Tomato Genome for Comparative Genomics
Authors: Dr. Amolkumar U Solanke and Dr. Amitha SV Mithra
NRC Plant Biotechnology, LBS Building, IARI, Pusa Campus, New Delhi

The tomato genome sequenced by International Tomato genome Sequencing Consortium (Tomato Genome Consortium, 2012) presently serves as a powerful resource to identify gene functions and clone agronomically important genes and alleles not only from tomato but also from less studied crop species through comparative analysis across the Solanaceae species.

Diversity in Solanaceae:
The Solanaceae is the third most economically important plant taxon and an important family in relation to vegetable crops. It consists of ~3000 species belonging to 90 genera. Members of Solanaceae are extremely diverse in nature. These species are found in hot deserts as well as in wettest tropical rain forests and are very small herbs to very tall trees. The diversity among these family members is also found in terms of its utilization. Most of the species are used for vegetable purpose. Some species also have medicinal properties producing various important secondary metabolites.

Many Solanaceae species have a basic set of 12 chromosomes and are diploid in nature, indicating an absence of large genome duplications and polyploidizations during the evolutionary history of this family (Wu and Tanksley, 2010). There are many methods to analyse the relationship between species which do not hybridize, like use of morphological, cytological and molecular markers. However, the comparisons of plant species via their genetic maps or DNA sequences in a phylogenetic context can provide the most meaningful insights into their comparative biology. Different markers like RAPD, ISSR, AFLP, SSR, SNPs have been employed to analyse genetic relationships among the Solanaceae species. Several phylogenetic studies of Solanaceae family members revealed close relationship among their genomes and suggested that the deep understanding of one genome can provide information about genome structure and function of the entire Solanaceae family (Mueller et al., 2005).

Genetic maps:
Closely linked genes in one species have a propensity to be closely linked in other species too while loosely linked genes in one species tend to be unlinked in other related species. This is the basis of comparative gene mapping. Conservation and disruption of linkage and synteny depends on the chromosomal rearrangements. Gene order is often conserved among related species. Relative positions of major genes and QTLs controlling qualitative and quantitative traits on comparative alignment clearly show that across Solanaceae species their positions are the same. Identification of genes for a trait in one species helps to isolate corresponding candidate genes from other related species. Comparison of QTLs governing fruit weight, shape and colour with the positions of similar loci in tomato, potato and pepper revealed that 40% of the different loci have putative orthologous counterparts in at least one of these crop species, indicating conservation of gene function (Doganlar et al., 2002a). These QTLs from tomato also have been reported to have orthologs in other plants (Zygier et al., 2005). Comparisons of tomato and eggplant maps revealed large scale conservation with 28 rearrangements in their genomes (Doganlar et al., 2002b). Comparison of Capsicum and tomato genetic maps revealed 18 homeologous linkage blocks. There are 5 translocations, 10 paracentric inversions, 2 pericentric inversions and 4 dissociations/associations in genomic regions of tomato, potato and pepper genomes which differentiate them from one another (Livingstone et al., 1999).

Comparative genomics:
Fully sequenced high quality tomato genome serves as reference to map onto its sequenced data, such as ESTs, methyl-filtered sequences or low Cot sequences from other species. Clustering and assembly of all the available ESTs into gene indices has revealed high degree of sequence conservation as well as species-specific transcripts among Solanaceae (Rensink et al., 2005). Complete sequence information, coupled with increasing number of EST projects, now allows for inter-species sequence comparisons at micro- as well as macro-levels. Wang et al. (2008) sequenced and did comparative analysis of conserved syntenic segments in the Solanaceae. Analysis of GC content of Solanaceae gene indices revealed a narrow deviation in GC content. Microarrays based on expressed sequences have also been used for comparative expression analysis in closely related heterologous species of Solanaceae (Moore et al., 2005).

Thus the beauty of Solanaceae family is that the gene content of the different species is similar despite the different phenotypic outcomes. Thus the basic features of the Solanaceae species and closely related species are helpful to address fundamental questions in plant biology through comparative genomics approach for which tomato is emerging as the potential model reference genome.

Doganlar S, Frary A, Daunay MC, Lester RN and Tanksley SD (2002a) Conservation of gene function in the Solanaceae as revealed by comparative mapping of domestication traits in eggplant. Genetics 161, 1713-1726
Doganlar S, Frary A, Daunay MC, Lester RN and Tanksley SD (2002b) A comparative genetic linkage map of eggplant (Solanum melongena) and its implications for genome evolution in the Solanaceae. Genetics 161, 1697-1711
Livingstone KD, Lackney VK, Blauth JR, Van Wijk R and Jahn MK (1999) Genome mapping in capsicum and the evolution of genome structure in the Solanaceae. Genetics 152, 1183-1202
Moore S, Payton P, Wright M, Tanksley S and Giovannoni J (2005) Utilization of tomato microarrays for comparative gene expression analysis in the Solanaceae. J. Exp. Bot. 56, 2885-2895
Mueller LA, Solow TH, Taylor N, Skwarecki B, Buels R, Binns J, Lin C, Wright MH, Ahrens R and Wang Y (2005) The SOL Genomics Network. a comparative resource for Solanaceae biology and beyond. Plant Physiol. 138, 1310-1317
Rensink WA, Lee Y, Liu J, Iobst S, Ouyang S, and Buell CR (2005) Comparative analyses of six solanaceous transcriptomes reveal a high degree of sequence conservation and species-specific transcripts. BMC Genomics 6, 124
The Tomato Genome Consortium (2012) Tomato genome sequencing and comparative analysis reveal two consecutive triplications that spawned genes influencing fruit characteristics. Nature 485, 635-641 (Solanke AU is one of the author in the consortium)
Wang Y, Diehl A, Wu FN, Vrebalov J, Giovannoni J, Siepel A, Tanksley SD (2008) Sequencing and comparative analysis of a conserved syntenic segment in the Solanaceae. Genetics 180, 391-408
Wu F and Tanksley SD (2010) Chromosomal evolution in the plant family Solanaceae. BMC Genomics 11, 182
Zygier S, Chaim AB, Efrati A, Kaluzky G, Borovsky Y and Paran I (2005) QTLs mapping for fruit size and shape in chromosomes 2 and 4 in pepper and a comparison of the pepper QTL map with that of tomato. Theor. Appl. Genet. 111, 437-445

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