SummaryLong noncoding RNAs (lncRNAs) regulate gene expression and biological processes. With the development of high-throughput RNA sequencing technology, lncRNAs have been extensively studied in recent years. Nevertheless, the expression and evolution of lncRNAs in plants remain poorly understood.Here, we identified 413 and 709 multi-exon noncoding transcripts from 353 and 595 loci of the cultivar tomato Heinz1706 and its wild relative LA1589, respectively. Systematic comparison of the sequence and expression of lncRNAs showed that they are poorly conserved in Solanaceae, with only < 0.4% lncRNAs present in all sequenced genomes of tomato and potato. Sequence analysis of Lycopersicon-specific lncRNA loci in Solanum lycopersicum and S. pennellii showed that the origins of these molecules are associated with transposable elements (TEs).LncRNA-314, a fruit-specific lncRNA expressed in S. lycopersicum and S. pimpinellifolium, but not in S. pennellii, originated through two evolutionary events: speciation of S. pennellii resulted in insertion of a long terminal repeat (LTR) retrotransposon into chromosome 10 and contributed to most of the transcribed region of lncRNA-314; and a large deletion in Lycopersicon generated the promoter region and part of the transcribed region of lncRNA-314.These results provide novel insights into the evolution of lncRNAs in plants.

The inflorescences and lateral branches of higher plants are generated by lateral meristems. The structure of the inflorescence has a direct effect on fruit yield in tomato (Solanum lycopersicum). We previously demonstrated that miR156a plays important roles in determining the structures of the inflorescences and lateral branches in tomato by suppressing the expression of the SQUAMOSA PROMOTER BINDING PROTEIN LIKE (SPL) transcription factor gene family. However, information on regulatory pathways associated with inflorescence morphogenesis is still lacking. In this study, we demonstrate that SPL13 is the major SPL involved in miR156a-regulated tomato inflorescence structure determination and lateral branch production. Suppressing the expression of SPL13 in tomato increases the number of inflorescences on vegetative branches and lateral branches, decreases the number of flowers and fruit, and reduces fruit size and yield. Genetic and biochemical evidence indicate that SPL13 controls inflorescence development by positively regulating the expression of the tomato inflorescence-associated gene SINGLE FLOWER TRUSS (SFT) by directly binding to its promoter region. Thus, our findings provide a major advance to our understanding of the miR156a-SlSPL-based mechanism that regulates plant architecture and yield in tomato.

Summary NF‐Y transcription factors are reported to play diverse roles in a wide range of biological processes in plants. However, only a few active NF‐Y complexes are known in plants and the precise functions of NF‐Y complexes in flavonoid biosynthesis have not been determined. Using various molecular, genetic and biochemical approaches, we found that NF‐YB8a, NF‐YB8b and NF‐YB8c – a NF‐YB subgroup – can interact with a specific subgroup of NF‐YC and then recruit either of two distinct NF‐YAs to form NF‐Y complexes that bind the CCAAT element in the CHS1 promoter. Furthermore, suppressing the expression of particular NF‐YB genes increased the levels of H3K27me3 at the CHS1 locus and significantly suppressed the expression of CHS1 during tomato fruit ripening, which led to the development of pink‐coloured fruit with colourless peels. Altogether, by demonstrating that NF‐Y transcription factors play essential roles in flavonoid biosynthesis and by providing significant molecular insight into the regulatory mechanisms that drive the development of pink‐coloured tomato fruit, we provide a major advance to our fundamental knowledge and information that has considerable practical value for horticulture.

Summary Efficient genetic transformation has the potential to advance research and breeding in watermelon (Citrullus lanatus), but regeneration from tissue culture remains challenging. Previous work showed that expressing a fusion of two interacting transcription factors, GROWTH‐REGULATING FACTOR4 (GRF4) and GRF‐INTERACTING FACTOR1 (GIF1), improved regeneration in wheat (Triticum aestivum). By overexpressing a chimeric fusion of ClGRF4 and ClGIF1, we achieved highly efficient transformation in watermelon. Mutating the mi396 microRNA target site in ClGRF further boosted the transformation efficiency up to 67.27% in a genotype‐independent manner. ClGRF4‐GIF1 can also be combined with clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR‐associated protein 9 (Cas9) genome editing tools to achieve highly efficient gene editing in watermelon, which we used to successfully create diploid seedless watermelon. This research thus puts forward a powerful transformation tool for future watermelon research and breeding.

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