Sample sequencing of vascular plants demonstrates widespread conservation and divergence of microRNAs

Abstract

Small RNAs are pivotal regulators of gene expression that guide transcriptional and posttranscriptional silencing mechanisms in eukaryotes, including plants. Here we report a comprehensive atlas of sRNA and miRNA from 3 species of algae and 31 representative species across vascular plants, including non-model plants. We sequence and quantify sRNAs from 99 different tissues or treatments across species, resulting in a data set of over 132 million distinct sequences. Using miRBase mature sequences as a reference, we identify the miRNA sequences present in these libraries. We apply diverse profiling methods to examine critical sRNA and miRNA features, such as size distribution, tissue-specific regulation and sequence conservation between species, as well as to predict putative new miRNA sequences. We also develop database resources, computational analysis tools and a dedicated website, http://smallrna.udel.edu/. This study provides new insights on plant sRNAs and miRNAs, and a foundation for future studies.

The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea

“…In parallel, novel potential DCL1/ AGO1-dependent miRNAs were enriched by selecting 5′-U 20-22 nt small RNAs from three different sequenced libraries from Z. marina described in ref. 12. A subset of these small RNAs with abundance ≥10 TPM (transcripts per million) was retained and aligned to the genome with no mismatches.…”

“…A novel variant of miR528 (not present in Spirodela) was found to be the only member of this miRNA family, and demonstrates that this conserved miRNA is the only one ancestral to the entire monocot lineage. Most likely, Z. marina did not take part in the subsequent birth of miRNAs that are common to several other monocots 12 ; nor did it experience or retain traces of prominent miRNA duplications.…”

The pivotal role of small non-coding RNAs in the regulation of seed development

“…Recently, a comprehensive analysis of the sRNA data from different organs, tissues, developmental stages or treatments in 3 green algae and 31 vascular plant species revealed that the size distribution of the sRNA sequences expressed by angiosperms typically shows two peaks, at 21-and 24-nt, whereas non-angiosperm species may show different patterns (Chávez-Montes et al 2014). However, within each plant species the sRNA profile varies with the stage of the plant life cycle and the tissues or cells being studied.…”

“…Reports on sRNA studies in gymnosperm seeds have been lacking so far, but previous work on conifer sRNAs have reached different and contradicting conclusions regarding the presence of 24-nt sRNAs, typically associated with hetsiRNAs, in the sRNA transcriptome of the conifers clade Morin et al 2008;Lee et al 2011;Chávez-Montes et al 2014;Wan et al 2012;Zhang et al 2012bZhang et al , 2013bNystedt et al 2013;Niu et al 2015). In somatic embryo-derived material from the conifer Japanese larch (Larix leptolepis) the presence of significant amounts of 24-nt sRNAs has been reported (Zhang et al 2012b(Zhang et al , 2013b, but it would be interesting to check for the presence of these sRNAs in conifer seeds.…”

Asymmetric bulges and mismatches determine 20-nt microRNA formation in plants

“…25,26 Arabidopsis thaliana has 4 DCL proteins which have some unique and redundant functions in small RNA pathways. 27 The majority of plant miRNAs are 21-nt long and the biogenesis of plant miRNAs depends on DCL1, [28][29][30][31] implying that plant DCL1 functions as a 21-nt molecular ruler. In addition to the properties of DCR or DCL proteins, miRNA length is also affected by DCR-binding proteins and pre-miRNA structure.…”