scholarly journals Novel phylogeny of angiosperms inferred from whole-genome microsynteny analysis

2020 ◽  
Author(s):  
Tao Zhao ◽  
Jiayu Xue ◽  
Shu-min Kao ◽  
Zhen Li ◽  
Arthur Zwaenepoel ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Genome Structure ◽  
Flowering Plants ◽  
Novel Approach ◽  
Genome Wide ◽  
Core Eudicots ◽  
Alternative Hypotheses ◽  
Angiosperm Species ◽  
Phylogenetic Character ◽  
Relative Gene

AbstractDespite the wealth of genomic and transcriptomic data of pivotal angiosperm species, the phylogenetic relationships of flowering plants are still not fully resolved. Microsynteny, or the conservation of relative gene order, has been recognized as a valuable and alternative phylogenetic character to sequence-based characters (nucleotides or amino acids). Here, we present a novel approach for phylogenetic tree reconstruction based on genome-wide synteny network data. We generated and analyzed synteny networks from 123 species from 52 families across 31 orders of flowering plants, including several lineages for which phylogenetic relationships are ambiguous. We obtained a stable and highly resolved phylogeny that is largely congruent with sequence-based phylogenies. However, our results unveiled several novel relationships for some key clades, such as magnoliids sister to monocots, Vitales as sister to core-eudicots, and Saxifragales sister to Santalales, in turn both sister to Caryophyllales. Our results highlight that phylogenies based on genome structure and organization are complementary to sequence-based phylogenies and provide alternative hypotheses of angiosperm relationships to be further tested.

Reconstructing Phylogenetic Relationships Based on Repeat Sequence Similarities

2019 ◽  
Author(s):  
Daniel Vitales ◽  
Sònia Garcia ◽  
Steven Dodsworth
Keyword(s):  
Phylogenetic Relationships ◽  
Sequence Similarity ◽  
Information Source ◽  
Repeat Sequence ◽  
Combined Application ◽  
Novel Approach ◽  
Genome Wide ◽  
History Of ◽  
Sequence Similarities ◽  
Phylogenetic Method

AbstractA recent phylogenetic method based on genome-wide abundance of different repeat types proved to be useful in reconstructing the evolutionary history of several plant and animal groups. Here, we demonstrate that an alternative information source from the repeatome can also be employed to infer phylogenetic relationships among taxa. Specifically, this novel approach makes use of the repeat sequence similarity matrices obtained from the comparative clustering analyses of RepeatExplorer 2, which are subsequently transformed to between-taxa distance matrices. These pairwise matrices are used to construct neighbour-joining trees for each of the top most-abundant clusters and they are finally summarized in a consensus network. This methodology was tested on three groups of angiosperms and one group of insects, resulting in congruent evolutionary hypotheses compared to more standard systematic analyses based on commonly used DNA markers. We propose that the combined application of these phylogenetic approaches based on repeat abundances and repeat sequence similarities could be helpful to understand mechanisms governing genome and repeatome evolution.

scholarly journals Subtype-associated epigenomic landscape and 3D genome structure in bladder cancer

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Tejaswi Iyyanki ◽  
Baozhen Zhang ◽  
Qixuan Wang ◽  
Ye Hou ◽  
Qiushi Jin ◽  
...  
Keyword(s):  
Bladder Cancer ◽  
Transcription Factor ◽  
Cancer Cell ◽  
Genome Structure ◽  
Transcription Factor Binding ◽  
Specific Gene ◽  
Open Chromatin ◽  
Factor Binding ◽  
3D Genome ◽  
Genome Wide

Abstract Muscle-invasive bladder cancers are characterized by their distinct expression of luminal and basal genes, which could be used to predict key clinical features such as disease progression and overall survival. Transcriptionally, FOXA1, GATA3, and PPARG are shown to be essential for luminal subtype-specific gene regulation and subtype switching, while TP63, STAT3, and TFAP2 family members are critical for regulation of basal subtype-specific genes. Despite these advances, the underlying epigenetic mechanisms and 3D chromatin architecture responsible for subtype-specific regulation in bladder cancer remain unknown. Result We determine the genome-wide transcriptome, enhancer landscape, and transcription factor binding profiles of FOXA1 and GATA3 in luminal and basal subtypes of bladder cancer. Furthermore, we report the first-ever mapping of genome-wide chromatin interactions by Hi-C in both bladder cancer cell lines and primary patient tumors. We show that subtype-specific transcription is accompanied by specific open chromatin and epigenomic marks, at least partially driven by distinct transcription factor binding at distal enhancers of luminal and basal bladder cancers. Finally, we identify a novel clinically relevant transcription factor, Neuronal PAS Domain Protein 2 (NPAS2), in luminal bladder cancers that regulates other subtype-specific genes and influences cancer cell proliferation and migration. Conclusion In summary, our work identifies unique epigenomic signatures and 3D genome structures in luminal and basal urinary bladder cancers and suggests a novel link between the circadian transcription factor NPAS2 and a clinical bladder cancer subtype.

scholarly journals Czechoslovakian Wolfdog Genomic Divergence from Its Ancestors Canis lupus, German Shepherd Dog, and Different Sheepdogs of European Origin

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 832
Author(s):  
Nina Moravčíková ◽  
Radovan Kasarda ◽  
Radoslav Židek ◽  
Luboš Vostrý ◽  
Hana Vostrá-Vydrová ◽  
...  
Keyword(s):  
Demographic History ◽  
Genome Structure ◽  
Principal Component ◽  
Genetic Distances ◽  
Nucleotide Polymorphisms ◽  
German Shepherd ◽  
German Shepherd Dog ◽  
Genome Wide ◽  
Scale Population ◽  
History Effect

This study focused on the genomic differences between the Czechoslovakian wolfdog (CWD) and its ancestors, the Grey wolf (GW) and German Shepherd dog. The Saarloos wolfdog and Belgian Shepherd dog were also included to study the level of GW genetics retained in the genome of domesticated breeds. The dataset consisted of 131 animals and 143,593 single nucleotide polymorphisms (SNPs). The effects of demographic history on the overall genome structure were determined by screening the distribution of the homozygous segments. The genetic variance distributed within and between groups was quantified by genetic distances, the FST index, and discriminant analysis of principal components. Fine-scale population stratification due to specific morphological and behavioural traits was assessed by principal component and factorial analyses. In the CWD, a demographic history effect was manifested mainly in a high genome-wide proportion of short homozygous segments corresponding to a historical load of inbreeding derived from founders. The observed proportion of long homozygous segments indicated that the inbreeding events shaped the CWD genome relatively recently compared to other groups. Even if there was a significant increase in genetic similarity among wolf-like breeds, they were genetically separated from each other. Moreover, this study showed that the CWD genome carries private alleles that are not found in either wolves or other dog breeds analysed in this study.

scholarly journals Type 2 Diabetes Subtype Responsive to ACCORD Intensive Glycemia Treatment

2021 ◽  
Author(s):  
Arshiya Mariam ◽  
Galen Miller-Atkins ◽  
Kevin M. Pantalone ◽  
Robert S. Zimmerman ◽  
John Barnard ◽  
...  
Keyword(s):  
Type 2 Diabetes ◽  
Mendelian Randomization ◽  
Controlled Trial ◽  
Clinical Group ◽  
Cvd Risk ◽  
Group 4 ◽  
Novel Approach ◽  
Genome Wide ◽  
Design And Methods

Objective <p>Current type 2 diabetes (T2D) management contraindicates intensive glycemia treatment in patients with high cardiovascular disease (CVD) risk, and is partially motivated by evidence of harms in the Action to Control Cardiovascular Risk in Diabetes (ACCORD) trial. Heterogeneity in response to intensive glycemia treatment has been observed, suggesting potential benefit for some individuals.</p> <p>Research Design and Methods</p> <p>ACCORD was a randomized controlled trial that investigated whether intensively treating glycemia in individuals with T2D reduced CVD outcomes. Using a novel approach to cluster HbA1c trajectories, we identified groups in the intensive glycemia arm with modified CVD risk. Genome-wide analysis and polygenic score (PS) were developed to predict group membership. Mendelian randomization was performed to infer causality. </p> <p>Results</p> <p>We identified four clinical groupings in the intensive glycemia arm, and clinical group 4 (C4) displayed fewer CVD outcomes (HR=0.34, <i>P</i>=2.01x10<sup>-3</sup>) and microvascular outcomes (HR=0.86, <i>P</i>=.015) than standard treatment. A single nucleotide polymorphism, rs220721, in <i>MAS1, </i>reached suggestive significance<i> </i>with C4 (<i>P</i>=4.34x10<sup>-7</sup>). The PS predicted C4 with high accuracy (AUC=0.98), and predicted C4 displayed reduced CVD risk on intensive versus standard glycemia treatment (HR=0.53, <i>P</i>=4.02x10<sup>-6</sup>), but not for microvascular outcomes (<i>P</i><.05). Mendelian randomization indicated causality between the PS, on-trial HbA1c, and reduction in CVD outcomes (<i>P</i><.05). </p> <p>Conclusions</p> <p>We found evidence of a T2D clinical group in ACCORD that benefited from intensive glycemia treatment, and membership of this group can be predicted using genetic variants. This study generates new hypotheses with implications for precision medicine in T2D and represents an important development for this landmark clinical trial warranting further investigation.</p>

scholarly journals Early diversification and permeable species boundaries in the Mediterranean firs

2019 ◽  
Vol 125 (3) ◽  
pp. 495-507 ◽  
Author(s):  
Francisco Balao ◽  
María Teresa Lorenzo ◽  
José Manuel Sánchez-Robles ◽  
Ovidiu Paun ◽  
Juan Luis García-Castaño ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Evolutionary History ◽  
Taxonomic Status ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Early Diversification ◽  
Genome Wide ◽  
History Of ◽  
The Mediterranean ◽  
Independent Species

Abstract Background and Aims Inferring the evolutionary relationships of species and their boundaries is critical in order to understand patterns of diversification and their historical drivers. Despite Abies (Pinaceae) being the second most diverse group of conifers, the evolutionary history of Circum-Mediterranean firs (CMFs) remains under debate. Methods We used restriction site-associated DNA sequencing (RAD-seq) on all proposed CMF taxa to investigate their phylogenetic relationships and taxonomic status. Key Results Based on thousands of genome-wide single nucleotide polymorphisms (SNPs), we present here the first formal test of species delimitation, and the first fully resolved, complete species tree for CMFs. We discovered that all previously recognized taxa in the Mediterranean should be treated as independent species, with the exception of Abies tazaotana and Abies marocana. An unexpectedly early pulse of speciation in the Oligocene–Miocene boundary is here documented for the group, pre-dating previous hypotheses by millions of years, revealing a complex evolutionary history encompassing both ancient and recent gene flow between distant lineages. Conclusions Our phylogenomic results contribute to shed light on conifers’ diversification. Our efforts to resolve the CMF phylogenetic relationships help refine their taxonomy and our knowledge of their evolution.

scholarly journals PHANOTATE: a novel approach to gene identification in phage genomes

2019 ◽  
Vol 35 (22) ◽  
pp. 4537-4542 ◽  
Author(s):  
Katelyn McNair ◽  
Carol Zhou ◽  
Elizabeth A Dinsdale ◽  
Brian Souza ◽  
Robert A Edwards
Keyword(s):  
Gene Prediction ◽  
Optimal Path ◽  
Genome Structure ◽  
Weighted Graph ◽  
Open Reading Frames ◽  
Supplementary Information ◽  
Functional Protein ◽  
Protein Database ◽  
Protein Coding ◽  
Novel Approach

Abstract Motivation Currently there are no tools specifically designed for annotating genes in phages. Several tools are available that have been adapted to run on phage genomes, but due to their underlying design, they are unable to capture the full complexity of phage genomes. Phages have adapted their genomes to be extremely compact, having adjacent genes that overlap and genes completely inside of other longer genes. This non-delineated genome structure makes it difficult for gene prediction using the currently available gene annotators. Here we present PHANOTATE, a novel method for gene calling specifically designed for phage genomes. Although the compact nature of genes in phages is a problem for current gene annotators, we exploit this property by treating a phage genome as a network of paths: where open reading frames are favorable, and overlaps and gaps are less favorable, but still possible. We represent this network of connections as a weighted graph, and use dynamic programing to find the optimal path. Results We compare PHANOTATE to other gene callers by annotating a set of 2133 complete phage genomes from GenBank, using PHANOTATE and the three most popular gene callers. We found that the four programs agree on 82% of the total predicted genes, with PHANOTATE predicting more genes than the other three. We searched for these extra genes in both GenBank’s non-redundant protein database and all of the metagenomes in the sequence read archive, and found that they are present at levels that suggest that these are functional protein-coding genes. Availability and implementation https://github.com/deprekate/PHANOTATE Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Linked genetic variation and not genome structure causes widespread differential expression associated with chromosomal inversions

2018 ◽  
Vol 115 (21) ◽  
pp. 5492-5497 ◽  
Author(s):  
Iskander Said ◽  
Ashley Byrne ◽  
Victoria Serrano ◽  
Charis Cardeno ◽  
Christopher Vollmers ◽  
...  
Keyword(s):  
Gene Expression ◽  
Natural Selection ◽  
Differential Expression ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Genome Structure ◽  
Regulatory Domains ◽  
Chromosomal Inversions ◽  
Important Variation ◽  
Genome Wide

Chromosomal inversions are widely thought to be favored by natural selection because they suppress recombination between alleles that have higher fitness on the same genetic background or in similar environments. Nonetheless, few selected alleles have been characterized at the molecular level. Gene expression profiling provides a powerful way to identify functionally important variation associated with inversions and suggests candidate phenotypes. However, altered genome structure itself might also impact gene expression by influencing expression profiles of the genes proximal to inversion breakpoint regions or by modifying expression patterns genome-wide due to rearranging large regulatory domains. In natural inversions, genetic differentiation and genome structure are inextricably linked. Here, we characterize differential expression patterns associated with two chromosomal inversions found in natural Drosophila melanogaster populations. To isolate the impacts of genome structure, we engineered synthetic chromosomal inversions on controlled genetic backgrounds with breakpoints that closely match each natural inversion. We find that synthetic inversions have negligible effects on gene expression. Nonetheless, natural inversions have broad-reaching regulatory impacts in cis and trans. Furthermore, we find that differentially expressed genes associated with both natural inversions are enriched for loci associated with immune response to bacterial pathogens. Our results support the idea that inversions in D. melanogaster experience natural selection to maintain associations between functionally related alleles to produce complex phenotypic outcomes.

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