The Caesalpinioideae subfamily contains many well-known trees that are important for the sustainability of the economy and human health, but the lack of genomic resources hindered the breeding and utilization of these plants. Here, we present chromosome-level reference genomes for two food and industrial trees Gleditsia sinensis (921 Mb) and Biancaea sappan (872 Mb), three shade and ornamental trees Albizia julibrissin (705 Mb), Delonix regia (580 Mb) and Acacia confusa (566 Mb), as well as two pioneer and hedgerow trees Leucaena leucocephala (1,338 Mb) and Mimosa bimucronata (641 Mb). Phylogeny inference showed that the mimosoid clade has a much higher evolution rate than the other clades of Caesalpinioideae. Macrosynteny comparison showed that the fusion and broken of an unstable chromosome was responsible for the difference in the basic chromosome number 13 and 14 for Caesalpinioideae. After the ancient whole genome duplication shared by all Caesalpinioideae species (CWGD, ∼72.0 MYA), we found two recent successive WGD events LWGD-1 (16.2-19.5 MYA) and LWGD-2 (7.1-9.5 MYA) in L. leucocephala. Then, ∼40% gene loss and genome size contraction occurred during the diploidization process in L. leucocephala. For the secondary metabolites, we identified all the gene copies involved in mimosine metabolism for these species and revealed that the abundance of mimosine biosynthesis genes in L. leucocephala largely explains its high mimosine production. Moreover, we identified all the potential genes involved in triterpenoid saponin biosynthesis in G. sinensis, which is more complete than the previous transcriptome-derived unigenes. Our analyzing results and the genomic resources will facilitate the biological studies of Caesalpinioideae and promote the utilization of valuable secondary metabolites.
Keywords: Caesalpinioideae; chromosome rearrangement; hybridization origin; mimosine biosynthesis genes; triterpenoid saponin.
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