobal Dubcovsky, Jorge Genome Biol Research 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% 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% 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% 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. BioMed Central 2013 2013-06-25 /pmc/articles/PMC4053977/ /pubmed/23800085 http://dx.doi.org/10.1186/gb-2013-14-6-r66 Text en Copyright © 2013 Krasileva et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Krasileva, Ksenia V Buffalo, Vince Bailey, Paul Pearce, Stephen Ayling, Sarah Tabbita, Facundo Soria, Marcelo Wang, Shichen Akhunov, Eduard Uauy, Cristobal Dubcovsky, Jorge Separating homeologs by phasing in the tetraploid wheat transcriptome |
title | 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_short | Separating homeologs by phasing in the tetraploid wheat transcriptome |
title_sort | separating homeologs by phasing in the tetraploid wheat transcriptome |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053977/ https://www.ncbi.nlm.nih.gov/pubmed/23800085 http://dx.doi.org/10.1186/gb-2013-14-6-r66 |
work_keys_str_mv | AT krasilevakseniav separatinghomeologsbyphasinginthetetraploidwheattranscriptome AT buffalovince separatinghomeologsbyphasinginthetetraploidwheattranscriptome AT baileypaul separatinghomeologsbyphasinginthetetraploidwheattranscriptome AT pearcestephen separatinghomeologsbyphasinginthetetraploidwheattranscriptome AT aylingsarah separatinghomeologsbyphasinginthetetraploidwheattranscriptome AT tabbitafacundo separatinghomeologsbyphasinginthetetraploidwheattranscriptome AT soriamarcelo separatinghomeologsbyphasinginthetetraploidwheattranscriptome AT wangshichen separatinghomeologsbyphasinginthetetraploidwheattranscriptome AT separatinghomeologsbyphasinginthetetraploidwheattranscriptome AT akhunoveduard separatinghomeologsbyphasinginthetetraploidwheattranscriptome AT uauycristobal separatinghomeologsbyphasinginthetetraploidwheattranscriptome AT dubcovskyjorge separatinghomeologsbyphasinginthetetraploidwheattranscriptome |