Bioinformatics, Comparative Genomics and Molecular Evolution
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Bioinformatics, Comparative Genomics and Molecular Evolution
A page dedicated at the dispersal of papers and facts related to these fascinating Scientific Endeavours
Curated by Arjen ten Have
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Special Collection on Molecular Evolution: Evolutionary Bioinformatics

Subscription and open access journals from SAGE Publishing, the world's leading independent academic publisher.
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Rescooped by Arjen ten Have from Plant Pathogenomics
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Current Opinion Microbiology: The birth and death of effectors in rapidly evolving filamentous pathogen genomes (2018)

Current Opinion Microbiology: The birth and death of effectors in rapidly evolving filamentous pathogen genomes (2018) | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
• Plant pathogens produce effectors to interfere with host defences and metabolism.• Effector genes are among the most rapidly evolving genes in pathogen populations.• Transcriptional control evolved in tandem with the chromosomal location of effectors.• Chromosomal rearrangements are at the origin of high effector gain and loss rates.

Plant pathogenic fungi and oomycetes are major risks to food security due to their evolutionary success in overcoming plant defences. Pathogens produce effectors to interfere with host defences and metabolism. These effectors are often encoded in rapidly evolving compartments of the genome. We review how effector genes emerged and were lost in pathogen genomes drawing on the links between effector evolution and chromosomal rearrangements. Some new effectors entered pathogen genomes via horizontal transfer or introgression. However, new effector functions also arose through gene duplication or from previously non-coding sequences. The evolutionary success of an effector is tightly linked to its transcriptional regulation during host colonization. Some effectors converged on an epigenetic control of expression imposed by genomic defences against transposable elements. Transposable elements were also drivers of effector diversification and loss that led to mosaics in effector presence–absence variation. Such effector mosaics within species was the foundation for rapid pathogen adaptation.


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Disulfide Bonds Enable Accelerated Protein Evolution | Molecular Biology and Evolution | Oxford Academic

Disulfide Bonds Enable Accelerated Protein Evolution | Molecular Biology and Evolution | Oxford Academic | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Abstract. The different proteins of any proteome evolve at enormously different rates. What factors contribute to this variability, and to what extent, is stil
Arjen ten Have's insight:
This makes perfect sense: "We hypothesized that disulfide bonds, by increasing protein stability, should make proteins’ structures relatively independent of their amino acid sequences, thus acting as buffers of deleterious mutations and enabling accelerated sequence evolution." It is indeed well know that robustness of folds is positively correlated with function diversification.
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Complex evolutionary footprints revealed in an analysis of reused protein segments of diverse lengths

Complex evolutionary footprints revealed in an analysis of reused protein segments of diverse lengths | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
National Academy of Sciences
Arjen ten Have's insight:
Why would the domain be the unit of selection? I have always doubted that hypothesis and here seems to be the evidence! It is likely that domains will be more often successfully recombined but that does not mean they generate as such a lot of change, change as in evolution
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The evolution of cooperation in simple molecular replicators. - PubMed - NCBI

The evolution of cooperation in simple molecular replicators. - PubMed - NCBI | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Proc Biol Sci. 2017 Oct 11;284(1864). pii: 20171967. doi: 10.1098/rspb.2017.1967.
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Barriers to Integration of Bioinformatics into Undergraduate Life Sciences Education

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
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imagine this is a survey done in the US.
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Clinical Knowledgebase (CKB)

Clinical Knowledgebase (CKB) | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it

JAX-CKB is a powerful tool for interpreting complex genomic profiles, and represents a valuable resource for clinicians and translational and clinical researchers. JAX-CKB advances JAX’s mission to discover genomic solutions for disease and empower the global biomedical community in the shared quest to improve human health.


jaxmoleculardx@jax.org | 1.860.837.2320
Arjen ten Have's insight:
Future of personalized medicine includes comparative analysis for which we need to gather data and make them available for medical teams (i.e. that lack knowledge in Bioinformatics). We will also need bioinformaticians specialized in medicine.
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Alternative evolutionary histories in the sequence space of an ancient protein

Alternative evolutionary histories in the sequence space of an ancient protein | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
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Joe Thornton strikes again. He is the leader in ancestral sequence  reconstruction and now exploited the brilliant idea of letting an ancestral sequence evolve. "To understand why molecular evolution turned out as it did, we must characterize not only the path that evolution followed across the space of possible molecular sequences but also the many alternative trajectories that could have been taken but were not." " We find hundreds of alternative protein sequences that use diverse biochemical mechanisms to perform the derived function at least as well as the historical outcome. These alternatives all require prior permissive substitutions that do not enhance the derived function, but not all require the same permissive changes that occurred during history."

Amazing and in full concordance with the work of that other brilliant evolutionary biologist, Andreas Wagner. Iḿ Flabbergasted!
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The dark side of the human genome : Nature : Nature Research

The dark side of the human genome : Nature : Nature Research | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Scientists are uncovering the hidden switches in our genome that dial gene expression up and down, but much work lies ahead to peel back the many layers of regulation.
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RNA Structural Determinants of Optimal Codons Revealed by MAGE-Seq

RNA Structural Determinants of Optimal Codons Revealed by MAGE-Seq | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Kelsic et al. develop and apply MAGE-seq to identify RNA structures that determine optimal codon preferences in an essential E. coli gene.
Arjen ten Have's insight:
Yet another type of functional constraint acting at the level of translation efficiency. or is it rna stability?
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Protein Assembly and Building Blocks: Beyond the Limits of the LEGO Brick Metaphor

Protein Assembly and Building Blocks: Beyond the Limits of the LEGO Brick Metaphor | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Protein Assembly and Building Blocks: Beyond the Limits of the LEGO Brick Metaphor
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Genome Expression Balance in a Triploid Trihybrid Vertebrate | Genome Biology and Evolution | Oxford Academic

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Sex is the emerging property of evolution. It is not meant for propagation but rather for maintaining high variation.
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Rescooped by Arjen ten Have from Plants and Microbes
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Science: Genomic-scale exchange of mRNA between a parasitic plant and its hosts (2014)

Science: Genomic-scale exchange of mRNA between a parasitic plant and its hosts (2014) | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it

Movement of RNAs between cells of a single plant is well documented, but cross-species RNA transfer is largely unexplored. Cuscuta pentagona (dodder) is a parasitic plant that forms symplastic connections with its hosts and takes up host messenger RNAs (mRNAs). We sequenced transcriptomes of Cuscuta growing on Arabidopsis and tomato hosts to characterize mRNA transfer between species and found that mRNAs move in high numbers and in a bidirectional manner. The mobile transcripts represented thousands of different genes, and nearly half the expressed transcriptome of Arabidopsis was identified in Cuscuta. These findings demonstrate that parasitic plants can exchange large proportions of their transcriptomes with hosts, providing potential mechanisms for RNA-based interactions between species and horizontal gene transfer.


Via Kamoun Lab @ TSL
Arjen ten Have's insight:
Sharing stuff is key yo any interaction. The higher the mutual dependency, the more partners will share. What I do not have clear yet is whether pathogenic relationships will differ substantially from mutualistic ones. miRNA has been shown in plant pathogen relationships, but I can also envisage these in a mutualistic symbiosis. Quite a conundrum. But that' s what  plant-pathogen relations are about anyway.
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Rescooped by Arjen ten Have from Papers
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Comparing two classes of biological distribution systems using network analysis

Comparing two classes of biological distribution systems using network analysis | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it

Distribution networks such as vasculature systems or urban transportation pathways are prevalent in our world. Understanding how different kinds of transport systems are organized to allow for efficient function in their environments and in the presence of constraints on material costs is currently an open area of investigation. In this study, we use methods from network science to compare and contrast the structure of two different classes of biological distribution networks: mycelial fungi and rodent brain vasculature. While each of these systems have been studied separately, less work has focused on understanding the diversity of their network organization. Here, we first examine several measures that characterize network connectivity on varying scales, finding that—although both systems have highly constrained network layouts—there are quantifiable differences in their architectures. Furthermore, using network analyses that specifically consider the embedding of these transport networks into real space, we observe that the two types of systems display distinct tradeoffs in network correlates of material cost, efficiency, and robustness. Together, our results provide evidence that while different distribution networks have general resemblances, they also exhibit variable design features that could reflect differences in their functions, environmental conditions, or development.

 

Papadopoulos L, Blinder P, Ronellenfitsch H, Klimm F, Katifori E, Kleinfeld D, et al. (2018) Comparing two classes of biological distribution systems using network analysis. PLoS Comput Biol 14(9): e1006428. https://doi.org/10.1371/journal.pcbi.1006428


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Phylogenomics from Whole Genome Sequences Using aTRAM | Systematic Biology | Oxford Academic

Phylogenomics from Whole Genome Sequences Using aTRAM | Systematic Biology | Oxford Academic | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Abstract. Novel sequencing technologies are rapidly expanding the size of data sets that can be applied to phylogenetic studies. Currently the most commonly us
Arjen ten Have's insight:
Very nice work with lots of applications. Basically they use paired end sequences, cluster them locally (meaning no large contigs are searched), the short contigs are put in a BLAST database that is searched with TBLASTN using a set of user specified queries. Hits are then further assembled. Love it!
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Biological Species Are Universal across Life’s Domains | Genome Biology and Evolution | Oxford Academic

Biological Species Are Universal across Life’s Domains | Genome Biology and Evolution | Oxford Academic | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Delineation of species is fundamental to organizing and understanding biological diversity. The most widely applied criterion for distinguishing species is the
Arjen ten Have's insight:
The fact that bacteria show horizontal gene transfer should be used in species determination.

This, the principle, is what I have been teaching in my postgrad course since five years. I actually suggest to include conjugation in the species determination. The original paper this piece comments on suggests a more thorough analysis! Great to see I am right once in a while!
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Evidence of evolutionary selection for cotranslational folding

National Academy of Sciences
Arjen ten Have's insight:
Very interesting stuff, Codon preference seems to affect not so much the speed at the start of translation of proteins but even guides cotranslational folding when we look at domains. Makes sense, of course.
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A most wanted list of conserved protein families with no known domains

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
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Algorithmically probable mutations reproduce aspects of evolution such as convergence rate, genetic memory, modularity, diversity explosions, and mass extinction

We show that if evolution is algorithmic in any form and can thus be considered a program in software space, the emergence of a natural algorithmic probability distribution has the potential to become an accelerating mechanism. We simulate the application of algorithmic mutations to binary matrices based on numerical approximations to algorithmic probability, comparing the evolutionary speed to the alternative hypothesis of uniformly distributed mutations for a series of matrices of varying complexity. When the algorithmic mutation produces unfit organisms---because mutations may lead to, for example, syntactically useless evolutionary programs---massive extinctions may occur. We show that modularity provides an evolutionary advantage also evolving a genetic memory. We demonstrate that such regular structures are preserved and carried on when they first occur and can also lead to an accelerated production of diversity and extinction, possibly explaining natural phenomena such as periods of accelerated growth of the number of species (e.g. the Cambrian explosion) and the occurrence of massive extinctions (e.g. the End Triassic) whose causes are a matter of considerable debate. The approach introduced here appears to be a better approximation to actual biological evolution than models based upon the application of mutation from uniform probability distributions, and because evolution by algorithmic probability converges faster to regular structures (both artificial and natural, as tested on a small biological network), it also approaches a formal version of open-ended evolution based on previous results. The results validate the motivations and results of Chaitin's Metabiology programme. We also show that the procedure has the potential to significantly accelerate solving optimization problems in the context of artificial evolutionary algorithms.

 

Algorithmically probable mutations reproduce aspects of evolution such as convergence rate, genetic memory, modularity, diversity explosions, and mass extinction

Santiago Hernández-Orozco, Hector Zenil, Narsis A. Kiani

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Molecular Evolution of Antifungal Drug Resistance | Annual Review of Microbiology

Molecular Evolution of Antifungal Drug Resistance | Annual Review of Microbiology | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
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Wham: Identifying Structural Variants of Biological Consequence

Wham: Identifying Structural Variants of Biological Consequence | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Existing methods for identifying structural variants (SVs) from short read datasets are inaccurate. This complicates disease-gene identification and efforts to understand the consequences of genetic variation. In response, we have created Wham (Whole-genome Alignment Metrics) to provide a single, integrated framework for both structural variant calling and association testing, thereby bypassing many of the difficulties that currently frustrate attempts to employ SVs in association testing. Here we describe Wham, benchmark it against three other widely used SV identification tools–Lumpy, Delly and SoftSearch–and demonstrate Wham’s ability to identify and associate SVs with phenotypes using data from humans, domestic pigeons, and vaccinia virus. Wham and all associated software are covered under the MIT License and can be freely downloaded from github (https://github.com/zeeev/wham), with documentation on a wiki (http://zeeev.github.io/wham/). For community support please post questions to https://www.biostars.org/.
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Epigenetics and the evolution of instincts

Epigenetics and the evolution of instincts | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
An animal mind is not born as an empty canvas: Bottlenose dolphins know how to swim and honey bees know how to dance without ever having learned these skills. Little is known about how animals acquire the instincts that enable such innate behavior. Instincts are widely held to be ancestral to learned behavior. Some have been elegantly analyzed at the cellular and molecular levels, but general principles do not exist. Based on recent research, we argue instead that instincts evolve from learning and are therefore served by the same general principles that explain learning.
Arjen ten Have's insight:
Not a big fan of epigenetics, this makes sense. Moreover, it would be a more feasible explanation for the language instinct than Chomsky' s hypothesis (indeed not a theory) thst claims we are hardwired. Epigenetics would be a go between.
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Gene Expression Regulation by Upstream Open Reading Frames and Human Disease

Gene Expression Regulation by Upstream Open Reading Frames and Human Disease | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Upstream open reading frames (uORFs) are major gene expression regulatory elements. In many eukaryotic mRNAs, one or more uORFs precede the initiation codon of the main coding region. Indeed, several studies have revealed that almost half of human transcripts present uORFs. Very interesting examples have shown that these uORFs can impact gene expression of the downstream main ORF by triggering mRNA decay or by regulating translation. Also, evidence from recent genetic and bioinformatic studies implicates disturbed uORF-mediated translational control in the etiology of many human diseases, including malignancies, metabolic or neurologic disorders, and inherited syndromes. In this review, we will briefly present the mechanisms through which uORFs regulate gene expression and how they can impact on the organism's response to different cell stress conditions. Then, we will emphasize the importance of these structures by illustrating, with specific examples, how disturbed uORF-mediated translational control can be involved in the etiology of human diseases, giving special importance to genotype-phenotype correlations. Identifying and studying more cases of uORF-altering mutations will help us to understand and establish genotype-phenotype associations, leading to advancements in diagnosis, prognosis, and treatment of many human disorders.
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Protein Assembly and Building Blocks: Beyond the Limits of the LEGO Brick Metaphor

Protein Assembly and Building Blocks: Beyond the Limits of the LEGO Brick Metaphor | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Protein Assembly and Building Blocks: Beyond the Limits of the LEGO Brick Metaphor
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Membrane fission by protein crowding

National Academy of Sciences
Arjen ten Have's insight:
This makes a lot of sense and can explain how effectors are trafficked. Proteins are selected based on a certain subsequence, gathered and send to (where ever they need to go). BI can help identifying these subsequences.
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