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

The circadian clock is a critical regulator of plant physiology and development, controlling key agricultural traits in crop plants. In addition, natural variation in circadian rhythms is important for local adaptation. However, quantitative modulation of circadian rhythms due to artificial selection has not yet been reported. Here we show that the circadian clock of cultivated tomato (Solanum lycopersicum) has slowed during domestication. Allelic variation of the tomato homolog of the Arabidopsis gene EID1 is responsible for a phase delay. Notably, the genomic region harboring EID1 shows signatures of a selective sweep. We find that the EID1 allele in cultivated tomatoes enhances plant performance specifically under long day photoperiods, suggesting that humans selected slower circadian rhythms to adapt the cultivated species to the long summer days it encountered as it was moved away from the equator.

VvMATE1 and VvMATE2 encode putative PA transporters expressed during seed development in grapevine. The subcellular localization of these MATE proteins suggests different routes for the intracellular transport of PAs. Proanthocyanidins (PAs), also called condensed tannins, protect plants against herbivores and are important quality components of many fruits. PAs biosynthesis is part of the flavonoid pathway that also produces anthocyanins and flavonols. In grape fruits, PAs are present in seeds and skin tissues. PAs are synthesized in the cytoplasm and accumulated into the vacuole and apoplast; however, little is known about the mechanisms involved in the transport of these compounds to such cellular compartments. A gene encoding a Multidrug And Toxic compound Extrusion (MATE) family protein suggested to transport anthocyanins-named VvMATE1-was used to identify a second gene of the MATE family, VvMATE2. Analysis of their deduced amino acid sequences and the phylogenetic relationship with other MATE-like proteins indicated that VvMATE1 and VvMATE2 encode putative PA transporters. Subcellular localization assays in Arabidopsis protoplasts transformed with VvMATE-GFP fusion constructs along with organelle-specific markers revealed that VvMATE1 is localized in the tonoplast whereas VvMATE2 is localized in the Golgi complex. Major expression of both genes occurs during the early stages of seed development concomitant with the accumulation of PAs. Both genes are poorly expressed in the skin of berries while VvMATE2 is also expressed in leaves. The presence of putative cis-acting elements in the promoters of VvMATE1 and VvMATE2 may explain the differential transcriptional regulation of these genes in grapevine. Altogether, these results suggest that these MATE proteins could mediate the transport and accumulation of PAs in grapevine through different routes and cellular compartments.

Komagataeibacter species are well‐recognized bionanocellulose ( BNC ) producers. This bacterial genus, formerly assigned to Gluconacetobacter , is known for its phenotypic diversity manifested by strain‐dependent carbon source preference, BNC production rate, pellicle structure, and strain stability. Here, we performed a comparative study of nineteen Komagataeibacter genomes, three of which were newly contributed in this work. We defined the core genome of the genus, clarified phylogenetic relationships among strains, and provided genetic evidence for the distinction between the two major clades, the K . xylinus and the K. hansenii . We found genomic traits, which likely contribute to the phenotypic diversity between the Komagataeibacter strains. These features include genome flexibility, carbohydrate uptake and regulation of its metabolism, exopolysaccharides synthesis, and the c‐di‐ GMP signaling network. In addition, this work provides a comprehensive functional annotation of carbohydrate metabolism pathways, such as those related to glucose, glycerol, acetan, levan, and cellulose. Findings of this multi‐genomic study expand understanding of the genetic variation within the Komagataeibacter genus and facilitate exploiting of its full potential for bionanocellulose production at the industrial scale.