Genome-wide annotation and comparative analysis of miniature inverted-repeat transposable elements (MITEs) in six pear species.

Abstract

Main conclusion: Through multi-faceted comparative analysis of MITEs across six pear genomes, we revealed their distribution patterns, functional impacts and their significant role as genomic origins for miRNAs, with copy number being the most critical factor for MITE-miRNA transformation, providing valuable insights for future research. Miniature inverted-repeat transposable elements (MITEs) are prevalent in plant genomes and play a significant role in genome evolution and diversity. The availability of high-quality genome sequences for six pear species-Pyrus bretschneideri Rehd cv. 'Dangshan Suli', Pyrus communis L. cv. 'Bartlett', Pyrus pyrifolia Nakai cv. 'Nijisseiki' and 'Cuiguan', Pyrus ussuriensis maxim cv. 'Zhongai No.1', Pyrus betulifolia Bunge cv. 'Duli'-has facilitated the annotation and comparative analysis of MITEs in these species. Consequently, we identified 12,759 intact MITEs belonging to 750 families. Sequence diversity analysis revealed that these MITEs underwent one or two rounds of amplification burst events within the pear genomes. Among them, 10,368 intact MITEs demonstrated collinearity across six pear species. Further investigation indicated that MITEs are predominantly located upstream regions of genes. Notably, 1832 genes exhibited potential regulation (either up-regulation or down-regulation) due to MITE insertions. Additionally, 4421 previously missing genes, disrupted by MITE insertions, were restored and re-annotated. We identified 8855 MITE-miRNAs belonging to 370 families across all six species, with approximately 75% of miRNAs originating from MITEs. Machine learning analysis revealed copy number as the most influential feature for MITE-miRNA transformation, followed by MITE length and structure stability. These findings provide valuable insights into transposable elements' role in shaping genome diversity and their impact on functional genes and miRNA genesis within pear genomes.