// Tomato

Tomato PAN genome consortium 

Tomato is one of the most consumed berry fruits in the world with global production of 35 million tons in 2018. It’s also the most studied edible fruit crop with thousands of publications. The reference genome of the tomato, “Heinz 1706”, was first published in Nature, May 2012. Due to the broad diversity of tomato uses and different food characteristics, there is a high need to better understand its varieties, as only a minor part is captured by one reference genome.

The tomato breeding and research community needs an affordable and fast means to supplement the already assembled reference genomes with other genomes representing the genetic diversity and a comprehensive means to fully capture and explore the intra species genetic variance of cultivated tomato.

By joining this consortium, you can expand your genomic research efforts - you will benefit from access to its de novo assembled genomes, pseudo chromosome construction, direct linear mappings between genomes, homology based annotation for each of them and full gene Presence Absence, copy number and Structural variation analysis (PAV CNV and SV) and their visualization.

  • Consortium leaders

Prof. David Francis (The Ohio State University)
Prof. Samuel Hutton (University of Florida)
Prof. Tong Geon Lee (University of Florida)

  • Current participants

4 Leading multinational seed companies

2 Academic institutes

LA0407 (L. habroachites)Wild
LA 1416 (S. pimp.)Wild

Frequently Asked Questions

How can I submit a sample?

Optimal genome assembly relies on high-quality High Molecular Weight (HMW) gDNA extraction which is suitable for our sequencing procedures. For swift and high standard results, we are offering DNA extraction as part of the service.

please contact our representative and request the documentation for tissue collection specifications and instructions.

Can hybrids be submitted?

The consortium offer is for the assembly of a homozygote sample (inbred or DH) using DeNovoMAX. Assembling a heterozygote sample requires the usage of DeNovoMAGIC which applies different sequencing data and assembly procedures. If your research requires the assembly of a heterozygote sample, we would be happy to provide it yet it is not in the scope of the consortium.

When will the project begin?

The project already started independently with each consortium member to sequence and assemble its own genome of interests.

The pan-genome analysis will start after finalizing the list of members who join the consortium and conclusion of all assemblies.

What type of files will be distributed?

Please request a detailed Technical Data Sheet from our representative. In short: The assembled sequence is delivered as .fasta, linear mappings are delivered in TSV files, annotation and gene comparison files are delivered in gff3 format.

Will data be published?

Yes. The results will be published as academic publications of the scientific committee.

What is the minimum number of participants?

5 participants are the minimum. please contact our representative and request for the latest updates of the number of genomes.

What is the payment schedule?

Payment is done in 2 installments, one 30 days after signature and the second after completion of the assembly.

Can a company join another to submit a single sample?

Companies and researchers from academia are welcome to join their budget together to be able to sequence and assemble their own genome of interest and get access to all the genomes which included in the consortium, pending approval of the consortium leadership.