The Neurospora crassa genome: Cosmid libraries sorted by chromosome

Hemant S. Kelkar, James Griffith, Mary E. Case, Sarah F. Covert, Robert D. Hall, Charles H. Keith, J. Steve Oliver, Marc J. Orbach, Matthew S. Sachs, Jeff R. Wagner, Michael J. Weise, John K. Wunderlich, Jonathan Arnold

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Abstract

A Neurospora crassa cosmid library of 12,000 clones (at least nine genome equivalents) has been created using an improved cosmid vector pLorist6Xh, Milch contains a bacteriophage λ origin of replication for lowcopy-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.

Original languageEnglish (US)
Pages (from-to)979-990
Number of pages12
JournalGenetics
Volume157
Issue number3
StatePublished - Mar 31 2001

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ASJC Scopus subject areas

  • Genetics

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Kelkar, H. S., 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. (2001). The Neurospora crassa genome: Cosmid libraries sorted by chromosome. Genetics, 157(3), 979-990.