Fluctuations in genomic repetitive fractions (repeatome) are known to impact several facets of evolution, such as ecological adaptation and speciation processes. Therefore, investigating the divergence of repetitive elements can provide insights into an important evolutionary force. However, it is not clear how the different repetitive element lineages are impacted by the ecological changes. To discuss this, we used the Neotropical legume genus Erythrostemon (Caesalpinioideae) as a model, given its ancient origin (~33 Mya), lineage-specific niche conservatism, macroecological heterogeneity, and disjunct distribution in Meso- and South American (MA and SA, respectively) lineages. We performed a comparative repeatomic analysis of 18 Erythrostemon species to test the impact of environmental variables over repeats diversification. Overall, repeatome composition was diverse, with high abundances of satDNAs and Ty3/gypsy-Tekay transposable elements, predominantly in the MA and SA lineages, respectively. Remarkably the first divergent lineages (E. pannosus and E. placidus) of the MA clade preserve plesiomorphic Tekay and satDNA patterns. This pattern was altered in the MA-sensu stricto subclade with a striking genomic differentiation (expansion of satDNA and retraction of Tekay) associated with the colonization of a new environment in Central America around 20 Mya. Our data reveal that the current species-specific Tekay pool was the result of two bursts of amplification probably in the Miocene, with distinct patterns for the MA and SA repeatomes. This suggests a strong role of the Tekay elements as modulators of the genome-environment interaction in Erythrostemon, providing macroevolutionary insights about mechanisms of repeatome differentiation and plant diversification across space and time.

Holocentric organisms, unlike typical monocentric organisms, have kinetochore activity distributed along almost the whole length of the chromosome. Because of this, chromosomal rearrangements through fission and fusion are more likely to become fixed in holocentric species, which may account for their extraordinary rates of chromosome evolution. Genome synteny has been reported to be conserved in animals with holocentric chromosomes despite high rates of chromosome rearrangements. Comparing genomes of Carex species and a genome of a distantly related Cyperaceae we have characterised conserved vs. rearranged genome regions across pairs of species that range in time since divergence between 2 and 50 million years. We have compared a C. scoparia genome with a linkage map of the same species to study rearrangements at a population level and suppression of recombination patterns. We found a surprisingly conserved genome synteny even between very distantly related species and extraordinarily high rates of chromosome evolution in genus Carex. Comparing the distribution of repetitive DNA and gene density between conserved and rearranged genomic regions, we found repetitive DNA to be related to holocentromeres and as well as rearranged regions of the genome. This evidence of extremely conserved synteny in sedges and the massive events of chromosome fission and fusion found across the evolution of genus Carex suggests the presence of common genomic hotspots of chromosome evolution related to repetitive DNA.