Abstract：
The Xishuangbanna (XIS) cucumber (Cucumis sativus var. xishuangbannanesis) is a semiwild variety that has many distinct agronomic traits. Here, long reads generated by Nanopore sequencing technology helped assembling a high-quality genome (contig N50 = 8.7 Mb) of landrace XIS49. A total of 10,036 structural/sequence variations (SVs) were identified when comparing with Chinese Long (CL), and known SVs controlling spines, tubercles, and carpel number were confirmed in XIS49 genome. Two QTLs of hypocotyl elongation under low light, SH3.1 and SH6.1, were fine-mapped using introgression lines (donor parent, XIS49; recurrent parent, CL). SH3.1 encodes a red-light receptor Phytochrome B (PhyB, CsaV3_3G015190). A ∼4 kb region with large deletion and highly divergent regions (HDRs) were identified in the promoter of the PhyB gene in XIS49. Loss of function of this PhyB caused a super-long hypocotyl phenotype. SH6.1 encodes a CCCH-type zinc finger protein FRIGIDA-ESSENTIAL LIKE (FEL, CsaV3_6G050300). FEL negatively regulated hypocotyl elongation but it was transcriptionally suppressed by long terminal repeats retrotransposon insertion in CL cucumber. Mechanistically, FEL physically binds to the promoter of CONSTITUTIVE PHOTOMORPHOGENIC 1a (COP1a), regulating the expression of COP1a and the downstream hypocotyl elongation. These above results demonstrate the genetic mechanism of cucumber hypocotyl elongation under low light.
摘要：
西双版纳（XIS）黄瓜（Cucumissativusvar。xishuangbannanesis）是具有许多独特农艺性状的半野生品种。这里,Nanopore测序技术产生的长读数有助于组装LandraceXIS49的高质量基因组（重叠群N50=8.7Mb）。与中国龙（CL）进行比较时，总共鉴定出10,036种结构/序列变异（SV），和已知的控制脊椎的SV，结节,和心皮编号在XIS49基因组中得到证实。弱光下胚轴伸长的两个QTL，SH3.1和SH6.1使用渗入系进行精细定位(供体亲本，XIS49；轮回生父母，CL)。SH3.1编码红光受体植物色素B(PhyB，CsaV3_3G015190)。在XIS49中的PhyB基因的启动子中鉴定出一个〜4kb的大缺失（DEL）和高度发散的区域（HDRs）。这种PhyB功能的丧失导致超长下胚轴表型。SH6.1编码CCCH型锌指蛋白FRIGIDA-基本样（FEL，CsaV3_6G050300)。FEL负调控下胚轴伸长，但在CL黄瓜中被长末端重复序列（LTR）逆转录转座子插入转录抑制。机械上,FEL与本构光致形态1a（COP1a）的启动子物理结合，调节COP1a的表达和下游下胚轴伸长。以上结果说明了弱光下黄瓜下胚轴伸长的遗传机制。
