The genomes of seven economic Caesalpinioideae trees provide insights into polyploidization history and secondary metabolite biosynthesis

The Caesalpinioideae subfamily contains many well-known trees that are important for economic sustainability and human health,but a lack of genomic resources has hindered their breeding and utilization.Here,we present chromosome-level reference genomes for the two food and industrial trees Gleditsia sinensis(921 Mb)and Biancaea sappan(872 Mb),the three shade and ornamental trees Albizia julibrissin(705 Mb),Delonix regia(580 Mb),and Acacia confusa(566 Mb),and the two pioneer and hedgerow trees Leucaena leucocephala(1338 Mb)and Mimosa bimucronata(641 Mb).Phylogenetic inference shows that the mimosoid clade has a much higher evolutionary rate than the other clades of Caesalpinioideae.Macrosynteny comparison suggests that the fusion and breakage of an unstable chromosome are responsible for the difference in basic chromosome number(13 or 14)for Caesalpinioideae.After an ancient whole-genome duplication(WGD)shared by all Caesalpinioideae species(CWGD,~72.0 million years ago[MYA]),there were two recent successive WGD events,LWGD-1(16.2-19.5 MYA)and LWGD-2(7.1-9.5 MYA),in L.leucocephala.Thereafter,~40%gene loss and genome-size contraction have occurred during the diploidization process in L.leucocephala.To investigate secondary metabolites,we identified all gene copies involved in mimosine metabolism in these species and found that the abundance of mimosine biosynthesis genes in L.leucocephala largely explains its high mimosine production.We also identified the set of all potential genes involved in triterpenoid saponin biosynthesis in G.sinensis,which is more complete than that based on previous transcriptome-derived unigenes.Our results and genomic resources will facilitate biological studies of Caesalpinioideae and promote the utilization of valuable secondary metabolites.

Haplotype-resolved chromosome-level genome of hexaploid Jerusalem artichoke provides insights into its origin,evolution,and inulin metabolism

Jerusalem artichoke(Helianthus tuberosus)is a global multifunctional crop.It has wide applications in the food,health,feed,and biofuel industries and in ecological protection;it also serves as a germplasm pool for breeding of the global oil crop common sunflower(Helianthus annuus).However,biological studies of Je-rusalem artichoke have been hindered by a lack of genome sequences,and its high polyploidy and large genome size have posed challenges to genome assembly.Here,we report a 21-Gb chromosome-level as-sembly of the hexaploid Jerusalem artichoke genome,which comprises 17 homologous groups,each with 6 pseudochromosomes.We found multiple large-scale chromosome rearrangements between Jerusalem artichoke and common sunflower,and our results show that the hexaploid genome of Jerusalem artichoke was formed by a hybridization event between a tetraploid and a diploid Helianthus species,followed by chromosome doubling of the hybrid,which occurred approximately 2 million years ago.Moreover,we iden-tied more copies of actively expressed genes involved in inulin metabolism and showed that these genes may still be undergoing loss of function or sub-or neofunctionalization.These genomic resources will pro-mote further biological studies,breeding improvement,and industrial utilization of Helianthus crops.