title: BAC library construction, screening and clone sequencing of lake whitefish (Coregonus clupeaformis, Salmonidae) towards the elucidation of adaptive species divergence.
abstract: Genomic DNA sequences and other genomic resources are essential towards the elucidation of the genomic bases of adaptive divergence and reproductive isolation. Here, we describe the construction, characterization and screening of a nonarrayed BAC library for lake whitefish (Coregonus clupeaformis). We then show how the combined use of BAC library screening and next-generation sequencing can lead to efficient full-length assembly of candidate genes. The lake whitefish BAC library consists of 181,050 clones derived from a single heterozygous fish. The mean insert size is 92 Kb, representing 5.2 haploid genome equivalents. Ten BAC clones were isolated following a quantitative real-time PCR screening approach that targeted five previously identified candidate genes. Sequencing of these clones on a 454 GS FLX system yielded 178,000 reads with a mean length of 358 bp, for a total of 63.8 Mb. De novo assembly and annotation then allowed retrieval of contigs corresponding to each candidate gene, which also contained up- and/or downstream noncoding sequences. These results suggest that the lake whitefish BAC library combined with next-generation sequencing technologies will be key resources to achieve a better understanding of both adaptive divergence and reproductive isolation in lake whitefish species pairs as well as salmonid evolution in general.
authors.affiliation: Institut de biologie intégrative et des systèmes (IBIS), 1030 av. de la Médecine, Québec City, Québec, G1V 0A6, Canada. julie.jeukens.1@ulaval.ca
authors.forename: J
authors.initials: J
authors.lastname: Jeukens
authors.forename: B
authors.initials: B
authors.lastname: Boyle
authors.forename: I
authors.initials: I
authors.lastname: Kukavica-Ibrulj
authors.forename: J
authors.initials: J
authors.lastname: St-Cyr
authors.forename: R C
authors.initials: RC
authors.lastname: Lévesque
authors.forename: L
authors.initials: L
authors.lastname: Bernatchez
mesh_terms: D000220:Adaptation, Biological; D000818:Animals; D022202:Chromosomes, Artificial, Bacterial; D004247:DNA / Q000737:chemistry / Q000235:genetics; D019143:Evolution, Molecular; D015723:Gene Library; D049810:Genetic Speciation; D005822:Genetic Vectors; D008969:Molecular Sequence Data; D010802:Phylogeny; D012487:Salmonidae / Q000235:genetics*; D017422:Sequence Analysis, DNA
chemical_list: D004247:DNA