Michelmore R

References (2)

Title : The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut - Bertioli_2016_Nat.Genet_48_438
Author(s) : Bertioli DJ , Cannon SB , Froenicke L , Huang G , Farmer AD , Cannon EK , Liu X , Gao D , Clevenger J , Dash S , Ren L , Moretzsohn MC , Shirasawa K , Huang W , Vidigal B , Abernathy B , Chu Y , Niederhuth CE , Umale P , Araujo AC , Kozik A , Kim KD , Burow MD , Varshney RK , Wang X , Zhang X , Barkley N , Guimaraes PM , Isobe S , Guo B , Liao B , Stalker HT , Schmitz RJ , Scheffler BE , Leal-Bertioli SC , Xun X , Jackson SA , Michelmore R , Ozias-Akins P
Ref : Nat Genet , 48 :438 , 2016
Abstract : Cultivated peanut (Arachis hypogaea) is an allotetraploid with closely related subgenomes of a total size of -2.7 Gb. This makes the assembly of chromosomal pseudomolecules very challenging. As a foundation to understanding the genome of cultivated peanut, we report the genome sequences of its diploid ancestors (Arachis duranensis and Arachis ipaensis). We show that these genomes are similar to cultivated peanut's A and B subgenomes and use them to identify candidate disease resistance genes, to guide tetraploid transcript assemblies and to detect genetic exchange between cultivated peanut's subgenomes. On the basis of remarkably high DNA identity of the A. ipaensis genome and the B subgenome of cultivated peanut and biogeographic evidence, we conclude that A. ipaensis may be a direct descendant of the same population that contributed the B subgenome to cultivated peanut.
ESTHER : Bertioli_2016_Nat.Genet_48_438
PubMedSearch : Bertioli_2016_Nat.Genet_48_438
PubMedID: 26901068
Gene_locus related to this paper: aradu-a0a6p4dix2 , aradu-a0a6p4dpj0 , aradu-a0a6p4dix7

Title : The genome sequence of the outbreeding globe artichoke constructed de novo incorporating a phase-aware low-pass sequencing strategy of F1 progeny - Scaglione_2016_Sci.Rep_6_19427
Author(s) : Scaglione D , Reyes-Chin-Wo S , Acquadro A , Froenicke L , Portis E , Beitel C , Tirone M , Mauro R , Lo Monaco A , Mauromicale G , Faccioli P , Cattivelli L , Rieseberg L , Michelmore R , Lanteri S
Ref : Sci Rep , 6 :19427 , 2016
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 (30x) of globe artichoke and cultivated cardoon (C. cardunculus var. altilis) parental genotypes and low-coverage (0.5 to 1x) 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 important genes from related species.
ESTHER : Scaglione_2016_Sci.Rep_6_19427
PubMedSearch : Scaglione_2016_Sci.Rep_6_19427
PubMedID: 26786968
Gene_locus related to this paper: cyncs-a0a103ymi4 , cyncs-a0a103ymk3 , cyncs-a0a103y8j9 , cyncs-a0a118jxn5 , cyncs-a0a103ylr0 , cyncs-a0a103y277 , cyncs-a0a103xay4 , cyncs-a0a118jvt7 , cyncs-a0a103ynz3 , cyncs-a0a103xkm8 , cyncs-a0a103xww5 , cyncs-a0a103yb15