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Transcriptome and proteome profiling of adventitious root development in hybrid larch (Larix kaempferi × Larix olgensis)

BACKGROUND: Hybrids of larch (Larix kaempferi × Larix olgensis) are important afforestation species in northeastern China. They are routinely propagated via rooted stem cuttings. Despite the importance of rooting, little is known about the regulation of adventitious root development in larch hybrids...

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Autores principales: Han, Hua, Sun, Xiaomei, Xie, Yunhui, Feng, Jian, Zhang, Shougong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4253636/
https://www.ncbi.nlm.nih.gov/pubmed/25425065
http://dx.doi.org/10.1186/s12870-014-0305-4
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author Han, Hua
Sun, Xiaomei
Xie, Yunhui
Feng, Jian
Zhang, Shougong
author_facet Han, Hua
Sun, Xiaomei
Xie, Yunhui
Feng, Jian
Zhang, Shougong
author_sort Han, Hua
collection PubMed
description BACKGROUND: Hybrids of larch (Larix kaempferi × Larix olgensis) are important afforestation species in northeastern China. They are routinely propagated via rooted stem cuttings. Despite the importance of rooting, little is known about the regulation of adventitious root development in larch hybrids. 454 GS FLX Titanium technology represents a new method for characterizing the transcriptomes of non-model species. This method can be used to identify differentially expressed genes, and then two-dimensional difference gel electrophoresis (2D-DIGE) and matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF/TOF MS) analyses can be used to analyze their corresponding proteins. In this study, we analyzed semi-lignified cuttings of two clones of L. kaempferi × L. olgensis with different rooting capacities to study the molecular basis of adventitious root development. RESULTS: We analyzed two clones; clone 25-5, with strong rooting capacity, and clone 23-12, with weak rooting capacity. We constructed four cDNA libraries from 25-5 and 23-12 at two development stages. Sequencing was conducted using the 454 pyrosequencing platform. A total of 957832 raw reads was produced; 95.07% were high-quality reads, and were assembled into 45137 contigs and 61647 singletons. The functions of the unigenes, as indicated by their Gene Ontology annotation, included diverse roles in the molecular functions, biological processes, and cellular component categories. We analyzed 75 protein spots (-fold change ≥2, P ≤0.05) by 2D-DIGE, and identified the differentially expressed proteins using MALDI-TOF/TOF MS. A joint analysis of transcriptome and proteome showed genes related to two pathways, polyamine synthesis and stress response, might play an important role on adventitious root development. CONCLUSIONS: These results provide fundamental and important information for research on the molecular mechanism of adventitious root development. We also demonstrated for the first time the combined use of two important technologies as a powerful approach to advance research on non-model, but otherwise important, larch species. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12870-014-0305-4) contains supplementary material, which is available to authorized users.
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spelling pubmed-42536362014-12-04 Transcriptome and proteome profiling of adventitious root development in hybrid larch (Larix kaempferi × Larix olgensis) Han, Hua Sun, Xiaomei Xie, Yunhui Feng, Jian Zhang, Shougong BMC Plant Biol Research Article BACKGROUND: Hybrids of larch (Larix kaempferi × Larix olgensis) are important afforestation species in northeastern China. They are routinely propagated via rooted stem cuttings. Despite the importance of rooting, little is known about the regulation of adventitious root development in larch hybrids. 454 GS FLX Titanium technology represents a new method for characterizing the transcriptomes of non-model species. This method can be used to identify differentially expressed genes, and then two-dimensional difference gel electrophoresis (2D-DIGE) and matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF/TOF MS) analyses can be used to analyze their corresponding proteins. In this study, we analyzed semi-lignified cuttings of two clones of L. kaempferi × L. olgensis with different rooting capacities to study the molecular basis of adventitious root development. RESULTS: We analyzed two clones; clone 25-5, with strong rooting capacity, and clone 23-12, with weak rooting capacity. We constructed four cDNA libraries from 25-5 and 23-12 at two development stages. Sequencing was conducted using the 454 pyrosequencing platform. A total of 957832 raw reads was produced; 95.07% were high-quality reads, and were assembled into 45137 contigs and 61647 singletons. The functions of the unigenes, as indicated by their Gene Ontology annotation, included diverse roles in the molecular functions, biological processes, and cellular component categories. We analyzed 75 protein spots (-fold change ≥2, P ≤0.05) by 2D-DIGE, and identified the differentially expressed proteins using MALDI-TOF/TOF MS. A joint analysis of transcriptome and proteome showed genes related to two pathways, polyamine synthesis and stress response, might play an important role on adventitious root development. CONCLUSIONS: These results provide fundamental and important information for research on the molecular mechanism of adventitious root development. We also demonstrated for the first time the combined use of two important technologies as a powerful approach to advance research on non-model, but otherwise important, larch species. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12870-014-0305-4) contains supplementary material, which is available to authorized users. BioMed Central 2014-11-26 /pmc/articles/PMC4253636/ /pubmed/25425065 http://dx.doi.org/10.1186/s12870-014-0305-4 Text en © Han et al.; licensee BioMed Central Ltd. 2014 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Han, Hua
Sun, Xiaomei
Xie, Yunhui
Feng, Jian
Zhang, Shougong
Transcriptome and proteome profiling of adventitious root development in hybrid larch (Larix kaempferi × Larix olgensis)
title Transcriptome and proteome profiling of adventitious root development in hybrid larch (Larix kaempferi × Larix olgensis)
title_full Transcriptome and proteome profiling of adventitious root development in hybrid larch (Larix kaempferi × Larix olgensis)
title_fullStr Transcriptome and proteome profiling of adventitious root development in hybrid larch (Larix kaempferi × Larix olgensis)
title_full_unstemmed Transcriptome and proteome profiling of adventitious root development in hybrid larch (Larix kaempferi × Larix olgensis)
title_short Transcriptome and proteome profiling of adventitious root development in hybrid larch (Larix kaempferi × Larix olgensis)
title_sort transcriptome and proteome profiling of adventitious root development in hybrid larch (larix kaempferi × larix olgensis)
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4253636/
https://www.ncbi.nlm.nih.gov/pubmed/25425065
http://dx.doi.org/10.1186/s12870-014-0305-4
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