The tomato genome sequence provides insights into fleshy fruit evolution

Abstract

Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera(1) and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium(2), and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness

Quantitative analysis of the tomato nuclear proteome during Phytophthora capsici infection unveils regulators of immunity

“…Protein identification and quantification were carried out using maxquant software version 1.4.1.2 (Cox & Mann, 2008). Raw MS data files were searched against a combined S. lycopersicum (Tomato Genome, 2012) and P. capsici (Lamour et al ., 2012) genome file (Notes S1) and quantification data were acquired using the label‐free quantification tool (LFQ) within maxquant (settings outlined in Notes S2) (Cox et al ., 2014). Full details of how maxquant generates peak lists and determines false discovery rates are detailed in Cox & Mann (2008).…”

“…A detailed description, including scripts used and analysed data, can be found on the GitHub page (Stam, 2015). In short, amino acid sequences for those proteins identified by MS were extracted from the SOL genomics protein database v. ITAG2.4 (Tomato Genome, 2012). This data set was subjected to predictnls (default settings) (Cokol et al ., 2000) and nlstradamus (two‐state model; posterior threshold 0.6) (Nguyen Ba et al ., 2009) to identify proteins with nuclear localization signals, and the Nucleolar Localization Sequence Detector ( nod ) (default settings) (Scott et al ., 2010, 2011) to identify proteins with nucleolar localization signals.…”

Physiological characterization, transcriptomic profiling, and microsatellite marker mining of Lycium ruthenicum

“…The transcriptome dataset is a valuable resource not only for the construction of expression profiles but also for novel gene discovery as well as for a large number of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers, which are highly useful for variety identification, population structure analysis, and linkage map development, and will contribute to the acceleration of breeding programs. To date, certain important plants of the Solanaceae family have been sequenced, such as the tomato and the potato (Xu et al, 2011;Sato et al, 2012). The deep RNAsequencing of L. ruthenicum will aid in understanding the key aspects of the biology and evolution of Lyceum, especially the molecular basis underlying its high saline-alkaline stress tolerance.…”

The tomato genome: implications for plant breeding, genomics and evolution

“…Solanaceous crop genomics is in an exciting phase of development following the recent sequencing of the potato and tomato genomes [6,7]. Tomato ( Solanum lycopersicum L.), originated in South America, and was spread around the world to become one of the most extensively used vegetable crops.…”