Genome-Wide Identification and Characterization of miRNAs and Natural Antisense Transcripts Show the Complexity of Gene Regulatory Networks for Secondary Metabolism in Aristolochia contorta .

Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067 (Electronic) Linking ISSN: 14220067 NLM ISO Abbreviation: Int J Mol Sci Subsets: MEDLINE

Original Publication: Basel, Switzerland : MDPI, [2000-

MicroRNAs*/genetics ; MicroRNAs*/metabolism ; Aristolochia*/genetics ; Gene Regulatory Networks* ; Gene Expression Regulation, Plant* ; Secondary Metabolism*/genetics; RNA, Antisense/genetics ; Genome, Plant ; RNA, Plant/genetics

Aristolochia contorta Bunge is an academically and medicinally important plant species. It belongs to the magnoliids, with an uncertain phylogenetic position, and is one of the few plant species lacking a whole-genome duplication (WGD) event after the angiosperm-wide WGD. A. contorta has been an important traditional Chinese medicine material. Since it contains aristolochic acids (AAs), chemical compounds with nephrotoxity and carcinogenicity, the utilization of this plant has attracted widespread attention. Great efforts are being made to increase its bioactive compounds and reduce or completely remove toxic compounds. MicroRNAs (miRNAs) and natural antisense transcripts (NATs) are two classes of regulators potentially involved in metabolism regulation. Here, we report the identification and characterization of 223 miRNAs and 363 miRNA targets. The identified miRNAs include 51 known miRNAs belonging to 20 families and 172 novel miRNAs belonging to 107 families. A negative correlation between the expression of miRNAs and their targets was observed. In addition, we identified 441 A. contorta NATs and 560 NAT-sense transcript (ST) pairs, of which 12 NATs were targets of 13 miRNAs, forming 18 miRNA-NAT-ST modules. Various miRNAs and NATs potentially regulated secondary metabolism through the modes of miRNA-target gene-enzyme genes, NAT-STs, and NAT-miRNA-target gene-enzyme genes, suggesting the complexity of gene regulatory networks in A. contorta . The results lay a solid foundation for further manipulating the production of its bioactive and toxic compounds.

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32370275 National Natural Science Foundation of China; 2021-I2M-1-022 The CAMS Innovation Fund for Medical Sciences (CIFMS)

Keywords: Aristolochia contorta; aristolochic acid; benzylisoquinoline alkaloid; long non-coding RNA; microRNA; natural antisense transcript

0 (MicroRNAs)
0 (RNA, Antisense)
0 (RNA, Plant)

Date Created: 20240619 Date Completed: 20240619 Latest Revision: 20240620

20240620

PMC11172604

10.3390/ijms25116043

38892231