DOI: 10.5061/dryad.8100
title: Data from: BAC library construction, screening and clone sequencing of lake whitefish (Coregonus clupeaformis, Salmonidae) towards the elucidation of adaptive species divergence

description: 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.
description: CARB assembly (ace)
 fileDe novo assembly of
 pyrosequencing data (454 Genome Sequencer FLX System, with long-read GS
 FLX Titanium chemistry) for 2 pooled BAC clones targeted for
 carboxylesterase (CARB). GS De novo Assembler software (Roche, Basel,
 Switzerland) was used with the following parameters: large or complex
 genome option, trimming database of the pCC1BAC HindIII vector, screening
 database of the E. coli str. K12 substr. DH10B genome (GenBank [accession
 number CP000948]), minimum overlap length 200 bp, minimum overlap identity
 98% and minimum contig length 500 bp. Raw data available at Sequence Read
 Archive at NCBI: SRP003484CARB.aceHSC assembly (ace) fileDe novo assembly of pyrosequencing data (454 Genome Sequencer FLX System, with long-read GS FLX Titanium chemistry) for 2 pooled BAC clones targeted for heat shock cognate 70 kDa protein (HSC). GS De novo Assembler software (Roche, Basel, Switzerland) was used with the following parameters: large or complex genome option, trimming database of the pCC1BAC HindIII vector, screening database of the E. coli str. K12 substr. DH10B genome (GenBank [accession number CP000948]), minimum overlap length 200 bp, minimum overlap identity 98% and minimum contig length 500 bp. Raw data available at Sequence Read Archive at NCBI: SRP003484HSC.aceMDH assembly (ace) fileDe novo assembly of pyrosequencing data (454 Genome Sequencer FLX System, with long-read GS FLX Titanium chemistry) for 2 pooled BAC clones targeted for cytoplasmic malate dehydrogenase (MDH). GS De novo Assembler software (Roche, Basel, Switzerland) was used with the following parameters: large or complex genome option, trimming database of the pCC1BAC HindIII vector, screening database of the E. coli str. K12 substr. DH10B genome (GenBank [accession number CP000948]), minimum overlap length 200 bp, minimum overlap identity 98% and minimum contig length 500 bp. Raw data available at Sequence Read Archive at NCBI: SRP003484MDH.aceGAPDH assembly (ace) fileDe novo assembly of pyrosequencing data (454 Genome Sequencer FLX System, with long-read GS FLX Titanium chemistry) for 2 pooled BAC clones targeted for glyceraldehyde-3-phosphate dehydrogenase (GAPDH). GS De novo Assembler software (Roche, Basel, Switzerland) was used with the following parameters: large or complex genome option, trimming database of the pCC1BAC HindIII vector, screening database of the E. coli str. K12 substr. DH10B genome (GenBank [accession number CP000948]), minimum overlap length 200 bp, minimum overlap identity 98% and minimum contig length 500 bp. Raw data available at Sequence Read Archive at NCBI: SRP003484GAPDH.aceMHC assembly (ace) fileDe novo assembly of pyrosequencing data (454 Genome Sequencer FLX System, with long-read GS FLX Titanium chemistry) for 2 pooled BAC clones targeted for MHC classII beta (MHC). GS De novo Assembler software (Roche, Basel, Switzerland) was used with the following parameters: large or complex genome option, heterozygosity option, trimming database of the pCC1BAC HindIII vector, screening database of the E. coli str. K12 substr. DH10B genome (GenBank [accession number CP000948]), minimum overlap length 200 bp, minimum overlap identity 98% and minimum contig length 500 bp. Raw data available at Sequence Read Archive at NCBI: SRP003484MHC.ace