Fosmid-based physical mapping of the Histoplasma capsulatum genome.

TitleFosmid-based physical mapping of the Histoplasma capsulatum genome.
Publication TypeJournal Article
Year of Publication2004
AuthorsMagrini, V, Warren, WC, Wallis, J, Goldman, WE, Xu, J, Mardis, ER, McPherson, JD
JournalGenome Res
Volume14
Issue8
Pagination1603-9
Date Published2004 Aug
ISSN1088-9051
KeywordsContig Mapping, DNA Fingerprinting, Genetic Vectors, Genome, Fungal, Genomic Library, Histoplasma, Restriction Mapping
Abstract

A fosmid library representing 10-fold coverage of the Histoplasma capsulatum G217B genome was used to construct a restriction-based physical map. The data obtained from three restriction endonuclease fingerprints, generated from each clone using BamHI, HindIII, and PstI endonucleases, were combined and used in FPC for automatic and manual contig assembly builds. Concomitantly, a whole-genome shotgun (WGS) sequencing of paired-end reads from plasmids and fosmids were assembled with PCAP, providing a predicted genome size of up to 43.5 Mbp and 17% repetitive DNA. Fosmid paired-end sequences in the WGS assembly provide anchoring information to the physical map and result in joining of existing physical map contigs into 84 clusters containing 9551 fosmid clones. Here, we detail mapping the Histoplasma capsulatum genome comprehensively in fosmids, resulting in an efficient paradigm for de novo sequencing that uses a map-assisted whole genome shotgun approach.

DOI10.1101/gr.2361404
Alternate JournalGenome Res.
PubMed ID15289478
PubMed Central IDPMC509269
Grant ListR01 AI025584 / AI / NIAID NIH HHS / United States
R56 AI025584 / AI / NIAID NIH HHS / United States
AI25584 / AI / NIAID NIH HHS / United States