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Plant genomes are known to be mainly composed of repetitive DNA sequences. Regardless of the non-genic function of these sequences, they are important for chromosome structure and stability during cell-cycle. Based on the recent available whole-genome assembly of white lupin (Lupinus albus L.; WL), we have in silico annotated and in situ mapped the main classes of DNA repeats identified with RepeatExplorer. A highly diverse and an abundance of satellite DNAs were found representing more than 10 families, where three of them were highly associated with CENH3-immunoprecipitated chromatin. Applying a strategy of several re-hybridization steps with different combinations of satDNA, rDNA, and LTR-RTs probes, we were able to construct a repeat-based chromosome map for the identification of most chromosome pairs. Two families of LTR retrotransposons, Ty1/copia SIRE and Ty3/gypsy Tekay, were highly abundant at pericentromeric regions, while the centromeric retrotransposon of WL (CRWL) from the CRM clade showed strong centromere-specific localization in most chromosomes and was also highly enriched with CENH3-immunoprecipitated chromatin. FISH mapping of repeat DNA showed some incongruences with the reference genome, which can be further used for improving the current version of the genome. Our results demonstrate that despite the relatively small genome of WL, a high diversity of pericentromeric repeats was found, emphasizing the rapid evolution of repeat sequences in plant genomes. [ABSTRACT FROM AUTHOR]

Plant genomes are known to be mainly composed of repetitive DNA sequences. Regardless of the non-genic function of these sequences, they are important for chromosome structure and stability during cell-cycle. Based on the recent available whole-genome assembly of white lupin (Lupinus albus L.; WL), we have in silico annotated and in situ mapped the main classes of DNA repeats identified with RepeatExplorer. A highly diverse and an abundance of satellite DNAs were found representing more than 10 families, where three of them were highly associated with CENH3-immunoprecipitated chromatin. Applying a strategy of several re-hybridization steps with different combinations of satDNA, rDNA, and LTR-RTs probes, we were able to construct a repeat-based chromosome map for the identification of most chromosome pairs. Two families of LTR retrotransposons, Ty1/copia SIRE and Ty3/gypsy Tekay, were highly abundant at pericentromeric regions, while the centromeric retrotransposon of WL (CRWL) from the CRM clade showed strong centromere-specific localization in most chromosomes and was also highly enriched with CENH3-immunoprecipitated chromatin. FISH mapping of repeat DNA showed some incongruences with the reference genome, which can be further used for improving the current version of the genome. Our results demonstrate that despite the relatively small genome of WL, a high diversity of pericentromeric repeats was found, emphasizing the rapid evolution of repeat sequences in plant genomes.

These genome comparisons show that the two descending dysploidies were not mediated by simple recombination between two ancestral chromosomes, but that multiple steps were required to generate the extant genome structures; the evolution of plant chromosomes can be complex and does not necessarily follow the most parsimonious pathways. Genome skimming and whole-genome sequencing elevated classical cytogenetics to a new level of modern evolutionary cytogenomics (see also Hu et al., [1]). Keywords: chromosomal rearrangements; cytogenomics; karyotype evolution; next generation sequencing; paleogenomics; polyploidy; repeatome; repetitive DNA EN chromosomal rearrangements cytogenomics karyotype evolution next generation sequencing paleogenomics polyploidy repeatome repetitive DNA 1 4 4 08/02/21 20210729 NES 210729 Chromosomal evolution is a driving force underlying diversification and speciation in plants. Altogether these studies fall into one of the four broader intersecting topics: (1) Pathways of karyotype and genome evolution and their role in plant speciation (2) Polyploidy and post-polyploid genome diploidization (3) Paleogenomics and paleogenomes (4) Repeatome and genome size evolution. [Extracted from the article]