Abstract
BackgroundSmall 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.ResultsHere, 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.ConclusionsCassava 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2391-1) contains supplementary material, which is available to authorized users.
Highlights
Small RNAs are endogenous sRNAs that play regulatory roles in plant growth, development, and biotic and abiotic stress responses
It is important to note that 69 % of the cassava genome has been shotgun sequenced [19], consistent with the proportion of cassava sRNAs matching the genome in this study
In this work, using high-resolution sequencing and analyses of sRNA libraries from leaf, stem, callus, male and female flower tissues, we have identified 38 new cassava miRNAs, including two miRNAs not previously reported in any plant species
Summary
Small RNAs (sRNAs) are endogenous sRNAs that play regulatory roles in plant growth, development, and biotic and abiotic stress responses. Plant sRNAs are processed from noncoding transcripts into the size range of 21 to 24 nucleotides These sRNAs play crucial roles in a variety of biological regulation processes, such as development, plant defense, and epigenetic modifications. Based on their origin and biogenesis, sRNAs are categorized into several major classes, predominantly including microRNAs (miRNAs), heterochromatic small interfering RNAs (hc-siRNAs), and secondary siRNAs such as trans-acting siRNAs (tasiRNAs) that are phased [1, 2]. The regulatory roles played by miRNAs in growth, development, organogenesis, and responses to biotic and abiotic stresses, have provided us new opportunities in crop improvement of especially crops with major production constraints as cassava (Manihot esculenta Crantz). Many cassava genotypes are recalcitrant to transformation and it has been suggested that regulatory molecules and associated gene networks during somatic embryogenesis may provide a long-term understanding of embryogenic competence and regenerability necessary for crop improvement via biotechnology [14]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
