{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T15:45:27Z","timestamp":1753890327426,"version":"3.41.2"},"reference-count":65,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,1,6]],"date-time":"2025-01-06T00:00:00Z","timestamp":1736121600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Bioinform."],"abstract":"<jats:p>Phytoplasma, a potentially hazardous pathogen associated with witches\u2019 broom, is an economically harmful disease-producing bacteria that damages chilli cultivation. Phytoplasma-infected plants display various symptoms that indicate significant disruptions in normal plant physiology and behaviour. Diseases caused by phytoplasma are widespread and have a major economic impact on crop quality and yield. This work focuses on identifying and examining chilli microRNAs (miRNAs) as potential targets against the 16S rRNA and <jats:italic>secA<\/jats:italic> gene of \u201c<jats:italic>Candidatus<\/jats:italic> Phytoplasma trifolii\u201d (\u201c<jats:italic>Ca<\/jats:italic>. P. trifolii\u201d) through plant miRNA prediction algorithms. Mature chilli miRNAs (CA-miRNAs) were collected and used to hybridise the 16S rRNA and <jats:italic>secA<\/jats:italic> genes. A total of four common CA-miRNAs were picked according to genetic consensus. Three algorithms applied in the present study suggested that the physiologically relevant, top-ranked miR169b_2 has a possibly specific site at nucleotide position 1,006 for targeting the \u2018<jats:italic>Ca<\/jats:italic>. P. trifolii\u2019 16S rRNA gene. The circos algorithm was then utilised to create the miRNA-mRNA regulatory network. The free energy between the miRNA:mRNA duplex was also computed, and the best value of \u221217.46 kcal\/mol was obtained for CA-miR166c_2. Currently, there are no suitable commercial \u2018<jats:italic>Ca<\/jats:italic>. P. trifolii\u2019-resistant chilli crops. As a result, the expected biological data provide useful evidence for developing \u2018<jats:italic>Ca<\/jats:italic>. P. trifolii\u2019-resistant chilli plants.<\/jats:p>","DOI":"10.3389\/fbinf.2024.1493712","type":"journal-article","created":{"date-parts":[[2025,1,6]],"date-time":"2025-01-06T06:59:14Z","timestamp":1736146754000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["In silico identification of chilli genome encoded MicroRNAs targeting the 16S rRNA and secA genes of \u201cCandidatus phytoplasma trifolii\u201d"],"prefix":"10.3389","volume":"4","author":[{"given":"Vineeta","family":"Pandey","sequence":"first","affiliation":[]},{"given":"Aarshi","family":"Srivastava","sequence":"additional","affiliation":[]},{"given":"Ramwant","family":"Gupta","sequence":"additional","affiliation":[]},{"given":"Haitham E. 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