Fragaria chiloensis KIB CAS Genome v2.0

Publication:

Xin Jin, Haiyuan Du, Maoxian Chen, Xu Zheng, Yiying He, Andan Zhu.  A fully phased octoploid strawberry genome reveals the evolutionary dynamism of centromeric satellites. Accepted to Genome Biology.

Abstract: We systematically examine the application of different phasing strategies to decrypt strawberry genome organization and produce a fully phased and accurate reference genome for Fragaria x ananassa cv. ‘EA78’ (EA78 was derived from synthetic allopolyploids by artificial hybridization between two genetically-distinct F. x ananassa cultivars, paternal material 'Albion' and maternal material 'Akihime'). We identify 147 bp canonical centromeric repeats across 50 strawberry chromosomes and uncover the formation of six neocentromeres through centromere turnover. Our findings indicate strawberry genomes have diverged centromeric satellite arrays among chromosomes, particularly across homoeologs, while maintaining high sequence similarity between homologs. We generated ONT ultra-long reads for F. chiloensis and F. virginiana and reassembled nearly complete genomes. We trace the evolutionary dynamics of centromeric repeats and find substantial centromere size expansion in wild and cultivated octoploids compared to the diploid ancestor, F. vesca.