Tomato (Solanum lycopersicum) is a major crop and an important model plant for scientific research on fruit development and quality. Tomato is also an important model crop for classical genetics and genome research due to its wide environmental adaptability, short life cycle, photoperiod sensitivity, high self-pollination, and small genome (950 Mb). The availability of the genome sequence has revolutionized the paradigm of genetics and genomics of this species. A draft genome of the tomato cultivar Heinz 1706 produced using shotgun sequencing technology was released in 2012 and widely used as a reference genome for scientific research. Scientists identified a total of approximately 34,727 genes in the decoded tomato genome, 97.4% of which have been accurately mapped to chromosomes.

CD Genomics is a leading service provider for agricultural genomics research, offering reliable tomato genome sequencing services to support research and breeding efforts in the field of tomato genomics for clients worldwide. Our services help breed new tomato varieties with excellent traits such as high yield, high quality, pests and diseases resistance, and stress resistance.

Our tomato genome sequencing service

CD Genomics offers comprehensive and customizable tomato genome sequencing services using cutting-edge technology and expertise to characterize the tomato genome at the cytogenetic, genetic, and molecular levels. Our services cover all stages of the sequencing process, from library preparation to data analysis, ensuring high-quality and accurate results.

With our advanced next-generation sequencing and long-read sequencing technology platforms, as well as bioinformatics tools, we can sequence the genomes of cultivated tomatoes and wild tomatoes, compare and analyze the domestication process of tomatoes, and discover alleles in wild tomatoes to provide rich reference resources for tomato breeding. The goal of our tomato genome sequencing project is to generate new information and resources to elucidate how a common set of genes gives rise to a wide range of morphologically and ecologically unique organisms, and how to better understand the genetic basis of plant diversity to meet The demand for sustainable food crop production for a rapidly growing world population.

Our sequencing strategies for tomato

We integrate tomato genome results combining BAC-by-BAC and WGS data to ensure the highest quality assembly and become a valuable resource for basic and applied research efforts.

• BAC-by-BAC strategy

The process of sequencing the tomato genome begins with careful planning and strategy development. We initially adopted a BAC-by-BAC approach, leveraging dense genetic and physical maps to ensure accurate assembly of the genome. This strategy allowed us to systematically sequence and analyze individual bacterial artificial chromosome (BAC) clones, providing a detailed understanding of the tomato genetic landscape.

• Whole-genome shotgun (WGS) strategy

Based on NGS technology, we offer WGS strategies for rapid and cost-effective sequencing of the entire tomato genome, providing a comprehensive snapshot of its genetic makeup.

Applications of tomato genome sequencing

• As a reference for adaptability and diversification of the Solanaceae family

The tomato genome can serve as a reference for studying the adaptability and diversification of the Solanaceae family. By comparing the genome sequences of different tomato varieties and wild relatives, researchers can identify genetic variations associated with important traits such as disease resistance, fruit quality, and environmental adaptation.

• Analyze biochemical pathways and gene networks

Genome sequencing can comprehensively explore the biochemical pathways and gene networks behind various biological processes in tomatoes. By deciphering the genetic basis of important physiological and developmental traits, researchers can gain a deeper understanding of the molecular mechanisms that control these processes.

• Marker-assisted breeding

The availability of the tomato genome sequence has revolutionized breeding programs by enabling marker-assisted selection. By identifying genetic markers associated with desired traits, breeders can accelerate the development of new tomato varieties with enhanced agronomic properties.

• Comparative genomics and evolutionary studies

The tomato genome serves as a valuable resource for comparative genomics and evolutionary studies. By comparing the tomato genome with those of other Solanaceae species, researchers can gain insights into the evolutionary relationships, gene family expansions, and genomic rearrangements that have shaped the Solanaceae family. This comparative approach enhances our understanding of plant evolution and provides a foundation for further research in diverse plant species.

Case study of tomato genome sequencing

The Tomato Genome Consortium sequenced and analyzed the tomato genome, revealing its genomic characteristics and its evolutionary relationships. The researchers compared the genomes of domesticated tomato (Solanum lycopersicum), its wild relative tomato (S. pimpinellifolium) and potato (S. tuberosum). The tomato genomes show minor nucleotide differences from their wild relatives as well as signs of recent mixing. However, they show significant differences from the potato genome.

The tomato genome, with a predicted size of about 900 Mb, was found to be highly homozygous with other economically important lycophytes. Annotation of the tomato and potato genomes predicted similar numbers of protein-coding genes, supported by RNA-seq data. Comparative genomic studies identified nucleotide divergence, inversions, and orthologous gene pairs between tomato and potato. These findings provide insights into the evolutionary relationships and genetic differences between these species.

• Gene family evolution and subfunctionalization: The tomato genome sequence provides a starting point for studying gene family evolution and subfunctionalization in the Solanaceae. A notable example is the self-pruning (SP) gene family, which includes a homolog of Arabidopsis FT (encoding the mobile flowering hormone florigenin) and its antagonist SP (encoding a direct homolog of TFL1).
• Genetic diversity and domestication: The genome sequences of tomato and its wild relative S. pimpinellifolium have unlocked the genetic bottleneck that has narrowed genetic diversity in tomato.

Fig. 1. The genome of the inbred tomato cultivar 'Heinz 1706' was sequenced and assembled using a combination of Sanger and "next generation" technologies. (Tomato Genome Consortium, 2012)

CD Genomics offers cutting-edge tomato genome sequencing services to provide comprehensive genomic information to researchers and breeders for their studies. We aim to provide data to support basic research on the genetics of important tomato traits and to promote tomato improvement. If you are interested, please feel free to contact us.

Reference

1. Tomato Genome Consortium. The tomato genome sequence provides insights into fleshy fruit evolution. Nature. 485.7400 (2012): 635.