Repeat-based holocentromeres of Luzula sylvatica

Although the centromere is restricted to a single region of the chromosome in most studied eukaryotes, members of the rush family (Juncaceae) harbor either monocentric (Juncus) or holocentric (Luzula) chromosomes. This provides an opportunity to study the evolutionary mechanisms involved in the transition to holocentricity. Here by combining chromosome-scale genome assembly, epigenetic analyses, immuno-FISH, and super-resolution microscopy, we report the occurrence of repeat-based holocentromeres in L. sylvatica. We found an irregular distribution of genes, centromeric units, and most repeats along the chromosomes. We determined the centromere function predominantly associated with two satellite DNA repeats, Lusy1 and Lusy2 of 124- and 174-bp monomer length, respectively, while CENH3 also binds repeat-free gene-poor regions. Comparative repeat analysis revealed that Lusy1 is present in most Luzula species, suggesting a conserved centromere role of this repeat. Synteny between L. sylvatica (n = 6) and J. effusus (n = 21) genomes further evidenced a chromosome number reduction in Luzula derived from multiple chromosome fusions of ancestral J. effusus-like chromosomes. We propose that the transition to holocentricity in Luzula involves: (i) fusion of small chromosomes resembling Juncus-like centromeres; (ii) expansion of atypical centromeric units; and (iii) colonization of satellite DNA for centromere stabilization.

Description of the data and file structure

Chromosome-scale reference genome:

Luzula_sylvatica_asm.hic.chr.FINAL.fasta

Repeat annotation files:

Luzula_sylvatica_asm.hic.chr.FINAL.TE_domains_full_output.gff3

Luzula_sylvatica_asm.hic.chr.FINAL.LTR_retrotransposons_annotation.gff3

Luzula_sylvatica_asm.hic.chr.FINAL.TideCluster_tandem_repeats.gff3

DNA methylation files are coded as below:

6261_A*

R1 and R2 stands for forward (R1) and reverse (R2), respectively.

Code/Software

The original code used in this study is available on GitHub at https://github.com/437364/Repeat-based-holocentromeres-of-Luzula-sylvatica (opens in new window). Any additional information required to re-analyze the data reported in this paper is available from the corresponding author upon request.