Cargando…
Deep RNA-Seq profile reveals biodiversity, plant–microbe interactions and a large family of NBS-LRR resistance genes in walnut (Juglans regia) tissues
Deep RNA-Seq profiling, a revolutionary method used for quantifying transcriptional levels, often includes non-specific transcripts from other co-existing organisms in spite of stringent protocols. Using the recently published walnut genome sequence as a filter, we present a broad analysis of the RN...
Autores principales: | , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Springer Berlin Heidelberg
2016
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4755957/ https://www.ncbi.nlm.nih.gov/pubmed/26883051 http://dx.doi.org/10.1186/s13568-016-0182-3 |
_version_ | 1782416239121924096 |
---|---|
author | Chakraborty, Sandeep Britton, Monica Martínez-García, P. J. Dandekar, Abhaya M. |
author_facet | Chakraborty, Sandeep Britton, Monica Martínez-García, P. J. Dandekar, Abhaya M. |
author_sort | Chakraborty, Sandeep |
collection | PubMed |
description | Deep RNA-Seq profiling, a revolutionary method used for quantifying transcriptional levels, often includes non-specific transcripts from other co-existing organisms in spite of stringent protocols. Using the recently published walnut genome sequence as a filter, we present a broad analysis of the RNA-Seq derived transcriptome profiles obtained from twenty different tissues to extract the biodiversity and possible plant–microbe interactions in the walnut ecosystem in California. Since the residual nature of the transcripts being analyzed does not provide sufficient information to identify the exact strain, inferences made are constrained to the genus level. The presence of the pathogenic oomycete Phytophthora was detected in the root through the presence of a glyceraldehyde-3-phosphate dehydrogenase. Cryptococcus, the causal agent of cryptococcosis, was found in the catkins and vegetative buds, corroborating previous work indicating that the plant surface supported the sexual cycle of this human pathogen. The RNA-Seq profile revealed several species of the endophytic nitrogen fixing Actinobacteria. Another bacterial species implicated in aerobic biodegradation of methyl tert-butyl ether (Methylibium petroleiphilum) is also found in the root. RNA encoding proteins from the pea aphid were found in the leaves and vegetative buds, while a serine protease from mosquito with significant homology to a female reproductive tract protease from Drosophila mojavensis in the vegetative bud suggests egg-laying activities. The comprehensive analysis of RNA-seq data present also unraveled detailed, tissue-specific information of ~400 transcripts encoded by the largest family of resistance (R) genes (NBS-LRR), which possibly rationalizes the resistance of the specific walnut plant to the pathogens detected. Thus, we elucidate the biodiversity and possible plant–microbe interactions in several walnut (Juglans regia) tissues in California using deep RNA-Seq profiling. |
format | Online Article Text |
id | pubmed-4755957 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Springer Berlin Heidelberg |
record_format | MEDLINE/PubMed |
spelling | pubmed-47559572016-02-26 Deep RNA-Seq profile reveals biodiversity, plant–microbe interactions and a large family of NBS-LRR resistance genes in walnut (Juglans regia) tissues Chakraborty, Sandeep Britton, Monica Martínez-García, P. J. Dandekar, Abhaya M. AMB Express Original Article Deep RNA-Seq profiling, a revolutionary method used for quantifying transcriptional levels, often includes non-specific transcripts from other co-existing organisms in spite of stringent protocols. Using the recently published walnut genome sequence as a filter, we present a broad analysis of the RNA-Seq derived transcriptome profiles obtained from twenty different tissues to extract the biodiversity and possible plant–microbe interactions in the walnut ecosystem in California. Since the residual nature of the transcripts being analyzed does not provide sufficient information to identify the exact strain, inferences made are constrained to the genus level. The presence of the pathogenic oomycete Phytophthora was detected in the root through the presence of a glyceraldehyde-3-phosphate dehydrogenase. Cryptococcus, the causal agent of cryptococcosis, was found in the catkins and vegetative buds, corroborating previous work indicating that the plant surface supported the sexual cycle of this human pathogen. The RNA-Seq profile revealed several species of the endophytic nitrogen fixing Actinobacteria. Another bacterial species implicated in aerobic biodegradation of methyl tert-butyl ether (Methylibium petroleiphilum) is also found in the root. RNA encoding proteins from the pea aphid were found in the leaves and vegetative buds, while a serine protease from mosquito with significant homology to a female reproductive tract protease from Drosophila mojavensis in the vegetative bud suggests egg-laying activities. The comprehensive analysis of RNA-seq data present also unraveled detailed, tissue-specific information of ~400 transcripts encoded by the largest family of resistance (R) genes (NBS-LRR), which possibly rationalizes the resistance of the specific walnut plant to the pathogens detected. Thus, we elucidate the biodiversity and possible plant–microbe interactions in several walnut (Juglans regia) tissues in California using deep RNA-Seq profiling. Springer Berlin Heidelberg 2016-02-17 /pmc/articles/PMC4755957/ /pubmed/26883051 http://dx.doi.org/10.1186/s13568-016-0182-3 Text en © Chakraborty et al. 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. |
spellingShingle | Original Article Chakraborty, Sandeep Britton, Monica Martínez-García, P. J. Dandekar, Abhaya M. Deep RNA-Seq profile reveals biodiversity, plant–microbe interactions and a large family of NBS-LRR resistance genes in walnut (Juglans regia) tissues |
title | Deep RNA-Seq profile reveals biodiversity, plant–microbe interactions and a large family of NBS-LRR resistance genes in walnut (Juglans regia) tissues |
title_full | Deep RNA-Seq profile reveals biodiversity, plant–microbe interactions and a large family of NBS-LRR resistance genes in walnut (Juglans regia) tissues |
title_fullStr | Deep RNA-Seq profile reveals biodiversity, plant–microbe interactions and a large family of NBS-LRR resistance genes in walnut (Juglans regia) tissues |
title_full_unstemmed | Deep RNA-Seq profile reveals biodiversity, plant–microbe interactions and a large family of NBS-LRR resistance genes in walnut (Juglans regia) tissues |
title_short | Deep RNA-Seq profile reveals biodiversity, plant–microbe interactions and a large family of NBS-LRR resistance genes in walnut (Juglans regia) tissues |
title_sort | deep rna-seq profile reveals biodiversity, plant–microbe interactions and a large family of nbs-lrr resistance genes in walnut (juglans regia) tissues |
topic | Original Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4755957/ https://www.ncbi.nlm.nih.gov/pubmed/26883051 http://dx.doi.org/10.1186/s13568-016-0182-3 |
work_keys_str_mv | AT chakrabortysandeep deeprnaseqprofilerevealsbiodiversityplantmicrobeinteractionsandalargefamilyofnbslrrresistancegenesinwalnutjuglansregiatissues AT brittonmonica deeprnaseqprofilerevealsbiodiversityplantmicrobeinteractionsandalargefamilyofnbslrrresistancegenesinwalnutjuglansregiatissues AT martinezgarciapj deeprnaseqprofilerevealsbiodiversityplantmicrobeinteractionsandalargefamilyofnbslrrresistancegenesinwalnutjuglansregiatissues AT dandekarabhayam deeprnaseqprofilerevealsbiodiversityplantmicrobeinteractionsandalargefamilyofnbslrrresistancegenesinwalnutjuglansregiatissues |