Rare genetic variants are abundant in genomes but less tractable in genome-wide association study. Here we exploit a strategy of rare variation mapping to discover a gene essential for tendril development in cucumber (Cucumis sativus L.). In a collection of >3000 lines, we discovered a unique tendril-less line that forms branches instead of tendrils and, therefore, loses its climbing ability. We hypothesized that this unusual phenotype was caused by a rare variation and subsequently identified the causative single nucleotide polymorphism. The affected gene TEN encodes a TCP transcription factor conserved within the cucurbits and is expressed specifically in tendrils, representing a new organ identity gene. The variation occurs within a protein motif unique to the cucurbits and impairs its function as a transcriptional activator. Analyses of transcriptomes from near-isogenic lines identified downstream genes required for the tendril's capability to sense and climb a support. This study provides an example to explore rare functional variants in plant genomes.

Histone deacetylase (HDAC) proteins participate in diverse and tissue-specific developmental processes by forming various corepressor complexes with different regulatory subunits. An important HDAC machinery hub, the Histone Deacetylase Complex1 (HDC1) protein, participates in multiple protein-protein interactions and regulates organ size in plants. However, the mechanistic basis for this regulation remains unclear. Here, we identified a cucumber (Cucumis sativus) short-fruit mutant (sf2) with a phenotype that includes repressed cell proliferation. SF2 encodes an HDC1 homolog, and its expression is enriched in meristematic tissues, consistent with a role in regulating cell proliferation through the HDAC complex. A weak sf2 allele impairs HDAC targeting to chromatin, resulting in elevated levels of histone acetylation. Genome-wide mapping revealed that SF2 directly targets and promotes histone deacetylation associated with key genes involved in multiple phytohormone pathways and cell cycle regulation, by either directly repressing or activating their expression. We further show that SF2 controls fruit cell proliferation through targeting the biosynthesis and metabolism of cytokinin and polyamines. Our findings reveal a complex regulatory network of fruit cell proliferation mediated by HDC1 and elucidate patterns of HDC1-mediated regulation of gene expression.

Protein-coding gene annotation. To search for homologous genes, the protein sequences from all ferns and lycophytes transcriptomes in the OneKP project 1 were retrieved and aligned to the A. capillus-veneris genome, using GeneWise 2 . For transcriptome-based prediction, nineteen transcriptomes covering the entire life cycle of A. capillus-veneris were generated in this study (Supplementary Table 8). RNA was extracted using the Qiagen RNeasy protocol and sequenced on an Illumina HiSeq 4000 with a 300 bp insert size. For transcriptome-based prediction, the HISAT2 3 and StringTie 4 programs were used for transcript assembly 5 . The program PASA (http://pasapipeline.github.io) was used to align spliced transcripts and annotate candidate genes. Ab initio prediction was performed with AUGUSTUS 6 , GlimmerHMM 7 , and SNAP 8 . Finally, nonredundant gene models were obtained with EVidenceModeler (version 1.1.0) 9 to integrate the gene models developed by different datasets.To validate the assembly quality, RNA-seq reads from nineteen tissues (Supplementary Table 8), together with publicly available EST sequences from the NCBI database (downloaded from http://togodb.dbcls.jp/library), were mapped to the A. capillus-veneris genome using HISAT2 3 and BLAT 10 with default parameters, respectively. The BLAT results were filtered with an identity and coverage cutoff of 0.9.Identification of noncoding RNAs. We used tRNAscan-SE (version 2.0rc2) 11 , with default parameters, to search for tRNAs in the A. capillus-veneris genome. A total of 1,624 tRNAs were found. Moreover, the Rfam14.0 database 12 , including 3,445 noncoding RNA families, was used to annotate additional noncoding RNAs (ncRNAs), including miRNAs, snRNAs, and tRNAs, using INFERNAL (version 1.1.2) 13 program.We predicted rRNA (5S, 5.8S, 28S, 18S) by using HMM searching based rRNA predicator Barrnap (version 0.9, https://github.com/tseemann/barrnap#barrnap), with default parameters. We finally identified 145 5S, 75 5.8S, 155 28S, and 165 18S sequences and their locations within the genome assembly of A. capillus-veneris.