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Items tagged with: Genomics
Unraveling the tangled #evolution of #figs.
#genomics #phylogenetics #introgression #Ficus
phys.org/news/2023-07-unraveli…
Unraveling the tangled evolution of figs
Containing more than 850 species, fig trees are one of the most diverse groups of plants in the world.Amanda Morris (Phys.org)
Hello everyone!
I’m an associate prof at Virginia Tech studying viral diversity. Lately my group has been focusing on giant viruses, but we are also interested in other protist viruses, and the role of viral endogenization in host genome evolution.
#GiantViruses #ViralDiversity #TreeOfLife #Protists #Microbiology #Bioinformatics #Evolution #Virology #Genomics
Recently we have been examining the strange and complex genes encoded in giant virus genomes!
doi.org/10.1093/femsre/fuad053
Studying some phage genes with scattered, partial alignments in varying degrees (40~+90%) of ID against closely related cousins (~93% ANI).
I'm thinking intragenic insertion/shuffling - but what kind of signals could I look for here? Common scars? Models to reference? #phage #bioinformatics #genomics
biorxiv.org/content/10.1101/20… #bioinformatics #HumanGenome #genomics
miniBUSCO: a faster and more accurate reimplementation of BUSCO
Motivation Assembly completeness evaluation of genome assembly is a critical assessment of the accuracy and reliability of genomic data. An incomplete assembly can lead to errors in gene predictions, annotation, and other downstream analyses.bioRxiv
Empirical Evidence That Complexity Limits Horizontal Gene Transfer
academic.oup.com/gbe/article/1…
Empirical Evidence That Complexity Limits Horizontal Gene Transfer
Abstract. Horizontal gene transfer (HGT) is a major contributor to bacterial genome evolution, generating phenotypic diversity, driving the expansion of proteinBurch, Christina L (Oxford University Press)
Built Into the Genome of the Microbes – Scientists Uncover Over 30,000 “Hidden” Viruses
scitechdaily.com/built-into-th…
Built Into the Genome of the Microbes – Scientists Uncover Over 30,000 “Hidden” Viruses
Unveiled within the DNA of unicellular organisms lie thousands of enigmatic viruses. Researchers at the University of Innsbruck, utilizing the high-performance computing cluster known as "Leo," have identified more than 30,000 new viruses embedded wi…Colin Collins (SciTechDaily)
Important study from Bellas et al showing that protists have a huge diversity of endogenous DNA viruses in their genomes!
Large-scale invasion of unicellular eukaryotic genomes by integrating DNA viruses
pnas.org/doi/10.1073/pnas.2300…
And a commentary about these exciting findings from @giant_virus and myself -
Endogenous DNA viruses take center stage in eukaryotic genome evolution
Mobile element variation contributes to population-specific genome diversification, gene regulation and disease risk
nature.com/articles/s41588-023…
Mobile element variation contributes to population-specific genome diversification, gene regulation and disease risk - Nature Genetics
MEGAnE is a new tool to detect and genotype mobile element variants (MEVs) from short-read whole-genome sequencing datasets. Genetic analyses implicate MEVs as population-specific drivers of gene expression variation and disease risk.Nature
Every base everywhere all at once: pangenomics comes of age
nature.com/articles/d41586-023…
Every base everywhere all at once: pangenomics comes of age
Multi-genome assemblies called pangenomes can capture genetic diversity in a species, but researchers are still working out how best to build and explore them.Eisenstein, Michael
JASPER: A fast genome polishing tool that improves accuracy of genome assemblies
journals.plos.org/ploscompbiol…
JASPER: A fast genome polishing tool that improves accuracy of genome assemblies
Advances in long-read sequencing technologies have dramatically improved the contiguity and completeness of genome assemblies.journals.plos.org
NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes
academic.oup.com/bioinformatic…
NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes
AbstractSummary. Large-scale comparative genomic studies have provided important insights into species evolution and diversity, but also lead to a great challenHe, Weiming (Oxford University Press)
Linking prokaryotic genome size variation to metabolic potential and environment
nature.com/articles/s43705-023…
Linking prokaryotic genome size variation to metabolic potential and environment - ISME Communications
ISME Communications - Linking prokaryotic genome size variation to metabolic potential and environmentNature
Fascinating study!
The methanogen core and pangenome: conservation and variability across biology’s growth temperature extremes
"Increased methanogenic growth temperature is associated with reduced genome size, and thermotolerant organisms...have larger core genome fractions, suggesting that genome size is governed by temperature rather than phylogeny. "
academic.oup.com/dnaresearch/a…
#genomics #pangenomics #microbiology
The methanogen core and pangenome: conservation and variability across biology’s growth temperature extremes
Abstract. Temperature is a key variable in biological processes. However, a complete understanding of biological temperature adaptation is lacking, in part becaProndzinsky, Paula (Oxford University Press)
Fascinating study on #genome #evolution :
Scaling of Protein Function Across the Tree of Life
"The abundance of functional categories in a given genome scales with genome size, suggesting that universal constraints shape category abundance. Here we look across the tree of life to understand how genome evolution may be related to functional scaling. "
biorxiv.org/content/10.1101/20…
Scaling of Protein Function Across the Tree of Life
Scaling laws are a powerful way to compare genomes because they put all organisms onto a single curve and reveal non-trivial generalities as genomes change in size.bioRxiv
It turns out that a section of our #DNA that we received from Neanderthals is particularly associated with outcomes (mild, severe) of #COVID19 infections.
This paper outlines an approach ranging from population genetics to functional #genomics in which the researchers identified four important #alleles and their likely #regulatory function.
Title: "Regulatory dissection of the severe #COVID-19 risk locus introgressed by #Neanderthals" (Jagoda et al. 2023)
Link: elifesciences.org/articles/712…
Regulatory dissection of the severe COVID-19 risk locus introgressed by Neanderthals
Key functional variants, discovered using Massively Parallel Reporter Assay (MPRA) and reporter assays in the context of SARS-CoV-2 infection, support the importance of two critical chemokine receptor genes CCR1 and CCR5 in severe Covid-19 illness.Evelyn Jagoda (eLife Sciences Publications, Ltd)
If you've ever wondered EXACTLY what is in
@NCBI
nt and nr (I certainly have!)
From youtu.be/2FW1dk5YQ3I?t=484 and youtu.be/KLBE0AuH-Sk?t=692 (cued to the right spots in the video)
NCBI Minute: Using BLAST Well
Presented October 3, 2018. In this webinar, the NCBI BLAST team lead will show you how to be more effective with NCBI’s standalone BLAST applications. You wi...YouTube
Decades-old #crustaceans coaxed from lake mud give up genetic secrets revealing #evolution in action
phys.org/news/2023-02-decades-…
Resurrection #genomics provides molecular and phenotypic evidence of rapid adaptation to #salinization in a keystone aquatic species pnas.org/doi/10.1073/pnas.2217…
They revived decades-old #Daphnia resting eggs from lake sediments. Tanners Lake has suffered significant salt #pollution, stemming from the widespread use of road deicing salts in its watershed.
Decades-old crustaceans coaxed from lake mud give up genetic secrets revealing evolution in action
Human actions are changing the environment at an unprecedented rate. Plant and animal populations must try to keep up with these human-accelerated changes, often by trying to rapidly evolve tolerance to changing conditions.Science X (Phys.org)
#Microbiology #Evolution #ExperimentalEvolution #EcoEvo #popgen #PopulationDynamics #Genomics
Quantifying the local adaptive landscape of a nascent bacterial community - Nature Communications
Fitness landscapes largely shape the dynamics of evolution, but it is unclear how they shift upon ecological diversification. By engineering genome-wide knockout libraries of a nascent bacterial community, Ascensao et al.Nature
Nice review on the increasing importance of large #transposons :
Giant Transposons in Eukaryotes: Is Bigger Better?
academic.oup.com/gbe/article/1…
"...the size limitations previously placed on mobilizable DNA units in eukaryotes may have been due in part to our inability to assemble large contiguous stretches of repetitive DNA in complex genomes."
Giant Transposons in Eukaryotes: Is Bigger Better?
Abstract. Transposable elements (TEs) are ubiquitous in both prokaryotes and eukaryotes, and the dynamic character of their interaction with host genomes bringsArkhipova, Irina R (Oxford University Press)
Current advances in primate genomics: novel approaches for understanding evolution and disease
nature.com/articles/s41576-022…
#genomics #genetics #evolution
Current advances in primate genomics: novel approaches for understanding evolution and disease - Nature Reviews Genetics
In this Review, the authors describe how advances in comparative primate genomics — complemented by multi-layered omic resources and primate cell systems — are providing insights into the evolution of primates and the genetic underpinnings of key tra…Nature
Reading up on the role of transposons in genome evolution, and finding this classic review from a few years ago very helpful:
Ten things you should know about transposable elements
genomebiology.biomedcentral.co…
#genomics #transposons #evolution #genetics
Ten things you should know about transposable elements - Genome Biology
Transposable elements (TEs) are major components of eukaryotic genomes. However, the extent of their impact on genome evolution, function, and disease remain a matter of intense interrogation.BioMed Central
When I started my lab a few years ago I started building up an in-house library for students. Two of the first books I bought are The Logic of Chance (Eugene Koonin) and The Origins of Genome Architecture (Michael Lynch). Both are remarkable books that discuss genomics in the context of microbial diversity and the tree of life.
What other genomics/evolution classics do people always keep around?
#genomics #bioinformatics #evolution #microbiology
