The evolutionary dynamics and conservation of the secondary structure of ITS rDNA vary across the different haplotypes of Lentinula edodes that are globally distributed.

• Mohammed M. Hawash*, Nadher A. Abed, Y. A. Obaid

  Author

This study relied on an integrated analysis of sequence characteristics, haplotype diversity, phylogenetic relationships, RNA secondary-structure modelling, and paired-site screening to analyse ITS rDNA variation and structural conservation across 19 geographically diverse Lentinula edodes accessions, including three from Iraq. A crucial component of fungal ITS evolution is the evolutionary accommodation of nucleotide diversity within structurally constrained ribosomal RNA sections. The ITS sequences were aligned, yielding 567 locations, with 330 remaining after gaps and incomplete data were eliminated. Seven haplotypes were discovered, with a haplotype diversity of 0.544 ± 0.136 and a nucleotide diversity of 0.03931 ± 0.03120. This reveals significant sequence variation among the analysed accessions. Given this distinction, both RNAfold and RNAalifold projected a well-conserved stem-loop structure. The consensus structure is anticipated to be thermodynamically stable (MFE = −263.78 kcal/mol; ensemble free energy = −272.45 kcal/mol), with a high level of concordance established across haplotypes (Pearson r = 0.995, P < 0.001). The expected stability of haplotype-specific structures differed; the Iraqi Maysan accession demonstrated somewhat less stability, whereas the Nepalese accession had the maximum stability. After screening 6,903 variable-site pairings, lineage-specific GC–CG state reversals were discovered; however, these were restricted to a single haplotype and did not exhibit statistical evidence for compensatory covariation. Overall, outcomes reveal that ITS sequence variation in L. edodes is accommodated within a projected RNA structural framework that is largely retained in the absence of direct evidence of compensatory evolution.

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