The evolutionary history of small RNAs in Solanaceae

Patricia Baldrich, Sébastien Bélanger, Shuyao Kong, Suresh Pokhrel, Saleh Tamim, Chong Teng, Courtney Schiebout, Sai Guna Ranjan Gurazada, Pallavi Gupta, Parth Patel, Hamid Razifard, Mayumi Nakano, Ayush Dusia, Blake C. Meyers, Margaret H. Frank

Research output: Contribution to journalArticlepeer-review

9 Scopus citations


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.

Original languageEnglish
Pages (from-to)644-665
Number of pages22
JournalPlant Physiology
Issue number2
StatePublished - Jun 2022


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