Supporting data for "The genomes of five underutilized Papilionoideae crops provide insights into root nodulation and disease resistance"

The Papilionoideae subfamily contains a large amount of underutilized legume crops, which are important for food security and human sustainability. However, the lack of genomic resources has hindered the breeding and utilization of these crops. <br>Here, we present chromosome-level reference genomes for five underutilized Papilionoideae crops: sword bean, scarlet runner bean, winged bean, smooth rattlebox and butterfly pea, with assembled genome sizes of 0.62, 0.59, 0.71, 1.22, 1.72 Gb, respectively. We found that long period of higher LTR activity is the major reason that enlarges the genome size of smooth rattlebox and butterfly pea, and there is no recent whole duplication (WGD) event in these 5 species except for the shared papilionoid-specific WGD event (PWGD, ~55 Mya). Then, we identified 6,710 and 669 unique genes between scarlet runner bean and common bean for each species, which may be responsible for their phenotypic differences and species-specific functions. Furthermore, we identified the key genes involved in root nodule symbiosis in all 5 species, and found that the <i>NIN</i> gene was duplicated in the early Papilionoideae ancestor, followed by the loss of one gene copy in smooth rattlebox and butterfly pea. At last, we identified the resistance (R) genes for plant defenses in these 5 species, and characterized their evolutionary history. <br>In summary, this study provides chromosome-scale reference genomes for three grain and vegetable beans (sword bean, scarlet runner bean, winged bean), along with genomes for a green manure crop (smooth rattlebox) and a food dyeing crop (butterfly pea). These genomes are crucial for studying phylogenetic history, unraveling nitrogen-fixing nodule symbiosis (RNS) evolution, and advancing plant defense research.