18 papers · ranked by Valyu relevance
Nicolas S. M. Robert, Fatih Sarigol, Bob Zimmermann, Axel Meyer + 2 more
Background Animal genomes are strikingly conserved in terms of local gene order (microsynteny). While some of these microsyntenies have been shown to be coregulated or to form gene regulatory blocks, the diversity of their genomic and regulatory properties across the metazoan tree of life remains largely unknown.…
Zhe Yu, Chunfang Zheng, Victor A. Albert, David Sankoff
We take advantage of synteny blocks, the analytical construct enabled at the evolutionary moment of speciation or polyploidization, to follow the independent loss of duplicate genes in two sister species or the loss through fractionation of syntenic paralogs in a doubled genome. By examining how much sequence remains…
S. N. Fatakia, Ishita Mehta, Basuthkar J. Rao
We investigate a densely packed, non-random arrangement of forty-six chromosomes (46,XY) in human nuclei. Here, we model systems-level chromosomal crosstalk by unifying intrinsic parameters (chromosomal length and number of genes) across all pairs of chromosomes in the genome to derive an extrinsic parameter called…
Di Guo, Xiaoming Song, Min Yuan, Zhenyi Wang + 4 more
'Jinpeng Wang' 'Xiyin Wang'] Plants growing under high-density (HD) conditions experience increased competition for water, nutrients, and light, possibly leading to changes in size, biomass, morphology, and productivity. However, no research has focused on the relationship between whole-genome expression patterns and…
Nereide Stela Santos-Magalhães, H. M. de Oliveira, Moraes Rêgo
- An approach for approximately calculating the number of genes in a genome is presented, which takes into account the average protein length expected for the species. A number of virus, bacterial and eukaryotic genomes are scrutinized. Genome figures are presented, which support the average protein size of a species…
Leandros Boukas, Hans T. Bjornsson, Kasper D. Hansen
The aggregation and joint analysis of large numbers of exome sequences has recently made it possible to derive estimates of intolerance to loss-of-function (LoF) variation for human genes. Here, we demonstrate strong and widespread coupling between genic LoF-intolerance and promoter CpG density across the human genome.…
Amy R Ellison, Tamsyn M Uren Webster, Olivier Rey, Carlos Garcia de Leaniz + 3 more
'Carlos Garcia de Leaniz' 'Sofia Consuegra' 'Pablo Orozco-terWengel' 'Jo Cable'] Background Captive animal populations, be it for food production or conservation programmes, are often maintained at densities far beyond those in natural environments, which can have profound effects on behaviour, immune and stress…
Aditi Gupta, Thomas LaBar, Miriam Miyagi, Christoph Adami
Genome sizes have evolved to vary widely, from 250 bases in viroids to 670 billion bases in amoeba. This remarkable variation in genome size is the outcome of complex interactions between various evolutionary factors such as point mutation rate, population size, insertions and deletions, and genome editing mechanisms…
Gideon S. Bradburd, Peter L. Ralph
Many questions that we have about the history and dynamics of organisms have a geographical component: How many are there, and where do they live? How do they move and interbreed across the landscape? How were they moving a thousand years ago, and where were the ancestors of a particular individual alive today? Answers…
Magdalena Fraszczak, Jakub Liu, Magda Mielczarek, Paula Dobosz + 1 more
Among all types of mutations, single nucleotide polymorphisms are the most common type of genomic variation. In our study, we explore the counts of single nucleotide polymorphisms in particular exons and introns of the human genome based on the data set of 1,222 individuals of Polish origin that comprises 41,836,187…
Daniel R. Garza, F. A. Bastiaan von Meijenfeldt, Bram van Dijk, Annemarie Boleij + 2 more
Microbial pan-genomes are shaped by a complex combination of stochastic and deterministic forces. Even closely related genomes often exhibit extensive variation in their gene content. Understanding what drives this variation requires exploring the interactions of genes with each other and with their external…
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Livestock agriculture generally operates as a linear economy, consuming large quantities of nonrenewable energy and nutrients while generating waste that often pollutes the environment. In this work, we propose approaches to help mitigate nutrient pollution via the development of cyanobacteria-based processes that…
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Molecular mechanisms governing initiation steps of the assembly of thousands of endogenous multi-protein complexes (EMCs) remain incompletely understood. Here, multiple lines of observations are reported reflecting the biological functions-aligned initiation sequence of hybrid assembly pathways (HAPs) of EMCs. HAPs…
Dominik Merges, Francesco Dal Grande, Henrique Valim, Garima Singh + 1 more
Intraspecific genomic variability affects a species’ adaptive potential towards climatic conditions. Variation in gene content across populations and environments may point at genomic adaptations to specific environments. The lichen symbiosis, a stable association of fungal and photobiont partners, offers an excellent…
Erik Bot, Jose Davila-Velderrain
Gene expression specificity is a biological parameter relevant for understanding the molecular basis of evolutionary constraints and tissue-selective pathogenesis. Many efforts have tried to quantify the degree of tissue specificity of individual genes. The growing availability of single-cell transcriptomic data…
Ying Chen Eyre‐Walker, Adam Eyre‐Walker
We have investigated the role that the mutation rate and the structure of genetic variation at a locus play in determining whether a gene is involved in disease. We predict that the mutation rate and its genetic diversity should be higher in genes associated with disease, unless all genes that could cause disease have…
Ehigbai Oikeh, Jesse Ziebarth, Daniel Kirchhoff, Yongmei Wang + 1 more
In nature, DNA exists primarily in a highly compacted form. The compaction of DNA in vivo is mediated by cationic proteins; histone in somatic nuclei and protamines in sperm chromatin. The extreme, near-crystalline packaging of DNA by protamines in spermatozoa is thought essential for both efficient genetic delivery as…
Amanda R. De La Torre, Yao-Cheng Lin, Yves Van de Peer, Pär K. Ingvarsson
'Pär K. Ingvarsson'] The recent sequencing of several gymnosperm genomes has greatly facilitated studying the evolution of their genes and gene families. In this study, we examine the evidence for expression-mediated selection in the first two fully sequenced representatives of the gymnosperm plant clade (Picea abies…