PmiR-Select® - a computational approach to plant pre-miRNA identification in genomes

• Published in: Molecular genetics and genomics : MGG 2025-12, Vol.300 (1), p.12, Article 12
• Main Authors: Bambil, Deborah, Costa, Mirele, Alencar Figueiredo, Lúcio Flávio de
• Format: Article
• Language: English
• Subjects: Algae; Angiosperms; Animal Genetics and Genomics; Biochemistry; Biomedical and Life Sciences; Computational Biology - methods; Computer applications; Conserved Sequence - genetics; Genome, Plant - genetics; Gymnosperms; Human Genetics; Life Sciences; Microbial Genetics and Genomics; MicroRNAs; MicroRNAs - genetics; miRNA; New families; Nucleic Acid Conformation; Original Article; Oryza - genetics; Plant Genetics and Genomics; Rice; RNA Precursors - genetics; RNA, Plant - chemistry; RNA, Plant - genetics
• ISSN: 1617-4615; 1617-4623; 1617-4623
• DOI: 10.1007/s00438-024-02221-7

Precursors of microRNAs (pre-miRNAs) are less used in silico to mine miRNAs. This study developed PmiR-Select ® based on covariance models (CMs) to identify new pre-miRNAs, detecting conserved secondary structural features across RNA sequences and eliminating the redundancy. The pipeline preceded PmiR-Select ® filtered 20% plant pre-miRNAs (from 38589 to 8677) from miRBase. The second filter reduced pre-miRNAs by 7% (from 8677 to 8045) through length limit to pre-miRNAs (70–300 nt) and miRNAs (20–24 nt). The 80% redundancy threshold was statistically the best, eliminating 55% pre-miRNAs (from 8045 to 3608). Angiosperms retained the highest number of pre-miRNAs and their families (2981 and 2202), followed by gymnosperms (362 and 271), bryophytes (183 and 119), and algae (82 and 78). Thirty-seven conserved pre-miRNA families happened among plant land clades, but none with algae. The PmiR-Select ® was applied to the rice genome, producing 8536 pre-miRNAs from 36 families. The 80% redundancy threshold retained 3% pre-miRNAs ( n  = 264) from 36 families, valuable experimental and computational research resources. 14% ( n  = 1216) of 8536 were new pre-miRNAs from 19 new families in rice. Only 16 new sequences from six families overlapped (39 to 54% identities) with rice pre-miRNAs and five species on miRBase. The validation against mature miRNAs identified 8086 pre-miRNAs from 13 families. Eleven ones have already been recorded, but two new and abundant pre-miRNAs [miR437 ( n  = 296) and miR1435 ( n  = 725)] scattered in all 12-rice chromosomes. PmiR-Select ® identified pre-miRNAs, decreased the redundancy, and discovered new miRNAs. These findings pave the way to delineating benchtop and computational experiments.