title: The 19 genomes of Drosophila: a BAC library resource for genus-wide and genome-scale comparative evolutionary research.
abstract: The genus Drosophila has been the subject of intense comparative phylogenomics characterization to provide insights into genome evolution under diverse biological and ecological contexts and to functionally annotate the Drosophila melanogaster genome, a model system for animal and insect genetics. Recent sequencing of 11 additional Drosophila species from various divergence points of the genus is a first step in this direction. However, to fully reap the benefits of this resource, the Drosophila community is faced with two critical needs: i.e., the expansion of genomic resources from a much broader range of phylogenetic diversity and the development of additional resources to aid in finishing the existing draft genomes. To address these needs, we report the first synthesis of a comprehensive set of bacterial artificial chromosome (BAC) resources for 19 Drosophila species from all three subgenera. Ten libraries were derived from the exact source used to generate 10 of the 12 draft genomes, while the rest were generated from a strategically selected set of species on the basis of salient ecological and life history features and their phylogenetic positions. The majority of the new species have at least one sequenced reference genome for immediate comparative benefit. This 19-BAC library set was rigorously characterized and shown to have large insert sizes (125-168 kb), low nonrecombinant clone content (0.3-5.3%), and deep coverage (9.1-42.9×). Further, we demonstrated the utility of this BAC resource for generating physical maps of targeted loci, refining draft sequence assemblies and identifying potential genomic rearrangements across the phylogeny.
authors.affiliation: Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA.
authors.forename: Xiang
authors.initials: X
authors.lastname: Song
authors.forename: Jose Luis
authors.initials: JL
authors.lastname: Goicoechea
authors.forename: Jetty S S
authors.initials: JS
authors.lastname: Ammiraju
authors.forename: Meizhong
authors.initials: M
authors.lastname: Luo
authors.forename: Ruifeng
authors.initials: R
authors.lastname: He
authors.forename: Jinke
authors.initials: J
authors.lastname: Lin
authors.forename: So-Jeong
authors.initials: SJ
authors.lastname: Lee
authors.forename: Nicholas
authors.initials: N
authors.lastname: Sisneros
authors.forename: Tom
authors.initials: T
authors.lastname: Watts
authors.forename: David A
authors.initials: DA
authors.lastname: Kudrna
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Golser
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Ashley
authors.forename: Kristi
authors.initials: K
authors.lastname: Collura
authors.forename: Michele
authors.initials: M
authors.lastname: Braidotti
authors.forename: Yeisoo
authors.initials: Y
authors.lastname: Yu
authors.forename: Luciano M
authors.initials: LM
authors.lastname: Matzkin
authors.forename: Bryant F
authors.initials: BF
authors.lastname: McAllister
authors.forename: Therese Ann
authors.initials: TA
authors.lastname: Markow
authors.forename: Rod A
authors.initials: RA
authors.lastname: Wing
mesh_terms: D000818:Animals; D005075:Biological Evolution; D002874:Chromosome Mapping; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics*; D059006:Chromosomes, Insect / Q000235:genetics*; D004331:Drosophila melanogaster / Q000235:genetics*; D017344:Genes, Insect; D049750:Genome, Insect; D015698:Genomic Library; D010802:Phylogeny; D017422:Sequence Analysis, DNA