Distinct patterns of satDNA distribution in spike-sedges (Eleocharis, Cyperaceae): evidence of repeat-based holocentromeres

Abstract Eleocharis R. Br. (Cyperaceae) species are known for having holocentric chromosomes, which enable rapid karyotype differentiation. Indeed, high intra- and interspecific variations in chromosome numbers and genome sizes are documented for different Eleocharis species, frequently accompanied by fluctuations in the repetitive DNA fraction. However, a lack of detailed analysis has hampered a better understanding of the interplay between holocentricity and repetitive DNA evolution in the genus. In this study, we confirmed the holocentricity of Eleocharis chromosomes by immunostaining against KNL1, histone H2AThr121ph and H3S10ph. We further studied the composition and chromosomal distribution of the main satellite DNA repeats found in five newly sequenced species. Five of the six satellites discovered were arranged in clusters, while EmaSAT14 was dispersed irregularly along the chromatid length in a line-like manner. This satDNA was accumulated exclusively by species belonging to the series Maculosae of the subgenus Eleocharis. The chromosomal distribution and genomic organization of EmaSAT14 suggest that it is a potential holocentromeric repeat. Our findings suggest that repeat-based holocentromeres are likely to evolve in a similar way across holocentric plants.