A de-novo-assembly-based Data Analysis Pipeline for Plant Obligate Parasite Metatranscriptomic Studies
Current and emerging plant diseases caused by obligate parasitic microbes such as rusts, downy mildews, and powdery mildews threaten worldwide crop production and food safety. These obligate parasites are typically unculturable in the laboratory, posing technical challenges to characterize them at t...
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2016-07-01
|
| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fpls.2016.00925/full |
| _version_ | 1811261679342714880 |
|---|---|
| author | Li Guo Kelly S Allen Kelly S Allen Greg A Deiulio Greg A Deiulio Yong Zhang Yong Zhang Angela M Madeiras Robert L Wick Li-Jun Ma |
| author_facet | Li Guo Kelly S Allen Kelly S Allen Greg A Deiulio Greg A Deiulio Yong Zhang Yong Zhang Angela M Madeiras Robert L Wick Li-Jun Ma |
| author_sort | Li Guo |
| collection | DOAJ |
| description | Current and emerging plant diseases caused by obligate parasitic microbes such as rusts, downy mildews, and powdery mildews threaten worldwide crop production and food safety. These obligate parasites are typically unculturable in the laboratory, posing technical challenges to characterize them at the genetic and genomic level. Here we have developed a data analysis pipeline integrating several bioinformatic software programs. This pipeline facilitates rapid gene discovery and expression analysis of a plant host and its obligate parasite simultaneously by next generation sequencing of mixed host and pathogen RNA (i.e. metatranscriptomics). We applied this pipeline to metatranscriptomic sequencing data of sweet basil (Ocimum basilicum) and its obligate downy mildew parasite Peronospora belbahrii, both lacking a sequenced genome. Even with a single data point, we were able to identify both candidate host defense genes and pathogen virulence genes that are highly expressed during infection. This demonstrates the power of this pipeline for identifying genes important in host-pathogen interactions without prior genomic information for either the plant host or the obligate biotrophic pathogen. The simplicity of this pipeline makes it accessible to researchers with limited computational skills and applicable to metatranscriptomic data analysis in a wide range of plant-obligate-parasite systems. |
| first_indexed | 2024-04-12T19:10:03Z |
| format | Article |
| id | doaj.art-3dcc5f0d40f24026bb39d1f8eca6aa5f |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-12T19:10:03Z |
| publishDate | 2016-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-3dcc5f0d40f24026bb39d1f8eca6aa5f2022-12-22T03:19:55ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2016-07-01710.3389/fpls.2016.00925198901A de-novo-assembly-based Data Analysis Pipeline for Plant Obligate Parasite Metatranscriptomic StudiesLi Guo0Kelly S Allen1Kelly S Allen2Greg A Deiulio3Greg A Deiulio4Yong Zhang5Yong Zhang6Angela M Madeiras7Robert L Wick8Li-Jun Ma9University of Massachusetts AmherstUniversity of Massachusetts Amherst,University of Massachusetts AmherstUniversity of Massachusetts Amherst,University of Massachusetts AmherstUniversity of Massachusetts AmherstUniversity of Massachusetts AmherstUniversity of Massachusetts AmherstUniversity of Massachusetts AmherstUniversity of Massachusetts AmherstCurrent and emerging plant diseases caused by obligate parasitic microbes such as rusts, downy mildews, and powdery mildews threaten worldwide crop production and food safety. These obligate parasites are typically unculturable in the laboratory, posing technical challenges to characterize them at the genetic and genomic level. Here we have developed a data analysis pipeline integrating several bioinformatic software programs. This pipeline facilitates rapid gene discovery and expression analysis of a plant host and its obligate parasite simultaneously by next generation sequencing of mixed host and pathogen RNA (i.e. metatranscriptomics). We applied this pipeline to metatranscriptomic sequencing data of sweet basil (Ocimum basilicum) and its obligate downy mildew parasite Peronospora belbahrii, both lacking a sequenced genome. Even with a single data point, we were able to identify both candidate host defense genes and pathogen virulence genes that are highly expressed during infection. This demonstrates the power of this pipeline for identifying genes important in host-pathogen interactions without prior genomic information for either the plant host or the obligate biotrophic pathogen. The simplicity of this pipeline makes it accessible to researchers with limited computational skills and applicable to metatranscriptomic data analysis in a wide range of plant-obligate-parasite systems.http://journal.frontiersin.org/Journal/10.3389/fpls.2016.00925/fullhost-pathogen interactionRNA-SeqmetatranscriptomicsDowny mildewde novo assemblyobligate biotroph |
| spellingShingle | Li Guo Kelly S Allen Kelly S Allen Greg A Deiulio Greg A Deiulio Yong Zhang Yong Zhang Angela M Madeiras Robert L Wick Li-Jun Ma A de-novo-assembly-based Data Analysis Pipeline for Plant Obligate Parasite Metatranscriptomic Studies Frontiers in Plant Science host-pathogen interaction RNA-Seq metatranscriptomics Downy mildew de novo assembly obligate biotroph |
| title | A de-novo-assembly-based Data Analysis Pipeline for Plant Obligate Parasite Metatranscriptomic Studies |
| title_full | A de-novo-assembly-based Data Analysis Pipeline for Plant Obligate Parasite Metatranscriptomic Studies |
| title_fullStr | A de-novo-assembly-based Data Analysis Pipeline for Plant Obligate Parasite Metatranscriptomic Studies |
| title_full_unstemmed | A de-novo-assembly-based Data Analysis Pipeline for Plant Obligate Parasite Metatranscriptomic Studies |
| title_short | A de-novo-assembly-based Data Analysis Pipeline for Plant Obligate Parasite Metatranscriptomic Studies |
| title_sort | de novo assembly based data analysis pipeline for plant obligate parasite metatranscriptomic studies |
| topic | host-pathogen interaction RNA-Seq metatranscriptomics Downy mildew de novo assembly obligate biotroph |
| url | http://journal.frontiersin.org/Journal/10.3389/fpls.2016.00925/full |
| work_keys_str_mv | AT liguo adenovoassemblybaseddataanalysispipelineforplantobligateparasitemetatranscriptomicstudies AT kellysallen adenovoassemblybaseddataanalysispipelineforplantobligateparasitemetatranscriptomicstudies AT kellysallen adenovoassemblybaseddataanalysispipelineforplantobligateparasitemetatranscriptomicstudies AT gregadeiulio adenovoassemblybaseddataanalysispipelineforplantobligateparasitemetatranscriptomicstudies AT gregadeiulio adenovoassemblybaseddataanalysispipelineforplantobligateparasitemetatranscriptomicstudies AT yongzhang adenovoassemblybaseddataanalysispipelineforplantobligateparasitemetatranscriptomicstudies AT yongzhang adenovoassemblybaseddataanalysispipelineforplantobligateparasitemetatranscriptomicstudies AT angelammadeiras adenovoassemblybaseddataanalysispipelineforplantobligateparasitemetatranscriptomicstudies AT robertlwick adenovoassemblybaseddataanalysispipelineforplantobligateparasitemetatranscriptomicstudies AT lijunma adenovoassemblybaseddataanalysispipelineforplantobligateparasitemetatranscriptomicstudies AT liguo denovoassemblybaseddataanalysispipelineforplantobligateparasitemetatranscriptomicstudies AT kellysallen denovoassemblybaseddataanalysispipelineforplantobligateparasitemetatranscriptomicstudies AT kellysallen denovoassemblybaseddataanalysispipelineforplantobligateparasitemetatranscriptomicstudies AT gregadeiulio denovoassemblybaseddataanalysispipelineforplantobligateparasitemetatranscriptomicstudies AT gregadeiulio denovoassemblybaseddataanalysispipelineforplantobligateparasitemetatranscriptomicstudies AT yongzhang denovoassemblybaseddataanalysispipelineforplantobligateparasitemetatranscriptomicstudies AT yongzhang denovoassemblybaseddataanalysispipelineforplantobligateparasitemetatranscriptomicstudies AT angelammadeiras denovoassemblybaseddataanalysispipelineforplantobligateparasitemetatranscriptomicstudies AT robertlwick denovoassemblybaseddataanalysispipelineforplantobligateparasitemetatranscriptomicstudies AT lijunma denovoassemblybaseddataanalysispipelineforplantobligateparasitemetatranscriptomicstudies |