KNOTTEDI-like homeobox (KNOXI) genes regulate development of the leaf from the shoot apical meristem (SAM) and may regulate leaf form. We examined KNOXI expression in SAMs of various vascular plants and found that KNOXI expression correlated with complex leaf primordia. However, complex primordia may mature into simple leaves. Therefore, not all simple leaves develop similarly, and final leaf morphology may not be an adequate predictor of homology.

The Knotted-1 (Kn1) locus is defined by several dominant gain-of-function mutations that alter leaf development. Foci of cells along the lateral veins do not differentiate properly, but continue to divide, forming outpocketings or knots. The ligule, a fringe normally found at the junction of leaf blade and sheath, is often displaced and perpendicular to its normal position. The phenotype is manifested in all cell layers of the leaf blade, but is controlled by a subgroup of cells of the inner layer. Mutations result from the insertion of transposable elements or a tandem duplication. We show that the Kn1 gene encodes a homeodomain-containing protein, the first identified in the plant kingdom. Sequence comparisons strongly suggest that Kn1 acts as a transcription factor. Here we use the Kn1 homeobox to isolate other expressed homeobox genes in maize. The Kn1 homeobox may permit the isolation of genes that, like animal and fungal counterparts, regulate cell fate determination.

Solanum pennellii is a wild tomato species endemic to Andean regions in South America, where it has evolved to thrive in arid habitats. Because of its extreme stress tolerance and unusual morphology, it is an important donor of germplasm for the cultivated tomato Solanum lycopersicum 1 . Introgression lines (ILs) in which large genomic regions of S. lycopersicum are replaced with the corresponding segments from S. pennellii can show remarkably superior agronomic performance 2 . Here we describe a high-quality genome assembly of the parents of the IL population. By anchoring the S. pennellii genome to the genetic map, we define candidate genes for stress tolerance and provide evidence that transposable elements had a role in the evolution of these traits. Our work paves a path toward further tomato improvement and for deciphering the mechanisms underlying the myriad other agronomic traits that can be improved with S. pennellii germplasm.Crosses between distantly related plants can lead to substantial improvements in performance. Notably, S. pennellii × S. lycopersicum ILs have been used to define numerous quantitative trait loci (QTLs) for superior yield, chemical composition, morphology, abiotic stress tolerance and extreme heterosis 3,4 . Although genetic studies have proven informative, few genes underlying specific QTLs have been cloned, largely because of the lack of a S. pennellii genome sequence. To support QTL analyses, we sequenced the genome of S. pennellii using Illumina sequencing with ~190-fold coverage ( Fig. 1 and Supplementary Tables 1-5). The initial assembly size was 942 Mb, with a scaffold N50 value of 1.7 Mb and N90 value of 0.43 Mb (Table 1 and Supplementary Tables 6 and 7). We estimated the total genome size to be about 1.2 Gb using a k-mer-based analysis ( Supplementary Fig. 1 and Supplementary Table 8), in accordance with previous estimations 3,4 . We anchored 97.1% of the genome assembly to chromosomes using genetic maps and restriction site-associated DNA sequencing (RAD-seq)-based markers from the IL population 5 (Supplementary Note). Comparison of the assembly to publicly available BAC sequences indicated an accuracy of >99.9%, and a satisfactory accuracy of gap-filled regions was shown by realigning reads (Supplementary Fig. 2 and Supplementary Table 9). Of the 307,350 S. lycopersicum and 7,812 S. pennellii publicly available ESTs, 93% and >96% could be aligned to the genome, respectively (Supplementary Table 10), indicating comprehensive coverage of the gene-rich regions. We predicted 32,273 high-confidence genes and a potential set of 44,966 protein-coding genes and checked these

Long-distance movement of RNA through the phloem is known to occur, but the functional importance of these transported RNAs has remained unclear. Grafting experiments with a naturally occurring dominant gain-of-function leaf mutation in tomato were used to demonstrate long-distance movement of mutant messenger RNA (mRNA) into wild-type scions. The stock-specific pattern of mRNA expression was graft transmissible, indicating that the mRNA accumulation pattern is inherent to the transcript and not attributable to the promoter. The translocated mRNA caused changes in leaf morphology of the wild-type scions, suggesting that the translocated RNA is functional.

The KNOTTED-1 (KN1) locus of maize is defined by dominant mutations that affect leaf cell fates. Transposon tagging led to the isolation of the gene and the discovery that KN1 encodes a homeo domain. Immunolocalization studies showed that in wild-type maize plants, KN1 protein is present in nuclei of apical meristems and immature shoot axes but is down-regulated as lateral organs, such as leaves, are initiated. The protein is not immunohistochemically detectable in wild-type leaves at any stage. In developing leaves of plants carrying the dominant Knl mutation, temporally and spatially restricted ectopic expression of KN1 causes the mutant phenotype. To better understand the function of KN1 in plant development, we sought to determine the phenotype of plants in which KN1 was constitutively expressed. We find that tobacco plants transformed with the KN1 cDNA driven by the CaMV 35S promoter have a dramatically altered phenotype. The phenotypes are variable and depend on the level of KN1 protein. Plants expressing moderate levels of KN1 are reduced in stature with rumpled or lobed leaves. Plants with relatively high levels of KN1 lack apical dominance and are severely dwarfed in overall height and leaf size. Small shoots originate from the surface of these diminutive leaves. On the basis of phenotypes in maize and tobacco, we propose that the KN1 homeo box gene plays a role in determining cell fate. The consequences of KN1 overexpression appear to depend on the concentration of KN1 and the timing of its expression during organogenesis.