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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

Length distribution (A), first nucleotide bias (B) and composition (C) of the small RNA in CK and Cd libraries.A, Average percentage (Y-axis) of redundant sequences of 14–30 nt length (X-axis) in CK and TR libraries. B, Base bias on the first position among small RNA with certain length. Each color in the figure shows the sRNA tags whose first base is a certain base. C, Summarization of all alignments. To make every unique small RNA mapped to only one annotation, we follow the following priority rule: rRNA etc (in which Genbank >Rfam) > known miRNA > repeat > exon > intron.
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pone.0125462.g003: Length distribution (A), first nucleotide bias (B) and composition (C) of the small RNA in CK and Cd libraries.A, Average percentage (Y-axis) of redundant sequences of 14–30 nt length (X-axis) in CK and TR libraries. B, Base bias on the first position among small RNA with certain length. Each color in the figure shows the sRNA tags whose first base is a certain base. C, Summarization of all alignments. To make every unique small RNA mapped to only one annotation, we follow the following priority rule: rRNA etc (in which Genbank >Rfam) > known miRNA > repeat > exon > intron.

Mentions: Two separate sRNA libraries were generated from T. angustifolia seedlings treated with (Cd) or without (CK) Cd-exposure and sequenced by Illumina sequencing technology. The sequencing acquired 12,128,241 reads from the CK library and 12,392,054 reads from the Cd library. After removing adaptor/acceptor sequences, filtering out low quality tags and cleaning up the contamination formed by the adaptor-adaptor ligation, 11,412,343 clean reads and 11,799,855 clean reads were obtained from CK library and Cd library respectively (S6 Table). In both libraries, the 21-nt and 24-nt classes showed the highest degree of redundancy (Fig 3A), suggesting that sRNAs in these size classes are often produced from precursors. The size distribution of all sRNAs was found to be uneven with a length range of 14–30, where the majority was 20–24 nt long. Analysis of the first nucleotide of 18–25 nt long sRNAs revealed that many sRNAs started with uridine (U) at their 5’-ends (Fig 3B). We further screened the clean data against rRNAs, snoRNAs, snRNAs and tRNAs in the NCBI Genebank database and Rfam database (Fig 3C; S6 Table) resulting in 7,856,512 (CK) and 8,275,444 (Cd) reads remaining for further analyses. Among the remaining sequences, 1,836,897 sequences of CK library and 1,813,553 sequences of Cd library were similar to known miRNAs from other plant species that had previously been deposited in miRBase 21.


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)

Length distribution (A), first nucleotide bias (B) and composition (C) of the small RNA in CK and Cd libraries.A, Average percentage (Y-axis) of redundant sequences of 14–30 nt length (X-axis) in CK and TR libraries. B, Base bias on the first position among small RNA with certain length. Each color in the figure shows the sRNA tags whose first base is a certain base. C, Summarization of all alignments. To make every unique small RNA mapped to only one annotation, we follow the following priority rule: rRNA etc (in which Genbank >Rfam) > known miRNA > repeat > exon > intron.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0125462.g003: Length distribution (A), first nucleotide bias (B) and composition (C) of the small RNA in CK and Cd libraries.A, Average percentage (Y-axis) of redundant sequences of 14–30 nt length (X-axis) in CK and TR libraries. B, Base bias on the first position among small RNA with certain length. Each color in the figure shows the sRNA tags whose first base is a certain base. C, Summarization of all alignments. To make every unique small RNA mapped to only one annotation, we follow the following priority rule: rRNA etc (in which Genbank >Rfam) > known miRNA > repeat > exon > intron.
Mentions: Two separate sRNA libraries were generated from T. angustifolia seedlings treated with (Cd) or without (CK) Cd-exposure and sequenced by Illumina sequencing technology. The sequencing acquired 12,128,241 reads from the CK library and 12,392,054 reads from the Cd library. After removing adaptor/acceptor sequences, filtering out low quality tags and cleaning up the contamination formed by the adaptor-adaptor ligation, 11,412,343 clean reads and 11,799,855 clean reads were obtained from CK library and Cd library respectively (S6 Table). In both libraries, the 21-nt and 24-nt classes showed the highest degree of redundancy (Fig 3A), suggesting that sRNAs in these size classes are often produced from precursors. The size distribution of all sRNAs was found to be uneven with a length range of 14–30, where the majority was 20–24 nt long. Analysis of the first nucleotide of 18–25 nt long sRNAs revealed that many sRNAs started with uridine (U) at their 5’-ends (Fig 3B). We further screened the clean data against rRNAs, snoRNAs, snRNAs and tRNAs in the NCBI Genebank database and Rfam database (Fig 3C; S6 Table) resulting in 7,856,512 (CK) and 8,275,444 (Cd) reads remaining for further analyses. Among the remaining sequences, 1,836,897 sequences of CK library and 1,813,553 sequences of Cd library were similar to known miRNAs from other plant species that had previously been deposited in miRBase 21.

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