scholarly journals Comparative Repeat Profiling of Two Closely Related Conifers (Larix decidua and Larix kaempferi) Reveals High Genome Similarity With Only Few Fast-Evolving Satellite DNAs

2021 ◽  
Vol 12 ◽  
Author(s):  
Tony Heitkam ◽  
Luise Schulte ◽  
Beatrice Weber ◽  
Susan Liedtke ◽  
Sarah Breitenbach ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Large Scale ◽  
Larix Decidua ◽  
Larix Kaempferi ◽  
Base Pairs ◽  
Satellite Dnas ◽  
Genomic Changes ◽  
Repeat Class ◽  
Organizational Patterns ◽  
Low Coverage

In eukaryotic genomes, cycles of repeat expansion and removal lead to large-scale genomic changes and propel organisms forward in evolution. However, in conifers, active repeat removal is thought to be limited, leading to expansions of their genomes, mostly exceeding 10 giga base pairs. As a result, conifer genomes are largely littered with fragmented and decayed repeats. Here, we aim to investigate how the repeat landscapes of two related conifers have diverged, given the conifers’ accumulative genome evolution mode. For this, we applied low-coverage sequencing and read clustering to the genomes of European and Japanese larch, Larix decidua (Lamb.) Carrière and Larix kaempferi (Mill.), that arose from a common ancestor, but are now geographically isolated. We found that both Larix species harbored largely similar repeat landscapes, especially regarding the transposable element content. To pin down possible genomic changes, we focused on the repeat class with the fastest sequence turnover: satellite DNAs (satDNAs). Using comparative bioinformatics, Southern, and fluorescent in situ hybridization, we reveal the satDNAs’ organizational patterns, their abundances, and chromosomal locations. Four out of the five identified satDNAs are widespread in the Larix genus, with two even present in the more distantly related Pseudotsuga and Abies genera. Unexpectedly, the EulaSat3 family was restricted to L. decidua and absent from L. kaempferi, indicating its evolutionarily young age. Taken together, our results exemplify how the accumulative genome evolution of conifers may limit the overall divergence of repeats after speciation, producing only few repeat-induced genomic novelties.

scholarly journals Comparative repeat profiling of two closely related conifers (Larix decidua and Larix kaempferi) reveals high genome similarity with only few fast-evolving satellite DNAs

2021 ◽  
Author(s):  
Tony Heitkam ◽  
Luise Schulte ◽  
Beatrice Weber ◽  
Susan Liedtke ◽  
Sarah Breitenbach ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Large Scale ◽  
Larix Decidua ◽  
Larix Kaempferi ◽  
Satellite Dnas ◽  
Genomic Changes ◽  
Repeat Class ◽  
Organizational Patterns ◽  
Low Coverage

ABSTRACTIn eukaryotic genomes, cycles of repeat expansion and removal lead to large-scale genomic changes and propel organisms forward in evolution. However, in conifers, active repeat removal is thought to be limited, leading to expansions of their genomes, mostly exceeding 10 gigabasepairs. As a result, conifer genomes are largely littered with fragmented and decayed repeats. Here, we aim to investigate how the repeat landscapes of two related conifers have diverged, given the conifers’ accumulative genome evolution mode. For this, we applied low coverage sequencing and read clustering to the genomes of European and Japanese larch, Larix decidua (Lamb.) Carrière and Larix kaempferi (Mill.), that arose from a common ancestor, but are now geographically isolated. We found that both Larix species harbored largely similar repeat landscapes, especially regarding the transposable element content. To pin down possible genomic changes, we focused on the repeat class with the fastest sequence turnover: satellite DNAs (satDNAs). Using comparative bioinformatics, Southern, and fluorescent in situ hybridization, we reveal the satDNAs’ organizational patterns, their abundances, and chromosomal locations. Four out of the five identified satDNAs are widespread in the Larix genus, with two even present in the more distantly related Pseudotsuga and Abies genera. Unexpectedly, the EulaSat3 family was restricted to L. decidua and absent from L. kaempferi, indicating its evolutionarily young age. Taken together, our results exemplify how the accumulative genome evolution of conifers may limit the overall divergence of repeats after speciation, producing only few repeat-induced genomic novelties.

Modeling cell-free DNA fragment size densities for non-invasive detection of cancer.

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. 3058-3058
Author(s):  
Jacob Carey ◽  
Bryan Chesnick ◽  
Denise Butler ◽  
Michael Rongione ◽  
Giovanni Parmigiani ◽  
...  
Keyword(s):  
Fragment Size ◽  
Length Distribution ◽  
Mixture Component ◽  
Base Pairs ◽  
Machine Model ◽  
Cell Free Dna ◽  
Non Invasive ◽  
Free Dna ◽  
Genome Wide ◽  
Low Coverage

3058 Background: Circulating cell-free DNA (cfDNA) is largely nucleosomal in origin with typical fragment lengths of 167 base-pairs reflecting the length of DNA wrapped around-the histone and H1 linker. Given the nucleosomal origin of cfDNA, we have previously used low coverage whole genome sequencing to evaluate DNA fragmentation profiles to sensitively and specifically detect tumor-derived DNA with altered fragment lengths or coverage. Methods: Here we evaluate the use of Bayesian finite mixtures to model the fragment length distribution and demonstrate how the parameters from these models can be useful to distinguish between individuals with and without cancer. We examined the number of cfDNA fragments by size ranging from 100-220bp and approximated the mixture component location, scale, and weight using Markov Chain Monte Carlo. The performance of the method was determined using a ten-fold, ten repeat cross-validation of Gradient Boosted Machine model using 1) our previously described genome-wide fragmentation profile approach, 2) the parameters from the mixture model and 3) a combination of approaches 1) and 2) as features. Results: In this study of 215 cancer patients and 208 cancer-free individuals, we observed cross-validated AUCs of 1) 0.94, 2) 0.95, and 3) 0.97 among the three approaches. Conclusions: Our findings indicate that parsimonious mixture models may improve detection of cancer in conjunction with fragmentation profile analyses across the genome.

Host defense mechanisms induce genome instability leading to rapid evolution in an opportunistic fungal pathogen

2021 ◽  
Author(s):  
Amanda Smith ◽  
Levi Morran ◽  
Meleah A. Hickman
Keyword(s):  
Fungal Pathogen ◽  
Defense Mechanisms ◽  
Large Scale ◽  
Genome Instability ◽  
Rapid Evolution ◽  
Genomic Changes ◽  
Opportunistic Fungal Pathogen ◽  
Immunocompromised Hosts ◽  
Stressful Environments

The ability to generate genetic variation facilitates rapid adaptation in stressful environments. The opportunistic fungal pathogen Candida albicans frequently undergoes large-scale genomic changes, including aneuploidy and loss-of heterozygosity (LOH), following exposure to host environments. However, the specific host factors inducing C. albicans genome instability remain largely unknown. Here, we leveraged the genetic tractability of nematode hosts to investigate whether innate immune components, including antimicrobial peptides (AMPs) and reactive oxygen species (ROS), induced host-associated C. albicans genome instability. C. albicans associated with immunocompetent hosts carried multiple large-scale genomic changes including LOH, whole chromosome, and segmental aneuploidies. In contrast, C. albicans associated with immunocompromised hosts deficient in AMPs or ROS production had reduced LOH frequencies and fewer, if any, additional genomic changes. To evaluate if extensive host-induced genomic changes had long-term consequences for C. albicans adaptation, we experimentally evolved C. albicans in either immunocompetent or immunocompromised hosts and selected for increased virulence. C. albicans evolved in immunocompetent hosts rapidly increased virulence, but not in immunocompromised hosts. Taken together, this work suggests that host-produced ROS and AMPs induces genotypic plasticity in C. albicans which facilitates rapid evolution.

scholarly journals Common adaptive strategies underlie within-host evolution of bacterial pathogens

2020 ◽  
Author(s):  
Yair E Gatt ◽  
Hanah Margalit
Keyword(s):  
Bacterial Infections ◽  
Large Scale ◽  
Bacterial Species ◽  
Adaptive Strategies ◽  
Single Species ◽  
Adaptive Strategy ◽  
Host Immune System ◽  
Glycerol Phosphate ◽  
Genomic Changes ◽  
Virulence Attenuation

Abstract Within-host adaptation is a hallmark of chronic bacterial infections, involving substantial genomic changes. Recent large-scale genomic data from prolonged infections allow the examination of adaptive strategies employed by different pathogens and open the door to investigate whether they converge towards similar strategies. Here, we compiled extensive data of whole-genome sequences of bacterial isolates belonging to miscellaneous species sampled at sequential time points during clinical infections. Analysis of these data revealed that different species share some common adaptive strategies, achieved by mutating various genes. While the same genes were often mutated in several strains within a species, different genes related to the same pathway, structure or function were changed in other species utilizing the same adaptive strategy (e.g. mutating flagellar genes). Strategies exploited by various bacterial species were often predicted to be driven by the host immune system, a powerful selective pressure that is not species-specific. Remarkably, we find adaptive strategies identified previously within single species to be ubiquitous. Two striking examples are shifts from siderophore-based to heme-based iron scavenging (previously shown for Pseudomonas aeruginosa), and changes in glycerol-phosphate metabolism (previously shown to decrease sensitivity to antibiotics in Mycobacterium tuberculosis). Virulence factors were often adaptively affected in different species, indicating shifts from acute to chronic virulence and virulence attenuation during infection. Our study presents a global view on common within-host adaptive strategies employed by different bacterial species and provides a rich resource for further studying these processes.

scholarly journals The role of semen and seminal plasma in inducing large-scale genomic changes in the female porcine peri-ovulatory tract

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
M. Álvarez-Rodríguez ◽  
C. A. Martinez ◽  
D. Wright ◽  
H. Rodríguez-Martinez
Keyword(s):  
Seminal Plasma ◽  
Genital Tract ◽  
Large Scale ◽  
Enrichment Analysis ◽  
Estrogen Signaling ◽  
Cell Recognition ◽  
Genomic Changes ◽  
Expression Of Genes ◽  
Microarray Analyses

AbstractSemen modifies the expression of genes related to immune function along the porcine female internal genital tract. Whether other pathways are induced by the deposition of spermatozoa and/or seminal plasma (SP), is yet undocumented. Here, to determine their relative impact on the uterine and tubal transcriptomes, microarray analyses were performed on the endocervix, endometrium and endosalpinx collected from pre-ovulatory sows 24 h after either mating or artificial insemination (AI) with specific ejaculate fractions containing spermatozoa or sperm-free SP. After enrichment analysis, we found an overrepresentation of genes and pathways associated with sperm transport and binding, oxidative stress and cell-to-cell recognition, such as PI3K-Akt, FoxO signaling, glycosaminoglycan biosynthesis and cAMP-related transcripts, among others. Although semen (either after mating or AI) seemed to have the highest impact along the entire genital tract, our results demonstrate that the SP itself also modifies the transcriptome. The detected modifications of the molecular profiles of the pre/peri-ovulatory endometrium and endosalpinx suggest an interplay for the survival, transport and binding of spermatozoa through, for instance the up-regulation of the Estrogen signaling pathway associated with attachment and release from the oviductal reservoir.

scholarly journals Isolation of a Pericentromeric Satellite DNA Family in Chnootriba argus (Henosepilachna argus) with an Unusual Short Repeat Unit (TTAAAA) for Beetles

Insects ◽  
2019 ◽  
Vol 10 (9) ◽  
pp. 306 ◽  
Author(s):  
Pablo Mora ◽  
Jesús Vela ◽  
Areli Ruiz-Mena ◽  
Teresa Palomeque ◽  
Pedro Lorite
Keyword(s):  
Repetitive Dna ◽  
Satellite Dna ◽  
Repeat Unit ◽  
Pericentromeric Region ◽  
Fish Analysis ◽  
Agricultural Pests ◽  
Base Pairs ◽  
Satellite Dnas ◽  
Repeat Units

Ladybird beetles (Coccinellidae) are one of the largest groups of beetles. Among them, some species are of economic interest since they can act as a biological control for some agricultural pests whereas other species are phytophagous and can damage crops. Chnootriba argus (Coccinellidae, Epilachnini) has large heterochromatic pericentromeric blocks on all chromosomes, including both sexual chromosomes. Classical digestion of total genomic DNA using restriction endonucleases failed to find the satellite DNA located on these heterochromatic regions. Cloning of C0t-1 DNA resulted in the isolation of a repetitive DNA with a repeat unit of six base pairs, TTAAAA. The amount of TTAAAA repeat in the C. argus genome was about 20%. Fluorescence in situ hybridization (FISH) analysis and digestion of chromosomes with the endonuclease Tru9I revealed that this repetitive DNA could be considered as the putative pericentromeric satellite DNA (satDNA) in this species. The presence of this satellite DNA was tested in other species of the tribe Epilachnini and it is also present in Epilachna paenulata. In both species, the TTAAAA repeat seems to be the main satellite DNA and it is located on the pericentromeric region on all chromosomes. The size of this satDNA, which has only six base pairs is unusual in Coleoptera satellite DNAs, where satDNAs usually have repeat units of a much larger size. Southern hybridization and FISH proved that this satDNA is conserved in some Epilachnini species but not in others. This result is in concordance with the controversial phylogenetic relationships among the genera of the tribe Epilachnini, where the limits between genera are unclear.

Rapid genomic changes in polyploid wheat and related species: implications for genome evolution and genetic improvement

2009 ◽  
Vol 36 (9) ◽  
pp. 519-528 ◽  
Author(s):  
Bao Liu ◽  
Chunming Xu ◽  
Na Zhao ◽  
Bao Qi ◽  
Josphert N. Kimatu ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Related Species ◽  
Genetic Improvement ◽  
Polyploid Wheat ◽  
Genomic Changes

scholarly journals Non-invasive prenatal testing as a valuable source of population specific allelic frequencies

2018 ◽  
Author(s):  
J Budis ◽  
J Gazdarica ◽  
J Radvanszky ◽  
M Harsanyova ◽  
I Gazdaricova ◽  
...  
Keyword(s):  
Large Scale ◽  
High Reliability ◽  
Low Cost ◽  
Variant Calling ◽  
Prenatal Testing ◽  
Data Set ◽  
Gold Standard Method ◽  
Non Invasive ◽  
Scale Population ◽  
Low Coverage

AbstractLow-coverage massively parallel genome sequencing for non-invasive prenatal testing (NIPT) of common aneuploidies is one of the most rapidly adopted and relatively low-cost DNA tests. Since aggregation of reads from a large number of samples allows overcoming the problems of extremely low coverage of individual samples, we describe the possible re-use of the data generated during NIPT testing for genome scale population specific frequency determination of small DNA variants, requiring no additional costs except of those for the NIPT test itself. We applied our method to a data set comprising of 1,548 original NIPT test results and evaluated the findings on different levels, from in silico population frequency comparisons up to wet lab validation analyses using a gold-standard method. The revealed high reliability of variant calling and allelic frequency determinations suggest that these NIPT data could serve as valuable alternatives to large scale population studies even for smaller countries around the world.

scholarly journals Hierarchical Discovery of Large-scale and Focal Copy Number Alterations in Low-coverage Cancer Genomes

2019 ◽  
Author(s):  
Ahmed Ibrahim Samir Khalil ◽  
Costerwell Khyriem ◽  
Anupam Chattopadhyay ◽  
Amartya Sanyal
Keyword(s):  
Copy Number ◽  
Large Scale ◽  
Simulated Data ◽  
Change Points ◽  
Copy Number Alterations ◽  
Biological Origin ◽  
Robust Detection ◽  
Cancer Data ◽  
Cancer Genomes ◽  
Low Coverage

AbstractMotivationDetection of copy number alterations (CNA) is critical to understand genetic diversity, genome evolution and pathological conditions such as cancer. Cancer genomes are plagued with widespread multi-level structural aberrations of chromosomes that pose challenges to discover CNAs of different length scales with distinct biological origin and function. Although several tools are available to identify CNAs using read depth (RD) of coverage, they fail to distinguish between large-scale and focal alterations due to inaccurate modeling of the RD signal of cancer genomes. These tools are also affected by RD signal variations, pronounced in low-coverage data, which significantly inflate false detection of change points and inaccurate CNA calling.ResultsWe have developed CNAtra to hierarchically discover and classify ‘large-scale’ and ‘focal’ copy number gain/loss from whole-genome sequencing (WGS) data. CNAtra provides an analytical and visualization framework for CNV profiling using single sequencing sample. CNAtra first utilizes multimodal distribution to estimate the copy number (CN) reference from the complex RD profile of the cancer genome. We utilized Savitzy-Golay filter and Modified Varri segmentation to capture the change points. We then developed a CN state-driven merging algorithm to identify the large segments with distinct copy number. Next, focal alterations were identified in each large segment using coverage-based thresholding to mitigate the adverse effects of signal variations. We tested CNAtra calls using experimentally verified segmental aneuploidies and focal alterations which confirmed CNAtra’s ability to detect and distinguish the two alteration phenomena. We used realistic simulated data for benchmarking the performance of CNAtra against other detection tools where we artificially spiked-in CNAs in the original cancer profiles. We found that CNAtra is superior in terms of precision, recall, and f-measure. CNAtra shows the highest sensitivity of 93% and 97% for detecting focal and large-scale alterations respectively. Visual inspection of CNAs showed that CNAtra is the most robust detection tool for low-coverage cancer data.Availability and implementationCNAtra is an open source software implemented in MATLAB, and is available at https://github.com/AISKhalil/CNAtra

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