Abstract:
:Gene duplication generates new genetic material, which has been shown to lead to major innovations in unicellular and multicellular organisms. A whole-genome duplication occurred in the ancestor of Saccharomyces yeast species but 92% of duplicates returned to single-copy genes shortly after duplication. The persisting duplicated genes in Saccharomyces led to the origin of major metabolic innovations, which have been the source of the unique biotechnological capabilities in the Baker's yeast Saccharomyces cerevisiae. What factors have determined the fate of duplicated genes remains unknown. Here, we report the first demonstration that the local genome mutation and transcription rates determine the fate of duplicates. We show, for the first time, a preferential location of duplicated genes in the mutational and transcriptional hotspots of S. cerevisiae genome. The mechanism of duplication matters, with whole-genome duplicates exhibiting different preservation trends compared to small-scale duplicates. Genome mutational and transcriptional hotspots are rich in duplicates with large repetitive promoter elements. Saccharomyces cerevisiae shows more tolerance to deleterious mutations in duplicates with repetitive promoter elements, which in turn exhibit higher transcriptional plasticity against environmental perturbations. Our data demonstrate that the genome traps duplicates through the accelerated regulatory and functional divergence of their gene copies providing a source of novel adaptations in yeast.
journal_name
Genome Biol Evoljournal_title
Genome biology and evolutionauthors
Fares MA,Sabater-Muñoz B,Toft Cdoi
10.1093/gbe/evx085subject
Has Abstractpub_date
2017-05-01 00:00:00pages
1229-1240issue
5issn
1759-6653pii
3770955journal_volume
9pub_type
杂志文章abstract::The chloroplast is an essential plant organelle responsible for photosynthesis. Gene duplication, relocation, and loss in the chloroplast genome (cpDNA) are useful for exploring the evolution and phylogeny of plant species. In this study, the complete chloroplast genome of Paris verticillata was sequenced using the 45...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evu138
更新日期:2014-06-19 00:00:00
abstract::We sequenced mitochondrial genomes from five diverse diatoms (Toxarium undulatum, Psammoneis japonica, Eunotia naegelii, Cylindrotheca closterium, and Nitzschia sp.), chosen to fill important phylogenetic gaps and help us characterize broadscale patterns of mitochondrial genome evolution in diatoms. Although gene cont...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy103
更新日期:2018-06-01 00:00:00
abstract::Recent whole-genome approaches to microbial phylogeny have emphasized partitioning genes into functional classes, often focusing on differences between a stable core of genes and a variable shell. To rigorously address the effects of partitioning and combining genes in genome-level analyses, we developed a novel techn...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evr121
更新日期:2012-01-01 00:00:00
abstract::Population bottlenecks leading to a drastic reduction of the population size are common in the evolutionary dynamics of natural populations; their occurrence is known to have implications for genome evolution due to genetic drift, the consequent reduction in genetic diversity, and the rate of adaptation. Nevertheless,...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evz243
更新日期:2019-11-01 00:00:00
abstract::The Piwi-interacting RNA (piRNA) pathway is responsible for germline specification, gametogenesis, transposon silencing, and genome integrity. Transposable elements can disrupt genome and its functions. However, piRNA pathway evolution and its adaptation to transposon diversity in the teleost fish remain unknown. This...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evu105
更新日期:2014-05-19 00:00:00
abstract::The evolution of a mechanically resilient epidermis was a key adaptation in the transition of amniotes to a fully terrestrial lifestyle. Skin appendages usually form via a specialized type of programmed cell death known as cornification which is characterized by the formation of an insoluble cornified envelope (CE). M...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evz054
更新日期:2019-03-01 00:00:00
abstract::Coevolution between hosts and pathogens generates strong selection pressures to maintain resistance and infectivity, respectively. Genomes of plant pathogens often encode major effect loci for the ability to successfully infect specific host genotypes. Hence, spatial heterogeneity in host genotypes coupled with abioti...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy087
更新日期:2018-04-01 00:00:00
abstract::Previous studies of the evolution of genes expressed at different life-cycle stages of Drosophila melanogaster have not been able to disentangle adaptive from nonadaptive substitutions when using nonsynonymous sites. Here, we overcome this limitation by combining whole-genome polymorphism data from D. melanogaster and...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evz086
更新日期:2019-05-01 00:00:00
abstract::The phylum Apicomplexa is a quintessentially parasitic lineage, whose members infect a broad range of animals. One exception to this may be the apicomplexan genus Nephromyces, which has been described as having a mutualistic relationship with its host. Here we analyze transcriptome data from Nephromyces and its parasi...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy251
更新日期:2019-01-01 00:00:00
abstract::The hundreds of endemic species of cichlid fishes in the East African Great Lakes Tanganyika, Malawi, and Victoria are a prime model system in evolutionary biology. With five genomes currently being sequenced, eastern African cichlids also represent a forthcoming genomic model for evolutionary studies of genotype-to-p...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evr047
更新日期:2011-01-01 00:00:00
abstract::The genome of the bladderwort Utricularia gibba provides an unparalleled opportunity to uncover the adaptive landscape of an aquatic carnivorous plant with unique phenotypic features such as absence of roots, development of water-filled suction bladders, and a highly ramified branching pattern. Despite its tiny size, ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evu288
更新日期:2015-01-09 00:00:00
abstract::Experimental evolution allows the observation of change over time as laboratory populations evolve in response to novel, controlled environments. Microbial evolution experiments take advantage of cryopreservation to archive experimental populations in glycerol media, creating a frozen, living "fossil" record. Prior re...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evaa121
更新日期:2020-08-01 00:00:00
abstract::Analysis of more than 150 Clostridium botulinum Group II type E genomes identified a small fraction (6%) where neurotoxin-encoding genes were located on plasmids. Seven closely related (134-144 kb) neurotoxigenic plasmids of subtypes E1, E3, and E10 were characterized; all carried genes associated with plasmid mobilit...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evw017
更新日期:2016-03-02 00:00:00
abstract::Many organisms have a global mechanism for dosage compensation (DC) operating along the entire male X chromosome, which equalizes gene expression on the male X with that on the two Xs in females and/or on autosomes. At the initial stage of sex chromosome evolution, however, gene-by-gene (or localized) DC may also be n...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy148
更新日期:2018-08-01 00:00:00
abstract::Oxidative phosphorylation (OXPHOS), the major energy-producing pathway in aerobic organisms, includes protein subunits encoded by both mitochondrial (mt) and nuclear (nu) genomes. How these independent genomes have coevolved is a long-standing question in evolutionary biology. Although mt genes evolve faster than most...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evt129
更新日期:2013-01-01 00:00:00
abstract::Genome reduction is a hallmark of symbiotic genomes, and the rate and patterns of gene loss associated with this process have been investigated in several different symbiotic systems. However, in long-term host-associated coevolving symbiont clades, the genome size differences between strains are normally quite small ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evv108
更新日期:2015-05-28 00:00:00
abstract::The selective impact of pathogen epidemics on host defenses can be strong but remains transient. By contrast, life-history shifts can durably and continuously modify the balance between costs and benefits of immunity, which arbitrates the evolution of host defenses. Their impact on the evolutionary dynamics of host im...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy124
更新日期:2018-09-01 00:00:00
abstract::Bacteria of the Planctomycetes phylum have many unique cellular features, such as extensive membrane invaginations and the ability to import macromolecules. These features raise intriguing questions about the composition of their cell envelopes. In this study, we have used microscopy, phylogenomics, and proteomics to ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evaa159
更新日期:2020-09-01 00:00:00
abstract::As most genes are shared between females and males, DNA methylation is assumed to play a crucial role in sex-biased gene expression. DNA methylation exclusively occurs at CpG dinucleotides, and therefore, we would expect that CpG density around transcription start sites (TSSs) relate to sex-biased gene expression. Her...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evx083
更新日期:2017-05-01 00:00:00
abstract::Because of its highly repetitive nature, the human male-specific Y chromosome remains understudied. It is important to investigate variation on the Y chromosome to understand its evolution and contribution to phenotypic variation, including infertility. Approximately 20% of the human Y chromosome consists of ampliconi...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy086
更新日期:2018-05-01 00:00:00
abstract::Gene duplication is the primary source of new genes, but the mechanisms underlying the functional divergence and retention of duplicate genes are not well understood. Because eukaryotic proteins are localized to subcellular structures and localization can be altered by a single amino acid replacement, it was recently ...
journal_title:Genome biology and evolution
pub_type: 信件
doi:10.1093/gbe/evp021
更新日期:2009-07-22 00:00:00
abstract::Immunity genes have repeatedly experienced natural selection during mammalian evolution. Galectins are carbohydrate-binding proteins that regulate diverse immune responses, including maternal-fetal immune tolerance in placental pregnancy. Seven human galectins, four conserved across vertebrates and three specific to p...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evz183
更新日期:2019-09-01 00:00:00
abstract::Sex determination evolves rapidly, often because of turnover of the genes at the top of the pathway. The house fly, Musca domestica, has a multifactorial sex determination system, allowing us to identify the selective forces responsible for the evolutionary turnover of sex determination in action. There is a male dete...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evv128
更新日期:2015-07-02 00:00:00
abstract::Chlamydiae are an example of obligate intracellular bacteria that possess highly reduced, compact genomes (1.0-3.5 Mbp), reflective of their abilities to sequester many essential nutrients from the host that they no longer need to synthesize themselves. The Chlamydiae is a phylum with a very wide host range spanning m...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy195
更新日期:2018-10-01 00:00:00
abstract::The genus Campylobacter includes some of the most relevant pathogens for human and animal health; the continuous effort in their characterization has also revealed new species putatively involved in different kind of infections. Nowadays, the available genomic data for the genus comprise a wide variety of species with...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evu195
更新日期:2014-09-04 00:00:00
abstract::In clonal systems, interpreting driver genes in terms of molecular networks helps understanding how these drivers elicit an adaptive phenotype. Obtaining such a network-based understanding depends on the correct identification of driver genes. In clonal systems, independent evolved lines can acquire a similar adaptive...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evw010
更新日期:2016-01-23 00:00:00
abstract::Cnidarians represent one of the few groups of venomous animals that lack a centralized venom transmission system. Instead, they are equipped with stinging capsules collectively known as nematocysts. Nematocysts vary in abundance and type across different tissues; however, the venom composition in most species remains ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evw155
更新日期:2016-08-25 00:00:00
abstract::Seed storage proteins (SSP) in cereals provide essential nutrition for humans and animals. Genes encoding these proteins have undergone rapid evolution in different grass species. To better understand the degree of divergence, we analyzed this gene family in the subfamily Chloridoideae, where the genome of teff (Eragr...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evw117
更新日期:2016-06-13 00:00:00
abstract::The story of how preColumbian civilizations developed goes hand-in-hand with the process of plant domestication by Mesoamerican inhabitants. Here, we present the almost complete sequence of a mitochondrial genome and a partial chloroplast genome from an archaeological maize sample collected at the Valley of Tehuacán, ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evx048
更新日期:2017-04-01 00:00:00
abstract::Biodegradation of the phenylurea herbicide linuron appears a specialization within a specific clade of the Variovorax genus. The linuron catabolic ability is likely acquired by horizontal gene transfer but the mechanisms involved are not known. The full-genome sequences of six linuron-degrading Variovorax strains isol...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evaa085
更新日期:2020-06-01 00:00:00