Skip to main content
NCBI home page
Genetics logoLink to Genetics
. 2001 Mar;157(3):979–990. doi: 10.1093/genetics/157.3.979

The Neurospora crassa genome: cosmid libraries sorted by chromosome.

H S Kelkar 1, J Griffith 1, M E Case 1, S F Covert 1, R D Hall 1, C H Keith 1, J S Oliver 1, M J Orbach 1, M S Sachs 1, J R Wagner 1, M J Weise 1, J K Wunderlich 1, J Arnold 1
PMCID: PMC1461552  PMID: 11238388

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.

Full Text

The Full Text of this article is available as a PDF (311.6 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Adams M. D., Celniker S. E., Holt R. A., Evans C. A., Gocayne J. D., Amanatides P. G., Scherer S. E., Li P. W., Hoskins R. A., Galle R. F. The genome sequence of Drosophila melanogaster. Science. 2000 Mar 24;287(5461):2185–2195. doi: 10.1126/science.287.5461.2185. [DOI] [PubMed] [Google Scholar]
  2. Aign V., Schulte U., Hoheisel J. D. Hybridization-based mapping of Neurospora crassa linkage groups II and V. Genetics. 2001 Mar;157(3):1015–1020. doi: 10.1093/genetics/157.3.1015. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. doi: 10.1016/S0022-2836(05)80360-2. [DOI] [PubMed] [Google Scholar]
  4. Aramayo R., Metzenberg R. L. Meiotic transvection in fungi. Cell. 1996 Jul 12;86(1):103–113. doi: 10.1016/s0092-8674(00)80081-1. [DOI] [PubMed] [Google Scholar]
  5. Balding D. J., Torney D. C. The design of pooling experiments for screening a clone map. Fungal Genet Biol. 1997 Jun;21(3):302–307. doi: 10.1006/fgbi.1997.0985. [DOI] [PubMed] [Google Scholar]
  6. Beadle G. W., Tatum E. L. Genetic Control of Biochemical Reactions in Neurospora. Proc Natl Acad Sci U S A. 1941 Nov 15;27(11):499–506. doi: 10.1073/pnas.27.11.499. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Bean L. E., Dvorachek W. H., Jr, Braun E. L., Errett A., Saenz G. S., Giles M. D., Werner-Washburne M., Nelson M. A., Natvig D. O. Analysis of the pdx-1 (snz-1/sno-1) region of the Neurospora crassa genome: correlation of pyridoxine-requiring phenotypes with mutations in two structural genes. Genetics. 2001 Mar;157(3):1067–1075. doi: 10.1093/genetics/157.3.1067. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Bean P. Role of viral load blips, drug boosting, and therapeutic holidays in HIV patient management. Am Clin Lab. 2001 Sep;20(8):11–13. [PubMed] [Google Scholar]
  9. Bhandarkar S. M., Machaka S. A., Shete S. S., Kota R. N. Parallel computation of a maximum-likelihood estimator of a physical map. Genetics. 2001 Mar;157(3):1021–1043. doi: 10.1093/genetics/157.3.1021. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Brody H., Griffith J., Cuticchia A. J., Arnold J., Timberlake W. E. Chromosome-specific recombinant DNA libraries from the fungus Aspergillus nidulans. Nucleic Acids Res. 1991 Jun 11;19(11):3105–3109. doi: 10.1093/nar/19.11.3105. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. C. elegans Sequencing Consortium Genome sequence of the nematode C. elegans: a platform for investigating biology. Science. 1998 Dec 11;282(5396):2012–2018. doi: 10.1126/science.282.5396.2012. [DOI] [PubMed] [Google Scholar]
  12. Case M. E., Schweizer M., Kushner S. R., Giles N. H. Efficient transformation of Neurospora crassa by utilizing hybrid plasmid DNA. Proc Natl Acad Sci U S A. 1979 Oct;76(10):5259–5263. doi: 10.1073/pnas.76.10.5259. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Centola M., Carbon J. Cloning and characterization of centromeric DNA from Neurospora crassa. Mol Cell Biol. 1994 Feb;14(2):1510–1519. doi: 10.1128/mcb.14.2.1510. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Enkerli J., Bhatt G., Covert S. F. Nht1, a transposable element cloned from a dispensable chromosome in Nectria haematococca. Mol Plant Microbe Interact. 1997 Aug;10(6):742–749. doi: 10.1094/MPMI.1997.10.6.742. [DOI] [PubMed] [Google Scholar]
  15. Ewing B., Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 1998 Mar;8(3):186–194. [PubMed] [Google Scholar]
  16. Ewing B., Hillier L., Wendl M. C., Green P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 1998 Mar;8(3):175–185. doi: 10.1101/gr.8.3.175. [DOI] [PubMed] [Google Scholar]
  17. Gibson T. J., Rosenthal A., Waterston R. H. Lorist6, a cosmid vector with BamHI, NotI, ScaI and HindIII cloning sites and altered neomycin phosphotransferase gene expression. Gene. 1987;53(2-3):283–286. doi: 10.1016/0378-1119(87)90017-5. [DOI] [PubMed] [Google Scholar]
  18. Goffeau A., Barrell B. G., Bussey H., Davis R. W., Dujon B., Feldmann H., Galibert F., Hoheisel J. D., Jacq C., Johnston M. Life with 6000 genes. Science. 1996 Oct 25;274(5287):546, 563-7. doi: 10.1126/science.274.5287.546. [DOI] [PubMed] [Google Scholar]
  19. Hoheisel J. D., Maier E., Mott R., McCarthy L., Grigoriev A. V., Schalkwyk L. C., Nizetic D., Francis F., Lehrach H. High resolution cosmid and P1 maps spanning the 14 Mb genome of the fission yeast S. pombe. Cell. 1993 Apr 9;73(1):109–120. doi: 10.1016/0092-8674(93)90164-l. [DOI] [PubMed] [Google Scholar]
  20. Huiet L., Tyler B. M., Giles N. H. A leucine tRNA gene adjacent to the QA gene cluster of Neurospora crassa. Nucleic Acids Res. 1984 Jul 25;12(14):5757–5765. doi: 10.1093/nar/12.14.5757. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Krumlauf R., Marzluf G. A. Characterization of the sequence complexity and organization of the Neurospora crassa genome. Biochemistry. 1979 Aug 21;18(17):3705–3713. doi: 10.1021/bi00584a011. [DOI] [PubMed] [Google Scholar]
  22. Krumlauf R., Marzluf G. A. Genome organization and characterization of the repetitive and inverted repeat DNA sequences in Neurospora crassa. J Biol Chem. 1980 Feb 10;255(3):1138–1145. [PubMed] [Google Scholar]
  23. Kupfer D. M., Reece C. A., Clifton S. W., Roe B. A., Prade R. A. Multicellular ascomycetous fungal genomes contain more than 8000 genes. Fungal Genet Biol. 1997 Jun;21(3):364–372. doi: 10.1006/fgbi.1997.0982. [DOI] [PubMed] [Google Scholar]
  24. Lee K., Loros J. J., Dunlap J. C. Interconnected feedback loops in the Neurospora circadian system. Science. 2000 Jul 7;289(5476):107–110. doi: 10.1126/science.289.5476.107. [DOI] [PubMed] [Google Scholar]
  25. Mahairas G. G., Wallace J. C., Smith K., Swartzell S., Holzman T., Keller A., Shaker R., Furlong J., Young J., Zhao S. Sequence-tagged connectors: a sequence approach to mapping and scanning the human genome. Proc Natl Acad Sci U S A. 1999 Aug 17;96(17):9739–9744. doi: 10.1073/pnas.96.17.9739. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Maier E., Hoheisel J. D., McCarthy L., Mott R., Grigoriev A. V., Monaco A. P., Larin Z., Lehrach H. Complete coverage of the Schizosaccharomyces pombe genome in yeast artificial chromosomes. Nat Genet. 1992 Jul;1(4):273–277. doi: 10.1038/ng0792-273. [DOI] [PubMed] [Google Scholar]
  27. Mizukami T., Chang W. I., Garkavtsev I., Kaplan N., Lombardi D., Matsumoto T., Niwa O., Kounosu A., Yanagida M., Marr T. G. A 13 kb resolution cosmid map of the 14 Mb fission yeast genome by nonrandom sequence-tagged site mapping. Cell. 1993 Apr 9;73(1):121–132. doi: 10.1016/0092-8674(93)90165-m. [DOI] [PubMed] [Google Scholar]
  28. Nelson M. A., Kang S., Braun E. L., Crawford M. E., Dolan P. L., Leonard P. M., Mitchell J., Armijo A. M., Bean L., Blueyes E. Expressed sequences from conidial, mycelial, and sexual stages of Neurospora crassa. Fungal Genet Biol. 1997 Jun;21(3):348–363. doi: 10.1006/fgbi.1997.0986. [DOI] [PubMed] [Google Scholar]
  29. Orbach M. J. A cosmid with a HyR marker for fungal library construction and screening. Gene. 1994 Dec 2;150(1):159–162. doi: 10.1016/0378-1119(94)90877-x. [DOI] [PubMed] [Google Scholar]
  30. Orbach M. J., Vollrath D., Davis R. W., Yanofsky C. An electrophoretic karyotype of Neurospora crassa. Mol Cell Biol. 1988 Apr;8(4):1469–1473. doi: 10.1128/mcb.8.4.1469. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Patel V. B., Schweizer M., Dykstra C. C., Kushner S. R., Giles N. H. Genetic organization and transcriptional regulation in the qa gene cluster of Neurospora crassa. Proc Natl Acad Sci U S A. 1981 Sep;78(9):5783–5787. doi: 10.1073/pnas.78.9.5783. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Perkins D. D. Chromosome rearrangements in Neurospora and other filamentous fungi. Adv Genet. 1997;36:239–398. doi: 10.1016/s0065-2660(08)60311-9. [DOI] [PubMed] [Google Scholar]
  33. Prade R. A., Ayoubi P., Krishnan S., Macwana S., Russell H. Accumulation of stress and inducer-dependent plant-cell-wall-degrading enzymes during asexual development in Aspergillus nidulans. Genetics. 2001 Mar;157(3):957–967. doi: 10.1093/genetics/157.3.957. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Radford A., Parish J. H. The genome and genes of Neurospora crassa. Fungal Genet Biol. 1997 Jun;21(3):258–266. doi: 10.1006/fgbi.1997.0979. [DOI] [PubMed] [Google Scholar]
  35. Randall T. A., Metzenberg R. L. The mating type locus of Neurospora crassa: identification of an adjacent gene and characterization of transcripts surrounding the idiomorphs. Mol Gen Genet. 1998 Oct;259(6):615–621. doi: 10.1007/s004380050855. [DOI] [PubMed] [Google Scholar]
  36. Rosa A. L., Haedo S. D., Temporini E. D., Borioli G. A., Mautino M. R. Mapping chromosome landmarks in the centromere I region of Neurospora crassa. Fungal Genet Biol. 1997 Jun;21(3):315–322. doi: 10.1006/fgbi.1997.0987. [DOI] [PubMed] [Google Scholar]
  37. Russell P. J., Wagner S., Rodland K. D., Feinbaum R. L., Russell J. P., Bret-Harte M. S., Free S. J., Metzenberg R. L. Organization of the ribosomal ribonucleic acid genes in various wild-type strains and wild-collected strains of Neurospora. Mol Gen Genet. 1984;196(2):275–282. doi: 10.1007/BF00328060. [DOI] [PubMed] [Google Scholar]
  38. Schmidhauser T. J., Liu Y. Z., Liu H., Zhou S. Genome analysis in Neurospora crassa; cloning of four loci arginine-1 (arg-1), methionine-6 (met-6), unknown-7 (un-7), and ribosome production-1 (rip-1) and associated chromosome walking. Fungal Genet Biol. 1997 Jun;21(3):323–328. doi: 10.1006/fgbi.1997.0974. [DOI] [PubMed] [Google Scholar]
  39. Selker E. U. Premeiotic instability of repeated sequences in Neurospora crassa. Annu Rev Genet. 1990;24:579–613. doi: 10.1146/annurev.ge.24.120190.003051. [DOI] [PubMed] [Google Scholar]
  40. Smulian A. G., Sesterhenn T., Tanaka R., Cushion M. T. The ste3 pheromone receptor gene of Pneumocystis carinii is surrounded by a cluster of signal transduction genes. Genetics. 2001 Mar;157(3):991–1002. doi: 10.1093/genetics/157.3.991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Vollmer S. J., Yanofsky C. Efficient cloning of genes of Neurospora crassa. Proc Natl Acad Sci U S A. 1986 Jul;83(13):4869–4873. doi: 10.1073/pnas.83.13.4869. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Wan Y., Liu H., Li C., Schmidhauser T. J. Genome analysis on linkage group VI of Neurospora crassa. Fungal Genet Biol. 1997 Jun;21(3):329–336. doi: 10.1006/fgbi.1997.0988. [DOI] [PubMed] [Google Scholar]
  43. Yelton M. M., Hamer J. E., Timberlake W. E. Transformation of Aspergillus nidulans by using a trpC plasmid. Proc Natl Acad Sci U S A. 1984 Mar;81(5):1470–1474. doi: 10.1073/pnas.81.5.1470. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Zabarovsky E. R., Allikmets R. L. An improved technique for the efficient construction of gene libraries by partial filling-in of cohesive ends. Gene. 1986;42(1):119–123. doi: 10.1016/0378-1119(86)90158-7. [DOI] [PubMed] [Google Scholar]
  45. Zhu H., Nowrousian M., Kupfer D., Colot H. V., Berrocal-Tito G., Lai H., Bell-Pedersen D., Roe B. A., Loros J. J., Dunlap J. C. Analysis of expressed sequence tags from two starvation, time-of-day-specific libraries of Neurospora crassa reveals novel clock-controlled genes. Genetics. 2001 Mar;157(3):1057–1065. doi: 10.1093/genetics/157.3.1057. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Zolan M. E., Crittenden J. R., Heyler N. K., Seitz L. C. Efficient isolation and mapping of rad genes of the fungus Coprinus cinereus using chromosome-specific libraries. Nucleic Acids Res. 1992 Aug 11;20(15):3993–3999. doi: 10.1093/nar/20.15.3993. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Genetics are provided here courtesy of Oxford University Press

RESOURCES