Parental origin of de novo chromosome rearrangements

1980 ◽  
Vol 53 (3) ◽  
pp. 343-347 ◽  
Author(s):  
J. Chamberlin ◽  
R. E. Magenis
GigaScience ◽  
2020 ◽  
Vol 9 (8) ◽  
Author(s):  
Eugenie C Yen ◽  
Shane A McCarthy ◽  
Juan A Galarza ◽  
Tomas N Generalovic ◽  
Sarah Pelan ◽  
...  

ABSTRACT Background Diploid genome assembly is typically impeded by heterozygosity because it introduces errors when haplotypes are collapsed into a consensus sequence. Trio binning offers an innovative solution that exploits heterozygosity for assembly. Short, parental reads are used to assign parental origin to long reads from their F1 offspring before assembly, enabling complete haplotype resolution. Trio binning could therefore provide an effective strategy for assembling highly heterozygous genomes, which are traditionally problematic, such as insect genomes. This includes the wood tiger moth (Arctia plantaginis), which is an evolutionary study system for warning colour polymorphism. Findings We produced a high-quality, haplotype-resolved assembly for Arctia plantaginis through trio binning. We sequenced a same-species family (F1 heterozygosity ∼1.9%) and used parental Illumina reads to bin 99.98% of offspring Pacific Biosciences reads by parental origin, before assembling each haplotype separately and scaffolding with 10X linked reads. Both assemblies are contiguous (mean scaffold N50: 8.2 Mb) and complete (mean BUSCO completeness: 97.3%), with annotations and 31 chromosomes identified through karyotyping. We used the assembly to analyse genome-wide population structure and relationships between 40 wild resequenced individuals from 5 populations across Europe, revealing the Georgian population as the most genetically differentiated with the lowest genetic diversity. Conclusions We present the first invertebrate genome to be assembled via trio binning. This assembly is one of the highest quality genomes available for Lepidoptera, supporting trio binning as a potent strategy for assembling heterozygous genomes. Using our assembly, we provide genomic insights into the geographic population structure of A. plantaginis.


Author(s):  
Philip D. Cotter ◽  
Michele Caggana ◽  
Judith P. Willner ◽  
Arvind Babu ◽  
Robert J. Desnick

Author(s):  
R. J McKinlay Gardner ◽  
David J Amor

Complex chromosome rearrangements (CCRs) include most of the rearrangements that would not be accounted for as “straightforward” classical categories. They may be translocations with three or more segments involved; or they may comprise a mix of translocation and, for example, inversion. Some can be extraordinarily complex. CCRs are classified as types I–IV, most falling into the “least complex” type I category, while types II–IV are grouped as “exceptional CCRs.” Many unbalanced CCRs have arisen de novo and imply no increased reproductive risk. The identification of the clinically normal balanced CCR carrier is less frequent, and for these people, the reproductive risks can be very high.


2020 ◽  
Vol 189 (12) ◽  
pp. 1451-1460
Author(s):  
Dimitry Bazyka ◽  
Maureen Hatch ◽  
Natalia Gudzenko ◽  
Elizabeth K Cahoon ◽  
Vladimir Drozdovitch ◽  
...  

Abstract Although transgenerational effects of exposure to ionizing radiation have long been a concern, human research to date has been confined to studies of disease phenotypes in groups exposed to high doses and high dose rates, such as the Japanese atomic bomb survivors. Transgenerational effects of parental irradiation can be addressed using powerful new genomic technologies. In collaboration with the Ukrainian National Research Center for Radiation Medicine, the US National Cancer Institute, in 2014–2018, initiated a genomic alterations study among children born in selected regions of Ukraine to cleanup workers and/or evacuees exposed to low–dose-rate radiation after the 1986 Chornobyl (Chernobyl) nuclear accident. To investigate whether parental radiation exposure is associated with germline mutations and genomic alterations in the offspring, we are collecting biospecimens from father-mother-offspring constellations to study de novo mutations, minisatellite mutations, copy-number changes, structural variants, genomic insertions and deletions, methylation profiles, and telomere length. Genomic alterations are being examined in relation to parental gonadal dose, reconstructed using questionnaire and measurement data. Subjects are being recruited in exposure categories that will allow examination of parental origin, duration, and timing of exposure in relation to conception. Here we describe the study methodology and recruitment results and provide descriptive information on the first 150 families (mother-father-child(ren)) enrolled.


1996 ◽  
Vol 97 (5) ◽  
pp. 568-572 ◽  
Author(s):  
Thomas Eggermann ◽  
Hartmut Engels ◽  
Barbara Moskalonek ◽  
Markus M. Nöthen ◽  
Jutta Müller-Navia ◽  
...  

2011 ◽  
Vol 54 (1) ◽  
pp. 19-24 ◽  
Author(s):  
Bernhard Horsthemke ◽  
Michaela Wawrzik ◽  
Stephanie Groß ◽  
Christina Lich ◽  
Birgitta Sauer ◽  
...  

2009 ◽  
Vol 29 (3) ◽  
pp. 257-265 ◽  
Author(s):  
Daniela Giardino ◽  
Cecilia Corti ◽  
Lucia Ballarati ◽  
Daniela Colombo ◽  
Elena Sala ◽  
...  

2003 ◽  
Vol 12 (1) ◽  
pp. 52-58 ◽  
Author(s):  
Stefan Aretz ◽  
Siegfried Uhlhaas ◽  
Reiner Caspari ◽  
Elisabeth Mangold ◽  
Constanze Pagenstecher ◽  
...  

Development ◽  
1988 ◽  
Vol 104 (2) ◽  
pp. 235-244
Author(s):  
A. Collick ◽  
W. Reik ◽  
S.C. Barton ◽  
A.H. Surani

The process of X-inactivation in mammals requires at least two events, the initiation of inactivation and the maintenance of the inactive state. One possible mechanism of control is by methylation of DNA at CpG dinucleotides to maintain the inactive state. Furthermore, the paternal X-chromosome is frequently inactivated in the extraembryonic membranes. The relationship between the parental origin of the chromosome, nonrandom inactivation and DNA methylation is not clear. In this paper, we report on the CpG methylation of an X-linked transgene, CAT-32. The levels of methylation in embryonic, extraembryonic and germline cells indicates that the modifications of the transgene are broadly similar to those reported for endogenous X-linked genes. Interestingly, the methylation of CAT-32 transgene in extraembryonic tissues displays patterns that could be linked to the germline origin of each allele. Hence, the maternally derived copy of CAT-32 was relatively undermethylated when compared to the paternal one. The changes in DNA methylation were attributed to de novo methylation occurring after fertilization, most probably during differentiation of extraembryonic tissues. In order to determine whether or not the patterns of DNA methylation reflected the germline origin of the X-chromosome, we constructed triploid embryos specifically to introduce two maternal X-chromosomes in the same embryo. In some of these triploid conceptuses, methylation patterns characteristic of the paternally derived transgene were observed. This observation indicates that the methylation patterns are not necessarily dependent on the parental origin of the X-chromosome, but could be changed by somatic events after fertilization. One of the more likely mechanisms is methylation of the transgene following inactivation of the X-chromosome in extraembryonic tissues.


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