Predictive role of noncoding RNAs in growth-development and stress mechanisms of Amaranthus hypochondriacus

The characterization of gene regulatory networks by noncoding RNAs (ncRNAs) may help understand the growth development and stress tolerance mechanisms of Amaranthus. The study aimed to identify (i) ncRNAs: long noncoding RNAs (lncRNAs), micro RNAs (miRNAs) and circular RNAs (circRNAs) on Amaranthus genome, (ii) ncRNA regulated genes and their role in plant processes, (iii) noncoding RNA bearing Simple Sequence Repeat (SSR) markers, and (iv) miRNA-lncRNA-mRNA triplet interactions, and study their involvement in growth development and stress tolerance mechanisms. We identified computationally a total of 2690 lncRNAs, 836 miRNAs, 31 circular RNAs and 3506 SSRs on genome and found SSRs on pre-miRNAs and lncRNAs. Majority of predicted lncRNAs were found specific to Amaranthus. The targeted genes of the identified ncRNAs are observed to be involved in growth-development and stress mechanisms. The lncRNA "Ahy_lnc_0021" acted as endogenous target mimic (eTM) to inhibit miRNA "ahy-mir8717" that targets the gene SHM6, largely involved in folate metabolism as well as in the synthesis of amino acids, vitamin B5 and nucleic acids. The likely involvement of lncRNAs and their targeted genes in growth development, phytophenols synthesis and stress tolerance mechanisms were validated. The key roles of lncRNA-miRNA-mRNA associations were also validated and found that the lncRNA "Ahy_lnc_2243" enhanced the expression of BRD-proteins by acting as RNA decoy for miRNA "ahy-mir5298". A database on findings from the study was populated and made available at https://cirssrdb.rf.gd/ and http://backlin.cabgrid.res.in/Amaranthus_database/index.php.

The online version contains supplementary material available at 10.1007/s13205-025-04515-y.