scholarly journals Mapping-Free and Assembly-Free Discovery of Inversion Breakpoints from Raw NGS Reads

2014 ◽  
pp. 119-130 ◽  
Author(s):  
Claire Lemaitre ◽  
Liviu Ciortuz ◽  
Pierre Peterlongo
Keyword(s):  
Inversion Breakpoints

scholarly journals Inversion breakpoints and the evolution of supergenes

2021 ◽  
Author(s):  
Romain Villoutreix ◽  
Diego Ayala ◽  
Mathieu Joron ◽  
Zachariah Gompert ◽  
Jeffrey L. Feder ◽  
...  
Keyword(s):  
Inversion Breakpoints

Fine-mapping complex inversion breakpoints and investigating somatic pairing in the Anopheles gambiae species complex using proximity-ligation sequencing

2019 ◽  
Author(s):  
Russell B. Corbett-Detig ◽  
Iskander Said ◽  
Maria Calzetta ◽  
Max Genetti ◽  
Jakob McBroome ◽  
...  
Keyword(s):  
Anopheles Gambiae ◽  
Species Complex ◽  
Cytological Study ◽  
Sequencing Data ◽  
Proximity Ligation ◽  
Chromosomal Inversions ◽  
History Of ◽  
Somatic Pairing ◽  
Inversion Breakpoints ◽  
Rich History

AbstractChromosomal inversions are fundamental drivers of genome evolution. In the main afro-tropical malaria vector species, belonging to the Anopheles gambiae species complex, inversions play an important role in local adaptation and have a rich history of cytological study. Despite the importance and ubiquity of some chromosomal inversions across the species complex, inversion breakpoints are often challenging to map molecularly due to the presence of large repetitive regions. Here, we develop an approach that uses Hi-C sequencing data to molecularly fine-map the breakpoints of inversions 2Rbc and 2Rd in A. coluzzii. We found that inversion breakpoints occur in large repetitive regions, and strikingly among three inversions analyzed, two breakpoints appear to be reused in two separate inversions. Additionally, we use heterozygous individuals to quantitatively investigate somatic pairing disruption in the regions immediately surrounding inversion breakpoints, and we find that pairing disruption is undetectable beyond approximately 250 Kb from the inversion breakpoints.

scholarly journals Fine-Mapping Complex Inversion Breakpoints and Investigating Somatic Pairing in the Anopheles gambiae Species Complex Using Proximity-Ligation Sequencing

Genetics ◽  
2019 ◽  
Vol 213 (4) ◽  
pp. 1495-1511 ◽  
Author(s):  
Russell B. Corbett-Detig ◽  
Iskander Said ◽  
Maria Calzetta ◽  
Max Genetti ◽  
Jakob McBroome ◽  
...  
Keyword(s):  
Anopheles Gambiae ◽  
Fine Mapping ◽  
Species Complex ◽  
Repeat Sequence ◽  
Relative Fitness ◽  
Sequencing Data ◽  
Satellite Repeat ◽  
Chromosomal Inversions ◽  
Somatic Pairing ◽  
Inversion Breakpoints

Chromosomal inversions are fundamental drivers of genome evolution. In the main Afrotropical malaria vector species, belonging to the Anopheles gambiae species complex, inversions play an important role in local adaptation and have a rich history of cytological study. Despite the importance and ubiquity of some chromosomal inversions across the species complex, inversion breakpoints are often challenging to map molecularly due to the presence of large repetitive regions. Here, we develop an approach that uses Hi-C sequencing data to molecularly fine-map the breakpoints of inversions. We demonstrate that this approach is robust and likely to be widely applicable for both identification and fine-mapping inversion breakpoints in species whose inversions have heretofore been challenging to characterize. We apply our method to interrogate the previously unknown inversion breakpoints of 2Rbc and 2Rd in An. coluzzii. We found that inversion breakpoints occur in large repetitive regions, and, strikingly, among three inversions analyzed, two breakpoints appear to be reused in two separate inversions. These breakpoint-adjacent regions are strongly enriched for the presence of a 30 bp satellite repeat sequence. Because low frequency inversion breakpoints are not correlated with genomic regions containing this satellite, we suggest that interrupting this particular repeat may result in arrangements with higher relative fitness. Additionally, we use heterozygous individuals to quantitatively investigate the impacts of somatic pairing in the regions immediately surrounding inversion breakpoints. Finally, we discuss important considerations for possible applications of this approach for inversion breakpoint identification in a range of organisms.

Precise detection of chromosomal translocation or inversion breakpoints by whole-genome sequencing

2014 ◽  
Vol 59 (12) ◽  
pp. 649-654 ◽  
Author(s):  
Toshifumi Suzuki ◽  
Yoshinori Tsurusaki ◽  
Mitsuko Nakashima ◽  
Noriko Miyake ◽  
Hirotomo Saitsu ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Chromosomal Translocation ◽  
Whole Genome ◽  
Inversion Breakpoints

Ultrastructure of E1 + 2 + 9 + 12 inversion breakpoints in Drosophila subobscura

1990 ◽  
Vol 70 (1-2) ◽  
pp. 39-51 ◽  
Author(s):  
Juan Bautista Cuenca ◽  
Anja O Saura ◽  
Veikko Sorsa ◽  
Rosa Frutos
Keyword(s):  
Drosophila Subobscura ◽  
Inversion Breakpoints

scholarly journals TECHNIQUES FOR MANIPULATING CHROMOSOMAL REARRANGEMENTS AND THEIR APPLICATION TO DROSOPHILA MELANOGASTER. II. TRANSLOCATIONS

Genetics ◽  
1984 ◽  
Vol 108 (3) ◽  
pp. 573-587
Author(s):  
Loring Craymer
Keyword(s):  
Tandem Duplication ◽  
Gene Dosage ◽  
Chromosomal Rearrangements ◽  
Region Of Interest ◽  
Reciprocal Translocations ◽  
The Third ◽  
Translocation Breakpoints ◽  
Inversion Breakpoints ◽  
Derivatives Of ◽  
Tandem Duplications

ABSTRACT Translocations have long been valued for their segregational properties. This paper extends the utility of translocations by considering recombinational derivatives of pairs of simple reciprocal translocations. Three major derivative structures are noted. One of these derivatives is suitable for use in half-tetrad experiments. A second should find use in recombining markers with translocation breakpoints. The third is an insertional-tandem duplication: it has a section of one chromosome inserted into a heterologue with a section of the latter chromosome tandemly repeated about the breaks of the insert. All of these structures are contained in "constellations" of chromosomes that regularly segregate aneuploid-1 products (informationally equivalent to nonrecombinant adjacent-1 segregants) for one of the parental translocations but do not segregate euploid products. This is in contrast to the parental T  1/T  2 constellations which segregate euploid products but not aneuploid-1 products. Methods are described for selecting translocation recombinants on the basis of this dichotomy. Several examples of translocation recombinants have been recovered with these techniques, and the recombination frequencies seem to be consistent with those observed for crossovers between inversion breakpoints. Recombinant chromosomes tend to disjoin, but it is observed that the tendency may vary according to the region involved in the recombination, and it is suggested that this difference reflects a difference in chiasmata terminalization times. Special consideration is given to insertional-tandem duplications. Large insertional-tandem duplications are useful in cytogenetic screens. Small insertional-tandem duplications are useful in gene dosage studies and other experiments that require an insert from one chromosome to another. Large duplications can be deleted to form small duplications. To generate a small insert for a specified region, it is only necessary to have one translocation with a breakpoint flanking the region of interest. The second translocation can have a breakpoint quite far from the region: an insertional-tandem duplication containing the region that has one closely flanking breakpoint can be deleted to create a smaller duplication that has two closely flanking breakpoints.

scholarly journals A nanopore based chromosome-level assembly representing Atlantic cod from the Celtic Sea

2019 ◽  
Author(s):  
Tina Graceline Kirubakaran ◽  
Øivind Andersen ◽  
Michel Moser ◽  
Mariann Arnyasi ◽  
Philip McGinnity ◽  
...  
Keyword(s):  
Gadus Morhua ◽  
Barents Sea ◽  
Atlantic Cod ◽  
Population Based ◽  
Linkage Groups ◽  
Long Read ◽  
Study Population ◽  
Celtic Sea ◽  
Genome Assemblies ◽  
Inversion Breakpoints

ABSTRACTCurrently available genome assemblies for Atlantic cod (Gadus morhua) have been constructed using DNA from fish belonging to the Northeast Arctic Cod (NEAC) population; a migratory population feeding in the cold Barents Sea. These assemblies have been crucial for the development of genetic markers which have been used to study population differentiation and adaptive evolution in Atlantic cod, pinpointing four discrete islands of genomic divergence located on linkage groups 1, 2, 7 and 12. In this paper, we present a high-quality reference genome from a male Atlantic cod representing a southern population inhabiting the Celtic sea. Structurally, the genome assembly (gadMor_Celtic) was produced from long-read nanopore data and has a combined contig size of 686 Mb with a N50 of 10 Mb. Integrating contigs with genetic linkage mapping information enabled us to construct 23 chromosome sequences which mapped with high confidence to the latest NEAC population assembly (gadMor3) and allowed us to characterize in detail large chromosomal inversions on linkage groups 1, 2, 7 and 12. In most cases, inversion breakpoints could be located within single nanopore contigs. Our results suggest the presence of inversions in Celtic cod on linkage groups 6, 11 and 21, although these remain to be confirmed. Further, we identified a specific repetitive element that is relatively enriched at predicted centromeric regions. Our gadMor_Celtic assembly provides a resource representing a ‘southern’ cod population which is complementary to the existing ‘northern’ population based genome assemblies and represents the first step towards developing pan-genomic resources for Atlantic cod.

GENETIC METHODS FOR ANALYSIS AND MANIPULATION OF INVERSION MUTATIONS IN BACTERIA

Genetics ◽  
1983 ◽  
Vol 105 (3) ◽  
pp. 517-537
Author(s):  
Molly B Schmid ◽  
John R Roth
Keyword(s):  
Type Strain ◽  
Wild Type Strain ◽  
Recipient Cell ◽  
Chromosome Segment ◽  
Large Chromosome ◽  
Good Resolution ◽  
Wild Type ◽  
Chromosomal Inversions ◽  
Inversion Breakpoints ◽  
Generalized Transduction

ABSTRACT A number of genetic methods for the isolation, characterization and manipulation of large chromosomal inversions in Salmonella typhimurium are described. One inversion-carrying mutant is characterized in detail and used to demonstrate a number of unique genetic properties of bacterial inversions.—Contrary to expectation, it was found that large inversion mutations can be repaired by generalized transduction. The repair results from the simultaneous introduction of two wild-type transduced fragments into a single recipient cell. Homologous recombination between the two transduced fragments and the two inversion breakpoints causes the inverted segment to be reinverted. This results in regeneration of the wild-type orientation of this chromosome segment. Similar recombination events allow a large inversion mutation to be introduced into a wild-type strain; two transduced fragments from an inversion strain cause recombination events resulting in inversion of a large chromosome segment.—Genetic methods for mapping the extent of a large inversion mutation by generalized transduction are described and tested. The methods are operationally simple and allow good resolution of the two inversion breakpoints.

Sign in / Sign up

Export Citation Format

Share Document