Dynamically expressed small RNAs, substantially driven by genomic structural variants, contribute to transcriptomic changes during tomato domestication.

Λεπτομέρειες βιβλιογραφικής εγγραφής
Τίτλος:	Dynamically expressed small RNAs, substantially driven by genomic structural variants, contribute to transcriptomic changes during tomato domestication.
Συγγραφείς:	Qing Y; Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China.; Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China., Zheng Y; Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China.; Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China.; Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA., Mlotshwa S; Department of Molecular Genetics, Ohio State University, Columbus, OH, 43210, USA., Smith HN; Department of Biological Sciences, Mississippi State University, Starkville, MS, 39759, USA., Wang X; Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA., Zhai X; Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China.; Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China., van der Knaap E; Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA.; Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA.; Department of Horticulture, University of Georgia, Athens, GA, 30602, USA., Wang Y; Department of Molecular Genetics, Ohio State University, Columbus, OH, 43210, USA.; Department of Biological Sciences, Mississippi State University, Starkville, MS, 39759, USA., Fei Z; Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA.; USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA.
Πηγή:	The Plant journal : for cell and molecular biology [Plant J] 2022 Jun; Vol. 110 (6), pp. 1536-1550. Date of Electronic Publication: 2022 May 24.
Τύπος έκδοσης:	Journal Article; Research Support, U.S. Gov't, Non-P.H.S.
Γλώσσα:	English
Στοιχεία περιοδικού:	Publisher: Blackwell Scientific Publishers and BIOS Scientific Publishers in association with the Society for Experimental Biology Country of Publication: England NLM ID: 9207397 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1365-313X (Electronic) Linking ISSN: 09607412 NLM ISO Abbreviation: Plant J Subsets: MEDLINE
Imprint Name(s):	Original Publication: Oxford : Blackwell Scientific Publishers and BIOS Scientific Publishers in association with the Society for Experimental Biology, c1991-
Ιατρικοί όροι (MeSH):	Solanum lycopersicum/genetics , Solanum lycopersicum/metabolism , MicroRNAs/genetics , MicroRNAs/metabolism, Gene Expression Regulation, Plant/genetics ; RNA, Plant/genetics ; RNA, Small Interfering/genetics ; Transcriptome/genetics ; Domestication ; Genomic Structural Variation ; Nucleotides
Περίληψη:	Tomato has undergone extensive selections during domestication. Recent progress has shown that genomic structural variants (SVs) have contributed to gene expression dynamics during tomato domestication, resulting in changes of important traits. Here, we performed comprehensive analyses of small RNAs (sRNAs) from nine representative tomato accessions. We demonstrate that SVs substantially contribute to the dynamic expression of the three major classes of plant sRNAs: microRNAs (miRNAs), phased secondary short interfering RNAs (phasiRNAs), and 24-nucleotide heterochromatic siRNAs (hc-siRNAs). Changes in the abundance of phasiRNAs and 24-nucleotide hc-siRNAs likely contribute to the alteration of mRNA gene expression in cis during tomato domestication, particularly for genes associated with biotic and abiotic stress tolerance. We also observe that miRNA expression dynamics are associated with imprecise processing, alternative miRNA-miRNA* selections, and SVs. SVs mainly affect the expression of less-conserved miRNAs that do not have established regulatory functions or low abundant members in highly expressed miRNA families. Our data highlight different selection pressures on miRNAs compared to phasiRNAs and 24-nucleotide hc-siRNAs. Our findings provide insights into plant sRNA evolution as well as SV-based gene regulation during crop domestication. Furthermore, our dataset provides a rich resource for mining the sRNA regulatory network in tomato. (© 2022 Society for Experimental Biology and John Wiley & Sons Ltd.)
Σχόλια:	Comment in: Plant J. 2022 Jun;110(6):1534-1535. doi: 10.1111/tpj.15857.. (PMID: 35751494)
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Contributed Indexing:	Keywords: Solanum lycopersicum; Solanum pimpinellifolium; 24-nucleotide hc-siRNA; domestication; genomic structural variant; miRNA; phasiRNA; tomato
Substance Nomenclature:	0 (MicroRNAs) 0 (Nucleotides) 0 (RNA, Plant) 0 (RNA, Small Interfering)
Entry Date(s):	Date Created: 20220506 Date Completed: 20220628 Latest Revision: 20221207
Update Code:	20260130
DOI:	10.1111/tpj.15798
PMID:	35514123
Βάση Δεδομένων:	MEDLINE

Περιγραφή
ISSN:	1365-313X
DOI:	10.1111/tpj.15798