High-resolution identification and abundance profiling of cassava (Manihot esculenta Crantz) microRNAs
Date
2016-01-28
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Publisher
BioMed Central
Abstract
BACKGROUND: Small RNAs (sRNAs) are endogenous sRNAs that play regulatory roles in plant growth, development, and
biotic and abiotic stress responses. In plants, one subset of sRNAs, microRNAs (miRNAs) exhibit tissue-differential
expression and regulate gene expression mainly through direct cleavage of mRNA or indirectly via production of
secondary phased siRNAs (phasiRNAs) that silence cognate target transcripts in trans.
RESULTS: Here, we have identified cassava (Manihot esculenta Crantz) miRNAs using high resolution sequencing of sRNA
libraries from leaf, stem, callus, male and female flower tissues. To analyze the data, we built a cassava genome database
and, via sequence analysis and secondary structure prediction, 38 miRNAs not previously reported in cassava were
identified. These new cassava miRNAs included two miRNAs not previously been reported in any plant species. The
miRNAs exhibited tissue-differential accumulation as confirmed by quantitative RT-PCR and Northern blot analysis, largely
reflecting levels observed in sequencing data. Some of the miRNAs identified were predicted to trigger production of
secondary phased siRNAs (phasiRNAs) from 80 PHAS loci.
CONCLUSIONS: Cassava is a woody perennial shrub, grown principally for its starch-rich storage roots, which are rich in
calories. In this study, new miRNAs were identified and their expression was validated using qRT-PCR of RNA from five
different tissues. The data obtained expand the list of annotated miRNAs and provide additional new resources for
cassava improvement research.
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Citation
Khatabi, Behnam, et al. "High-resolution identification and abundance profiling of cassava (Manihot esculenta Crantz) microRNAs." BMC genomics 17.1 (2016): 1.