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The miRNAome of globe artichoke: conserved and novel micro RNAs and target analysis.

De Paola D, Cattonaro F, Pignone D, Sonnante G - BMC Genomics (2012)

Bottom Line: In addition to conserved miRNAs, found in a wide range of plant species a number of novel species-specific miRNAs, displaying lower levels of expression can be found.New target genes were identified.We suggest that the generation of secondary short-interfering RNAs from miR393 target can be a general rule in the plant kingdom.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Plant Genetics (IGV), National Research Council (CNR), Via Amendola 165/A, 70126 Bari - Italy.

ABSTRACT

Background: Plant microRNAs (miRNAs) are involved in post-transcriptional regulatory mechanisms of several processes, including the response to biotic and abiotic stress, often contributing to the adaptive response of the plant to adverse conditions. In addition to conserved miRNAs, found in a wide range of plant species a number of novel species-specific miRNAs, displaying lower levels of expression can be found. Due to low abundance, non conserved miRNAs are difficult to identify and isolate using conventional approaches. Conversely, deep-sequencing of small RNA (sRNA) libraries can detect even poorly expressed miRNAs.No miRNAs from globe artichoke have been described to date. We analyzed the miRNAome from artichoke by deep sequencing four sRNA libraries obtained from NaCl stressed and control leaves and roots.

Results: Conserved and novel miRNAs were discovered using accepted criteria. The expression level of selected miRNAs was monitored by quantitative real-time PCR. Targets were predicted and validated for their cleavage site. A total of 122 artichoke miRNAs were identified, 98 (25 families) of which were conserved with other plant species, and 24 were novel. Some miRNAs were differentially expressed according to tissue or condition, magnitude of variation after salt stress being more pronounced in roots. Target function was predicted by comparison to Arabidopsis proteins; the 43 targets (23 for novel miRNAs) identified included transcription factors and other genes, most of which involved in the response to various stresses. An unusual cleaved transcript was detected for miR393 target, transport inhibitor response 1.

Conclusions: The miRNAome from artichoke, including novel miRNAs, was unveiled, providing useful information on the expression in different organs and conditions. New target genes were identified. We suggest that the generation of secondary short-interfering RNAs from miR393 target can be a general rule in the plant kingdom.

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Related in: MedlinePlus

Small RNA read size. Distribution and abundance of small RNA unique sequences in leaves (a) and roots (b). Light bars indicate control plants; dark bars refer to NaCl stressed plants.
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Figure 1: Small RNA read size. Distribution and abundance of small RNA unique sequences in leaves (a) and roots (b). Light bars indicate control plants; dark bars refer to NaCl stressed plants.

Mentions: To discover the artichoke miRNAome and the possible involvement of miRNAs in the response to saline stress, four sRNA libraries were generated from leaves and roots of young artichoke plants subjected or not to NaCl treatment. Deep sequencing yielded a total of almost 28 million reads (Table 1). After removing low quality reads, adapter sequences, and sequences shorter than 16 or longer than 30 nucleotides, reads were about 6 million (corresponding to 2,447,091 unique sequences) for control plant (CP) leaves, almost 7 million (2,151,783 unique sequences) for stressed plant (SP) leaves, almost 3 million (1,194,486 unique sequences) for CP roots, and about 3 million (734,396 unique sequences) for SP roots (Table 1). The length distribution of unique reads revealed a non homogeneous pattern, the majority of sRNAs in all libraries (on average 79%) being 20-25 nucleotide in length with 24-nt long sRNAs as the main peak (Figure 1). Reads from all artichoke libraries were annotated according to small non-coding RNAs contained in Rfam (Additional File 1). As a result, 16.16%, 19.88%, 20.32%, and 44.72% reads matching known sRNAs were identified in CP leaves, SP leaves, CP roots and SP roots, respectively. The most abundant class was rRNA, in agreement with the method used to obtain sRNA fraction for library preparation. tRNAs ranged from a minimum of 2.34% in CP roots to a maximum of 5.55% in SP roots; snRNA and snoRNA seemed to be equally distributed in the four sRNA libraries.


The miRNAome of globe artichoke: conserved and novel micro RNAs and target analysis.

De Paola D, Cattonaro F, Pignone D, Sonnante G - BMC Genomics (2012)

Small RNA read size. Distribution and abundance of small RNA unique sequences in leaves (a) and roots (b). Light bars indicate control plants; dark bars refer to NaCl stressed plants.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3285030&req=5

Figure 1: Small RNA read size. Distribution and abundance of small RNA unique sequences in leaves (a) and roots (b). Light bars indicate control plants; dark bars refer to NaCl stressed plants.
Mentions: To discover the artichoke miRNAome and the possible involvement of miRNAs in the response to saline stress, four sRNA libraries were generated from leaves and roots of young artichoke plants subjected or not to NaCl treatment. Deep sequencing yielded a total of almost 28 million reads (Table 1). After removing low quality reads, adapter sequences, and sequences shorter than 16 or longer than 30 nucleotides, reads were about 6 million (corresponding to 2,447,091 unique sequences) for control plant (CP) leaves, almost 7 million (2,151,783 unique sequences) for stressed plant (SP) leaves, almost 3 million (1,194,486 unique sequences) for CP roots, and about 3 million (734,396 unique sequences) for SP roots (Table 1). The length distribution of unique reads revealed a non homogeneous pattern, the majority of sRNAs in all libraries (on average 79%) being 20-25 nucleotide in length with 24-nt long sRNAs as the main peak (Figure 1). Reads from all artichoke libraries were annotated according to small non-coding RNAs contained in Rfam (Additional File 1). As a result, 16.16%, 19.88%, 20.32%, and 44.72% reads matching known sRNAs were identified in CP leaves, SP leaves, CP roots and SP roots, respectively. The most abundant class was rRNA, in agreement with the method used to obtain sRNA fraction for library preparation. tRNAs ranged from a minimum of 2.34% in CP roots to a maximum of 5.55% in SP roots; snRNA and snoRNA seemed to be equally distributed in the four sRNA libraries.

Bottom Line: In addition to conserved miRNAs, found in a wide range of plant species a number of novel species-specific miRNAs, displaying lower levels of expression can be found.New target genes were identified.We suggest that the generation of secondary short-interfering RNAs from miR393 target can be a general rule in the plant kingdom.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Plant Genetics (IGV), National Research Council (CNR), Via Amendola 165/A, 70126 Bari - Italy.

ABSTRACT

Background: Plant microRNAs (miRNAs) are involved in post-transcriptional regulatory mechanisms of several processes, including the response to biotic and abiotic stress, often contributing to the adaptive response of the plant to adverse conditions. In addition to conserved miRNAs, found in a wide range of plant species a number of novel species-specific miRNAs, displaying lower levels of expression can be found. Due to low abundance, non conserved miRNAs are difficult to identify and isolate using conventional approaches. Conversely, deep-sequencing of small RNA (sRNA) libraries can detect even poorly expressed miRNAs.No miRNAs from globe artichoke have been described to date. We analyzed the miRNAome from artichoke by deep sequencing four sRNA libraries obtained from NaCl stressed and control leaves and roots.

Results: Conserved and novel miRNAs were discovered using accepted criteria. The expression level of selected miRNAs was monitored by quantitative real-time PCR. Targets were predicted and validated for their cleavage site. A total of 122 artichoke miRNAs were identified, 98 (25 families) of which were conserved with other plant species, and 24 were novel. Some miRNAs were differentially expressed according to tissue or condition, magnitude of variation after salt stress being more pronounced in roots. Target function was predicted by comparison to Arabidopsis proteins; the 43 targets (23 for novel miRNAs) identified included transcription factors and other genes, most of which involved in the response to various stresses. An unusual cleaved transcript was detected for miR393 target, transport inhibitor response 1.

Conclusions: The miRNAome from artichoke, including novel miRNAs, was unveiled, providing useful information on the expression in different organs and conditions. New target genes were identified. We suggest that the generation of secondary short-interfering RNAs from miR393 target can be a general rule in the plant kingdom.

Show MeSH
Related in: MedlinePlus