The genomes of 5 underutilized Papilionoideae crops provide insights into root nodulation and disease resistance

文献类型： 外文期刊

第一作者： Yuan, Lihua

作者： Yuan, Lihua;Lei, Lihong;Jiang, Fan;Wang, Anqi;Chen, Rong;Wang, Hengchao;Meng, Sihan;Fan, Wei;Yuan, Lihua;Lei, Lihong;Yuan, Lihua;Lei, Lihong

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关键词： Papilionoideae; underutilized legume; whole genome duplication; root-nodule symbiosis; R genes

期刊名称：GIGASCIENCE （ 影响因子：3.9； 五年影响因子：11.1 ）

ISSN： 2047-217X

年卷期： 2024 年 13 卷

页码：

收录情况： SCI

摘要： Background 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.Results Here, we present chromosome-level reference genomes for 5 underutilized diploid Papilionoideae crops: sword bean (Canavalia gladiata), scarlet runner bean (Phaseolus coccineus), winged bean (Psophocarpus tetragonolobus), smooth rattlebox (Crotalaria pallida), and butterfly pea (Clitoria ternatea), with assembled genome sizes of 0.62 Gb, 0.59 Gb, 0.71 Gb, 1.22 Gb, and 1.72 Gb, respectively. We found that the long period of higher long terminal repeat retrotransposon activity is the major reason that the genome size of smooth rattlebox and butterfly pea is enlarged. Additionally, there have been no recent whole-genome duplication (WGD) events in these 5 species except for the shared papilionoid-specific WGD event (similar to 55 million years ago). Then, we identified 5,328 and 10,434 species-specific genes between scarlet runner bean and common bean, respectively, which may be responsible for their phenotypic and functional differences and species-specific functions. Furthermore, we identified the key genes involved in root-nodule symbiosis (RNS) in all 5 species and found that the NIN gene was duplicated in the early Papilionoideae ancestor, followed by the loss of 1 gene copy in smooth rattlebox and butterfly pea lineages. Last, we identified the resistance (R) genes for plant defenses in these 5 species and characterized their evolutionary history.Conclusions In summary, this study provides chromosome-scale reference genomes for 3 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 RNS evolution, and advancing plant defense research.

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