Identification of grapevine microRNAs and their targets using high throughput sequencing and degradome analysis

Abstract

In plants, microRNAs (miRNAs) comprise one of three classes of small RNAs regulating gene expression at the post-transcriptional level. Many plant miRNAs are conserved, and play a role in development, abiotic stress responses or pathogen responses. However, some miRNAs have only been found in certain species. Here, we use deep-sequencing, computational and molecular methods to identify, profile, and describe conserved and non-conserved miRNAs in four grapevine (Vitis vinifera) tissues. A total of 24 conserved miRNA families were identified in all four tissues, and 26 known but non-conserved miRNAs were also found. In addition to known miRNAs, we also found 21 new grapevine-specific miRNAs together with their star strands. We have also shown that almost all of them originated from single genes. Furthermore, 21 other plausible miRNA candidates have been described. We have found that many known and new miRNAs showed tissue-specific expression. Finally, 112 target mRNAs of known and 44 target mRNAs of new grapevine-specific miRNAs were identified by genomic-scale high-throughput sequencing of miRNA cleaved mRNAs.

Novel and Recently Evolved MicroRNA Clusters Regulate Expansive F-BOX Gene Networks through Phased Small Interfering RNAs in Wild Diploid Strawberry

“…In addition, unlike conserved miRNAs that often targeted multiple members of a gene family, most novel miRNAs targeted genes from different gene families. Similar observations were made in other plant species, reflecting the properties of young miRNAs (Pantaleo et al, 2010;Xia et al, 2012;Zhu et al, 2012).…”

miRNA profiling in leaf and cork tissues of Quercus suber reveals novel miRNAs and tissue-specific expression patterns

“…The tissue-dependent variation in the pools of 24 and 21-nt classes has also been observed in other plant species (Pantaleo et al 2010) and, in a few cases, striking variation has been detected (Slotkin et al 2009) reflecting the sRNA biogenesis pathways operating in such tissues. The determined level of non-redundancy further showed that in both cork oak tissue types the 21-nt class is less diverse than the 24-nt class, which is in agreement with previous reports in other species Martínez et al 2011;Pantaleo et al 2010;Rajagopalan et al 2006). …”

“…In fact, previous reports refer that the 24-nt sRNAs is the predominant size class, for instance in Arabidopsis thaliana, Nicothiana benthamiana, Solano lycopersicum, Oriza sativa and Olea europea (Morin et al 2008;Pantaleo et al 2010;Donaire et al 2011;Kasschau et al 2007), while the 21-nt class is more abundant in species such as Eschscholzia californica, Hordeum vulgare, Vitis vinifera, Pinus contorta and Panax gynseng (Pantaleo et al 2010;Morin et al 2008;Schreiber et al 2011;Barakat et al 2007). The tissue-dependent variation in the pools of 24 and 21-nt classes has also been observed in other plant species (Pantaleo et al 2010) and, in a few cases, striking variation has been detected (Slotkin et al 2009) reflecting the sRNA biogenesis pathways operating in such tissues. The determined level of non-redundancy further showed that in both cork oak tissue types the 21-nt class is less diverse than the 24-nt class, which is in agreement with previous reports in other species Martínez et al 2011;Pantaleo et al 2010;Rajagopalan et al 2006).…”

Homology-independent discovery of replicating pathogenic circular RNAs by deep sequencing and a new computational algorithm

“…GSM465746) and from a grapevine tree cultivar Pinot noir ENTAV115 (accession no. GSE18405) was downloaded from the Gene Expression Omnibus database of the NCBI (23,40). The reference sequences of PLMVd (accession no.…”