Isolation and mapping of DNA probes within the linkage group I gene cluster of Caenorhabditis elegans

Genome ◽  
1989 ◽  
Vol 32 (3) ◽  
pp. 365-372 ◽  
Author(s):  
T. Starr ◽  
A. M. Howell ◽  
J. McDowall ◽  
K. Peters ◽  
A. M. Rose
Keyword(s):  
Caenorhabditis Elegans ◽  
Linkage Group ◽  
Gene Cluster ◽  
Physical Map ◽  
Dna Polymorphisms ◽  
Caenorhabditis Briggsae ◽  
Coding Regions ◽  
Group I ◽  
Type Strains ◽  
I Gene

We have isolated probes for DNA polymorphisms across the linkage group I gene cluster in Caenorhabditis elegans, using Tc1-linkage selection. The probes detect strain polymorphism between the wild-type strains of var. Bristol and var. Bergerac. As a result of mapping the sites hP4, hP5, hP6, hP7, hP9, and sP1, more than 1000 kilobases (kb) of cloned cosmid DNA has been positioned on the genetic map. We found there is more DNA per map unit in the center of the gene cluster than expected on the basis of the genomic average. Furthermore, the amount is not constant across the entire region but reaches a peak in the hP9 unc-13 interval. To find the coding regions, we examined DNA cross-homology between two species, Caenorhabditis elegans and Caenorhabditis briggsae. Approximately one-third of the DNA in the hP5 hP9 interval was examined for coding regions and 21 sequences were identified within 318 kb of DNA.Key words: Caenorhabditis elegans, physical map, DNA polymorphisms, genetic mapping, Caenorhabditis briggsae.

The genetic and RFLP characterization of the left end of linkage group III in Caenorhabditis elegans

Genome ◽  
1993 ◽  
Vol 36 (4) ◽  
pp. 712-724 ◽  
Author(s):  
Dave Pilgrim
Keyword(s):  
Caenorhabditis Elegans ◽  
Linkage Group ◽  
Genetic Map ◽  
Physical Map ◽  
Group Iii ◽  
C Elegans ◽  
Genomic Regions ◽  
Caenorhabditis Elegans Genome ◽  
Selection Of

A genetic approach was taken to identify new transposable element Tc1 -dependent polymorphisms on the left end of linkage group III in the nematode Caenorhabditis elegans. The cloning of the genomic DNA surrounding the Tc1 allowed the selection of overlapping clones (from the collection being used to assemble the physical map of the C. elegans genome). A contig of approximately 600–800 kbp in the region has been identified, the genetic map of the region has been refined, and 10 new RFLPs as well as at least four previously characterized genetic loci have been positioned onto the physical map, to the resolution of a few cosmids. This analysis demonstrated the ability to combine physical and genetic mapping for the rapid analysis of large genomic regions (0.5–1 Mbp) in genetically amenable eukaryotes.Key words: Caenorhabditis elegans, genome analysis, RFLP, physical map, genetic map.

Genetic mapping of the 5S rRNA gene cluster of the nematode Caenorhabditis elegans

1986 ◽  
Vol 28 (4) ◽  
pp. 545-553 ◽  
Author(s):  
D. W. Nelson ◽  
B. M. Honda
Keyword(s):  
Caenorhabditis Elegans ◽  
Linkage Group ◽  
Gene Cluster ◽  
5S Rrna ◽  
Rrna Gene ◽  
Nematode Caenorhabditis Elegans ◽  
Group V ◽  
Length Difference ◽  
5S Rrna Gene ◽  
Restriction Fragment Length

We have identified a restriction fragment length difference (RFLD) affecting the genomic sequences immediately flanking the 5S rRNA gene cluster in the Bristol and Bergerac strains of the nematode Caenorhabditis elegans. We have used this RFLD as a molecular marker to follow the segregation of the 5S rRNA gene cluster through a series of two- and three-factor interstrain crosses. Our results show that the 5S rRNA gene cluster maps between unc-76 and dpy-21 on the right arm of linkage group V. This genetic localization provides a linkage group V "landmark" with which to localize other cloned sequences by in situ hybridization.Key words: Caenorhabditis elegans, 5S rRNA gene cluster, restriction fragment length difference, genetic mapping.

scholarly journals Half-tetrad analysis in zebrafish: mapping the ros mutation and the centromere of linkage group I.

Genetics ◽  
1995 ◽  
Vol 139 (4) ◽  
pp. 1727-1735 ◽  
Author(s):  
S L Johnson ◽  
D Africa ◽  
S Horne ◽  
J H Postlethwait
Keyword(s):  
Linkage Group ◽  
Genetic Linkage ◽  
Dna Polymorphisms ◽  
Tetrad Analysis ◽  
Significant Excess ◽  
Group I ◽  
Gynogenetic Diploid ◽  
Polymerase Chain ◽  
Linkage Relationships ◽  
New Mutations

Abstract Analysis of meiotic tetrads is routinely used to determine genetic linkage in various fungi. Here we apply tetrad analysis to the study of genetic linkage in a vertebrate. The half-tetrad genotypes of gynogenetic diploid zebrafish produced by early-pressure (EP) treatment were used to investigate the linkage relationships of two recessive pigment pattern mutations, leopard (leo) and rose (ros). The results showed that ros is tightly linked to its centromere and leo maps 31 cM from its centromere. Analysis of half-tetrads segregating for ros and leo in repulsion revealed no homozygous ros individuals among 32 homozygous leo half-tetrads--i.e., a parental ditype (PD) to nonparental ditype (NPD) ratio of 32:0. This result shows that ros is linked to leo, a mutation previously mapped to Linkage Group I. Investigation of PCR-based DNA polymorphisms on Linkage Group I confirmed the location of ros near the centromere of this linkage group. We propose an efficient, generally useful method to assign new mutations to a linkage group in zebrafish by determining which of 25 polymerase chain reaction (PCR)-based centromere markers shows a significant excess of PD to NPD in half-tetrad fish.

Physical Mapping of the liguleless Linkage Group in Sorghum bicolor Using Rice RFLP-Selected Sorghum BACs

Genetics ◽  
1998 ◽  
Vol 148 (4) ◽  
pp. 1983-1992
Author(s):  
Michael S Zwick ◽  
M Nurul Islam-Faridi ◽  
Don G Czeschin ◽  
Rod A Wing ◽  
Gary E Hart ◽  
...  
Keyword(s):  
Linkage Group ◽  
Linkage Map ◽  
Physical Mapping ◽  
Fluorescent In Situ Hybridization ◽  
Physical Map ◽  
Rflp Markers ◽  
Full Agreement ◽  
Group I ◽  
Chromosome I

Abstract Physical mapping of BACs by fluorescent in situ hybridization (FISH) was used to analyze the liguleless (lg-1) linkage group in sorghum and compare it to the conserved region in rice and maize. Six liguleless-associated rice restriction fragment length polymorphism (RFLP) markers were used to select 16 homeologous sorghum BACs, which were in turn used to physically map the liguleless linkage group in sorghum. Results show a basic conservation of the liguleless region in sorghum relative to the linkage map of rice. One marker which is distal in rice is more medial in sorghum, and another marker which is found within the linkage group in rice is on a different chromosome in sorghum. BACs associated with linkage group I hybridize to chromosome It, which was identified by using FISH in a sorghum cytogenetic stock trisomic for chromosome I (denoted It), and a BAC associated with linkage group E hybridized to an unidentified chromosome. Selected BACs, representing RFLP loci, were end-cloned for RFLP mapping, and the relative linkage order of these clones was in full agreement with the physical data. Similarities in locus order and the association of RFLP-selected BAC markers with two different chromosomes were found to exist between the linkage map of the liguleless region in maize and the physical map of the liguleless region in sorghum.

The synaptonemal complexes of Caenorhabditis elegans: duplication mutants sDp1 and mnDp1, disjunction regulator regions and aneuploidy

Nematology ◽  
2010 ◽  
Vol 12 (5) ◽  
pp. 759-766
Author(s):  
Paul Goldstein
Keyword(s):  
Caenorhabditis Elegans ◽  
Linkage Group ◽  
X Chromosome ◽  
Initiation Site ◽  
Genetic Maps ◽  
Wild Type ◽  
Pachytene Nucleus ◽  
Synaptonemal Complexes ◽  
Recombination Nodules ◽  
Group I

AbstractThe duplication mutants sDp1 and mnDp1 in Caenorhabditis elegans differ in their size and recombination/pairing strategies within the pachytene nucleus. mnDp1 is a duplication of approximately 18% of the X chromosome with the duplicated segment transposed and inserted into linkage group V. sDp1 is a free duplication which covers 30 map units of linkage group I and crossing-over has been determined genetically with its homologue. Analysis of the synaptonemal complexes (SC) and pachytene karyotypes of both duplication mutants reveal that there is an extension of one of the SCs in mnDp1 while the sDp1 free duplication partially pairs with its homologue along a small portion of its length. The remaining region exists as a univalent in the pachytene nucleus. This indicates that there is at least one SC initiation site on the sDp1 free duplication. Only bivalent pairing is permitted and there are no trivalents. To some extent, the autosomes preferentially pair at the exclusion of the sDp1 duplication. Switching of pairing partners was evident between the duplication and the homologue, probably because of the size of the duplication. Thus, the mechanism of chromosome segregation in the two duplications is different. The number of Disjunction Regulator Regions, which are associated with X-chromosome nondisjunction, was three in both mutants compared to six in wild-type. The number of males produced in mnDp1 was 1.0%, in sDp1 it was 2.0%, while in wild-type it is 0.3%. Recombination nodules were not observed in any nuclei. The ultimate goal of these studies is to correlate the physical and genetic maps and in this study linkage group I has been identified in the pachytene nucleus.

Maternal-effect lethal mutations on linkage group II of Caenorhabditis elegans.

Genetics ◽  
1988 ◽  
Vol 120 (4) ◽  
pp. 977-986
Author(s):  
K J Kemphues ◽  
M Kusch ◽  
N Wolf
Keyword(s):  
Caenorhabditis Elegans ◽  
Linkage Group ◽  
Maternal Effect ◽  
Essential Genes ◽  
The Other ◽  
C Elegans ◽  
Lethal Mutations ◽  
Embryonic Lethal ◽  
Embryonic Lethal Mutations ◽  
F1 Progeny

Abstract We have analyzed a set of linkage group (LG) II maternal-effect lethal mutations in Caenorhabditis elegans isolated by a new screening procedure. Screens of 12,455 F1 progeny from mutagenized adults resulted in the recovery of 54 maternal-effect lethal mutations identifying 29 genes. Of the 54 mutations, 39 are strict maternal-effect mutations defining 17 genes. These 17 genes fall into two classes distinguished by frequency of mutation to strict maternal-effect lethality. The smaller class, comprised of four genes, mutated to strict maternal-effect lethality at a frequency close to 5 X 10(-4), a rate typical of essential genes in C. elegans. Two of these genes are expressed during oogenesis and required exclusively for embryogenesis (pure maternal genes), one appears to be required specifically for meiosis, and the fourth has a more complex pattern of expression. The other 13 genes were represented by only one or two strict maternal alleles each. Two of these are identical genes previously identified by nonmaternal embryonic lethal mutations. We interpret our results to mean that although many C. elegans genes can mutate to strict maternal-effect lethality, most genes mutate to that phenotype rarely. Pure maternal genes, however, are among a smaller class of genes that mutate to maternal-effect lethality at typical rates. If our interpretation is correct, we are near saturation for pure maternal genes in the region of LG II balanced by mnC1. We conclude that the number of pure maternal genes in C. elegans is small, being probably not much higher than 12.

scholarly journals A genetic mapping system in Caenorhabditis elegans based on polymorphic sequence-tagged sites.

Genetics ◽  
1992 ◽  
Vol 131 (3) ◽  
pp. 609-624 ◽  
Author(s):  
B D Williams ◽  
B Schrank ◽  
C Huynh ◽  
R Shownkeen ◽  
R H Waterston
Keyword(s):  
Caenorhabditis Elegans ◽  
Genetic Mapping ◽  
Physical Map ◽  
Nematode Caenorhabditis Elegans ◽  
C Elegans ◽  
Sequence Tagged Sites ◽  
Mapping System ◽  
Polymerase Chain ◽  
Tc1 Element ◽  
Single Reaction

Abstract We devised an efficient genetic mapping system in the nematode Caenorhabditis elegans which is based upon the differences in number and location of the transposable element Tc1 between the Bristol and Bergerac strains. Using the nearly completed physical map of the C. elegans genome, we selected 40 widely distributed sites which contain a Tc1 element in the Bergerac strain, but not in the Bristol strain. For each site a polymerase chain reaction assay was designed that can distinguish between the Bergerac Tc1-containing site and the Bristol "empty" site. By combining appropriate assays in a single reaction, one can score multiple sites within single worms. This permits a mutation to be rapidly mapped, first to a linkage group and then to a chromosomal subregion, through analysis of only a small number of progeny from a single interstrain cross.

scholarly journals Mitochondrial Intronic Open Reading Frames in Podospora: Mobility and Consecutive Exonic Sequence Variations

Genetics ◽  
1996 ◽  
Vol 143 (2) ◽  
pp. 777-788 ◽  
Author(s):  
Carole H Sellem ◽  
Yves d'Aubenton-Carafa ◽  
Michèle Rossignol ◽  
Léon Belcour
Keyword(s):  
Mitochondrial Genome ◽  
Open Reading Frames ◽  
Nucleotide Substitutions ◽  
Sequence Comparisons ◽  
Modular Evolution ◽  
Group I ◽  
Sequence Variations ◽  
Type Strains ◽  
Reading Frames ◽  
Adjacent Exon

Abstract The mitochondrial genome of 23 wild-type strains belonging to three different species of The mitochondrial genome the filamentous fungus Podospora was examined. Among the 15 optional sequences identified are two intronic reading frames, nad1-i4-orf1 and cox1-i7-orf2. We show that the presence of these sequences was strictly correlated with tightly clustered nucleotide substitutions in the adjacent exon. This correlation applies to the presence or absence of closely related open reading frames (ORFs), found at the same genetic locations, in all the Pyrenomycete genera examined. The recent gain of these optional ORFs in the evolution of the genus Podospora probably account for such sequence differences. In the homoplasmic progeny from heteroplasmons constructed between Podospora strains differing by the presence of these optional ORFs, nad1-i4-orf1 and cox1-i7-orf2 appeared highly invasive. Sequence comparisons in the nad1-i4 intron of various strains of the Pyrenomycete family led us to propose a scenario of its evolution that includes several events of loss and gain of intronic ORFs. These results strongly reinforce the idea that group I intronic ORFs are mobile elements and that their transfer, and comcomitant modification of the adjacent exon, could participate in the modular evolution of mitochondrial genomes.

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