The genome sequence of the outbreeding globe artichoke constructed de novo incorporating a phase-aware low-pass sequencing strategy of F1 progeny

Scientific Reports
Davide ScaglioneSergio Lanteri

Abstract

Globe artichoke (Cynara cardunculus var. scolymus) is an out-crossing, perennial, multi-use crop species that is grown worldwide and belongs to the Compositae, one of the most successful Angiosperm families. We describe the first genome sequence of globe artichoke. The assembly, comprising of 13,588 scaffolds covering 725 of the 1,084 Mb genome, was generated using ~133-fold Illumina sequencing data and encodes 26,889 predicted genes. Re-sequencing (30×) of globe artichoke and cultivated cardoon (C. cardunculus var. altilis) parental genotypes and low-coverage (0.5 to 1×) genotyping-by-sequencing of 163 F1 individuals resulted in 73% of the assembled genome being anchored in 2,178 genetic bins ordered along 17 chromosomal pseudomolecules. This was achieved using a novel pipeline, SOILoCo (Scaffold Ordering by Imputation with Low Coverage), to detect heterozygous regions and assign parental haplotypes with low sequencing read depth and of unknown phase. SOILoCo provides a powerful tool for de novo genome analysis of outcrossing species. Our data will enable genome-scale analyses of evolutionary processes among crops, weeds, and wild species within and beyond the Compositae, and will facilitate the identification of economically ...Continue Reading

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Citations

May 28, 2016·Nature Genetics·Jordi Garcia-Mas, Manuel Rodriguez-Concepcion
Apr 13, 2017·Nature Communications·Sebastian Reyes-Chin-WoRichard W Michelmore
Oct 11, 2017·The Journal of Heredity·Brook T MoyersJohn K McKay
Jul 19, 2017·Scientific Reports·Alberto AcquadroSergio Lanteri
Aug 15, 2019·Scientific Reports·Lorenzo BarchiGiuseppe Leonardo Rotino
Oct 15, 2019·Database : the Journal of Biological Databases and Curation·Daniel VitalesSònia Garcia
Aug 21, 2020·G3 : Genes - Genomes - Genetics·Alberto AcquadroSergio Lanteri
Sep 29, 2020·Molecular Ecology Resources·Simei HeShengchao Yang
Feb 27, 2021·Frontiers in Plant Science·Xinwei WangJianwei Xiao
Nov 2, 2021·Nucleic Acids Research·Marco Di MarsicoRiccardo Aiese Cigliano

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Datasets Mentioned

BETA
PRJNA64989
SUB874020
PRJNA238069

Methods Mentioned

BETA
flow cytometry
RNAseq
whole-genome shotgun sequencing
genotyping
degradome sequencing
electrophoresis
PCR
RNA-seq

Software Mentioned

calls2csvr
qtl
Genome Tools
HMMER2
TopHat2 aligner
HAPCUT
RepeatMasker
ALLPATHS
AgriGo
SynMap

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