Oligo-barcode illuminates holocentric karyotype evolution in Rhynchospora (Cyperaceae)

Abstract

Holocentric karyotypes are assumed to rapidly evolve through chromosome fusions and fissions due to the diffuse nature of their centromeres. Here, we took advantage of the recent availability of a chromosome-scale reference genome for Rhynchospora breviuscula, a model species of this holocentric genus, and developed the first set of oligo-based barcode probes for a holocentric plant. These probes were applied to 13 additional species of the genus, aiming to investigate the evolutionary dynamics driving the karyotype evolution in Rhynchospora. The two sets of probes were composed of 27,392 (green) and 23,968 (magenta) oligonucleotides (45-nt long), and generated 15 distinct FISH signals as a unique barcode pattern for the identification of all five chromosome pairs of the R. breviuscula karyotype. Oligo-FISH comparative analyzes revealed different types of rearrangements, such as fusions, fissions, putative inversions and translocations, as well as genomic duplications among the analyzed species. Two rounds of whole genome duplication (WGD) were demonstrated in R. pubera, but both analyzed accessions differed in the complex chain of events that gave rise to its large, structurally diploidized karyotypes with 2n = 10 or 12. Considering the phylogenetic relationships and divergence time of the species, the specificity and synteny of the probes were maintained up to species with a divergence time of ~25 My. However, karyotype divergence in more distant species hindered chromosome mapping and the inference of specific events. This barcoding system is a powerful tool to study chromosomal variations and genomic evolution in holocentric chromosomes of Rhynchospora species.

Repeat-based holocentromeres of the woodrushLuzula sylvaticareveal new insights into the evolutionary transition from mono- to holocentricity

“…Although phylogenetic relationships are poorly resolved in the genus, descending dysploidy has been observed in species from different Luzula clades (L. elegans in the Marlenia clade and L. purpureo-splendens in the Nodulosae clade), indicating that this process of chromosomal evolution has occurred independently at least twice during the evolution of the genus(Bozek et al 2012). Our results support dysploidy as the main driver of karyotype evolution in holocentric organisms (Fig.S10;(Bozek et al 2012;Guerra 2016;Senaratne et al 2022), since fission and fusion events have been described in sedges, leading to dysploid karyotypes in the holocentric genera Rhynchospora(Hofstatter et al 2022;Mata-Sucre et al 2024) and Carex(Ning et al 2023;Escudero et al 2023), as well in some holocentric butterflies(Cicconardi et al 2021;Wright et al 2024). However, the fusion of ancestral chromosomes that resemble chromosomes from the sister genus Juncus resulting in the dysploid L. sylvatica is intriguing, since it involves a simultaneous shift of centromere organization.…”

“…2022), since fission and fusion events have been described in sedges, leading to dysploid karyotypes in the holocentric genera Rhynchospora (Hofstatter et al . 2022; Mata-Sucre et al . 2024) and Carex (Ning et al .…”

“…However, holocentric chromosomes lack a primary constriction and exhibit molecular and epigenetic features that allow kinetochore proteins and microtubules to bind extensively along the chromosomes (Heckmann et al 2013;Schubert et al 2020). Therefore, holocentric chromosomes can tolerate large-scale rearrangements, such as chromosome fusions and fissions, because the rearranged chromosomes can maintain kinetochore activity, avoiding segregation problems and preserving essential genetic information during cell divisions (Burchardt et al 2020;Hofstatter et al 2022;Escudero et al 2023;Mata-Sucre et al 2024).…”