title: Assembly and validation of the genome of the nonmodel basal angiosperm Amborella.
abstract: Genome sequencing with next-generation sequence (NGS) technologies can now be applied to organisms pivotal to addressing fundamental biological questions, but with genomes previously considered intractable or too expensive to undertake. However, for species with large and complex genomes, extensive genetic and physical map resources have, until now, been required to direct the sequencing effort and sequence assembly. As these resources are unavailable for most species, assembling high-quality genome sequences from NGS data remains challenging. We describe a strategy that uses NGS, fluorescence in situ hybridization, and whole-genome mapping to assemble a high-quality genome sequence for Amborella trichopoda, a nonmodel species crucial to understanding flowering plant evolution. These methods are applicable to many other organisms with limited genomic resources.
authors.affiliation: Department of Biology, University of Florida, Gainesville, FL 32611, USA.
authors.forename: Srikar
authors.initials: S
authors.lastname: Chamala
authors.forename: Andre S
authors.initials: AS
authors.lastname: Chanderbali
authors.forename: Joshua P
authors.initials: JP
authors.lastname: Der
authors.forename: Tianying
authors.initials: T
authors.lastname: Lan
authors.forename: Brandon
authors.initials: B
authors.lastname: Walts
authors.forename: Victor A
authors.initials: VA
authors.lastname: Albert
authors.forename: Claude W
authors.initials: CW
authors.lastname: dePamphilis
authors.forename: Jim
authors.initials: J
authors.lastname: Leebens-Mack
authors.forename: Steve
authors.initials: S
authors.lastname: Rounsley
authors.forename: Stephan C
authors.initials: SC
authors.lastname: Schuster
authors.forename: Rod A
authors.initials: RA
authors.lastname: Wing
authors.forename: Nianqing
authors.initials: N
authors.lastname: Xiao
authors.forename: Richard
authors.initials: R
authors.lastname: Moore
authors.forename: Pamela S
authors.initials: PS
authors.lastname: Soltis
authors.forename: Douglas E
authors.initials: DE
authors.lastname: Soltis
authors.forename: W Brad
authors.initials: WB
authors.lastname: Barbazuk
mesh_terms: D020451:Contig Mapping / Q000379:methods*; D018745:Genome, Plant; D017404:In Situ Hybridization, Fluorescence; D017422:Sequence Analysis, DNA / Q000379:methods*; D064028:Tracheophyta / Q000235:genetics*