Luffaspp.是南瓜科重要的世界性栽培蔬菜和药用植物。在这项研究中,我们报告了丝瓜高代近交系SG261的高质量染色体水平基因组。通过PacBio长读数确定基因组序列,Hi-C测序读数,和10倍基因组学测序,装配尺寸为739.82Mb,重叠群N50为18.38Mb,脚手架N50为56.08Mb。短句来源近角乳杆菌SG261的基因组预计含有27,312个蛋白质编码基因和72.56%的重复序列,其中长末端重复序列(LTR)是重复序列的重要形式,占基因组的67.84%。系统发育分析表明,acutangula的进化晚于丝瓜,Luffa与Momodicacharantia密切相关。将acutangulaSG261和cylindrica的基因组与PacBio数据进行比较,在SG261中鉴定出67,128个高质量的结构变异(SV)和55,978个存在-不存在变异(PAV),导致在CDS区域中具有变异的2424和1094个基因,分别,有287个相同的基因受到两种不同结构变异分析的影响。此外,我们发现转录因子FY(FLOWERINGLOCUSY)家族在L.acutangulaSG261(早晨开花)中的扩张幅度大于L.cylindrica(下午开花),这可能会导致落叶松SG261的开花时间提前。本研究为丝瓜的选育及泛基因组研究提供了有价值的参考。
Luffa spp. is an important worldwide cultivated vegetable and medicinal plant from the Cucurbitaceae family. In this study, we report a high-quality chromosome-level genome of the high-generation inbred line SG261 of Luffa acutangula. The genomic sequence was determined by PacBio long reads, Hi-C sequencing reads, and 10× Genomics sequencing, with an assembly size of 739.82 Mb, contig N50 of 18.38 Mb, and scaffold N50 of 56.08 Mb. The genome of L. acutangula SG261 was predicted to contain 27,312 protein-coding genes and 72.56% repetitive sequences, of which long terminal repeats (LTRs) were an important form of repetitive sequences, accounting for 67.84% of the genome. Phylogenetic analysis reveals that L. acutangula evolved later than Luffa cylindrica, and Luffa is closely related to Momodica charantia. Comparing the genome of L. acutangula SG261 and L. cylindrica with PacBio data, 67,128 high-quality structural variations (SVs) and 55,978 presence-absence variations (PAVs) were identified in SG261, resulting in 2424 and 1094 genes with variation in the CDS region, respectively, and there are 287 identical genes affected by two different structural variation analyses. In addition, we found that the transcription factor FY (FLOWERING LOCUS Y) families had a large expansion in L. acutangula SG261 (flowering in the morning) compared to L. cylindrica (flowering in the afternoon), which may result in the early flowering time in L. acutangula SG261. This study provides valuable reference for the breeding of and pan-genome research into Luffa species.