Kozik A

References (2)

Title : Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce - Reyes-Chin-Wo_2017_Nat.Commun_8_14953
Author(s) : Reyes-Chin-Wo S , Wang Z , Yang X , Kozik A , Arikit S , Song C , Xia L , Froenicke L , Lavelle DO , Truco MJ , Xia R , Zhu S , Xu C , Xu H , Xu X , Cox K , Korf I , Meyers BC , Michelmore RW
Ref : Nat Commun , 8 :14953 , 2017
Abstract : Lettuce (Lactuca sativa) is a major crop and a member of the large, highly successful Compositae family of flowering plants. Here we present a reference assembly for the species and family. This was generated using whole-genome shotgun Illumina reads plus in vitro proximity ligation data to create large superscaffolds; it was validated genetically and superscaffolds were oriented in genetic bins ordered along nine chromosomal pseudomolecules. We identify several genomic features that may have contributed to the success of the family, including genes encoding Cycloidea-like transcription factors, kinases, enzymes involved in rubber biosynthesis and disease resistance proteins that are expanded in the genome. We characterize 21 novel microRNAs, one of which may trigger phasiRNAs from numerous kinase transcripts. We provide evidence for a whole-genome triplication event specific but basal to the Compositae. We detect 26% of the genome in triplicated regions containing 30% of all genes that are enriched for regulatory sequences and depleted for genes involved in defence.
ESTHER : Reyes-Chin-Wo_2017_Nat.Commun_8_14953
PubMedSearch : Reyes-Chin-Wo_2017_Nat.Commun_8_14953
PubMedID: 28401891
Gene_locus related to this paper: lacsa-a0a2j6jnd3 , lacsa-a0a2j6l6y4 , lacsa-a0a2j6mjs5 , lacsa-a0a2j6mk82 , lacsa-a0a2j6k5z4 , lacsa-a0a2j6mk08 , lacsa-a0a2j6mhc5 , lacsa-a0a2j6m8d0 , lacsa-a0a2j6mdb6 , lacsa-a0a2j6mdh6 , lacsa-a0a2j6jnf0 , lacsa-a0a2j6mji4 , lacsa-a0a2j6ke81 , lacsa-a0a2j6jip3 , lacsa-a0a2j6jir5 , lacsa-a0a2j6ksa7 , lacsa-a0a2j6l4a3

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