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.

High-quality genome assemblies for two Australimusa bananas(Musa spp.)and insights into regulatory mechanisms of superior fiber properties

Bananas(Musa spp.)are monocotyledonous plants with high genetic diversity in the Musaceae family that are cultivated mainly in tropical and subtropical countries.The fruits are a popular food,and the plants themselves have diverse uses.Four genetic groups(genomes)are thought to have contributed to current banana cultivars:Musa acuminata(A genome),Musa balbisiana(B genome),Musa schizocarpa(S genome),and species of the Australimusa section(T genome).However,the T genome has not been effectively explored.Here,we present the high-quality TT genomes of two representative accessions,Abaca(Musa textilis),with high-quality naturalfiber,and Utafun(Musa troglodytarum,Fe’i group),with abundant b-carotene.Both the Abaca and Utafun assemblies comprise 10 pseudochromosomes,and their total genome sizes are 613 Mb and 619 Mb,respectively.Comparative genome analysis revealed that the larger size of the T genome is likely attributable to rapid expansion and slow removal of trans-posons.Compared with those of Musa AA or BB accessions or sisal(Agava sisalana),Abacafibers exhibit superior mechanical properties,mainly because of their thicker cell walls with a higher content of cellulose,lignin,and hemicellulose.Expression of MusaCesA cellulose synthesis genes peaks earlier in Abaca than in AA or BB accessions during plant development,potentially leading to earlier cellulose accumulation during secondary cell wall formation.The Abaca-specific expressed gene MusaMYB26,which is directly regulated by MusaMYB61,may be an important regulator that promotes precocious expression of secondary cell wall MusaCesAs.Furthermore,MusaWRKY2 and MusaNAC68,which appear to be involved in regulating expression of MusaLAC and MusaCAD,may at least partially explain the high accumulation of lignin in Abaca.This work contributes to a better understanding of banana domestica-tion and the diverse genetic resources in the Musaceae family,thus providing resources for Musa genetic improvement.

Two gap-free reference genomes and a global view of the centromere architecture in rice

Rice(Oryza sativa),a major staple throughout the world and a model system for plant genomics and breeding,was the first crop genome sequenced almost two decades ago.However,reference genomes for all higher organisms to date contain gaps and missing sequences.Here,we report the assembly and analysis of gap-free reference genome sequences for two elite O.sativa xian/indica rice varieties,Zhenshan 97 and Minghui 63,which are being used as a model system for studying heterosis and yield.Gap-free reference genomes provide the opportunity for a global view of the structure and function of centromeres.We show that all rice centromeric regions share conserved centromere-specific satellite motifs with different copy numbers and structures.In addition,the similarity of CentO repeats in the same chromosome is higher than across chromosomes,supporting a model of local expansion and homogenization.Both genomes have over 395 non-TE genes located in centromere regions,of which∼41%are actively transcribed.Two large structural variants at the end of chromosome 11 affect the copy number of resistance genes between the two genomes.The availability of the two gap-free genomes lays a solid foundation for further understanding genome structure and function in plants and breeding climate-resilient varieties.

GenomeSyn:a bioinformatics tool for visualizing genome synteny and structural variations

Advances in the next-generation and long-read sequencing technologies have promoted the development of genome-wide comparative genomics analysis,and constructing pangenomes and identifying structural variations(SVs)are becoming the frontier of genomics.Comparative genomics is of critical importance for determining the gene function and the evolutionary basis of traits.