Neurospora crassa chromosome walks
M.A. Nelson and D.O. Natvig - Department of Biology, University of New Mexico, Albuquerque, NM 87131
Chromosome walks have been executed for all seven chromosomes of N. crassa, but the amount of coverage varies greatly, from less than 3% (LG V) to about 25% (LG VII). Overall, about 10% of the genome has been covered by chromosome walks (Table 1). All chromosome walks are shown with respect to the position on the chromosome, oriented from the left telomere to the right. The standard nomenclature for these genomic libraries is followed: pSV50 (Vollmer and Yanofsky 1986 Proc. Natl. Acad. Sci. USA 83:4869-4873), pMOcosX (Orbach 1994 Gene 150:159-162), EMBL3 (Yeadon and Catcheside 1995 Curr. Genet. 28:155-163), pCRD103 (Davis et al. 1994 Genetics 136:1297-1306), CBM1 (Cabibbo et al. 1991 Fungal Genet. Newsl. 38:68-70), CBM2 (Ballario et al. 1996 EMBO J. 15:1650-1657) and yeast artificial chromosome (YAC; Centola et al. 1994 Fungal Genet. Newsl. 41:23-33). For precise map positions of the cited alleles, refer to Perkins et al. (1982 Microbiol. Rev. 46:426-570) and Perkins (1992 Fungal Genet. Newsl. 39:61-70).
A comparison of genetic and physical distances has been published recently (Radford and Parish 1997 Fungal Genet. Biol. 21:258-266). On average, 1 map unit (MU) corresponds to about 43 kb, but this value varies from about 20 to 80 kb per MU. In centromere-proximal regions, the crossover-suppressing effect of the centromere contributes to even larger distances per MU (Centola and Carbon 1994 Mol. Cell. Biol. 14:1510-1519). Regions corresponding to nearly 100 MU (of the ~1010 MU total for N. crassa) have been covered in the chromosome walks reported here.
Updated versions of chromosome walks will be available through the Neurospora Genome Project HomePage (http://biology.unm.edu/~ngp/home.html). Please share your chromosome walk information with Mary Anne Nelson (manelson@unm.edu) or Don Natvig (dnatvig@unm.edu), so that this important resource will be available to the whole community.
Acknowledgements
We thank Louise Glass for sharing unpublished results. This work was supported by the National Science Foundation RIMI (Research Improvements in Minority Institutions) Program Grant HRD-9550649.
Table 1. Chromosome walks
Position Markers spanned Cosmids, plasmids, lambda clones and YACsa Lengthb Referencec
LG IL eth-1, arg-3 X22:H2, L2, G19:G4, G13:C4, X17:D9, G6:F6, 230 kb 1
X1:F3, G4:G5, 28:12D, 26:11B, X10:H6,
G3:E9, G9:C4, G17:E10, X8:D4, X17:B1,
G15:B10, X9:C6, G8:D5, G1:A11
LG IL mei-3, T39311 G3:B5, X11:H2, G1:A7, 9:7G, 9:1H, X10:C2, 100 kb 1
X10:D3, G10:H5, X5:D9, X14:G3, G11:B1
LG IR un-2, his-2, 5:F10*, 22:F5*, 12:B6*, 14:D7*, 17:E2*, 500 kb 1
TAR173, 22:G2*,5:A10*, 5:D1*, 13:F7*, 12:C6*
LG IR his-2, TAR173 X20:D8, X7:H7, G2:B2, G13:B4, 10:6F, 125 kb 1
G19:B11, G13:H11, X11:B4, X21:G12
LG IR his-3 lJY25, lJY29, G3:6F, 23:3H 60 kb 2
LG IR hom, al-1 X1:7G, X9:3H, 3:11H, X24:3E, G2:8G, 270 kb 3
G10:10B, G16:11C, G8:7G, G16:8A
LG IIL un-24, het-6, X19:F1, G25:F11, X18:H11, X24:G9, G8:F7, 270 lb 4
TAR18 G12:E3, G8:G1, X14:C1, X5:F11, X7:G5
LG IIL het-C, pyr-4 X2:C1, G20:D11, G22:H5, X25:A1, X7:F1, 150 kb 5
X11:C6
LG IIIR ser-1, pro-1, 22:4D, 27:10H, 25:3G, 14:1C, 3-30:2B, 24:5G, 205 kb 6
ace-2 2-13:10B, 2-11:12A, 28:5H, 3:11A, 4:9C, 8:1E,
13:7C, 13:10A, 21:6D, 18:2C, 18:12G, 11:1B,
1:6G
LG IVR tol, trp-4 G13:C8, X25:D7, X7:C2, G1:E5, G6:E12, 350 kb 7
X4:E10, X14:C2, G4:A9, X17:B5, X10:A4,
X17:C11, G6:C9
LG VR am, gul-1, G9:A10, G9:D12, X12:D8, G15:A7, X8:H6, 240 kb 8
ace-5, ure-1 X4:A2, X15:D8, G18:D11, X25:B7, G24:H8,
G20:D6, X15:H8, X9:C3, G12:G1, X16:F6,
X13:F3, G17:B9, G17:H9, X21:D7, X23:F10
LG VILd Bml G14:11C, X9:9B, X5:7F, G12:10C 110 kb 9
LG VIL ylo-1, un-13, G7:5F, G13:4D, G2:3A, X7:8E, X16:12D, 420 kb 9
cpc-1 X10:5H, X5:9H, G22:2C, X3:9C, X13:5A,
G17:11E, G7:5F, G8:6D, G15:8E, pHL200,
2:5A, 22:11A
LG VIIe qa-2, met-7, 24-1-C*, 12-10-H*, 19-5-B*, 15-6-H*, 750 kb 10
met-9 24-3-G*, 7-10-D*
LG VIIR met-7, wc-1 20:D-7, p550, 2-I, 3:H-3, 22-F, 12:F-8, 230 kb 11
31:G-3, 54:E-6, G17:H7, 20:G-9, G7:G3, 56:E-7
LG VIIR oli, frq, for 2:10A, 15:12G, l3L10, l2L82, l19a, l13a, 190 kb 12
l13R, l7R, 30:1A, 26:2A, 8:3B, 6:5A, 31:5E,
26:1H, 23:9D
aSee text for clone references and nomenclature conventions. N. crassa YAC clones are
indicated
with an asterisk, to distinguish them from cosmid clones with similar nomenclature.
bThe approximate extent of the chromosome walk in kilobase pairs (kb) is indicated.
cReferences: [1] Rosa et al. 1997 Fungal Genet. Biol. 21:315-322. [2]
Yeadon and Catcheside 1995
Curr. Genet. 28:155-163. [3] Schmidhauser et al. 1997 Fungal Genet. Biol.
21:323-328. [4] Smith
et al. 1996 Genetics 144:523-531. [5] Saupe et al. 1996 Genetics
143:1589-1600. [6] Davis et al.
1994 Genetics 136:1297-1306. [7] N.L. Glass, personal communication. [8] Bowring and Catcheside
1995 Curr. Genet. 29:27-33. [9] Wan et al. 1997 Fungal Genet. Biol.
21:329-336. [10] Centola and
Carbon 1994 Mol. Cell. Biol. 14:1510-1519. [11] Ballario et al. 1996 EMBO J.
15:1650-1657. [12]
McClung, Fox and Dunlap 1989 Nature 339:558-562.
dOrientation of this walk is unknown.
eThis chromosome walk spans the LG VII centromere.