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Random selected markers for big gaps on chromosomes.
And there are some SDs that reside within 1 Mb of the "gaps" on chromosomes (Chrs 6, 14, 17 and 27), suggesting that SDs may be the problematic regions for both clone-based and whole-genome shotgun sequencing methods.
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In contrast, in our current linkage map for T. monococcum there was only two gaps on chromosome 4Am.
The coverage of the genome was rather homogeneous, with only few gaps on chromosome III and on the right arm of chromosome XIV.
A total of 96 DM BACs spanning scaffolding gaps on chromosome 4 were selected (using DM BAC-end hits; Potato Genome Sequencing Consortium 2011).
Compared with the previously published map [ 16], intervals of >10 cM remaining in the tetraploid map were reduced to 16 - nine in the At subgenome, and seven in the Dt subgenome, with the largest number of gaps on chromosome D8 (4 gaps >10 cM) and the largest overall gap on chromosome A3 (between two adjacent loci) 22.2 cM (Additional file 1: Table S1).
Since the published genetic map contains large gaps on chromosome 7, chromosome 2 and elsewhere, we also collated available cytogenetic map data from Fluorescence In Situ Hybridization with Tyramide Signal Amplification (FISH-TSA) analysis using cDNA probes [ 8, 10, 20], and evaluated read density on scaffolds anchored by known physical location of probes.
The average interval between consecutive loci is 5.48 cM, ranging from 0.0 cM between cosegregating markers to 25.7 cM in the largest gap (on chromosome 5).
There were examples of gap-filling: for example, FGX_OWB00091, mapped to a 17 cM gap on chromosome 7H in the Szűcs et al. [ 3] and incorporation of this marker reduced the distance between the two flanking markers to 10 cM.
Interestingly, the gap on chromosome 7 appears to contain the X. tropicalis sex determining locus [ 12], although an independent marker analysis suggests that there is not a large region of sex-specific sequence [ 13] which might interfere with meiotic mapping.
The overall size of an array of tandem 12 kb repeats which spanned a gap on chromosome 8 was found to be 600 kb to 1.7 Mbp in size, representing one of the largest non-centromeric arrays characterized.
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