scholarly journals Physical Mapping of the Anopheles (Nyssorhynchus) darlingi Genomic Scaffolds

Insects ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 164
Author(s):  
Míriam Silva Rafael ◽  
Leticia Cegatti Bridi ◽  
Igor V. Sharakhov ◽  
Osvaldo Marinotti ◽  
Maria V. Sharakhova ◽  
...  
Keyword(s):  
Physical Mapping ◽  
Genomic Dna ◽  
Chromosomal Rearrangements ◽  
Polytene Chromosomes ◽  
Anopheles Darlingi ◽  
Anopheles Albimanus ◽  
Anopheles Species ◽  
Homologous Sequences ◽  
Genome Assemblies

The genome assembly of Anopheles darlingi consists of 2221 scaffolds (N50 = 115,072 bp) and has a size spanning 136.94 Mbp. This assembly represents one of the smallest genomes among Anopheles species. Anopheles darlingi genomic DNA fragments of ~37 Kb were cloned, end-sequenced, and used as probes for fluorescence in situ hybridization (FISH) with salivary gland polytene chromosomes. In total, we mapped nine DNA probes to scaffolds and autosomal arms. Comparative analysis of the An. darlingi scaffolds with homologous sequences of the Anopheles albimanus and Anopheles gambiae genomes identified chromosomal rearrangements among these species. Our results confirmed that physical mapping is a useful tool for anchoring genome assemblies to mosquito chromosomes.

Interspecific chromosomal rearrangements in monosomic addition lines of Allium

Genome ◽  
2001 ◽  
Vol 44 (5) ◽  
pp. 929-935 ◽  
Author(s):  
L Barthes ◽  
A Ricroch
Keyword(s):  
Genomic Dna ◽  
Chromosomal Rearrangements ◽  
In Situ Hybridisation ◽  
Crossing Over ◽  
Dna Repeats ◽  
Addition Lines ◽  
Genomic In Situ Hybridisation ◽  
Chromatin Transfer ◽  
Alien Addition Lines

Monosomic alien addition lines (MAALs) are useful for assigning linkage groups to chromosomes. We examined whether the chromosomal rearrangements following the introduction of a single onion (Allium cepa) chromosome into the Allium fistulosum genome were produced by homeologous crossing over or by a nonreciprocal conversion event. Among the monosomic lines available, 17 were studied by fluorescent genomic in situ hybridisation, using total A. cepa genomic DNA as the probe and total A. fistulosum genomic DNA as the competitor. In this way, rearrangements such as chromosomal translocations between A. cepa and A. fistulosum were identified as terminal regions consisting of tandem DNA repeats. Homeologous crossing over between the two closely related genomes occurred in 4 of the 17 lines, suggesting that such events are not rare. On the basis of a detailed molecular cytogenetic characterisation, we identified true monosomic alien addition lines for A. cepa chromosomes 3, 4, 5, 7, and 8 that can reliably be used in genetic studies.Key words: chromatin transfer, genomic in situ hybridisation, GISH, monosomic alien addition lines, MAALs, Allium.

LOCATION OF THE LSP-1 GENES IN DROSOPHILA SPECIES BY IN SITU HYBRIDIZATION

Genetics ◽  
1983 ◽  
Vol 103 (1) ◽  
pp. 75-92
Author(s):  
Hugh W Brock ◽  
David B Roberts
Keyword(s):  
Drosophila Melanogaster ◽  
In Situ Hybridization ◽  
X Chromosome ◽  
Restriction Enzyme ◽  
Genomic Dna ◽  
Polytene Chromosomes ◽  
Enzyme Digestion ◽  
Restriction Enzyme Digestion ◽  
Larval Serum Protein

ABSTRACT The locations of the larval serum protein one (LSP-1) α, β and γ genes were determined in Drosophila melanogaster and in 14 other species of Drosophila by in situ hybridization to polytene chromosomes. The LSP-1 α gene mapped to bands 11B on the X chromosome, the LSP-1 β gene mapped to bands 21D-E on chromosome 2L, and the LSP-1 γ gene mapped to band 61A in all the melanogaster subgroup species. In eight other species, both the LSP-1α and β genes mapped to one site on Muller's element E which corresponds to chromosome 3R of D. melanogaster. No hybridization of LSP-1 γ was detected in these eight species. Restriction enzyme digestion and analysis of genomic DNA by filter transfer hybridization confirmed the presence of LSP-1 α-like and β-like genes in seven of these species. These results are discussed with respect to conservation of the chromosomal elements in the genus Drosophila.

The evolutionary history of Drosophila buzzatii. XXIII. High content of nonsatellite repetitive DNA in D. buzzatii and in its sibling D. koepferae

Genome ◽  
1992 ◽  
Vol 35 (6) ◽  
pp. 967-974 ◽  
Author(s):  
I. Marin ◽  
M. Labrador ◽  
A. Fontdevila
Keyword(s):  
Repetitive Dna ◽  
Sibling Species ◽  
Genomic Dna ◽  
Repetitive Sequences ◽  
Polytene Chromosomes ◽  
Drosophila Buzzatii ◽  
Repleta Group ◽  
Wide Variability ◽  
History Of

The frequency and types of repetitive nonsatellite DNA of two sibling species of the repleta group of Drosophila, D. buzzatii, and D. koepferae have been determined. For each species, the analysis is based on a sample of more than 100 clones (400 kb) obtained from genomic DNA. A theoretical model has been developed to correct for the presence of a mixture of repetitive and unique DNA in these clones. After correction, a high content of repetitive DNA has been demonstrated for both species (D. buzzatii, 19–26%; D. koepferae, 27–32%). The repetitive sequences have been classified according to their hybridization pattern when used as probes against genomic DNA and by their in situ hybridization signals on polytene chromosomes. Data suggest that the main nonsatellite component of these species is simpler and more repetitive than that of D. melanogaster, pointing to a wide variability in content and class size distribution of repetitive DNA among Drosophila species.Key words: repetitive DNA, DNA evolution, Drosophila, repleta group, sibling species.

A combined ultrastructural and gene molecular research for the relationship between human uterine cervical carcinoma and human papillomavirus

1990 ◽  
Vol 48 (3) ◽  
pp. 204-205
Author(s):  
Kun Lee ◽  
Jingyi Si ◽  
Ricai Han ◽  
Wei Zhang ◽  
Bingbing Tan ◽  
...  
Keyword(s):  
Cervical Cancer ◽  
Human Papillomavirus ◽  
Intraepithelial Neoplasia ◽  
Hpv Infection ◽  
Dot Blot ◽  
Homologous Sequences ◽  
Normal Cervical Epithelium ◽  
The Relationship ◽  
Chronic Cervicitis

There are more supports for the view that human papillomavirus (HPV) infection might be an etiological factor in the development of cervical cancer when the association of persistent condylomata is considered. Biopsies from 318 cases with squamous cell carcinoma of uterine cervix, 48 with cervical and vulvar condylomata, 14 with cervical intraepithelial neoplasia (CIN), 34 with chronic cervicitis and 24 normal cervical epithelium were collected from 5 geographic regions of China with different cervical cancer mortalities. All specimens were prepared for Dot blot, Southern blot and in situ DNA-DNA hybridizations by using HPV-11, 16, 18 DNA labelled with 32P and 3H as probes to detect viral homologous sequences in samples. Among them, 32 cases with cervical cancer, 27 with condyloma and 10 normal cervical epitheliums were randomly chosen for comparative EM observation. The results showed that: 1), 192 out of 318 (60.4%) cases of cervical cancer were positive for HPV-16 DNA probe (Table I)

scholarly journals Molecular Characterization of hobo-Mediated Inversions in Drosophila melanogaster

Genetics ◽  
1996 ◽  
Vol 144 (2) ◽  
pp. 647-656
Author(s):  
William B Eggleston ◽  
Nac R Rim ◽  
Johng K Lim
Keyword(s):  
X Chromosome ◽  
Polymerase Chain Reaction Amplification ◽  
Polytene Chromosomes ◽  
Chromosomal Inversions ◽  
Hobo Element ◽  
Reaction Amplification ◽  
Notch Locus ◽  
Polymerase Chain

Abstract The structure of chromosomal inversions mediated by hobo transposable elements in the Uc-1 X chromosome was investigated using cytogenetic and molecular methods. Uc-1 contains a phenotypically silent hobo element inserted in an intron of the Notch locus. Cytological screening identified six independent Notch mutations resulting from chromosomal inversions with one breakpoint at cytological position 3C7, the location of Notch. In situ hybridization to salivary gland polytene chromosomes determined that both ends of each inversion contained hobo and Notch sequences. Southern blot analyses showed that both breakpoints in each inversion had hobo-Notch junction fragments indistinguishable in structure from those present in the Uc-1 X chromosome prior to the rearrangements. Polymerase chain reaction amplification of the 12 hobo-Notch junction fragments in the six inversions, followed by DNA sequence analysis, determined that each was identical to one of the two hobo-Notch junctions present in Uc-1. These results are consistent with a model in which hobo-mediated inversions result from homologous pairing and recombination between a pair of hobo elements in reverse orientation.

scholarly journals Physical mapping of repetitive oligonucleotides facilitates the establishment of a genome map-based karyotype to identify chromosomal variations in peanut

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Liuyang Fu ◽  
Qian Wang ◽  
Lina Li ◽  
Tao Lang ◽  
Junjia Guo ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Physical Mapping ◽  
Tandem Repeats ◽  
Genetic Research ◽  
Diploid Species ◽  
Reference Sequence ◽  
A Genome ◽  
Genome Map ◽  
Chromosomal Variants

Abstract Background Chromosomal variants play important roles in crop breeding and genetic research. The development of single-stranded oligonucleotide (oligo) probes simplifies the process of fluorescence in situ hybridization (FISH) and facilitates chromosomal identification in many species. Genome sequencing provides rich resources for the development of oligo probes. However, little progress has been made in peanut due to the lack of efficient chromosomal markers. Until now, the identification of chromosomal variants in peanut has remained a challenge. Results A total of 114 new oligo probes were developed based on the genome-wide tandem repeats (TRs) identified from the reference sequences of the peanut variety Tifrunner (AABB, 2n = 4x = 40) and the diploid species Arachis ipaensis (BB, 2n = 2x = 20). These oligo probes were classified into 28 types based on their positions and overlapping signals in chromosomes. For each type, a representative oligo was selected and modified with green fluorescein 6-carboxyfluorescein (FAM) or red fluorescein 6-carboxytetramethylrhodamine (TAMRA). Two cocktails, Multiplex #3 and Multiplex #4, were developed by pooling the fluorophore conjugated probes. Multiplex #3 included FAM-modified oligo TIF-439, oligo TIF-185-1, oligo TIF-134-3 and oligo TIF-165. Multiplex #4 included TAMRA-modified oligo Ipa-1162, oligo Ipa-1137, oligo DP-1 and oligo DP-5. Each cocktail enabled the establishment of a genome map-based karyotype after sequential FISH/genomic in situ hybridization (GISH) and in silico mapping. Furthermore, we identified 14 chromosomal variants of the peanut induced by radiation exposure. A total of 28 representative probes were further chromosomally mapped onto the new karyotype. Among the probes, eight were mapped in the secondary constrictions, intercalary and terminal regions; four were B genome-specific; one was chromosome-specific; and the remaining 15 were extensively mapped in the pericentric regions of the chromosomes. Conclusions The development of new oligo probes provides an effective set of tools which can be used to distinguish the various chromosomes of the peanut. Physical mapping by FISH reveals the genomic organization of repetitive oligos in peanut chromosomes. A genome map-based karyotype was established and used for the identification of chromosome variations in peanut following comparisons with their reference sequence positions.

scholarly journals CHROMOSOMAL SEQUENCES AND INTERISLAND COLONIZATIONS IN HAWAIIAN DROSOPHILA

Genetics ◽  
1983 ◽  
Vol 103 (3) ◽  
pp. 465-482
Author(s):  
Hampton L Carson
Keyword(s):  
Polytene Chromosomes ◽  
Complex Species ◽  
Hawaiian Drosophila ◽  
On This Island ◽  
Break Points ◽  
Chromosomal Sequences ◽  
Founder Events ◽  
Paracentric Inversions ◽  
Single Set

ABSTRACT Of 103 picture-winged Drosophila species endemic to the high Hawaiian islands, all but three are endemic to single islands or island complexes. They are presumed to have evolved in situ on each island. The banding pattern sequences of the five major polytene chromosomes of these species have been mapped to a single set of Standard sequences. Sequential variation among these chromosomes is due to 213 paracentric inversions. An atlas of their break points is provided. Geographical, morphological and behavioral data may be used to supplement the cytological information in tracing ancestry. Starting at the newer end of the archipelago, the 26 species of the Island of Hawaii (less than 700,000 years old) are inferred to have been derived from 19 founders, 15 from the Maui complex, three from Oahu and one from Kauai. The existence of 40 Maui complex species is explicable as resulting from 12 founders, ten from Oahu and two from Kauai. The 29 Oahu species can be explained by 12 founder events, five from Kauai and seven from Maui complex (summary in Figure 5). Although the ancestry of two Kauai species can be traced to newer islands, the ten remaining ones on this island (age about 5.6 million years) are apparently ancient elements in the fauna, relating ultimately to Palearctic continental sources.

C-banding and fluorescence in situ hybridization studies of the wheat–alien hybrid 'Agrotana'

Genome ◽  
1994 ◽  
Vol 37 (3) ◽  
pp. 477-481 ◽  
Author(s):  
Jie Xu ◽  
R. L. Conner ◽  
A. Laroche
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Genomic Dna ◽  
Chromosome Engineering ◽  
C Banding ◽  
Chinese Spring Wheat ◽  
Mother Cells ◽  
Alien Chromatin ◽  
Chromosome Segments

'Agrotana', a wheat-alien hybrid (2n = 56), is a potential source of resistance to common root rot, stem rust, wheat streak mosaic virus, and the wheat curl mite. However, the origin of 'Agrotana', reported to be durum wheat × Agropyron trichophorum (pubescent wheatgrass), is uncertain. The objective of this investigation was to determine the chromosome constitution of 'Agrotana' using C-banding and fluorescence in situ hybridization techniques. The F1 hybrid of 'Agrotana' × 'Chinese Spring' wheat showed 7 I + 21 II in 14.9% of the pollen mother cells, evidence of the presence of the A, B, and D genomes in 'Agrotana'. The hybrid had 16 heavily C-banded chromosomes, namely 4A, and 1-7B of wheat, and a translocation that probably involved wheat chromosomes 2A and 2D. In situ hybridization using biotinylated genomic DNA of Ag. trichophorum cv. Greenleaf blocked with CS DNA failed to identify the alien chromosomes in 'Agrotana', indicating that the alien chromosomes were not likely derived from pubescent wheatgrass. In situ hybridization using labelled wheat genomic DNA blocked with 'Agrotana' DNA revealed that 'Agrotana' had 40 wheat, 14 alien, and 2 (a pair) wheat–alien translocated chromosomes. There was no homology between wheat and the alien chromosomes or chromosome segments involved in the wheat–alien recombinant. Two of the seven pairs of alien chromosomes were homoeologous to each other. The ability to identify alien chromatin in wheat using labelled wheat DNA instead of labelled alien DNA will be particularly useful in chromosome engineering of wheat germplasms having alien chromatin of unknown origin.Key words: wheat–alien hybrid, C-banding, fluorescence in situ hybridization, labelled wheat DNA as probe.

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