title: BAC sequencing using pooled methods.
abstract: Shotgun sequencing and assembly of a large, complex genome can be both expensive and challenging to accurately reconstruct the true genome sequence. Repetitive DNA arrays, paralogous sequences, polyploidy, and heterozygosity are main factors that plague de novo genome sequencing projects that typically result in highly fragmented assemblies and are difficult to extract biological meaning. Targeted, sub-genomic sequencing offers complexity reduction by removing distal segments of the genome and a systematic mechanism for exploring prioritized genomic content through BAC sequencing. If one isolates and sequences the genome fraction that encodes the relevant biological information, then it is possible to reduce overall sequencing costs and efforts that target a genomic segment. This chapter describes the sub-genome assembly protocol for an organism based upon a BAC tiling path derived from a genome-scale physical map or from fine mapping using BACs to target sub-genomic regions. Methods that are described include BAC isolation and mapping, DNA sequencing, and sequence assembly.
authors.affiliation: Clemson University Genomics Institute, Clemson, SC, 29634, USA.
authors.forename: Christopher A
authors.initials: CA
authors.lastname: Saski
authors.forename: F Alex
authors.initials: FA
authors.lastname: Feltus
authors.forename: Laxmi
authors.initials: L
authors.lastname: Parida
authors.forename: Niina
authors.initials: N
authors.lastname: Haiminen
mesh_terms: D022202:Chromosomes, Artificial, Bacterial / Q000737:chemistry* / Q000378:metabolism; D020451:Contig Mapping / Q000379:methods*; D016172:DNA Fingerprinting; D004262:DNA Restriction Enzymes / Q000378:metabolism; D004269:DNA, Bacterial / Q000235:genetics* / Q000378:metabolism; D004926:Escherichia coli / Q000187:drug effects / Q000235:genetics / Q000378:metabolism; D005697:Galactosides / Q000378:metabolism; D016680:Genome, Bacterial; D015698:Genomic Library; D059014:High-Throughput Nucleotide Sequencing; D007211:Indoles / Q000378:metabolism; D007544:Isopropyl Thiogalactoside / Q000494:pharmacology; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D004269:DNA, Bacterial; D005697:Galactosides; D007211:Indoles; D007544:Isopropyl Thiogalactoside; D004262:DNA Restriction Enzymes; C044888:5-bromo-4-chloro-3-indolyl beta-galactoside