YEAST

VOL. 8: 817-902 (1992)

Genetic and Physical Maps of Saccharomyces cerevisiae, Edition 11 ROBERT K. MORTIMER, C. REBECCA CONTOPOULOU AND JEFF S. KING Department of Molecular and Cell Biology and Lawrence Berkeley Laboratory, University of California, Berkeley, CA94720

INTRODUCTION In this article we present our most recent compilation of genetic mapping data for the yeast Saccharomyces cerevisiae. Three earlier publications (Mortimer and Schild 1980, 1985, Mortimer et al. 1989) included mapping data that appeared up to 1989 and this compilation presents data that has appeared since then. The data have been obtained from the literature and as personal communications from a large number of investigators. We surveyed on a regular basis several journals (Cell, Current Genetics, EMBO Journal, Genetics, Molecular and Cellular Biology, Molecular and General Genetics, Proceedings of the National Academy of Sciences and Yeast) and in addition used Melvyl to scan the broader literature. In May 1990, we sent out a solicitation for mapping information to over 1500 yeast researchers and many responded. In addition, we obtained other data by attending the XV International Conference of Yeast Genetics and Molecular Biology at The Hague in 1990, and the Yeast Genetics and Molecular Biology meetings held in Atlanta in 1989 and in San Francisco in 1991. In the current compilation, mapping results on 276 new genes are presented; 178 of these genes have been assigned to specific chromosomal sites and 98 have been assigned only to a chromosome or a chromosomal region. Twenty four of the new genes were discovered independently by two (21), three (1) or four (2) research groups. An additional 23 newly described genes were found to be alleles of already mapped genes. Five genes that had been described 0749-503X/92/1008 17-86$48.00 01992 by John Wiley & Sons Ltd

previously have been renamed. The total number of genes on the current genetic maps of yeast is 1046. The classical approach towards identifying genes is to mutate the wild type allele to a mutant allele. If the mutation has a recognizable phenotypic difference relative to wild type, and this difference shows normal Mendelian segregation, it can be studied further. This segregation serves to define the gene and if it is studied relative to the segregation of other genes can be used to map the gene. Once a gene is mapped to a specific site on one of the chromosomes it becomes more completely defined. It cannot be an allele of any gene that maps elsewhere in the yeast genome. Genes are also identified by cloning and sequencing the wild type allele and showing that this sequence is unique. Many new genes are now also being identified as chromosomal regions that hybridize to specific cDNAs or as open reading frames identified in sequencing projects. Tetrad analysis can be used in yeast to map genes rather precisely. In contrast to genetic analyses in most eucaryotic organisms, which involve the use of random gametes, all recombination events in a genetic interval can be detected with tetrad analysis. This type of genetic analysis involves studying the segregation of a gene, Ala, relative to the segregation of other genes, e.g. B/b, Clc etc. also segregating in the cross. For a given gene pair, e.g. Ala and B/b, and assuming only 2:2 segregations for both genes, only three types of tetrads are expected: parental ditype

818 (PD) AB AB ab ab, nonparental ditype (NPD) Ab Ab aB aB and tetratype (T) AB Ab aB ab. For two genes that are unlinked, either because they are far apart on the same chromosome or are on different chromosomes, PD : NPD : T = 1 : 1 : 4. If A/a and B/b are linked, PD is significantly greater than NPD. If both A/a and B/b are linked to their respective but different centromeres, PD = NPD and T is less than 2/3. Map distances for gene-gene and gene-centromere linkages were calculated using a recently described maximum likelihood (King and Mortimer 1991). This analysis yields values for map distance, x’, in centimorgans (cM) as well as an interference parameter, k, plus errors in these two parameters. k represents the reduced probability of a crossover event if that crossover is associated with another crossover event. It is approximately equivalent to the coincidence coefficient, C, defined for two-interval analyses. Strong interference is associated with low values of k and weak or no interference is associated with k values near or above 1. Several other approaches are available for localizing an unmapped gene to a specific chromosome or chromosomal site. In addition to tetrad analysis, these procedures include random spore analyses, trisomic or aneuploid analyses, mitotic crossing over procedures, methods involving chromosome loss and hybridization of a cloned gene to a chromosome blot. These procedures have been described in detail in previous publications (Mortimer and Hawthorne 1975, Mortimer and Schild 1980, 1985, Mortimer et al. 1989). The chromosome fragmentationmethod (Vollrath et al. 1988) and random breakage mapping (Game et al. 1991) yield gene-telomere physical distances. The latter method can also be used to determine the physical distance of a cloned gene from the ends of the Not I fragment on which it is located. Several genes were mapped in this compilation by showing that a portion of the adjoining sequence of the gene overlapped the flanking sequence of an already mapped gene. In almost every case, this type of analysis fails to determine the order of the gene on the chromosome relative to the gene against which it is mapped or relative to other nearby genes. Riles and Olson (personal communication) have introduced a new method that is widely used. They have developed a set of lamda clones containing inserts averaging 15 kb that cover almost the entire genome. These are available as a set of three nylon blots to which cloned genes can be hybridized. Many other genes have been identified by hybridizing cDNAs to portions of the physical map of chromosomes or chromosome segments. Still other

R. MORTIMER ET AL.

genes are being defined as open reading frames (ORFs) in chromosome sequencing projects. In nearly all of these cases, the function of the gene is identified secondarily or not at all. Most of these new genes have not been added to the map. DISCUSSION The genetic maps presented in Figures 1 to 16 represent our best estimate of the order and relative spacings of genes on the different chromosomes. To establish the position of a new gene relative to those of already mapped genes, it is necessary to carry out a three-point cross, where two of the three genes are already well mapped and appropriately placed. The correct order is that which requires the least number of crossovers to explain the observed segregations. Most of the tetrad data included in this review are of that type. However, some sets of data are based on combinations of two-point crosses and are not as informative. If only a single two-point cross is reported, order cannot be determined. In constructing the maps to include the new data, we reexamined the data in our three previous reviews. On many occasions, the new data required an adjustment of the relative spacings and even of order of previously mapped genes. Frequently, we adjusted the new map distances to be compatible with distances reported previously. For example, lys2 and tyrl have been used as reference markers to map many new genes. The spacing of these two genes, based on thousands of tetrads, is 38.3 cM. Consider a hypothetical gene that maps between these two genes and is 25 cM from lys2 and 20 cM from tyrl. We would place this gene 25/45 x 38.3 cM (21.3 cM) from lys2 and 20145 x 38.3 cM (17.0 cM) from tyrl. A gene whose neighboring sequence is found to overlap that of an already mapped gene cannot be ordered relative to other genes on the chromosome. We have placed such genes on the left side of the chromosome line and, if order is unknown, arbitrarily distal to the already mapped gene. Two gaps on chromosomes XI and XVI have been filled in by data appearing in this Edition. The gene mzj2 shows linkage to cdcl6, near the centromere of chromosome XI as well as to ural and trp3 further out on the left arm. It fails to show linakge to mak9, which establishes the left arm order mak9-fas2-trp3ura2-mifl-cdcl6-cenlI.Also, cly7, which had been mapped to this chromosome, failed to show linkage to either mifl or trp3 and has been removed from the map (Table 1 1 ) . In contrast to these genetic data, physical mapping data define the order tel-ural-

GENETIC MAP OF S. CEREVISIAE

819

trp3-fas2-cenll. The independently derived physical maps of L. Riles and M. V. Olson (personal communication) and B. Dujon (personal communication) place ural as the most distal marker. Also, M. Bell and J. Game (personal communication) have shown by Random Breakage Mapping that ural is only 48.5 kb from the telomere while fusl is 105 kb from the telomere. These physical distances agree closely with those obtained by Riles and Olson. The difference between the genetic and physical mapping results can be explained if the strain used to map mi$? carries an inversion relative to the strains (S288C, AB972) used in physical mapping. This is a reasonable explanation because the left arm of chromosome XI has been shown to have telomeric X and Y’ sequences near its midpoint (B. Dujon, personal communication). An intrachromosomal recombination event between this sequence and the normal telomere could generate such an inversion. On chromosome XVI, sptl4 shows linkage to gal4 near the left telomere as well as to sit3 which is linked to genes near the centromere. Chromosome XIV is shorter genetically than was shown in Edition 10. The gene SUP165, which had been mapped distal to holl on the right arm, has been removed from the map because of inconsistencies with the physical maps of Riles and Olson (personal communication) and because the tetrad ratio (17:3:20) is improbable; there are too many NPD tetrads relative to T tetrads. For chromosomes I, 111, V, VI, and VIII we have also presented physical maps which were redrawn from those of Riles et al. (1992). The genetic scale in all these as well as the other maps is the same, i.e. 1 cM/1 mm. The scales of the physical maps were

adjusted so that the end markers shared by both maps were the same distance apart. Because smaller chromosomes have higher cM/kb values than larger chromosomes (Kaback et al. 1992), this scaling factor was different for each of the chromosomes. For each of the chromosomes, the maps are colinear, although cM/kb varies several-fold along the chromosomes. .Kaback et al. (1992) have shown that chromosome 1, which has the highest cM/kb value (0.6), when bisected at the centromere yields two smaller chromosomes each with even higher cM/kb values. When these two pieces of chromosome I were attached to the much longer chromosome 11, the cM/kb values for the chromosome I regions were found to be lower than those for intact chromosome I. These authors conclude that crossing over is regulated at the whole chromosome level to assure that each bivalent has at least one crossover. In Figure 17, we present a plot of cM/kb vs kb for each of the sixteen yeast chromosomes. This log-log plot is linear with a negative slope indicating an inverse relationship between these two variables. Figure 18 is a log-log plot of average crossovers per mega base pair (co/mb) vs average mb/chromosome for ten genetically-studied organisms with average chromosome sizes varying by more than four orders of magnitude (King and Mortimer 1990). Again, a linear relationship is seen and the slope is close to -1. Figures 17 and 18 show that crossing over per chromosome is almost independent of chromosome size. Most organisms have on the average about two to three crossovers per chromosome, irrespective of chromosome size. Saccharomyces cerevisiae is unusual in this respect with an average of 5 to 6 crossovers per chromosome.

Figures 1 to 16. The genetic and physical maps (Figures 1 to 16) of the sixteen chromosomes of Saccharomyces cerevisiae are based on data presented in Tables 1 to 16 as well as on data presented in earlier reviews (Mortimer and Schild 1980, 1985, Mortimer et a f . 1989). Physical maps for chromosomes I, 111, V, VI and VIII were redrawn from Riles er al. (1992). Genetic maps are drawn as solid vertical lines at a scale of 1 cM/mm or dashed lines representing linkages established by mitotic crossing over. Centromeres are represented as circles on the genetic map line with the left arm above and the right arm below the centromere. Physical maps are drawn parallel and 3 cm to the left of the genetic maps and are distinguished by the scale (in kb) to the left of this line. Horizontal tick marks to the right of the genetic map lines indicate the positions of the genes: in crowded regions, these tick marks are joined to the gene symbol by a thin connecting line. Gene positions on the five physical maps are represented as short vertical bars. These bars are centered at the center of the physical region containing the

gene but their lengths are arbitrary. Dashed lines connect the same gene on the genetic and physical maps. Crowded regions on the genetic map are drawn as expansions, 2-fold for chromosome I1 and 5-fold for all other expanded regions. Gene symbols are defined in Table 19. Synonyms are separated by a comma. Genes added since Edition 10 are in bold type. Genes that have been mapped on the basis of sequence overlap relative to geneticallymapped genes are positioned to the left of the genetic map line and are connected to this line by tick marks; when the order of these genes relative to the mapped genes is unknown, they are arbitrarily placed distal to the mapped gene. Genes listed below the chromosome maps or expanded regions of these maps have been assigned to the chromosome or region either by genetic or physical methods but cannot be positioned more precisely. Some gene symbols in this category are capitalized; this does not necessarily indicate dominance but instead means that the wild type copy was used to map the gene.

820

R. MORTIMER ET AL.

Table 1. New mapping data for chromosome I Interval

rpal -adel leu2 -rpal leu2-adel

Segregation FD

SD

35 31

20 24

ssal -adel

233 tsvll.5-cenl tsvll.5-adel t~vll5-~d~lS 209 cenl -adel

Ascus Type PD NPD

Map Distance

T

x’(cM)

SE 2.2 0.7 1.0

49

0

7

6.3 20.6 25.6

32

0

3

4.3

231 17

1 0

24 4

0.2 5.1 9.5 5.3

0.0 1.0 4.3 0.0

61 42 61 44 143 119

1 1 1 1 0 0

78 78 81 79 5 5

30.1 34.9 30.3 34.2 1.7 2.0

2.5 2.8 2.5 2.7 0.7 0.9

1

24

cdcl S-pHISI cdcl 5-PHISI ~ d ~ l 5 - p hI o l ~dcl5-pholl pHISl -pholl PHIS1 -phol I

Interference k

Reference

SE Heyer et al. (1990)

2.4

Craig et al. (1987) Harris and Pringle (1991)

0.4

1.2

0.20 0.17 0.17 0.14 0.17 0.16 0.15 0.14

Steensma et al. (1989)

Other genes located on chromosome I; additional information:

60 transcribed regions have been physically mapped on 160 kb of the 250 kb of DNA on this chromosome.

D. Kaback, pers. comm.

FUN9, FUNlO, F U N l l , FUNI2, FUN19, FUN20, FUN21, FUN22; 8 transcribed regions physically mapped in relation to transcripts of already mapped genes on the left arm distal to mak9

Diehl and Pringle (1991)

cln3 is allelic to whil - dafl - fun10

G. Tokiwa, pers. comm.

FL0.5

F. Vezinhet and P. Barre, pers. comm.

ltel and makl6 are adjacent genes

Wickner et al. (1987, 1988)

pholl is 3.5 kb from the right end of chromosome; approximately 20 kb of the region of chromosome I containing phol I is repeated near one of the telomeres of chromosome VIII. phol2 is in this chromosome VIII region.

Steensma et al. ( 1989)

Physical map to the left of the genetic map is drawn at a scale of 0.65 cM/kb

Riles et al. (1992)

leu2-rpal data give the leu2-cen3 + cenl -rpal distance; leu2-adel data give the leu2-cen3 + cenl -adel distance. This places rpal 5 cM proximal to adel

Heyer et al. (1990)

ssal is allelic to YGlUU; YGlOU has been physically mapped between trnl and the centromere

Craig et al. ( 1987)

tsvl15 is a temperature-sensitive allele of FUN24

Hams and Pringle (1991)

GENETIC MAP OF S.CEREVISIAE

82 1

0

. puRA3

50 cdc24, cls4, tsll (WHI1, funl0, DAFI, cln3 -cyc3 ‘cdcl9, pykl 100

mak16

< ltel

ccr4

cy53

150

tsvll5, fun24

- let1 I

‘adel ‘cdcl5 ‘SUP56

200

229

FLOl phol 1

Figure 1. Genetic and physical maps of chromosome I. tRNA (Ser) IGA FL05

822

R. MORTIMER ETAL.

Table 2. New mapping data for chromosome I1 Interval

Segregation FD

SD

Ascus Type PD NPD

Map Distance

Interference

T

x’(cM)

SE

k

0.38 0.30

Reference

SE

pkcl-cd~27 pkcl - ~ l y 2 pkcl-lys2

27 11 10

0 1 5

19 25 21

20.7 42.3

3.6 7.0

tell -cdc27 tell -cdc2 7

16 32

0 0

0 3

4.6 4.3

2.4

pet9-pep1 pet9-pdr4 pet9-cen2 pet9-gall pepl -pdr4 pepl -cen2 pepl -gall pdr4-cen2 pdr4-gall cen2-gall

33 28

0 1

10 14

14 35

1 1

27 7

21

1

20

26

0

16

11.6 24.5 21.2 39.7 12.3 11.2 31.0 3.6 19.1 17.1

3.2 7.7 0.8 6.4 6.3 0.3 6.4 0.0 3.8 0.6

0

22

6.7 11.8 7.9

0.1 2.2 0.1

Fujimura (1990)

71

14

0

25

32.1 5.3

3.8 0.1

Bulawa (1992)

4

0

13

5.1

M. Breitenbach, pers. comm.

1.2 4.8 3.2

27

16

34

9

40

3

29

13

81

12

dac2-cen2 dac2-gall cen2-gall

79

14

pet9-csd2 cen2-csd2

35

4

33

31

Levin et al. (1990)

S . Kronmal and T. Petes, pers. comm. Preston et al. (1991)

1.6

0.8

0.39 0.31 2.4 1.2 0.69

0.57

15 35

0 0

5 21

38.2 29.3 12.5 18.8

fdpl-lys2

27

2

16

46.9

8.2

fdpl-ly~2 f d p l -tyrl lys2-tyrl

71 14 19

0 4 2

39 46 42

17.7 56.1 43.4

2.3 8.6 5.8

cmdl-lys2

72

0

9

5.6

1.8

T. Davis, pers. comm.

radl6-lys2

35

0

1

1.4

1.4

Schild et al. (1992)

l y ~-2c k ~ l 1 ~- ~ d2 ~ 2 8 CkSl -cdc28

21 14 22

0 1 0

19 25 18

23.8 39.1 22.5

3.9 6.6 3.9

iral-lys2

22

0

4

7.7

3.5

pet9-ditl01 cen2 -ditlOl gall 0-ditlO1 gall -ditlOl

1.6

.04 van de Poll and Schamhart (1977)

K. Luyten, S. Hohmann and

Genetic and physical maps of Saccharomyces cerevisiae, Edition 11.

YEAST VOL. 8: 817-902 (1992) Genetic and Physical Maps of Saccharomyces cerevisiae, Edition 11 ROBERT K. MORTIMER, C. REBECCA CONTOPOULOU AND JEFF S...
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