Telomere-to-telomere assembly of cassava genome reveals the evolution of cassava and divergence of allelic expression

Cassava is a crucial crop that makes a significant contribution to ensuring human food security.However,high-quality telomere-totelomere cassava genomes have not been available up to now,which has restricted the progress of haploid molecular breeding for cassava.In this study,we constructed two nearly complete haploid resolved genomes and an integrated,telomere-to-telomere gap-free reference genome of an excellent cassava variety,‘Xinxuan 048’,thereby providing a new high-quality genomic resource.Furthermore,the evolutionary history of several species within the Euphorbiaceae family was revealed.Through comparative analysis of haploid genomes,it was found that two haploid genomes had extensive differences in linear structure,transcriptome features,and epigenetic characteristics.Genes located within the highly divergent regions and differentially expressed alleles are enriched in the functions of auxin response and the starch synthesis pathway.The high heterozygosity of cassava‘Xinxuan 048’leads to rapid trait segregation in the first selfed generation.This study provides a theoretical basis and genomic resource for molecular breeding of cassava haploids.

Two haplotype-resolved genome assemblies for AAB allotriploid bananas provide insights into banana subgenome asymmetric evolution and Fusarium wilt control

Bananas(Musa spp.)are one of the world’s most important fruit crops and play a vital role in food security for many developing countries.Most banana cultivars are triploids derived from inter-and intraspecific hybrid-izations between the wild diploid ancestor species Musa acuminate(AA)and M.balbisiana(BB).We report two haplotype-resolved genome assemblies of the representative AAB-cultivated types,Plantain and Silk,and precisely characterize ancestral contributions by examining ancestry mosaics across the genome.Widespread asymmetric evolution is observed in their subgenomes,which can be linked to frequent homol-ogous exchange events.We reveal the genetic makeup of triploid banana cultivars and verify that subge-nome B is a rich source of disease resistance genes.Only 58.5%and 59.4%of Plantain and Silk genes,respectively,are present in all three haplotypes,with>50%of genes being differentially expressed alleles in different subgenomes.We observed that the number of upregulated genes in Plantain is significantly higher than that in Silk at one-week post-inoculation with Fusarium wilt tropical race 4(Foc TR4),which con-firms that Plantain can initiate defense responses faster than Silk.Additionally,we compared genomic and transcriptomic differences among the genes related to carotenoid synthesis and starch metabolism between Plantain and Silk.Our study provides resources for better understanding the genomic architecture of culti-vated bananas and has important implications for Musa genetics and breeding.