Isolation and identification of a centromeric tandemly repeated DNA sequence in Saccharina japonica

The centromere is a chromosomal locus essential for accurate chromosome segregation, typically composed of repetitive DNA sequences. To date, the centromeric DNA of the commercially important brown alga Saccharina japonica remains uncharacterized. In this study, we screened a candidate centromeric satellite DNA, Sjsat998, through bioinformatic analysis of male gametophyte genome data using RepeatExplorer2 and local BLAST against a centromeric BAC clone. Sjsat998 was organized as tandem repeats with a 998-bp monomer. Fluorescence in situ hybridization (FISH) confirmed its specific enrichment at centromeric regions. Immuno-FISH (IF-FISH) demonstrated precise co-localization of Sjsat998 with the centromeric histone H3 variant SjCENH3. Furthermore, electrophoretic mobility shift assays (EMSAs) confirmed the specific binding of recombinant SjCENH3 protein to Sjsat998. Sjsat998 was the first identified centromeric element in S. japonica . It provides a foundation for studying centromere evolution in brown algae and will facilitate the construction of a telomere-to-telomere (T2T) genome for this species. • Sjsat998 was identified as the first centromeric element in the brown alga Saccharina japonica . • Sjsat998 consisted of 998-bp tandem repeats, with specific enrichment at centromeres validated by FISH. • IF-FISH and EMSAs confirmed Sjsat998 co-localized with and specifically bound to the centromeric histone variant SjCENH3. • This study facilitated centromere evolution studies and T2T genome assembly in brown algae.