Report of the committee on linkage data and gene order

1987 ◽  
Vol 46 (1-4) ◽  
pp. 339-343
Author(s):  
B.J.B. Keats ◽  
P.M. Conneally ◽  
J.M. Lalouel
Keyword(s):  
Gene Order ◽  
Linkage Data

Tests of gene order from three-locus linkage data

1987 ◽  
Vol 51 (3) ◽  
pp. 235-249 ◽  
Author(s):  
G. M. LATHROP ◽  
J. CHOTAI ◽  
J. OTT ◽  
J. M. LALOUEL
Keyword(s):  
Gene Order ◽  
Linkage Data

Use of 4x–2x crosses to determine gene–centromere map distances of isozyme loci in Solanum species

Genome ◽  
1987 ◽  
Vol 29 (4) ◽  
pp. 519-527 ◽  
Author(s):  
David S. Douches ◽  
Carlos F. Quiros
Keyword(s):  
Key Words ◽  
Gene Order ◽  
2N Gametes ◽  
Solanum Species ◽  
Linkage Data ◽  
Tetrad Analysis ◽  
Potato Genome ◽  
Pooled Data ◽  
Meiotic Abnormality ◽  
Isozyme Loci

With the meiotic abnormality described as the parallel spindles mechanism operating during anaphase II, first division type restitution 2n gametes (FDR) were identified in selected diploid Solanum clones. Generating 4x–2x FDR testcrosses of the general form aaaa × Aa with these diploid parents provided a means of estimating gene–centromere linkages with the application of half-tetrad analysis to the segregating tetraploid progenies. In this study, gene–centromere map distances were obtained for 10 isozyme loci and the yellow tuber flesh locus (Y). Electrophoretic assay of the tetraploid progenies yielded pooled gene–centromere linkage estimates for Got-1 (0.9 map units, mu), Pgm-2 (2.0 mu), Sdh-1 (8.3 mu), Aps-1 (13.5 mu), Adh-1 (15.8 mu), Prx-3 (18.0 mu), Idh-1 (18.4 mu), Pgi-1 (26.0 mu), 6-Pgdh-3 (30.1 mu), Mdh-1 (33.5 mu), and y (16.8 mu). These linkage data were combined with previously reported diploid testcross linkage data to show that these 11 markers are distributed over at least 8 of the 24 chromosome arms in the potato genome. In addition, gene order for the Idh-1/Sdh-1 linkage block (36.8 mu) was predicted to be of the sequence Id1-1 –centromere–Sdh-1, which is similarly found in Lycopersicon. Because of the codominant nature of these enzyme-coding loci, the theoretical expectations for 4x–2x FDR segregation were tested in this crop. Tests for reciprocity of exchange products of pooled data for 6-Pgdh-3, Mdh-1, Pgi-1, Adh-1, and Sdh-1 families yielded good fits to the expected 1:1 ratio. With these defined electrophoretic markers available, more critical genetic analyses can be extended to a number of genetic and breeding problems concerning the potato. Key words: half-tetrad analysis, 4x–2x, isozymes, Solanum, linkages.

scholarly journals The localization of G6pd, glucose-6-phosphate dehydrogenase, and mdx, muscular dystrophy in the mouse X chromosome

1988 ◽  
Vol 52 (3) ◽  
pp. 195-201 ◽  
Author(s):  
J. Peters ◽  
S. T. Ball ◽  
D. J. Charles ◽  
W. Pretsch ◽  
Grahame Bulfield ◽  
...  
Keyword(s):  
Muscular Dystrophy ◽  
X Chromosome ◽  
Gene Order ◽  
Recombination Frequency ◽  
Linkage Data ◽  
Point Test ◽  
Glucose 6 Phosphate Dehydrogenase ◽  
Low Activity

SummaryA low activity mutant of glucose-6-phosphate dehydrogenase, G6pda-m1Neu has been used to position G6pd in the mouse X chromosome. Linkage tests with tabby, Ta and harlequin, Hq, indicate a likely gene order of Hq–G6pd–Ta. Muscular dystrophy, mdx, has been located by two-and three-point crosses using Hprt, Pgk-1 and Moblo and suggest a gene order of Hprt–mdx–Pgk-1–Moblo. Together with existing linkage data a tentative order for the seven loci is Hq–Hprt–G6pd–mdx–Ta–Pgk-1–Moblo. The relative positions of G6pd and mdx have not been directly tested and G6pd is assigned provisionally proximal to mdx. In the three point test using Hq, G6pd and Ta the recombination frequency found between Hq and Ta was 9·9 ± 2·6%, substantially less than the value of 20·5 ± 2·1% reported by Isaacson et al. (1974).

TANDEM DUPLICATION RANDOM LOSS EVENTS INFLUENCED TO GENE ORDER CHANGES IN BAIKALIAN AMPHIPODS

2018 ◽  
Author(s):  
E.A. SIROTININA ◽  
◽  
E.V. ROMANOVA ◽  
D. YU. SHERBAKOV ◽  
◽  
...  
Keyword(s):  
Gene Order ◽  
Tandem Duplication ◽  
Random Loss

Computer Programs for Analyses of Inheritance and Linkage Data 1

Crop Science ◽  
1978 ◽  
Vol 18 (3) ◽  
pp. 517-517 ◽  
Author(s):  
Wayne Hanna ◽  
Ben Mullinix ◽  
Larry Grimes
Keyword(s):  
Computer Programs ◽  
Linkage Data

scholarly journals Validation of Automated Chromosome Recovery in the Reconstruction of Ancestral Gene Order

Algorithms ◽  
2021 ◽  
Vol 14 (6) ◽  
pp. 160
Author(s):  
Qiaoji Xu ◽  
Lingling Jin ◽  
James H. Leebens-Mack ◽  
David Sankoff
Keyword(s):  
Phylogenetic Tree ◽  
Gene Order ◽  
Evolutionary Process ◽  
Gene Content ◽  
Ancestral Genome ◽  
Maximum Weight ◽  
Ancestral Gene ◽  
Maximum Weight Matching

The RACCROCHE pipeline reconstructs ancestral gene orders and chromosomal contents of the ancestral genomes at all internal vertices of a phylogenetic tree. The strategy is to accumulate a very large number of generalized adjacencies, phylogenetically justified for each ancestor, to produce long ancestral contigs through maximum weight matching. It constructs chromosomes by counting the frequencies of ancestral contig co-occurrences on the extant genomes, clustering these for each ancestor and ordering them. The main objective of this paper is to closely simulate the evolutionary process giving rise to the gene content and order of a set of extant genomes (six distantly related monocots), and to assess to what extent an updated version of RACCROCHE can recover the artificial ancestral genome at the root of the phylogenetic tree relating to the simulated genomes.

scholarly journals Not Frozen in the Ice: large and Dynamic Rearrangements in the Mitochondrial Genomes of the Antarctic Fish

2021 ◽  
Author(s):  
Chiara Papetti ◽  
Massimiliano Babbucci ◽  
Agnes Dettai ◽  
Andrea Basso ◽  
Magnus Lucassen ◽  
...  
Keyword(s):  
Gene Order ◽  
Hot Spot ◽  
Mitochondrial Gene ◽  
Antarctic Fish ◽  
Purifying Selection ◽  
Compositional Bias ◽  
Mitochondrial Genomes ◽  
Notothenioid Fish ◽  
Antarctic Notothenioids ◽  
The Antarctic

Abstract The vertebrate mitochondrial genomes generally present a typical gene order. Exceptions are uncommon and important to study the genetic mechanisms of gene order rearrangements and their consequences on phylogenetic output and mitochondrial function. Antarctic notothenioid fish carry some peculiar rearrangements of the mitochondrial gene order. In this first systematic study of 28 species, we analysed known and undescribed mitochondrial genome rearrangements for a total of eight different gene orders within the notothenioid fish. Our reconstructions suggest that transpositions, duplications and inversion of multiple genes are the most likely mechanisms of rearrangement in notothenioid mitochondrial genomes. In Trematominae, we documented an extremely rare inversion of a large genomic segment of 5300 bp that partially affected the gene compositional bias but not the phylogenetic output. The genomic region delimited by nad5 and trnF, close to the area of the Control Region, was identified as the hot spot of variation in Antarctic fish mitochondrial genomes. Analysing the sequence of several intergenic spacers and mapping the arrangements on a newly generated phylogeny showed that the entire history of the Antarctic notothenioids is characterized by multiple, relatively rapid, events of disruption of the gene order. We hypothesised that a pre-existing genomic flexibility of the ancestor of the Antarctic notothenioids may have generated a precondition for gene order rearrangement, and the pressure of purifying selection could have worked for a rapid restoration of the mitochondrial functionality and compactness after each event of rearrangement.

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