背景:Papilionoideae亚科包含大量未充分利用的豆科作物,这对粮食安全和人类可持续发展至关重要。然而,基因组资源的缺乏阻碍了这些作物的育种和利用。
结果:这里,我们提供了5种未充分利用的二倍体Papilionoideae作物的染色体水平参考基因组:剑豆(Canavaliagladiata),猩红色红花菜豆(菜豆),有翼豆(果蝇四虫),光滑的响尾蛇(鳄鱼),和蝴蝶豌豆(Clitoriaternatea),组装的基因组大小为0.62Gb,0.59Gb,0.71Gb,1.22Gb,和1.72Gb,分别。我们发现,长期较高的长末端重复反转录转座子活性是光滑响尾蛇和蝴蝶豌豆基因组大小扩大的主要原因。此外,在这5个物种中,没有最近的全基因组复制(WGD)事件,除了共有的类乳头虫特异性WGD事件(〜5500万年前)。然后,我们鉴定了红红红菜豆和普通豆之间的5,328和10,434种特异性基因,分别,这可能是它们的表型和功能差异以及物种特异性功能的原因。此外,我们在所有5个物种中鉴定了参与根瘤共生(RNS)的关键基因,并发现NIN基因在早期乳头科祖先中重复,随后在光滑的响尾蛇和蝴蝶豌豆谱系中丢失了1个基因拷贝。最后,我们确定了这5个物种中植物防御的抗性(R)基因,并描述了它们的进化史。
结论:总之,这项研究提供了3种谷物和菜豆(剑豆,猩红色红红豆,有翼豆),以及绿肥作物(光滑的响尾蛇箱)和食品染色作物(蝴蝶豌豆)的基因组。这些基因组对于研究系统发育史至关重要,解开固氮RNS的进化,推进植物防御研究。
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 (∼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.