Cargando…

De novo sequencing and analysis of root transcriptome using 454 pyrosequencing to discover putative genes associated with drought tolerance in Ammopiptanthus mongolicus

BACKGROUND: De novo assembly of transcript sequences produced by next-generation sequencing technologies offers a rapid approach to obtain expressed gene sequences for non-model organisms. Ammopiptanthus mongolicus, a super-xerophytic broadleaf evergreen wood, is an ecologically important foundation...

Descripción completa

Detalles Bibliográficos
Autores principales: Zhou, Yijun, Gao, Fei, Liu, Ran, Feng, Jinchao, Li, Hongjie
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3407029/
https://www.ncbi.nlm.nih.gov/pubmed/22721448
http://dx.doi.org/10.1186/1471-2164-13-266
_version_ 1782239274433773568
author Zhou, Yijun
Gao, Fei
Liu, Ran
Feng, Jinchao
Li, Hongjie
author_facet Zhou, Yijun
Gao, Fei
Liu, Ran
Feng, Jinchao
Li, Hongjie
author_sort Zhou, Yijun
collection PubMed
description BACKGROUND: De novo assembly of transcript sequences produced by next-generation sequencing technologies offers a rapid approach to obtain expressed gene sequences for non-model organisms. Ammopiptanthus mongolicus, a super-xerophytic broadleaf evergreen wood, is an ecologically important foundation species in desert ecosystems and exhibits substantial drought tolerance in Mid-Asia desert. Root plays an important role in water absorption of plant. There are insufficient transcriptomic and genomic data in public databases for understanding of the molecular mechanism underlying the drought tolerance of A. mongolicus. Thus, high throughput transcriptome sequencing from A. mongolicus root is helpful to generate a large amount of transcript sequences for gene discovery and molecular marker development. RESULTS: A total of 672,002 sequencing reads were obtained from a 454 GS XLR70 Titanium pyrosequencer with a mean length of 279 bp. These reads were assembled into 29,056 unique sequences including 15,173 contigs and 13,883 singlets. In our assembled sequences, 1,827 potential simple sequence repeats (SSR) molecular markers were discovered. Based on sequence similarity with known plant proteins, the assembled sequences represent approximately 9,771 proteins in PlantGDB. Based on the Gene ontology (GO) analysis, hundreds of drought stress-related genes were found. We further analyzed the gene expression profiles of 27 putative genes involved in drought tolerance using quantitative real-time PCR (qRT-PCR) assay. CONCLUSIONS: Our sequence collection represents a major transcriptomic resource for A. mongolicus, and the large number of genetic markers predicted should contribute to future research in Ammopiptanthus genus. The potential drought stress related transcripts identified in this study provide a good start for further investigation into the drought adaptation in Ammopiptanthus.
format Online
Article
Text
id pubmed-3407029
institution National Center for Biotechnology Information
language English
publishDate 2012
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-34070292012-07-28 De novo sequencing and analysis of root transcriptome using 454 pyrosequencing to discover putative genes associated with drought tolerance in Ammopiptanthus mongolicus Zhou, Yijun Gao, Fei Liu, Ran Feng, Jinchao Li, Hongjie BMC Genomics Research Article BACKGROUND: De novo assembly of transcript sequences produced by next-generation sequencing technologies offers a rapid approach to obtain expressed gene sequences for non-model organisms. Ammopiptanthus mongolicus, a super-xerophytic broadleaf evergreen wood, is an ecologically important foundation species in desert ecosystems and exhibits substantial drought tolerance in Mid-Asia desert. Root plays an important role in water absorption of plant. There are insufficient transcriptomic and genomic data in public databases for understanding of the molecular mechanism underlying the drought tolerance of A. mongolicus. Thus, high throughput transcriptome sequencing from A. mongolicus root is helpful to generate a large amount of transcript sequences for gene discovery and molecular marker development. RESULTS: A total of 672,002 sequencing reads were obtained from a 454 GS XLR70 Titanium pyrosequencer with a mean length of 279 bp. These reads were assembled into 29,056 unique sequences including 15,173 contigs and 13,883 singlets. In our assembled sequences, 1,827 potential simple sequence repeats (SSR) molecular markers were discovered. Based on sequence similarity with known plant proteins, the assembled sequences represent approximately 9,771 proteins in PlantGDB. Based on the Gene ontology (GO) analysis, hundreds of drought stress-related genes were found. We further analyzed the gene expression profiles of 27 putative genes involved in drought tolerance using quantitative real-time PCR (qRT-PCR) assay. CONCLUSIONS: Our sequence collection represents a major transcriptomic resource for A. mongolicus, and the large number of genetic markers predicted should contribute to future research in Ammopiptanthus genus. The potential drought stress related transcripts identified in this study provide a good start for further investigation into the drought adaptation in Ammopiptanthus. BioMed Central 2012-06-21 /pmc/articles/PMC3407029/ /pubmed/22721448 http://dx.doi.org/10.1186/1471-2164-13-266 Text en Copyright ©2012 Zhou 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 Article
Zhou, Yijun
Gao, Fei
Liu, Ran
Feng, Jinchao
Li, Hongjie
De novo sequencing and analysis of root transcriptome using 454 pyrosequencing to discover putative genes associated with drought tolerance in Ammopiptanthus mongolicus
title De novo sequencing and analysis of root transcriptome using 454 pyrosequencing to discover putative genes associated with drought tolerance in Ammopiptanthus mongolicus
title_full De novo sequencing and analysis of root transcriptome using 454 pyrosequencing to discover putative genes associated with drought tolerance in Ammopiptanthus mongolicus
title_fullStr De novo sequencing and analysis of root transcriptome using 454 pyrosequencing to discover putative genes associated with drought tolerance in Ammopiptanthus mongolicus
title_full_unstemmed De novo sequencing and analysis of root transcriptome using 454 pyrosequencing to discover putative genes associated with drought tolerance in Ammopiptanthus mongolicus
title_short De novo sequencing and analysis of root transcriptome using 454 pyrosequencing to discover putative genes associated with drought tolerance in Ammopiptanthus mongolicus
title_sort de novo sequencing and analysis of root transcriptome using 454 pyrosequencing to discover putative genes associated with drought tolerance in ammopiptanthus mongolicus
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3407029/
https://www.ncbi.nlm.nih.gov/pubmed/22721448
http://dx.doi.org/10.1186/1471-2164-13-266
work_keys_str_mv AT zhouyijun denovosequencingandanalysisofroottranscriptomeusing454pyrosequencingtodiscoverputativegenesassociatedwithdroughttoleranceinammopiptanthusmongolicus
AT gaofei denovosequencingandanalysisofroottranscriptomeusing454pyrosequencingtodiscoverputativegenesassociatedwithdroughttoleranceinammopiptanthusmongolicus
AT liuran denovosequencingandanalysisofroottranscriptomeusing454pyrosequencingtodiscoverputativegenesassociatedwithdroughttoleranceinammopiptanthusmongolicus
AT fengjinchao denovosequencingandanalysisofroottranscriptomeusing454pyrosequencingtodiscoverputativegenesassociatedwithdroughttoleranceinammopiptanthusmongolicus
AT lihongjie denovosequencingandanalysisofroottranscriptomeusing454pyrosequencingtodiscoverputativegenesassociatedwithdroughttoleranceinammopiptanthusmongolicus