scholarly journals Ultra-deep sequencing reveals dramatic alteration of organellar genomes in Physcomitrella patens due to biased asymmetric recombination

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Masaki Odahara ◽  
Kensuke Nakamura ◽  
Yasuhiko Sekine ◽  
Taku Oshima
Keyword(s):  
Deep Sequencing ◽  
Physcomitrella Patens ◽  
Genome Instability ◽  
Read Depth ◽  
Organelle Genome ◽  
Abnormal Growth ◽  
Genome Wide ◽  
Knockout Mutants ◽  
Organelle Genomes ◽  
Recombination Repair

AbstractDestabilization of organelle genomes causes organelle dysfunction that appears as abnormal growth in plants and diseases in human. In plants, loss of the bacterial-type homologous recombination repair (HRR) factors RECA and RECG induces organelle genome instability. In this study, we show the landscape of organelle genome instability in Physcomitrella patens HRR knockout mutants by deep sequencing in combination with informatics approaches. Genome-wide maps of rearrangement positions in the organelle genomes, which exhibited prominent mutant-specific patterns, were highly biased in terms of direction and location and often associated with dramatic variation in read depth. The rearrangements were location-dependent and mostly derived from the asymmetric products of microhomology-mediated recombination. Our results provide an overall picture of organelle-specific gross genomic rearrangements in the HRR mutants, and suggest that chloroplasts and mitochondria share common mechanisms for replication-related rearrangements.

scholarly journals Factors Affecting Organelle Genome Stability in Physcomitrella patens

Plants ◽  
2020 ◽  
Vol 9 (2) ◽  
pp. 145 ◽  
Author(s):  
Masaki Odahara
Keyword(s):  
Genome Stability ◽  
Physcomitrella Patens ◽  
Genome Structure ◽  
Land Plant ◽  
Factors Affecting ◽  
Organelle Genome ◽  
Organelle Genomes ◽  
Recombination Repair ◽  
The Relationship ◽  
Bacterial Type

Organelle genomes are essential for plants; however, the mechanisms underlying the maintenance of organelle genomes are incompletely understood. Using the basal land plant Physcomitrella patens as a model, nuclear-encoded homologs of bacterial-type homologous recombination repair (HRR) factors have been shown to play an important role in the maintenance of organelle genome stability by suppressing recombination between short dispersed repeats. In this review, I summarize the factors and pathways involved in the maintenance of genome stability, as well as the repeats that cause genomic instability in organelles in P. patens, and compare them with findings in other plant species. I also discuss the relationship between HRR factors and organelle genome structure from the evolutionary standpoint.

scholarly journals Single Nucleotide Polymorphism Discovery and Genetic Differentiation Analysis of Geese Bred in Poland, Using Genotyping-by-Sequencing (GBS)

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 1074
Author(s):  
Joanna Grzegorczyk ◽  
Artur Gurgul ◽  
Maria Oczkowicz ◽  
Tomasz Szmatoła ◽  
Agnieszka Fornal ◽  
...  
Keyword(s):  
Genotyping By Sequencing ◽  
Read Depth ◽  
Model Organisms ◽  
Single Nucleotide Polymorphism Discovery ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Polymorphism Discovery ◽  
Genome Wide ◽  
Plumage Development ◽  
Edar Gene

Poland is the largest European producer of goose, while goose breeding has become an essential and still increasing branch of the poultry industry. The most frequently bred goose is the White Kołuda® breed, constituting 95% of the country’s population, whereas geese of regional varieties are bred in smaller, conservation flocks. However, a goose’s genetic diversity is inaccurately explored, mainly because the advantages of the most commonly used tools are strongly limited in non-model organisms. One of the most accurate used markers for population genetics is single nucleotide polymorphisms (SNP). A highly efficient strategy for genome-wide SNP detection is genotyping-by-sequencing (GBS), which has been already widely applied in many organisms. This study attempts to use GBS in 12 conservative goose breeds and the White Kołuda® breed maintained in Poland. The GBS method allowed for the detection of 3833 common raw SNPs. Nevertheless, after filtering for read depth and alleles characters, we obtained the final markers panel used for a differentiation analysis that comprised 791 SNPs. These variants were located within 11 different genes, and one of the most diversified variants was associated with the EDAR gene, which is especially interesting as it participates in the plumage development, which plays a crucial role in goose breeding.

Evaluation of Four Methods to Identify the Homozygotic Sex Chromosome in Small Populations

2021 ◽  
Author(s):  
Charles Christian Riis Hansen ◽  
Kristen M. Westfall ◽  
Snaebjörn Pálsson
Keyword(s):  
Sex Chromosomes ◽  
Sex Chromosome ◽  
Read Depth ◽  
Mapping Method ◽  
Small Population ◽  
Genomic Variation ◽  
Z Chromosome ◽  
Effective Population ◽  
Organelle Genomes ◽  
Heterogametic Sex

Abstract BackgroundWhole genomes are commonly assembled into a collection of scaffolds and often lack annotations of autosomes, sex chromosomes, and organelle genomes (i.e., mitochondrial and chloroplast). As these chromosome types differ in effective population size and can have highly disparate evolutionary histories, it is imperative to take this information into account when analysing genomic variation. Here we assessed the accuracy of four methods for identifying the homogametic sex chromosome in a small population using two whole genome sequences (WGS) and 133 RAD sequences of white-tailed eagles (Haliaeetus albicilla): i) difference in read depth per scaffold in a male and a female, ii) heterozygosity per scaffold in a male and a female, iii) mapping to a reference genome of a related species (chicken) with identified sex chromosomes, and iv) analysis of SNP-loadings from a principal components analysis (PCA), based on the low-depth RADseq data. ResultsThe best performing approach was the reference mapping (method iii), which identified 98.12% of the expected homogametic sex chromosome (Z). The read depth per scaffold (method i) identified 86.41% of the homogametic sex chromosome with few false positives. The SNP-loading scores (method iv) found 78.6% of the Z-chromosome and had a false positive discovery rate of more than 10%. The heterozygosity per scaffold (method ii) did not provide clear results due to a lack of diversity in both the Z and autosomal chromosomes, and potential interference from the heterogametic sex chromosome (W). The evaluation of these methods also revealed 10 Mb of likely PAR and gametologous regions.ConclusionIdentification of the homogametic sex chromosome in a small population is best accomplished by reference mapping or examining read depth differences between sexes.

scholarly journals Genome-wide transcriptome analysis of gametophyte development in Physcomitrella patens

2011 ◽  
Vol 11 (1) ◽  
pp. 177 ◽  
Author(s):  
Lihong Xiao ◽  
Hui Wang ◽  
Ping Wan ◽  
Tingyun Kuang ◽  
Yikun He
Keyword(s):  
Transcriptome Analysis ◽  
Physcomitrella Patens ◽  
Gametophyte Development ◽  
Genome Wide

scholarly journals Emerging Technologies for Genome-Wide Profiling of DNA Breakage

2021 ◽  
Vol 11 ◽  
Author(s):  
Matthew J. Rybin ◽  
Melina Ramic ◽  
Natalie R. Ricciardi ◽  
Philipp Kapranov ◽  
Claes Wahlestedt ◽  
...  
Keyword(s):  
Genome Instability ◽  
Dna Double Strand Breaks ◽  
Single Nucleotide ◽  
Strand Breaks ◽  
Single Strand Breaks ◽  
Genome Wide ◽  
A Genome ◽  
Wide Scale ◽  
Nucleotide Resolution ◽  
Genomic Regions

Genome instability is associated with myriad human diseases and is a well-known feature of both cancer and neurodegenerative disease. Until recently, the ability to assess DNA damage—the principal driver of genome instability—was limited to relatively imprecise methods or restricted to studying predefined genomic regions. Recently, new techniques for detecting DNA double strand breaks (DSBs) and single strand breaks (SSBs) with next-generation sequencing on a genome-wide scale with single nucleotide resolution have emerged. With these new tools, efforts are underway to define the “breakome” in normal aging and disease. Here, we compare the relative strengths and weaknesses of these technologies and their potential application to studying neurodegenerative diseases.

scholarly journals ATM orchestrates the DNA-damage response to counter toxic non-homologous end-joining at broken replication forks

2018 ◽  
Author(s):  
Gabriel Balmus ◽  
Domenic Pilger ◽  
Julia Coates ◽  
Mukerrem Demir ◽  
Matylda Sczaniecka-Clift ◽  
...  
Keyword(s):  
Genetic Resistance ◽  
Resistance Mechanisms ◽  
Replication Forks ◽  
End Joining ◽  
Strand Breaks ◽  
Dna Damaging Agents ◽  
Genome Wide ◽  
Topoisomerase Poison ◽  
Recombination Repair ◽  
Non Homologous End Joining

SummaryMutations in the ATM tumor suppressor confer hypersensitivity to DNA-damaging agents. To explore genetic resistance mechanisms, we performed genome-wide CRISPR-Cas9 screens in cells treated with the DNA topoisomerase poison topotecan. Thus, we establish that loss of terminal components of the non-homologous end-joining (NHEJ) machinery or the BRCA1-A complex specifically confers topotecan resistance to ATM-deficient cells. We show that hypersensitivity of ATM-mutant cells to topotecan or the poly-(ADP-ribose) polymerase inhibitor olaparib is due to delayed homologous recombination repair at DNA-replication-fork-associated double-strand breaks (DSBs), resulting in toxic NHEJ-mediated chromosome fusions. Accordingly, restoring legitimate repair in ATM-deficient cells, either by preventing NHEJ DNA ligation or by enhancing DSB-resection by BRCA1-A complex inactivation, markedly suppresses this toxicity. Our work suggests opportunities for patient stratification in ATM-deficient cancers and when using ATM inhibitors in the clinic, and identifies additional therapeutic vulnerabilities that might be exploited when such cancers evolve drug resistance.One Sentence SummaryATM counteracts toxic NHEJ at broken replication forks

scholarly journals Genome-Wide Essentiality Analysis of Mycobacterium abscessus by Saturated Transposon Mutagenesis and Deep Sequencing

mBio ◽  
2021 ◽  
Author(s):  
Dalin Rifat ◽  
Liang Chen ◽  
Barry N. Kreiswirth ◽  
Eric L. Nuermberger
Keyword(s):  
Deep Sequencing ◽  
Mycobacterium Abscessus ◽  
Transposon Mutagenesis ◽  
Comprehensive Analysis ◽  
Data Sets ◽  
Similar Data ◽  
Intrinsic Resistance ◽  
Effective Strategies ◽  
Genome Wide

Limited knowledge regarding Mycobacterium abscessus pathogenesis and intrinsic resistance to most classes of antibiotics is a major obstacle to developing more effective strategies to prevent and mitigate disease. Using optimized procedures for Himar1 transposon mutagenesis and deep sequencing, we performed a comprehensive analysis to identify M. abscessus genetic elements essential for in vitro growth and compare them to similar data sets for M. tuberculosis and M. avium subsp. hominissuis .

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