The evolutionary history of small RNAs in Solanaceae.

Autor:	Baldrich P; Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA., Bélanger S; Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA., Kong S; School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA., Pokhrel S; Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA.; School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA.; Division of Plant Science and Technology, University of Missouri, Columbia, Missouri 65211, USA., Tamim S; Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware 19711, USA., Teng C; Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA., Schiebout C; Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA., Gurazada SGR; Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware 19711, USA.; Corteva Agriscience, Wilmington, Delaware 19805, USA., Gupta P; Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA.; Institute for Data Science & Informatics, University of Missouri, Columbia, Missouri 65211, USA., Patel P; Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware 19711, USA., Razifard H; School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA., Nakano M; Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA., Dusia A; Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware 19711, USA., Meyers BC; Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA.; Division of Plant Science and Technology, University of Missouri, Columbia, Missouri 65211, USA., Frank MH; Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA.
Jazyk:	angličtina
Zdroj:	Plant physiology [Plant Physiol] 2022 Jun 01; Vol. 189 (2), pp. 644-665.
DOI:	10.1093/plphys/kiac089
Abstrakt:	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. (© The Author(s) 2022. Published by Oxford University Press on behalf of American Society of Plant Biologists.)
Databáze:	MEDLINE
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