Neurospora crassa Genetic Map Description
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Genetic Maps
Description
Around 1,000 known genetic markers exist for Neurospora crassa. Some of these markers have been ordered on seven linkage group genetic maps. The genetic map information was kindly provided by Alan Radford, David Perkins and Matt Sachs. See the 1982 Compendium FGSC genetic maps for more details, or visit the updated 2000 version. Additional genetic map data was compiled by Roll Jean Cheng and Alex Harry as part of the Apprenticeships in Science and Engineering program.The gene order on these maps is based on recombination in multiple-point crosses or on duplication-coverage. The order is reliable but relative distances are often inaccurately determined and are variable in different genetic backgrounds. The overall length of the maps is estimated using meiotic recombination frequencies:
Marker Positions
Positions of markers on the genetic maps are only rough approximations. Different strains used for mapping exhibit different recombination frequencies and recombination values for the same interval have been shown to vary 10-fold or more in crosses of different parentage. For this reason, no attempt has been made to correct for undetected multiple crossovers in long intervals by using a mapping function.Distances between markers were estimated as composite or representative values based on all the crosses available and are shown on the scale where 10 map units = 7% recombination. It must be stressed that absolute and relative positions on the maps possess only limited predictive value, depending on the genotype of a particular cross with respect to genes that determine the frequency of recombination in each local region. In contrast, gene order is constant in the absence of rearrangement.
Units on the genetic map represent distance from the centromere.
- Negative distances denote positions on the left arm
- Positive distances denote positions on the right arm
Marker Sequence
252 genetic markers have associated sequence. Most of the available marker sequence is from Neurospora crassa itself, but in some cases the sequence is derived from a homologous gene in Saccharomyces cerevisiae.Genetic Marker Data
There are 928 known genetic markers assigned to linkage groups for Neurospora crassa. Of these markers:| # | % | Description |
|---|---|---|
| 409 | 44% | well-ordered within a genetic map linkage group |
| 252 | 27% | have associated sequence |
| 89 | 10% | well-ordered with sequence |
Breakpoint Naming
The naming of breakpoints on our maps differs slightly from the names on the published maps from the Compendium. We have included the linkage group in the name in some cases to make the name unique in the genome. For example, the breakpoint T(ALS176) that occurs on linkage groups II and V has been named T(ALS176)II and T(ALS176)V in our database. In addition, the superscripts in the breakpoint names, such as T(OY330)L, have been removed so that the name now looks like T(OY330)I(L).Correlation to Physical Map
Methodology
All genetic markers with associated sequence were compared to the current assembly using BLASTN. Where these matches were unique, were of high quality, and contained most or all of the gene, we assigned a marker position in one of our contigs. The resulting alignments were used to correlate contigs with linkage groups:- 240 of the 252 markers with sequence (95%) successfully mapped to the current assembly
- 67 supercontigs, representing 31.0 Mb (81% of the assembly), are anchored to a linkage group
- 88 of the 89 well-ordered markers (98%) successfully mapped to current assembly
- 43 supercontigs, representing 25.0 Mb (66% of the assembly), are ordered and oriented on a linkage group map
Special Cases
Markers in more than one contigIn several cases a marker spans more than one contig. This is to be expected as there are still gaps in between contigs that can occur in the middle of a gene. In these cases the marker is placed where the larger portion of the gene is, but a comment is added in the marker feature detail. The following markers have been split in this way:
| Marker | Contigs |
|---|---|
| cit-1 | 3.387, 3.73 |
| hsp30 | 3.592, 3.593 |
| mat A-1 | 3.87, 3.86 |
| mat a-1 | 3.87, 3.86 |
| nop-1 | 3.758, 3.759 |
In addition, several markers with sequence have not been assigned a position in the assembly. This may mean that the marker is not in the current assembly, or that the BLASTN results did not point to a unique location in the genome. The following markers have not been assigned a position:
| Marker | Linkage Group |
|---|---|
| Fsr-12 | I |
| Fsr-13 | IV |
| Fsr-16 | V |
| Fsr-17 | II |
| Fsr-20 | V |
| Fsr-45 | III |
| Fsr-51 | IV |
| Fsr-54 | II |
| cat-1 | III |
| cox-4 | III |
| cox-6 | V |
| tRNALEU | VII |
Lastly, a few supercontigs contain markers that have been assigned to 2 linkage groups. This could indicate a problem with the assembly, a problem with the genetic map, a problem assigning a sequence to marker, or a problem assigning a marker a position in the assembly. When the sequence is more complete we will be able to resolve these descrepancies. These supercontigs are currently displayed in the maps for two linkage groups. They are listed below:
| Supercontig | Markers in Different Linkage Groups |
|---|---|
| 1 | 7 in LGIII, 1 in LGVI (tom22) |
| 10 | 10 in LGII, 1 in LGV (nap) |
| 12 | 2 in LGI, 3 in LGVI |
| 14 | 3 in LGIV, 1 in LGVII (lacc) |
| 18 | 1 in LGII (vma-10), 1 in LGVI (nuo21.3c) |
| 28 | 3 in LGIII, 1 in LGV (gna-2) |
| 35 | 1 in LGIII (his-7), 1 in LGV (Tel-VR) |
| 4 | 11 in LGII, 1 in LGV (ppt-1) |
| 58 | 1 in LGII (con-6), 1 in LGIII (erg-3) |
Discrepancies
There are a few cases where marker order on the linkage group map conflicts with the locations of markers in supercontigs. These differences are indicated visually by crossed lines on the Correspondence of Physical to Genetic Maps. The discrepancies may be due to:- Errors in assembly of sequence into contigs or supercontigs
- Errors in order of markers on the linkage group map
- Correct but incomplete assembly data: for example, one supercontig may lie within a gap between contigs in another supercontig
Map Correlation Data
You can graphically view the correlation between the physical and genetic linkage maps from the Genetic Maps page.You can download a comma-separated file listing all markers (including GI numbers for those with sequence, and contig positions for those located in our assembly): markers.csv (see Download Markers for data details).
You may also search for genetic markers located on our current assembly.
A poster sized version of all of the physical & genetic maps is also available on the download page.