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PMID: 11238388 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

The Neurospora crassa genome: cosmid libraries sorted by chromosome.

Genetics ·Vol. 157 ·No. 3 ·2001-03-00 ·Pages 979-90

Kelkar HS, Griffith J, Case ME, Covert SF, Hall RD, Keith CH, Oliver JS, Orbach MJ, Sachs MS, Wagner JR, Weise MJ, Wunderlich JK, Arnold J

Abstract

A Neurospora crassa cosmid library of 12,000 clones (at least nine genome equivalents) has been created using an improved cosmid vector pLorist6Xh, which contains a bacteriophage lambda origin of replication for low-copy-number replication in bacteria and the hygromycin phosphotransferase marker for direct selection in fungi. The electrophoretic karyotype of the seven chromosomes comprising the 42.9-Mb N. crassa genome was resolved using two translocation strains. Using gel-purified chromosomal DNAs as probes against the new cosmid library and the commonly used medium-copy-number pMOcosX N. crassa cosmid library in two independent screenings, the cosmids were assigned to chromosomes. Assignments of cosmids to linkage groups on the basis of the genetic map vs. the electrophoretic karyotype are 93 +/- 3% concordant. The size of each chromosome-specific subcollection of cosmids was found to be linearly proportional to the size of the particular chromosome. Sequencing of an entire cosmid containing the qa gene cluster indicated a gene density of 1 gene per 4 kbp; by extrapolation, 11,000 genes would be expected to be present in the N. crassa genome. By hybridizing 79 nonoverlapping cosmids with an average insert size of 34 kbp against cDNA arrays, the density of previously characterized expressed sequence tags (ESTs) was found to be slightly <1 per cosmid (i.e., 1 per 40 kbp), and most cosmids, on average, contained an identified N. crassa gene sequence as a starting point for gene identification.

MeSH Terms
Bacteriophage lambda/genetics Chromosome Mapping Chromosomes/genetics Cosmids/genetics DNA, Complementary/genetics,metabolism Expressed Sequence Tags Gene Library Genetic Linkage Genetic Vectors Genome, Fungal Karyotyping Models, Genetic Molecular Sequence Data Neurospora crassa/genetics Nucleic Acid Hybridization Phosphotransferases (Alcohol Group Acceptor)/genetics Physical Chromosome Mapping Sequence Analysis, DNA
Chemicals
DNA, Complementary Phosphotransferases (Alcohol Group Acceptor) hygromycin-B kinase
Authors & Affiliations
13 authors, click to expand affiliations / ORCID
Kelkar H S
Department of Genetics, University of Georgia, Athens, Georgia 30602, USA.
Griffith J
Case M E
Covert S F
Hall R D
Keith C H
Oliver J S
Orbach M J
Sachs M S
Wagner J R
Weise M J
Wunderlich J K
Arnold J
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Article Info
Journal
Genetics
Abbr.
Genetics
ISSN
0016-6731
DOI
10.1093/genetics/157.3.979
Published
2001-03-00
Pages
979-90
Language
English
Region
United States
NLM ID
0374636
PMCID
PMC1461552
Subset
IM
Databases
GENBANK
AC006498, AF237704
External Links
PubMed source DOI: 10.1093/genetics/157.3.979 PMC Full Text View journal details
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