Informace o publikaci
Largest genome assembly in Brassicaceae: retrotransposon-driven genome expansion and karyotype evolution in Matthiola incana
| Autoři | |
|---|---|
| Rok publikování | 2025 |
| Druh | Článek v odborném periodiku |
| Časopis / Zdroj | PLANT BIOTECHNOLOGY JOURNAL |
| Fakulta / Pracoviště MU | |
| Citace | |
| www | https://onlinelibrary.wiley.com/doi/10.1111/pbi.70193 |
| Doi | https://doi.org/10.1111/pbi.70193 |
| Klíčová slova | genome assembly; genome obesity; Lineage III; Hesperodae; Cruciferae; retrotransposons |
| Přiložené soubory | |
| Popis | Matthiola incana, commonly known as stock and gillyflower, is a widely grown ornamental plant whose genome is significantly larger than that of other species in the mustard family. However, the evolutionary history behind such a large genome (similar to 2 Gb) is still unknown. Here, we have succeeded in obtaining a high-quality chromosome-scale genome assembly of M. incana by integrating PacBio HiFi reads, Illumina short reads and Hi-C data. The resulting genome consists of seven pseudochromosomes with a length of 1965 Mb and 38 245 gene models. Phylogenetic analysis indicates that M. incana and other taxa of the supertribe Hesperodae represent an early-diverging lineage in the evolutionary history of the Brassicaceae. Through a comparative analysis, we revisited the ancestral Hesperodae karyotype (AHK, n = 7) and found several differences from the well-established ancestral crucifer karyotype (ACK, n = 8) model, including extensive inter- and intra-chromosomal rearrangements. Our results suggest that the primary reason for genome obesity in M. incana is the massive expansion of long terminal repeat retrotransposons (LTR-RTs), particularly from the Angela, Athila and Retand families. CHG methylation modification is obviously reduced in the regions where the highest density of Copia-type LTR-RTs and the lowest density of Gypsy-type LTR-RTs overlap, corresponding to the putative centromeres. Based on insertion times and methylation profiling, recently inserted LTR-RTs were found to have a significantly different methylation pattern compared to older ones. |
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