// Pepper

new Pepper Pan GENOME consortium is currently open, join today and enjoy its full benefits!

The Genus Capsicum, commonly referred to as pepper, is a member of the Solanaceae family. The genus includes at least 32 different species, provides a variety of fruit shapes, sizes and tastes and used for culinary, medicinal and ornamental purposes. Total chili and bell pepper production in the US in 2018 was 1.6 Billion pounds on a total of 53,900 acres harvested, valued at $US628 million (NASS, 2018). The estimated world production in 2017 is 130 Billion pounds on a total of 11.5 million acres harvested (FAO). The species Capsicum annuum is the most common of the five domesticated capsicums, including popular varieties of both sweet peppers and hot chilis. It is a mainly self-pollinated diploid species with an estimated genome size of 3.48Gbp.

 

The pepper breeding and research community needs an affordable and fast means to supplement the publicly known reference genomes with other divergent genomes representing the pepper genetic diversity and a comprehensive means to fully capture and explore the intra species genetic variance in genic and nongenic regions alike.

By joining this consortium, you can expand your genomic research efforts - you will benefit from all its de novo assembled genomes, direct linear mappings between all these genomes, transcripts mapping for each of them, statistical report and reciprocal analysis between each genome.

Capsicum Webinar

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  • consortium leader

Ilan Paran, Ph.D.  (Volcani Center, ARO)

Allen Van Deynze, Ph.D (UC Davis) 

Current participant and lines

LineType
Maor- open pollinated (Capsicum L.)Blocky
Top Seeds International-commercial line 1Blocky
Pilpel Seeds-commercial line 2Blocky
Nunhems-commercial line 3Lamuyo
Publicly available Reference (pivot)

Latest results

Quality ParameterType
TOTAL ASSEMBLY SIZE3.1 Gbp
N50140 Mbp
N9062 Mbp
UNFILLED GAPS (%N)1.2%
COMPLETE BUSCOs97%

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.