Globe Artichoke Microsatellite DataBase - DISAFA

The globe artichoke genome has been recently sequenced.

D. Scaglione, S. Reyes-Chin-Wo, A. Acquadro, L. Froenicke, E. Portis, C. Beitel, M. Tirone, R. Mauro, A. Lo Monaco, G. Mauromicale, P. Faccioli, L. Cattivelli, L. Rieseberg, R. Michelmore & S Lanteri. The genome sequence of the outbreeding globe artichoke constructed de novo incorporating a phase-aware low-pass sequencing strategy of F1 progeny. Sci. Rep. 6, 19427; doi: 10.1038/srep19427 (2016)

It represents the first published genome sequence of a Compositae crop species fully available to the scientific community.

The genome sequence has been unravelled by a consortium including the University of Torino (DISAFA, Plant Genetics and Breeding, Italy, team leader Sergio Lanteri), the University of California (The Genome Center, Davis, CA, USA, team leader Richard Michelmore) and the Università di Catania (Di3A, Italy, team leader Giovanni Mauromicale) in the framework of the Compositae Genome Project (CGP).

The project started in 2011 and later on was joined by the University of British Columbia (Canada, team leader Loren Rieseberg) and Crea (Genomics Research Centre, Fiorenzuola d’Arda, Italy, team leader Luigi Cattivelli).

GlobeArtichokeGenome

The genome draft was assembled from ~133-fold next-generation sequencing data,  into 13K scaffolds (N50= 125 Kbp, L50=1411), which represent 725 Mb of genomic sequence with a de novo prediction of 26,906 gene models. Thanks to a low coverage whole genome-sequencing of an F1 highly segregating mapping population, a dense genetic map based on the two-way pseudo test cross strategy, was built up and used for anchoring and orienting 73% of the assembled scaffolds in 17 reconstructed pseudomolecules.

This was achieved thanks to the development of a novel pipeline, namely SOILoCo (Scaffold Ordering by Imputation with Low Coverage), which detects heterozygous regions and assigns parental haplotypes with low sequencing read depth (missing genotypes per block/type = 30-40%) and of unknown phase. In the manuscript major emphasis is given to the newly developed tool applied for genetically anchoring de novo assembled scaffolds without the availability of a validated reference genome, and whose accuracy and robustness was validated by aligning the two parental maps we independently generated. Although our pipeline was developed to analyze F1 progeny data, it may be also used for mapping with other progenies, such as F2, RILs, and BC populations. Actually, this scenario has not been approached in literature so far and can be of interest to a wide range of plant as well as animal genetics and genomics investigators.

Bioinformatics analyses have also provided insights on the globe artichoke genome biology in terms of: i) protein coding genes along with distribution of gene families and inferences on speciation time, ii) miRNA genes and their repetitive context, iii) repetitive elements and insertion time.

Genome Assemblies (FASTA Format),
(C. cardunculus var. scolymus, genotype ‘2C’)

Globe Artichoke Microsatellite Database

To gain benefit of the whole genome sequence the bulk mining of its markers in totality is imperative and critically required. Here we introduce the first microsatellite marker database CyMSatDB (Cynara cardunculus MicroSatellite DataBase) based on whole genome SSR mining.

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CyMsatDB has been presented at:
58th Italian Society of Agricultural Genetics Annual Congress Alghero
Portis E, Portis F, Valente L, Lanteri S, Acquadro A: The whole genome SSR markers database of globe artichoke. Proceedings of the 58th Italian Society of Agricultural Genetics Annual Congress, 15-18 September 2014, Alghero (Italy), Poster Communication Abstract – 1.21.
Conference Abstract
International Plant & Animal Genome Conference XXIII
Portis E, Portis F, Valente L, Gianoglio S, Cericola F, Lanteri S, Acquadro A: CyMSatDB: the globe artichoke (Cynara cardunculus var. scolymus) microsatellite database. Plant and Animal Genome XXIIIrd Conference, 10-14 January 2015, San Diego (California USA), Poster Communication.
Conference Abstract

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