Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Large scale sequencing of viroid derived small RNA in Potato spindle tuber viroid infected tomato plants

ABSTRACT: In order to analyze the production of small RNA (sRNA) by viroids upon infecting the plants, the tomato plants (Lycopersicum esculentum cv. Rutgers) were inoculated with the variants of Potato spindle tuber viroid (PSTVd). After 21-days of post inoculation, total RNA was extracted and subjected for deep-sequencing using Illumina platform. The primers were trimmed and only 21- to 24-nt long small RNAs were filtered after quality check of the raw data. The filtered 21- to 24-nt was mapped against the genomic and antigenomic strands of the respective PSTVd variants using standard pattern matching algorithm. The profiling of viroid derived sRNA (vd-sRNA) revealed that the viroids are susceptible to host RNA silencing mechanism. Evaluation of the vd-sRNA production in PSTVd infected tomato plants by high-throughput sequencing of small RNAs.

ORGANISM(S): Solanum lycopersicum

SUBMITTER: Charith Raj Adkar-Purushothama

PROVIDER: E-GEOD-69225 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Wheat leaf rust caused by the pathogenic fungus Puccinia triticina, is a serious threat to bread wheat and durum production in many areas of the world. This plant-pathogen interaction has been studied extensively at the molecular genetics level, however proteomics data are still relatively scarce. The present study investigated temporal changes in the abundance of the apoplastic fluid proteome of wheat leaves infected with either virulent or avirulent races of P. triticina, using a label-free LC-MS-based approach. In general, there was very little difference between inoculated and control apoplastic proteomes as a result of either race of pathogen, until haustoria had become well established in the incompatible interaction, although the resistant host responds to pathogen challenge sooner than the susceptible. In the earlier samplings (up to 72 h after inoculation), there were 46 host proteins with significantly changing abundance, however pathogen proteins were detected only rarely and not reproducibly. This is consistent with the hemi-biotrophic life-style of P. triticina; the pathogen infection is characterized by an early phase of a symbiosis-like relationship, followed by a later stage of pathogenesis, with tissue damage and parasitism. The majority of the host proteins with altered abundance up to 72 h post-inoculation were pathogen-response-related, including peroxidases, chitinases, β-1-3-endo-glucanases and PR-proteins. Five days after inoculation with the incompatible race it was possible to detect 150 PT proteins and 117 host proteins which had significantly increased in abundance as well as 33 host proteins which had significantly decreased in abundance and which represent potential targets of pathogen effectors. The pathogen-expressed proteins – seen most abundantly in the incompatible interaction – were mostly uncharacterized proteins, however many of their functions could be inferred through homology-matching with pBLAST. Pathogen proteins also included several candidate effector proteins, some novel and some which have been reported previously from the purified haustoria proteome.

Project description:Inoculation of endophyte-free (E-) Theobroma cacao leaves with Colletotrichum tropicale (E+), the dominant foliar fungal endophyte in healthy T. cacao, induced significant changes in the expression of hundreds of host genes. Further, E+ leaves exhibit enhanced pathogen resistance, increased lignin and cellulose content, reduced maximum rates of photosynthesis (Amax), and enrichment of nitrogen-15 and carbon-13 isotopes that all correspond to the changes in expression of specific functional genes in related pathways. Moreover, a cacao gene highly up-regulated in E+ leaves increases pathogen resistance apart from any direct endophyte effects. Thus, benefits of increased pathogen resistance in E+ plants are partially due to enhanced induction of intrinsic host defense pathways, and potential costs include reduced photosynthetic capacity and endophyte metabolism of host tissues. Similar effects are likely to be properties of most plant-endophyte interactions, suggesting general relevance to the design and interpretation of studies of genetic and phenotypic expression in plants. The objective of this experiment was to identify Theobroma cacao genes that are differentially expressed between leaves inoculated with fungal endophyte Colletotrichum tropicale (E+ leaves) and control un-inoculated leaves (E- leaves) 14 days post last endophyte inoculation. The experiment was conducted in a Percival growth chambers (model I35LL, 115 volts, 1/4 Hp, series: 8503122.16, Percival Scientific, Inc., Perry IA) with 12/12 h light/dark photoperiod and temperatures of 30M-BM-:C and 26M-BM-:C respectively. A total of four endophyte spore inoculations (1X10^6 spore/ml) were made by aspersion to a group of T. cacao seedlings and a second group of seedlings were maintained as un-inoculated. Then six biological replicates per treatment (E+ leaves and six E- leaves) each one belonging from a different seedling were collected and processed for a two color oligo microarray analysis. A total of six arrays were processed, each one hybridized to an inoculated and a control un-inoculated sample in a dye swap design.

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Large scale sequencing of viroid derived small RNA in Potato spindle tuber viroid infected tomato plants

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