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Analysis of small RNA production patterns among the two potato spindle tuber viroid variants in tomato plants.

Adkar-Purushothama CR, Perreault JP, Sano T - Genom Data (2015)

Bottom Line: The primers were trimmed and only 21- to 24-nt long sRNAs were filtered after quality check of the raw data.The profiling of viroid derived sRNA (vd-sRNA) revealed that the viroids are susceptible to host RNA silencing mechanism.High-throughput sequence data linked to this project have been deposited in the Gene Expression Omnibus (GEO) database under accession number GSE69225.

View Article: PubMed Central - PubMed

Affiliation: RNA Group/Groupe ARN, Département de Biochimie, Faculté de médecine des sciences de la santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, 3201 rue Jean-Mignault, Sherbrooke, Québec J1E 4K8, Canada.

ABSTRACT
In order to analyze the production of small RNA (sRNA) by viroids upon infecting the plants, the tomato plants (Solanum lycopersicum cultivar Rutgers) were inoculated with the variants of Potato spindle tuber viroid (PSTVd). After 21-days of postinoculation, total RNA was extracted and subjected for deep-sequencing using Illumina HiSeq platform. The primers were trimmed and only 21- to 24-nt long sRNAs were filtered after quality check of the raw data. The filtered sRNA population was then mapped against both 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. High-throughput sequence data linked to this project have been deposited in the Gene Expression Omnibus (GEO) database under accession number GSE69225.

No MeSH data available.


Sequence profiles of the genomic (+) and the antigenomic (−) PSTVd-sRNA populations recovered from the leaf tissues of infected tomato plants. (A) and (B) represent the profiles of the sRNAs derived from the (+) and the (−) strands of the PSTVd-M and PSTVd-I, respectively. Please note that different scales are used so as to compensate for the lower numbers of sRNA sequences recovered for the PSTVd-M infected plants.
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f0005: Sequence profiles of the genomic (+) and the antigenomic (−) PSTVd-sRNA populations recovered from the leaf tissues of infected tomato plants. (A) and (B) represent the profiles of the sRNAs derived from the (+) and the (−) strands of the PSTVd-M and PSTVd-I, respectively. Please note that different scales are used so as to compensate for the lower numbers of sRNA sequences recovered for the PSTVd-M infected plants.

Mentions: Sequence analysis of over 4.28 million sRNAs obtained from mock inoculated plants identified about 108 and 106 viroid specific small RNAs (vd-sRNA) of PSTVd-M and PSTVd-I type, respectively, matching the genomes of PSTVd-M and PSTVd-I. Analysis of 4.54 million sRNA reads obtained from the PSTVd-M inoculated plants against both the (+) and (−) strands of PSTVd-M revealed 103,933 vd-sRNAs. Similarly, analysis of 4.88 million reads obtained from the PSTVd-I inoculated plants against both the (+) and (−) strands of PSTVd-I underscored 488,146 vd-sRNAs. That said, PSTVd-I inoculated plants showed more vd-sRNA (11.3%) than PSTVd-M (2.3%) inoculated plants. This difference in the vd-sRNA recovery can be attributed to the lower accumulation of PSTVd-M compared to PSTVd-I, as described previously [2]. All 21- to 24-nt long vd-sRNAs were profiled on both polarity strands of the respective PSTVd variants using the standard pattern-matching algorithm in order to understand the production of the vd-sRNAs (Fig. 1). Although PSTVd-M and PSTVd-I produced different amount of sRNAs, both showed similar vd-sRNA profile. Further, profiling of vd-sRNA on the PSTVd genome revealed that certain region of PSTVd produced more sRNA than others, indicating that these regions are more susceptible to RNA silencing.


Analysis of small RNA production patterns among the two potato spindle tuber viroid variants in tomato plants.

Adkar-Purushothama CR, Perreault JP, Sano T - Genom Data (2015)

Sequence profiles of the genomic (+) and the antigenomic (−) PSTVd-sRNA populations recovered from the leaf tissues of infected tomato plants. (A) and (B) represent the profiles of the sRNAs derived from the (+) and the (−) strands of the PSTVd-M and PSTVd-I, respectively. Please note that different scales are used so as to compensate for the lower numbers of sRNA sequences recovered for the PSTVd-M infected plants.
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4664692&req=5

f0005: Sequence profiles of the genomic (+) and the antigenomic (−) PSTVd-sRNA populations recovered from the leaf tissues of infected tomato plants. (A) and (B) represent the profiles of the sRNAs derived from the (+) and the (−) strands of the PSTVd-M and PSTVd-I, respectively. Please note that different scales are used so as to compensate for the lower numbers of sRNA sequences recovered for the PSTVd-M infected plants.
Mentions: Sequence analysis of over 4.28 million sRNAs obtained from mock inoculated plants identified about 108 and 106 viroid specific small RNAs (vd-sRNA) of PSTVd-M and PSTVd-I type, respectively, matching the genomes of PSTVd-M and PSTVd-I. Analysis of 4.54 million sRNA reads obtained from the PSTVd-M inoculated plants against both the (+) and (−) strands of PSTVd-M revealed 103,933 vd-sRNAs. Similarly, analysis of 4.88 million reads obtained from the PSTVd-I inoculated plants against both the (+) and (−) strands of PSTVd-I underscored 488,146 vd-sRNAs. That said, PSTVd-I inoculated plants showed more vd-sRNA (11.3%) than PSTVd-M (2.3%) inoculated plants. This difference in the vd-sRNA recovery can be attributed to the lower accumulation of PSTVd-M compared to PSTVd-I, as described previously [2]. All 21- to 24-nt long vd-sRNAs were profiled on both polarity strands of the respective PSTVd variants using the standard pattern-matching algorithm in order to understand the production of the vd-sRNAs (Fig. 1). Although PSTVd-M and PSTVd-I produced different amount of sRNAs, both showed similar vd-sRNA profile. Further, profiling of vd-sRNA on the PSTVd genome revealed that certain region of PSTVd produced more sRNA than others, indicating that these regions are more susceptible to RNA silencing.

Bottom Line: The primers were trimmed and only 21- to 24-nt long sRNAs were filtered after quality check of the raw data.The profiling of viroid derived sRNA (vd-sRNA) revealed that the viroids are susceptible to host RNA silencing mechanism.High-throughput sequence data linked to this project have been deposited in the Gene Expression Omnibus (GEO) database under accession number GSE69225.

View Article: PubMed Central - PubMed

Affiliation: RNA Group/Groupe ARN, Département de Biochimie, Faculté de médecine des sciences de la santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, 3201 rue Jean-Mignault, Sherbrooke, Québec J1E 4K8, Canada.

ABSTRACT
In order to analyze the production of small RNA (sRNA) by viroids upon infecting the plants, the tomato plants (Solanum lycopersicum cultivar Rutgers) were inoculated with the variants of Potato spindle tuber viroid (PSTVd). After 21-days of postinoculation, total RNA was extracted and subjected for deep-sequencing using Illumina HiSeq platform. The primers were trimmed and only 21- to 24-nt long sRNAs were filtered after quality check of the raw data. The filtered sRNA population was then mapped against both 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. High-throughput sequence data linked to this project have been deposited in the Gene Expression Omnibus (GEO) database under accession number GSE69225.

No MeSH data available.