Update on linkage map given genome sequence assembly
Mohamed Noor, Duke University
7 February 2006
Since the publication of our linkage map [1], the genome of Drosophila mojavensis has been sequenced and assembled (see http://rana.lbl.gov/drosophila/tools.html). The physical assembly matches very well with our linkage map overall. We have prepared this comment to note a handful of minor inconsistencies between our linkage map and the new physical assembly.
First, sequences of four of the unmapped microsatellites that we suggested to be probably autosomal were assembled into contigs associated with the X-chromosome. These markers are DMOJA500, DMOJA513, DMOJA514, and DMOJA517. None of the microsatellites we localized to the X were assembled onto autosomal scaffolds, and none of the microsatellites we assigned to a particular chromosome based on our linkage map were assembled onto a different chromosome in the physical assembly.
Second, two linked pairs of microsatellites were assembled in the opposite (reversed) orientation in the genome sequence relative to our linkage map: DMOJ2020-DMOJ2030 and DMOJ3030-DMOJ3040. However, one or both of these differences could reflect chromosomal inversion differences between the strains used in our mapping study and the strain used for the genome sequence, as chromosomes 2 and 3 are known to segregate for multiple arrangements within D. mojavensis [2].
We are very excited at the prospect of now having the combination of an assembled genome sequence with our recombinational linkage map.
References
1. Staten R, Dixon Schully S, Noor MAF: A microsatellite linkage map of Drosophila mojavensis. BMC Genet 2004, 5:12.
2. Ruiz A, Heed WB, Wasserman M: Evolution of the mojavensis cluster of cactophilic Drosophila with descriptions of two new species. J Hered 1990, 81(1):30-42.
Update on linkage map given genome sequence assembly
7 February 2006
Since the publication of our linkage map [1], the genome of Drosophila mojavensis has been sequenced and assembled (see http://rana.lbl.gov/drosophila/tools.html). The physical assembly matches very well with our linkage map overall. We have prepared this comment to note a handful of minor inconsistencies between our linkage map and the new physical assembly.
First, sequences of four of the unmapped microsatellites that we suggested to be probably autosomal were assembled into contigs associated with the X-chromosome. These markers are DMOJA500, DMOJA513, DMOJA514, and DMOJA517. None of the microsatellites we localized to the X were assembled onto autosomal scaffolds, and none of the microsatellites we assigned to a particular chromosome based on our linkage map were assembled onto a different chromosome in the physical assembly.
Second, two linked pairs of microsatellites were assembled in the opposite (reversed) orientation in the genome sequence relative to our linkage map: DMOJ2020-DMOJ2030 and DMOJ3030-DMOJ3040. However, one or both of these differences could reflect chromosomal inversion differences between the strains used in our mapping study and the strain used for the genome sequence, as chromosomes 2 and 3 are known to segregate for multiple arrangements within D. mojavensis [2].
We are very excited at the prospect of now having the combination of an assembled genome sequence with our recombinational linkage map.
References
1. Staten R, Dixon Schully S, Noor MAF: A microsatellite linkage map of Drosophila mojavensis. BMC Genet 2004, 5:12.
2. Ruiz A, Heed WB, Wasserman M: Evolution of the mojavensis cluster of cactophilic Drosophila with descriptions of two new species. J Hered 1990, 81(1):30-42.
Competing interests
None declared