ArticlePlant physiology2022
The evolutionary history of small RNAs in Solanaceae.
Article in Plant physiology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers, 1 of them a synthesis that pooled it.
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Who cites it
11 citing papers in PubMed, 1 synthesis or guideline pooled it, 14 citations in OpenAlex.
- The role of microRNAs in responses to drought and heat stress in peanut (Arachis hypogaea).The plant genome · 2023Pooled it
- Transposon expansion is associated with reorganization of small RNA and DNA methylation landscapes in the morphologically minimal angiosperm Wolffia brasiliensis.The Plant journal : for cell and molecular biology · 2026Article
- Article
- Sulfate Deficiency-Responsive MicroRNAs in Tomato Uncover an Expanded and Functionally Integrated Regulatory Network.International journal of molecular sciences · 2025Article
- MicroRNA gatekeepers: Orchestrating rhizospheric dynamics.Journal of integrative plant biology · 2025Review
- Identification of Tomato microRNAs in Late Response toInternational journal of molecular sciences · 2024Article
- Phylogenetic analyses of seven protein families refine the evolution of small RNA pathways in green plants.Plant physiology · 2023Article
- Small RNAs >26 nt in length associate with AGO1 and are upregulated by nutrient deprivation in the alga Chlamydomonas.The Plant cell · 2023Article
- An atlas of small RNAs from potato.Plant direct · 2022Article
- Parasitic plant small RNA analyses unveil parasite-specific signatures of microRNA retention, loss, and gain.Plant physiology · 2022Article
- Heat-responsive microRNAs and phased small interfering RNAs in reproductive development of flax.Plant direct · 2022Article
Corrections and comments
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Authors and funding
15 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The Solanaceae or "nightshade" family is an economically important group with remarkable diversity. To gain a better understanding of how the unique biology of the Solanaceae relates to the family's small RNA (sRNA) genomic landscape, we downloaded over 255 publicly available sRNA data sets that comprise over 2.6 billion reads of sequence data. We applied a suite of computational tools to predict and annotate two major sRNA classes: (1) microRNAs (miRNAs), typically 20- to 22-nucleotide (nt) RNAs generated from a hairpin precursor and functioning in gene silencing and (2) short interfering RNAs (siRNAs), including 24-nt heterochromatic siRNAs typically functioning to repress repetitive regions of the genome via RNA-directed DNA methylation, as well as secondary phased siRNAs and trans-acting siRNAs generated via miRNA-directed cleavage of a polymerase II-derived RNA precursor. Our analyses described thousands of sRNA loci, including poorly understood clusters of 22-nt siRNAs that accumulate during viral infection. The birth, death, expansion, and contraction of these sRNA loci are dynamic evolutionary processes that characterize the Solanaceae family. These analyses indicate that individuals within the same genus share similar sRNA landscapes, whereas comparisons between distinct genera within the Solanaceae reveal relatively few commonalities.
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Registered trials
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