Identification of novel and conserved microRNAs in Coffea canephora and Coffea arabica

Loss-Morais, Guilherme; Ferreira, Daniela C.R.; Margis, Rogério; Alves‐Ferreira, Márcio; Corrêa, Régis L.

doi:10.1590/s1415-47572014005000020

Cited by 15 publications

(22 citation statements)

References 57 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In addition to that, recently, deepsequencing libraries have been generated using both genomic [11] and transcriptomic [29] data of C. canephora. In both cases, miRNA genes belonging to 33 families were found.…”

Section: Characteristics Of Potential Coffee Mirnas Identifiedmentioning

confidence: 99%

See 1 more Smart Citation

New Insights on Coffea miRNAs: Features and Evolutionary Conservation

Chaves

Fernandes-Brum

Silva³

et al. 2015

Appl Biochem Biotechnol

View full text Add to dashboard Cite

Small RNAs influence the gene expression at the post-transcriptional level by guiding messenger RNA (mRNA) cleavage, translational repression, and chromatin modifications. In addition to model plants, the microRNAs (miRNAs) have been identified in different crop species. In this work, we developed a specific pipeline to search for coffee miRNA homologs on expressed sequence tags (ESTs) and genome survey sequences (GSS) databases. As a result, 36 microRNAs were identified and a total of 616 and 362 potential targets for Coffea arabica and Coffea canephora, respectively. The evolutionary analyses of these molecules were performed by comparing the primary and secondary structures of precursors and mature miRNAs with their orthologs. Moreover, using a stem-loop RT-PCR assay, we evaluated the accumulation of mature miRNAs in genomes with different ploidy levels, detecting an increase in the miRNAs accumulation according to the ploidy raising. Finally, a 5' RACE (Rapid Amplification of cDNA Ends) assay was performed to verify the regulation of auxin responsive factor 8 (ARF8) by MIR167 in coffee plants. The great variety of target genes indicates the functional plasticity of these molecules and reinforces the importance of understanding the RNAi-dependent regulatory mechanisms. Our results expand the study of miRNAs and their target genes in this crop, providing new challenges to understand the biology of these species.

show abstract

Section: Characteristics Of Potential Coffee Mirnas Identifiedmentioning

confidence: 99%

“…Computer-based strategies have described 16 miRNA families in C. arabica [1,38]. In addition, deep-sequencing libraries have been generated using both genomic [11] and transcriptomic [29] data of C. canephora. In both cases, miRNA genes belonging to 33 families were described for that specie.…”

mentioning

confidence: 99%

New Insights on Coffea miRNAs: Features and Evolutionary Conservation

Chaves

Fernandes-Brum

Silva³

et al. 2015

Appl Biochem Biotechnol

View full text Add to dashboard Cite

show abstract

“…In Coffea arabica and Coffea canephora , the main economically important species of coffee, one of the most important crops in the world and the second most traded global commodity, MIR families have been identified based on Expressed Sequence Tags (EST), Genome Survey Sequences (GSS), and other transcript-based analyses [35–38]. …”

Section: Introductionmentioning

confidence: 99%

A genome-wide analysis of the RNA-guided silencing pathway in coffee reveals insights into its regulatory mechanisms

et al. 2017

View full text Add to dashboard Cite

microRNAs (miRNAs) are derived from self-complementary hairpin structures, while small-interfering RNAs (siRNAs) are derived from double-stranded RNA (dsRNA) or hairpin precursors. The core mechanism of sRNA production involves DICER-like (DCL) in processing the smallRNAs (sRNAs) and ARGONAUTE (AGO) as effectors of silencing, and siRNA biogenesis also involves action of RNA-Dependent RNA Polymerase (RDR), Pol IV and Pol V in biogenesis. Several other proteins interact with the core proteins to guide sRNA biogenesis, action, and turnover. We aimed to unravel the components and functions of the RNA-guided silencing pathway in a non-model plant species of worldwide economic relevance. The sRNA-guided silencing complex members have been identified in the Coffea canephora genome, and they have been characterized at the structural, functional, and evolutionary levels by computational analyses. Eleven AGO proteins, nine DCL proteins (which include a DCL1-like protein that was not previously annotated), and eight RDR proteins were identified. Another 48 proteins implicated in smallRNA (sRNA) pathways were also identified. Furthermore, we identified 235 miRNA precursors and 317 mature miRNAs from 113 MIR families, and we characterized ccp-MIR156, ccp-MIR172, and ccp-MIR390. Target prediction and gene ontology analyses of 2239 putative targets showed that significant pathways in coffee are targeted by miRNAs. We provide evidence of the expansion of the loci related to sRNA pathways, insights into the activities of these proteins by domain and catalytic site analyses, and gene expression analysis. The number of MIR loci and their targeted pathways highlight the importance of miRNAs in coffee. We identified several roles of sRNAs in C. canephora, which offers substantial insight into better understanding the transcriptional and post-transcriptional regulation of this major crop.

show abstract

“…It also has medicinal properties because of secondary metabolites like polyphenols, caffeine, theobromine, and chlorogenic acids (Ferrazzano, 2009). To our knowledge, although progress has been made on the genus Coffea, there is little knowledge about miRNAs in Coffea (Rebijith et al, 2013;Akter et al, 2014;Loss-Morais et al, 2014). In this study, we employed a well-defined comparative genomebased homolog search to identify Coffea miRNAs.…”

mentioning

confidence: 99%

Bioinformatics profiling and characterization of potentialmicroRNAs and their targets in the genus Coffea

Bibi¹,

Barozai²,

Din³

2017

Turk J Agric For

View full text Add to dashboard Cite

IntroductionMicroRNAs (miRNAs) are an extensive class of noncoding small endogenous RNAs of 18 to 26 nt in length that are derived from self-complementary fold-back structures of longer precursor sequences (pre-miRNAs) and are generated by Dicer-like 1 (DCL1) in plants (Bartel, 2004). Mature miRNAs inhibit gene expression at posttranscriptional levels by either targeting mRNAs for degradation or inhibiting protein translation. Both processes are accomplished by the complementary base pairing of miRNAs to their target mRNA sequences (Ambros, 2004). In plants, for a majority of cases, miRNAs interact with their targets through perfect or near-perfect base pairing and lead to target mRNA degradation (Jones-Rhoades et al., 2006). Increasing evidence has revealed that miRNAs play an important role in a wide range of development processes in plants, including cell proliferation, stress response, metabolism, inflammation, and signal transduction (Ambros, 2004;Jones-Rhoades et al., 2006;Zhang et al., 2007a;Ali et al., 2016) and crosskingdom gene regulation (Barozai and Din, 2017). To date, more than 28,645 miRNAs have been identified from 223 species of plants and animals and deposited in the publicly available database miRBase (Release 21) (Griffiths-Jones et al., 2008). The majority of plant miRNAs have been found in species with fully sequenced genomes including 713 from Oryza sativa, 401 from Populus trichocarpa, 384 from Arabidopsis thaliana, 343 from Solanum tuberosum, 321 from Zea mays, and 241 from Sorghum bicolor (Griffiths-Jones et al., 2008). miRNA-related research is continuously growing and miRNAs, along with their functions, are being identified and elucidated using a wide variety of computational tools and experimental methods including direct cloning, deep sequencing, and other approaches. Comparison of miRNAs across multiple plant species has demonstrated that some miRNAs are highly evolutionary conserved from species to species, such as from mosses to higher flowering eudicots in the plant kingdom (Floyd and Bowman, 2004;Zhang et al., 2006aZhang et al., , 2006b. Conservation of miRNA sequences has provided a powerful strategy for identifying miRNAs in other species. Currently, comparative genome-based homolog searches have been used to identify conserved miRNAs in many plant species, including cotton (

show abstract

Identification of novel and conserved microRNAs in Coffea canephora and Coffea arabica

Cited by 15 publications

References 57 publications

New Insights on Coffea miRNAs: Features and Evolutionary Conservation

New Insights on Coffea miRNAs: Features and Evolutionary Conservation

A genome-wide analysis of the RNA-guided silencing pathway in coffee reveals insights into its regulatory mechanisms

Bioinformatics profiling and characterization of potentialmicroRNAs and their targets in the genus Coffea

Contact Info

Product

Resources

About