Expert group meeting on “Sequencing the Saffron genome”
Rome, ENEA Headquarters, Dec 12-13, 2013
Present:
Giovanni Giuliano, ENEA
Marco Pietrella, ENEA
Sergio Lucretti, ENEA (only Dec 13)
Matteo Busconi, Catholic University of Piacenza
Silvia Fluch, Austrian Institute of Technology
Antonio Granell, University of Valencia
Gabino Sanchez Perez, Univ of Wageningen
Bahattin Tanyolac, Ege University
Thomas Schmidt, Technical University of Dresden
Carsten Pedersen, University of Copenhagen
Additional people contacted:
Jaroslav Dolezel, Plant Genomics Center, Olomouc
Josè Antonio Fernandez Perez, Univ. of Albacete
Pat Heslop-Harrison and Trude Schwarzacher, Leicester University
Stephane Rombauts, VIB Gent
Marcelino de los Mozos Pascual, CrocusBank curator
These people will form the provisional Steering Committee of the Saffron Genome Project. The committee
will meet regularly by Skype + once a year at Saffronomics WG1 meetings.
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Saffron genome size (3c): ca. 10,4 Gb (determined by JD on BCU001584 accession). Not yet known
if homo or allo-triploid.
Proposed accession for genome sequencing: BCU001722 (enough corms and leaves accessible).
Saffron resources available:
● RNA-Seq from 6 stigma developmental stages complete (ENEA, unknown Castilla-La Mancha
accession; on line by Mar 2014).
● SSR database on same material (ENEA, under construction).
● 2x Illumina coverage of BGU5084 accession (TS).
● Chloroplast sequencing os saffron and allied species under way by BT.
● C. cartwightianus genome sequencing of under way by Frank Blattner (Gatersleben): TS will invite
him to join the sequencing project and ask him about C. cartwightianus sequencing situation
Possible strategies:
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Whole genome shotgun (now possible)
Sort chromosomes and sequence each one separately (not possible for the moment: repeats have to
be found that discriminate homeologous chromosomes for sorting (FISHIS)
Whole genome shotgun
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Sequencing: 90x Illumina HiSeq: 2x100 Paired Ends (200 – 500 bp) + matepairs (1kb - 10kb). Cost:
approx 60 K€. Additional 3-5x MiSeq 2x300 (overlapping for the central 100 bases). Useful for
filling gaps and phasing the haplotypes. Cost: approx. 5-8 K€.
Assembly: w Allpaths or Soapdenovo. 1 machine available in Wageningen (max 1 Tb of shared
RAM). For larger RAM machines, we will contact Pittsburg supercomputing center (GG) or
Barcelona supercomputing center (AG).
Annotation: Additional tissues (leaves, roots, corms, anthers, tepals) will be subjected to RNA-Seq.
Proposed annotation pipelines: iTAG (S. Rombauts) and/or MakerP (iPlant).
WGS will be started ASAP and funded by own funds. Participating institutions and donating companies will
be asked to provide work and/or a financial contribution (approx. 5.000 €/institution/company). Target for
obtaining a first annotated assembly: September 2014. In the meanwhile.
Chromosome/genome sorting
Contributions :
ENEA: HMW DNA production, RNA-Seq, MiSeq, LC-MS metabolomics, chromosome sorting,
supercomputing (own and through Pittsburgh)
Wageningen: HiSeq sequencing (w financial contribution by others), assembly
Tulln: DNA production and distribution, MiSeq sequencing, project website
Valencia: GC-MS metabolomics, GBS setup, supercomputing (Barcelona), tissue culture for double haploid
or hexaploid production
Dresden: cytogenetics, annotation of major TE families
Olomouc: Chromosome sorting, MiSeq sequencing
Piacenza, Izmir: funding (to be verified)
Copenhagen: funding (to be verified), biodiversity collection
Crocusbank: Maintenance and distribution of biological material.
Additional activities:
Genotyping by sequencing of C. sativus and wild accessions using the Elshire protocol. Choice of enzymes
cutters and exploratory GBS on few samples: TG,
Sequencing gene-rich regions using methylation-sensitive enzymes: SF.
Epigenomics: MB.
10-15x PacBio long reads
40-Kb fosmid matepairs
Optical mapping.
White paper writing (coordination GG):
Introduction:
Botanical position od Iridaceae & Crocus (CP)
Chemical diversity in Iridaceae and Crocus (GG)
Status of angiosperm sequencing with reference to monocots (TG, BT)
History and uses of C. sativus, including medicinal uses (MB)
Repeats and chromosomes (TS)
Proposed project:
WGS, with time lines and deliverables (GSP, GG)
Chromosome-based strategies (JD, SL, PHH)
Additional activities (SF, BT, TG)
The target of the paper will be the saffron scientific community, funding agencies and companies. Possibility
of publication will be also explored.
Deadline for sending contributions to GG: Jan 7.