Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China.
State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China.
Gigascience. 2024 Jan 2;13. doi: 10.1093/gigascience/giae063.
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.
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 (∼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.
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.
紫葳科包含大量未充分利用的豆科作物，这些作物对粮食安全和人类可持续性至关重要。然而，缺乏基因组资源阻碍了这些作物的培育和利用。
在这里，我们为 5 种未充分利用的二倍体紫葳科作物提供了染色体水平的参考基因组：剑豆（Canavalia gladiata）、红花菜豆（Phaseolus coccineus）、四棱豆（Psophocarpus tetragonolobus）、光滑野百合（Crotalaria pallida）和蓝蝴蝶（Clitoria ternatea），组装的基因组大小分别为 0.62Gb、0.59Gb、0.71Gb、1.22Gb 和 1.72Gb。我们发现，长末端重复转座子活动的长期存在是导致光滑野百合和蓝蝴蝶基因组扩大的主要原因。此外，除了共享的豆科特异性全基因组复制事件（约 5500 万年前）外，这 5 个物种最近都没有发生全基因组复制事件。然后，我们分别在红花菜豆和普通菜豆之间鉴定出 5328 个和 10434 个种特异性基因，这些基因可能负责它们的表型和功能差异以及种特异性功能。此外，我们鉴定了所有 5 个物种中参与根瘤共生（RNS）的关键基因，发现 NIN 基因在早期紫葳科祖先中发生了复制，随后在光滑野百合和蓝蝴蝶谱系中丢失了 1 个基因拷贝。最后，我们鉴定了这 5 个物种中植物防御的抗性（R）基因，并对其进化历史进行了描述。
总之，本研究为 3 种粮食和蔬菜豆（剑豆、红花菜豆、四棱豆）以及绿肥作物（光滑野百合）和食用染料作物（蓝蝴蝶）提供了染色体水平的参考基因组。这些基因组对于研究系统发育历史、揭示固氮 RNS 进化以及推进植物防御研究至关重要。
