Gene_locus Report for: lacsa-a0a2j6mjs5

(Below N is a link to NCBI taxonomic web page and E link to ESTHER at designed phylum.)
> cellular organisms: N E > Eukaryota: N E > Viridiplantae: N E > Streptophyta: N E > Streptophytina: N E > Embryophyta: N E > Tracheophyta: N E > Euphyllophyta: N E > Spermatophyta: N E > Magnoliophyta: N E > Mesangiospermae: N E > eudicotyledons: N E > Gunneridae: N E > Pentapetalae: N E > asterids: N E > campanulids: N E > Asterales: N E > Asteraceae: N E > Cichorioideae: N E > Cichorieae: N E > Lactucinae: N E > Lactuca: N E > Lactuca sativa: N E

Title: Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce
Reyes-Chin-Wo S, Wang Z, Yang X, Kozik A, Arikit S, Song C, Xia L, Froenicke L, Lavelle DO and Michelmore RW <9 more 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 (- 9)
Ref: Nat Commun, 8:14953, 2017 : PubMed
Abstract


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

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.