By mapping translated metagenomic reads to a microbial metabolic network, we show that ruminal ecosystems that are rather dissimilar in their taxonomy can be considerably more similar at the ...metabolic network level. Using a new network bi-partition approach for linking the microbial network to a bovine metabolic network, we observe that these ruminal metabolic networks exhibit properties consistent with distinct metabolic communities producing similar outputs from common inputs. For instance, the closer in network space that a microbial reaction is to a reaction found in the host, the lower will be the variability of its enzyme copy number across hosts. Similarly, these microbial enzymes that are nearby to host nodes are also higher in copy number than are more distant enzymes. Collectively, these results demonstrate a widely expected pattern that, to our knowledge, has not been explicitly demonstrated in microbial communities: namely that there can exist different community metabolic networks that have the same metabolic inputs and outputs but differ in their internal structure.
After whole‐genome duplication (WGD), deletions return most loci to single copy. However, duplicate loci may survive through selection for increased dosage. Here, we show how the WGD increased copy ...number of some glycolytic genes could have conferred an almost immediate selective advantage to an ancestor of Saccharomyces cerevisiae, providing a rationale for the success of the WGD. We propose that the loss of other redundant genes throughout the genome resulted in incremental dosage increases for the surviving duplicated glycolytic genes. This increase gave post‐WGD yeasts a growth advantage through rapid glucose fermentation; one of this lineage's many adaptations to glucose‐rich environments. Our hypothesis is supported by data from enzyme kinetics and comparative genomics. Because changes in gene dosage follow directly from post‐WGD deletions, dosage selection can confer an almost instantaneous benefit after WGD, unlike neofunctionalization or subfunctionalization, which require specific mutations. We also show theoretically that increased fermentative capacity is of greatest advantage when glucose resources are both large and dense, an observation potentially related to the appearance of angiosperms around the time of WGD.
Synopsis
Gene duplication has long been recognized as an important route to evolutionary novelty and increased organismal complexity. It has also been recognized that the different scales of possible duplications have the potential to generate differing kinds of novel adaptations. New proteins may evolve from single‐gene duplications, while larger duplications, including WGDs, can, in addition, allow more global restructuring of regulatory or metabolic networks in the organism. We describe a potential example of such a global change after a WGD in the bakers’ yeast, S. cerevisiae. The pathway in question is one of the most central in eukaryotes: glycolysis. Our analysis was initially prompted by an apparently different pattern of duplicate gene loss in the glycolytic pathway after WGD, as compared to the remainder of the genome. After WGD, many duplicate genes were lost rapidly, such that, today, only 10% of the duplicates created by WGD survive in S. cerevisiae. However, we show that genes coding for enzymes in the glycolytic pathway are significantly more like to be retained in duplicate than genes in the genome at large (with approximately 45% of the genes in the pathway preserved). Moreover, those genes involved in glycolysis that were preserved in duplicate tend to have greater impact on flux than their non‐duplicated counterparts, according to a mathematical model of glycolysis that we adapt.
One potential explanation for this pattern of preservation in selection for gene dosage, whereby certain genes are maintained in duplicate because of a requirement for more copies of the proteins they code for. This possibility is of particular interest because it may relate to one of the more intriguing features of the physiology of bakers’ yeast. This yeast is unusual in that it prefers to ferment glucose to ethanol in the presence of oxygen rather than using the apparently more efficient respiratory pathways. Interestingly, several previous studies of fermentation in S. cerevisiae and related species have seemed to indicate a trend toward increased importance of fermentation around the time of the WGD.
We argue that the WGD and consequent changes in glycolytic enzyme concentrations may first have increased the overall flux through glycolysis. Because a cell's rate of respiration depends on many complex factors, including the size and location of the mitochondria, the concentration of oxygen and the kinetics of the enzymes involved, we argue that WGD would have had a much less pronounced effect on the rate of respiration than on that of fermentation. Indeed, several mutant strains of yeast seem to support this hypothesis: reducing the concentration of glycolytic enzymes increases the relative importance of respiration, increasing these concentrations decreases its importance. Thus, we believe that the bakers’ yeast's preference for fermentation was enhanced by WGD. This possibility may seem counter‐intuitive, given the greater efficiency (in terms of moles of ATP produced per mole of glucose) of respiration. However, we illustrate an example of the well‐known phenomenon where a less efficient, but faster growing population has a competitive advantage over a more efficient one (the ‘tragedy of the commons’). This selective advantage may have even been the reason the WGD survived and became fixed, as its survival is otherwise difficult to explain. Thus, in addition to suggesting how an important physiological change in an organism can be wrought by a duplication, our example provides a plausible mechanism by which evolution can generate a complex new adaptation.
Glycolysis genes survived in duplicate after the S. cerevisiae WGD in a higher proportion than did genes in the genome at large
Surviving duplicates in the glycolytic pathway tend to code for enzymes with a larger impact on flux than do genes returned to single copy
Respiration's compartmentalization in the mitochondria tends to limit that pathway's ability to accept increased flux from glycolysis.
Summary
Many crops are polyploid or have a polyploid ancestry. Recent phylogenetic analyses have found that polyploidy often preceded the domestication of crop plants. One explanation for this ...observation is that increased genetic diversity following polyploidy may have been important during the strong artificial selection that occurs during domestication.
In order to test the connection between domestication and polyploidy, we identified and examined candidate genes associated with the domestication of the diverse crop varieties of Brassica rapa. Like all ‘diploid’ flowering plants, B. rapa has a diploidized paleopolyploid genome and experienced many rounds of whole genome duplication (WGD). We analyzed transcriptome data of more than 100 cultivated B. rapa accessions.
Using a combination of approaches, we identified > 3000 candidate genes associated with the domestication of four major B. rapa crop varieties. Consistent with our expectation, we found that the candidate genes were significantly enriched with genes derived from the Brassiceae mesohexaploidy. We also observed that paleologs were significantly more diverse than non‐paleologs.
Our analyses find evidence for that genetic diversity derived from ancient polyploidy played a key role in the domestication of B. rapa and provide support for its importance in the success of modern agriculture.
The root-knot nematodes of the genus
are important and damaging parasites capable of infecting most flowering plants. Within this genus, several species of the
group show evidence of paleopolyploidy ...in their genomes. We used our software tool POInT, the Polyploidy Orthology Inference Tool, to phylogenetically model the gene losses that followed that polyploidy. These models, and simulations based on them, show that three of these species (
,
and
) descend from a single common hybridization event that yielded triplicated genomes with three distinguishable subgenomes. While one of the three subgenomes shows elevated gene loss rates relative to the other two, this subgenome does not show elevated sequence divergence. In all three species, ancestral loci where two of the three gene copies have been lost are less likely to have orthologs in
that are lethal when knocked down than are ancestral loci with surviving duplicate copies.
Several species of yeast, including the baker's yeast Saccharomyces cerevisiae, underwent a genome duplication roughly 100 million years ago. We analyze genetic networks whose members were involved ...in this duplication. Many networks show detectable redundancy and strong asymmetry in their interactions. For networks of co-expressed genes, we find evidence for network partitioning whereby the paralogs appear to have formed two relatively independent subnetworks from the ancestral network. We simulate the degeneration of networks after duplication and find that a model wherein the rate of interaction loss depends on the "neighborliness" of the interacting genes produces networks with parameters similar to those seen in the real partitioned networks. We propose that the rationalization of network structure through the loss of pair-wise gene interactions after genome duplication provides a mechanism for the creation of semi-independent daughter networks through the division of ancestral functions between these daughter networks.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Among yeasts that underwent whole-genome duplication (WGD), Kluyveromyces polysporus represents the lineage most distant from Saccharomyces cerevisiae. By sequencing the K. polysporus genome and ...comparing it with the S. cerevisiae genome using a likelihood model of gene loss, we show that these species diverged very soon after the WGD, when their common ancestor contained >9,000 genes. The two genomes subsequently converged onto similar current sizes (5,600 protein-coding genes each) and independently retained sets of duplicated genes that are strikingly similar. Almost half of their surviving single-copy genes are not orthologs but paralogs formed by WGD, as would be expected if most gene pairs were resolved independently. In addition, by comparing the pattern of gene loss among K. polysporus, S. cerevisiae, and three other yeasts that diverged after the WGD, we show that the patterns of gene loss changed over time. Initially, both members of a duplicate pair were equally likely to be lost, but loss of the same gene copy in independent lineages was increasingly favored at later time points. This trend parallels an increasing restriction of reciprocal gene loss to more slowly evolving gene pairs over time and suggests that, as duplicate genes diverged, one gene copy became favored over the other. The apparent low initial sequence divergence of the gene pairs leads us to propose that the yeast WGD was probably an autopolyploidization.
The Pecorans (higher ruminants) are believed to have rapidly speciated in the Mid-Eocene, resulting in five distinct extant families: Antilocapridae, Giraffidae, Moschidae, Cervidae, and Bovidae. Due ...to the rapid radiation, the Pecoran phylogeny has proven difficult to resolve, and 11 of the 15 possible rooted phylogenies describing ancestral relationships among the Antilocapridae, Giraffidae, Cervidae, and Bovidae have each been argued as representations of the true phylogeny. Here we demonstrate that a genome-wide single nucleotide polymorphism (SNP) genotyping platform designed for one species can be used to genotype ancient DNA from an extinct species and DNA from species diverged up to 29 million years ago and that the produced genotypes can be used to resolve the phylogeny for this rapidly radiated infraorder. We used a high-throughput assay with 54,693 SNP loci developed for Bos taurus taurus to rapidly genotype 678 individuals representing 61 Pecoran species. We produced a highly resolved phylogeny for this diverse group based upon 40,843 genome-wide SNP, which is five times as many informative characters as have previously been analyzed. We also establish a method to amplify and screen genomic information from extinct species, and place Bison priscus within the Bovidae. The quality of genotype calls and the placement of samples within a well-supported phylogeny may provide an important test for validating the fidelity and integrity of ancient samples. Finally, we constructed a phylogenomic network to accurately describe the relationships between 48 cattle breeds and facilitate inferences concerning the history of domestication and breed formation.
Much like humans, gene duplicates may be created equal, but they do not stay that way for long. For four completely sequenced genomes we show that 20%-30% of duplicate gene pairs show asymmetric ...evolution in the amino acid sequence of their protein products. That is, one of the duplicates evolves much faster than the other. The greater this asymmetry, the greater the ratio Ka/Ks of amino acid substitutions (Ka) to silent substitutions (Ks) in a gene pair. This indicates that most asymmetric divergence may be caused by relaxed selective constraints on one of the duplicates. However, we also find some candidate duplicates where positive (directional) selection of beneficial mutations (Ka/Ks > 1) may play a role in asymmetric divergence. Our analysis rests on a codon-based model of molecular evolution that allows a test for asymmetric divergence in Ka. The method is also more sensitive in detecting positive selection (Ka/Ks > 1) than models relying only on pairwise gene comparisons.
The abundance of detected ancient polyploids in extant genomes raises questions regarding evolution after whole-genome duplication (WGD). For instance, what rules govern the preservation or loss of ...the duplicated genes created by WGD? We explore this question by contrasting two possible preservation forces: selection on relative and absolute gene dosages. Constraints on the relative dosages of central network genes represent an important force for maintaining duplicates (the dosage balance hypothesis). However, preservation may also result from selection on the absolute abundance of certain gene products. The metabolic network of the model plant Arabidopsis thaliana is a powerful system for comparing these hypotheses. We analyzed the surviving WGD-produced duplicate genes in this network, finding evidence that the surviving duplicates from the most recent WGD (WGD-α) are clustered in the network, as predicted by the dosage balance hypothesis. A flux balance analysis suggests an association between the survival of duplicates from a more ancient WGD (WGD-β) and reactions with high metabolic flux. We argue for an interplay of relative and absolute dosage constraints, such that the relative constraints imposed by the recent WGD are still being resolved by evolution, while they have been essentially fully resolved for the ancient event.
Abstract
The Bovine Genome Database (BGD) (http://bovinegenome.org) has been the key community bovine genomics database for more than a decade. To accommodate the increasing amount and complexity of ...bovine genomics data, BGD continues to advance its practices in data acquisition, curation, integration and efficient data retrieval. BGD provides tools for genome browsing (JBrowse), genome annotation (Apollo), data mining (BovineMine) and sequence database searching (BLAST). To augment the BGD genome annotation capabilities, we have developed a new Apollo plug-in, called the Locus-Specific Alternate Assembly (LSAA) tool, which enables users to identify and report potential genome assembly errors and structural variants. BGD now hosts both the newest bovine reference genome assembly, ARS-UCD1.2, as well as the previous reference genome, UMD3.1.1, with cross-genome navigation and queries supported in JBrowse and BovineMine, respectively. Other notable enhancements to BovineMine include the incorporation of genomes and gene annotation datasets for non-bovine ruminant species (goat and sheep), support for multiple assemblies per organism in the Regions Search tool, integration of additional ontologies and development of many new template queries. To better serve the research community, we continue to focus on improving existing tools, developing new tools, adding new datasets and encouraging researchers to use these resources.
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