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Transcriptome-Wide Identification of miRNAs and Their Targets from Typha angustifolia by RNA-Seq and Their Response to Cadmium Stress.

Xu Y, Chu L, Jin Q, Wang Y, Chen X, Zhao H, Xue Z - PLoS ONE (2015)

Bottom Line: Based on transcriptome data of T. angustifolia, we catalogued and analyzed the sRNAs, resulting in the identification of 114 conserved miRNAs and 41 novel candidate miRNAs in both small RNA libraries.Combined with function of target genes, these results suggested that miRNAs might play a role in plant Cd stress response.This study provided the first transcriptome-based analysis of miRNAs and their targets responsive to Cd stress in T. angustifolia, which provide a framework for further analysis of miRNAs and their role in regulating plant responses to Cd stress.

View Article: PubMed Central - PubMed

Affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, P.R. China.

ABSTRACT
MicroRNAs (miRNAs) play important roles in plant responses to environmental stress. In this work, we used high-throughput sequencing to analyze transcriptome and small RNAs (sRNAs) in Typha angustifolia under cadmium (Cd) stress. 57,608,230 raw reads were obtained from deep sequencing of a pooled cDNA library. Sequence assembly and analysis yielded 102,473 unigenes. We subsequently sequenced two sRNA libraries from T. angustifolia with or without Cd exposure respectively. Based on transcriptome data of T. angustifolia, we catalogued and analyzed the sRNAs, resulting in the identification of 114 conserved miRNAs and 41 novel candidate miRNAs in both small RNA libraries. In silico analysis revealed 764 targets for 89 conserved miRNAs and 21 novel miRNAs. Statistical analysis on sequencing reads abundance and experimental validation revealed that 4 conserved and 6 novel miRNAs showed specific expression. Combined with function of target genes, these results suggested that miRNAs might play a role in plant Cd stress response. This study provided the first transcriptome-based analysis of miRNAs and their targets responsive to Cd stress in T. angustifolia, which provide a framework for further analysis of miRNAs and their role in regulating plant responses to Cd stress.

No MeSH data available.


Related in: MedlinePlus

Common and specific sequences between CK and Cd library.Summarise the common and specific tags of two libraries, including the summary of unique tags and total tags.
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pone.0125462.g006: Common and specific sequences between CK and Cd library.Summarise the common and specific tags of two libraries, including the summary of unique tags and total tags.

Mentions: To identify differently regulated sRNAs under Cd stress in T. angustifolia, we summarized the common and specific sequences between two libraries. CK and Cd library shared 18,329,135 (78.96%) sequences among the total sRNAs, which indicated that the majority of small RNAs were shared (Fig 6). However, the shared unique sRNAs were much smaller, only occupying 12.36% of the total unique sRNAs. In these unique sRNAs, the count of CK-specific sRNA was 2,286,986 reads (46.28%), which is higher than Cd-specific sRNAs 2,043,720 reads (41.36%). This means that Cd stress induces some small RNAs and represses other miRNAs, and that more unique small RNAs are repressed than induced. The size distribution of small RNAs in two libraries was slightly different (Fig 3). The contents of two most abundant small RNA classes, 21-nt and 24-nt, in CK library were increased compared to those in the Cd library.


Transcriptome-Wide Identification of miRNAs and Their Targets from Typha angustifolia by RNA-Seq and Their Response to Cadmium Stress.

Xu Y, Chu L, Jin Q, Wang Y, Chen X, Zhao H, Xue Z - PLoS ONE (2015)

Common and specific sequences between CK and Cd library.Summarise the common and specific tags of two libraries, including the summary of unique tags and total tags.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4414455&req=5

pone.0125462.g006: Common and specific sequences between CK and Cd library.Summarise the common and specific tags of two libraries, including the summary of unique tags and total tags.
Mentions: To identify differently regulated sRNAs under Cd stress in T. angustifolia, we summarized the common and specific sequences between two libraries. CK and Cd library shared 18,329,135 (78.96%) sequences among the total sRNAs, which indicated that the majority of small RNAs were shared (Fig 6). However, the shared unique sRNAs were much smaller, only occupying 12.36% of the total unique sRNAs. In these unique sRNAs, the count of CK-specific sRNA was 2,286,986 reads (46.28%), which is higher than Cd-specific sRNAs 2,043,720 reads (41.36%). This means that Cd stress induces some small RNAs and represses other miRNAs, and that more unique small RNAs are repressed than induced. The size distribution of small RNAs in two libraries was slightly different (Fig 3). The contents of two most abundant small RNA classes, 21-nt and 24-nt, in CK library were increased compared to those in the Cd library.

Bottom Line: Based on transcriptome data of T. angustifolia, we catalogued and analyzed the sRNAs, resulting in the identification of 114 conserved miRNAs and 41 novel candidate miRNAs in both small RNA libraries.Combined with function of target genes, these results suggested that miRNAs might play a role in plant Cd stress response.This study provided the first transcriptome-based analysis of miRNAs and their targets responsive to Cd stress in T. angustifolia, which provide a framework for further analysis of miRNAs and their role in regulating plant responses to Cd stress.

View Article: PubMed Central - PubMed

Affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, P.R. China.

ABSTRACT
MicroRNAs (miRNAs) play important roles in plant responses to environmental stress. In this work, we used high-throughput sequencing to analyze transcriptome and small RNAs (sRNAs) in Typha angustifolia under cadmium (Cd) stress. 57,608,230 raw reads were obtained from deep sequencing of a pooled cDNA library. Sequence assembly and analysis yielded 102,473 unigenes. We subsequently sequenced two sRNA libraries from T. angustifolia with or without Cd exposure respectively. Based on transcriptome data of T. angustifolia, we catalogued and analyzed the sRNAs, resulting in the identification of 114 conserved miRNAs and 41 novel candidate miRNAs in both small RNA libraries. In silico analysis revealed 764 targets for 89 conserved miRNAs and 21 novel miRNAs. Statistical analysis on sequencing reads abundance and experimental validation revealed that 4 conserved and 6 novel miRNAs showed specific expression. Combined with function of target genes, these results suggested that miRNAs might play a role in plant Cd stress response. This study provided the first transcriptome-based analysis of miRNAs and their targets responsive to Cd stress in T. angustifolia, which provide a framework for further analysis of miRNAs and their role in regulating plant responses to Cd stress.

No MeSH data available.


Related in: MedlinePlus