Publications of NIPGR Scientists

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Author: search.filters.author.Chattopadhyay, DebasisSubject: search.filters.subject.Solanum lycopersicum

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    Genome-wide sequence variations between wild and cultivated tomato species revisited by whole genome sequence mapping
    (BioMed Central Ltd, 2017) Sahu, Kamlesh Kumar; Chattopadhyay, Debasis
    BACKGROUND: Cultivated tomato (Solanum lycopersicum L.) is the second most important vegetable crop after potato and a member of thirteen interfertile species of Solanum genus. Domestication and continuous selection for desirable traits made cultivated tomato species susceptible to many stresses as compared to the wild species. In this study, we analyzed and compared the genomes of wild and cultivated tomato accessions to identify the genomic regions that encountered changes during domestication. RESULTS: Analysis was based on SNP and InDel mining of twentynine accessions of twelve wild tomato species and forty accessions of cultivated tomato. Percentage of common SNPs among the accessions within a species corresponded with the reproductive behavior of the species. SNP profiles of the wild tomato species within a phylogenetic subsection varied with their geographical distribution. Interestingly, the ratio of genic SNP to total SNPs increased with phylogenetic distance of the wild tomato species from the domesticated species, suggesting that variations in gene-coding region play a major role in speciation. We retrieved 2439 physical positions in 1594 genes including 32 resistance related genes where all the wild accessions possessed a common wild variant allele different from all the cultivated accessions studied. Tajima's D analysis predicted a very strong purifying selection associated with domestication in nearly 1% of its genome, half of which is contributed by chromosome 11. This genomic region with a low Tajima's D value hosts a variety of genes associated with important agronomic trait such as, fruit size, tiller number and wax deposition. CONCLUSION: Our analysis revealed a broad-spectrum genetic base in wild tomato species and erosion of that in cultivated tomato due to recurrent selection for agronomically important traits. Identification of the common wild variant alleles and the genomic regions undergoing purifying selection during cultivation would facilitate future breeding program by introgression from wild species.
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    The tomato genome sequence provides insights into fleshy fruit evolution
    (NPG, 2012) The Tomato Genome Consortium; Sato, Shusei; Zamir, Dani; Giuliano, Giovanni; Tyagi, Akhilesh K.; Chattopadhyay, Debasis; et al.
    Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera 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, 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.
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    The tomato sequencing project, the first cornerstone of the international Solanaceae project (SOL)
    (Wiley-Blackwell, 2005) Mueller, Lukas A.; Tanksley, Steven D.; Giovannoni, Jim J.; Eck, Joyce van; Stack, Stephen; Choi, Doil; Kim, Byung Dong; Chen, Mingsheng; Cheng, Zhukuan; Li, Chuanyou; Ling, Hongqing; Xue, Yongbiao; Seymour, Graham; Bishop, Gerard; Bryan, Glenn; Sharma, Rameshwar; Khurana, Jitendra; Tyagi, Akhilesh K.; Chattopadhyay, Debasis; Singh, Nagendra K.; Stiekema, Willem; Lindhout, P.; Jesse, Taco; Lankhorst, Rene Klein; Bouzayen, Mondher; Shibata, Daisuke; Tabata, Satoshi; Granell, Antonio; Botella, Miguel A.; Giuliano, Giovanni; Frusciante, Luigi; Causse, Mathilde; Zamir, Dani
    The genome of tomato (Solanum lycopersicum) is being sequenced by an international consortium of 10 countries (Korea, China, the United Kingdom, India, The Netherlands, France, Japan, Spain, Italy and the United States) as part of a larger initiative called the ‘International Solanaceae Genome Project (SOL): Systems Approach to Diversity and Adaptation’. The goal of this grassroots initiative, launched in November 2003, is to establish a network of information, resources and scientists to ultimately tackle two of the most significant questions in plant biology and agriculture: (1) How can a common set of genes/proteins give rise to a wide range of morphologically and ecologically distinct organisms that occupy our planet? (2) How can a deeper understanding of the genetic basis of plant diversity be harnessed to better meet the needs of society in an environmentally friendly and sustainable manner? The Solanaceae and closely related species such as coffee, which are included in the scope of the SOL project, are ideally suited to address both of these questions. The first step of the SOL project is to use an ordered BAC approach to generate a high quality sequence for the euchromatic portions of the tomato as a reference for the Solanaceae. Due to the high level of macro and micro-synteny in the Solanaceae the BAC-by-BAC tomato sequence will form the framework for shotgun sequencing of other species. The starting point for sequencing the genome is BACs anchored to the genetic map by overgo hybridization and AFLP technology. The overgos are derived from approximately 1500 markers from the tomato high density F2-2000 genetic map (http://sgn.cornell.edu/). These seed BACs will be used as anchors from which to radiate the tiling path using BAC end sequence data. Annotation will be performed according to SOL project guidelines. All the information generated under the SOL umbrella will be made available in a comprehensive website. The information will be interlinked with the ultimate goal that the comparative biology of the Solanaceae — and beyond — achieves a context that will facilitate a systems biology approach.