Aspergillus nidulans Genetic Map Description
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Genetic Maps
Description
Around 260 known genetic markers, which have associated sequences, exist for Aspergillus nidulans. Dr. John Clutterbuck, at University of Glasgow, kindly compiled and provided us with the map information. See The Aspergillus nidulans Linkage Map for more details.
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.
Units on the genetic map represent distance from the left arm to the right arm.
Genetic Marker Data
The 260 genetic markers were filtered to a set of 196 unambiguous sequences with accessions in GenBank. Of these 196 markers, 103 are ordered on the linkage group map whereas the remaining 93 are unordered. The file of genetic markers is available for download.
Correlation to Physical Map
Methodology
The 260 markers were filtered to a set of 201 unambiguous sequences with accessions in GenBank. These 201 markers were compared to the current assembly using BLASTN. Where these matches were unique, were of high quality, and contained most or all the gene, we assigned a marker position in one of our contigs. Of the 201 markers, 187 markers were placed uniquely within the assembly and 14 of the markers showed discrepancies. We used the 187 unique marker alignments to correlate contigs with linkage groups, creating the correlated genetic maps displayed here.
- 28.5 Mb (18 supercontigs) of the 30 Mb assembly or 95% of the assembly, are anchored to the genetic map.
- 26.8 Mb (12 supercontigs ) or 89% of the assembly are ordered and oriented.
- 1.7 Mb can only be placed on a linkage group without specifying order or orientation
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
See Genetic Map Errata for details of additional map information.
Special Cases
Supercontigs in more than one linkage group
43 genetic markers were located within supercontig 1.1. 42 of these 43 genetic markers are from linkage group VIII, however one genetic marker (aroG) is assigned to linkage group VII. This discrepancy could indicate an error in the genetic map or a misassembly.
There are 7 markers which show such discrepancies and would cause supercontigs to be placed on multiple linkage groups. Instead, we have placed each supercontig on the linkage group that contains the majority of its markers and we report here the 7 discrepant cases:
| Supercontig | Markers in Different Linkage Groups |
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| 1.2 | 24 in LGVII, 1 in LGI (chsD) |
| 1.3 | 16 in LGVI, 1 in LGIII (cmkB), 1 in LGVII (pgmB) |
| 1.4 | 9 in LGII, 1 in LGIV (cpcB) |
| 1.6 | 21 in LGI, 1 in LGII (acrA) |
| 1.7 | 13 in LGV, 1 in LGI (nudC) |
| 1.9 | 4 in LGIV, 1 in LGVIII (lipA) |
Map Correlation Data
You can graphically view the correlation between the physical and genetic linkage maps from the Genetic Maps page.You can download XML, tab-delimited and FASTA files for the markers used in creating the genetic map. (see Download Markers for data details).
A poster sized version of all of the physical & genetic maps is also available on the download page.