Mitochondrial-nuclear interactions: compensatory evolution or variable functional constraint among vertebrate oxidative phosphorylation genes?

abstract：:The plastid genomes of four related carnivorous plants (Drosera regia, Drosera erythrorhiza, Aldrovanda vesiculosa, and Dionaea muscipula) were sequenced to examine changes potentially induced by the transition to carnivory. The plastid genomes of the Droseraceae show multiple rearrangements, gene losses, and large ex...

journal_title：Genome biology and evolution

authors： Nevill PG,Howell KA,Cross AT,Williams AV,Zhong X,Tonti-Filippini J,Boykin LM,Dixon KW,Small I

更新日期：2019-02-01 00:00:00

abstract：:Population-level differences in the number of copies of genes resulting from gene duplication and loss have recently been recognized as an important source of variation in eukaryotes. However, except for a small number of cases, the phenotypic effects of this variation are unknown. Data from the Saccharomyces Genome R...

journal_title：Genome biology and evolution

authors： Ames RM,Rash BM,Hentges KE,Robertson DL,Delneri D,Lovell SC

更新日期：2010-01-01 00:00:00

abstract：:Whole-genome duplications are radical evolutionary events that have driven speciation and adaptation in many taxa. Higher-order polyploids have complex histories often including interspecific hybridization and dynamic genomic changes. This chromosomal reshuffling is poorly understood for most polyploid species, despit...

journal_title：Genome biology and evolution

authors： Tennessen JA,Govindarajulu R,Ashman TL,Liston A

更新日期：2014-12-04 00:00:00

abstract：:Increasing evidence from sequence data from various environments, including the human gut, suggests the existence of a previously unknown putative seventh order of methanogens. The first genomic data from members of this lineage, Methanomassiliicoccus luminyensis and "Candidatus Methanomethylophilus alvus," provide in...

journal_title：Genome biology and evolution

authors： Borrel G,O'Toole PW,Harris HM,Peyret P,Brugère JF,Gribaldo S

更新日期：2013-01-01 00:00:00

abstract：:The propensity of protein sites to be occupied by any of the 20 amino acids is known as site-specific amino acid preferences (SSAP). Under the assumption that SSAP are conserved among homologs, they can be used to parameterize evolutionary models for the reconstruction of accurate phylogenetic trees. However, simulati...

journal_title：Genome biology and evolution

authors： Ferrada E

更新日期：2019-01-01 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

authors： Pérez-Zamorano B,Vallebueno-Estrada M,Martínez González J,García Cook A,Montiel R,Vielle-Calzada JP,Delaye L

更新日期：2017-04-01 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

authors： Qian W,Zhang J

更新日期：2009-07-22 00:00:00

abstract：:Animals interact with a diverse array of both beneficial and detrimental microorganisms. In insects, these symbioses in many cases allow feeding on nutritionally unbalanced diets. It is, however, still not clear how are obligate symbioses maintained at the cellular level for up to several hundred million years. Exact ...

journal_title：Genome biology and evolution

authors： Husnik F,Hypsa V,Darby A

更新日期：2020-04-01 00:00:00

abstract：:Parasitoid wasps are among the most speciose animals, yet have relatively few available genomic resources. We report a draft genome assembly of the wasp Diachasma alloeum (Hymenoptera: Braconidae), a host-specific parasitoid of the apple maggot fly Rhagoletis pomonella (Diptera: Tephritidae), and a developing model fo...

journal_title：Genome biology and evolution

authors： Tvedte ES,Walden KKO,McElroy KE,Werren JH,Forbes AA,Hood GR,Logsdon JM,Feder JL,Robertson HM

更新日期：2019-10-01 00:00:00

abstract：:DNA methylation is an evolutionary ancient epigenetic modification that is phylogenetically widespread. Comparative studies of the methylome across a diverse range of non-conventional and conventional model organisms is expected to help reveal how the landscape of DNA methylation and its functions have evolved. Here, ...

journal_title：Genome biology and evolution

authors： Kvist J,Gonçalves Athanàsio C,Shams Solari O,Brown JB,Colbourne JK,Pfrender ME,Mirbahai L

更新日期：2018-08-01 00:00:00

abstract：:Fungi expressing P450nor, an unconventional nitric oxide (NO) reducing cytochrome P450, are considered significant contributors to environmental nitrous oxide (N2O) emissions. Despite extensive efforts, fungal contributions to N2O emissions remain uncertain. For example, the majority of N2O emitted from antibiotic-ame...

journal_title：Genome biology and evolution

authors： Higgins SA,Schadt CW,Matheny PB,Löffler FE

更新日期：2018-09-01 00:00:00

abstract：:Some photosynthetic organisms live in extremely low light environments. Light limitation is associated with selective forces as well as reduced exposure to mutagens, and over evolutionary timescales it can leave a footprint on species' genomes. Here, we present the chloroplast genomes of four green algae (Bryopsidales...

journal_title：Genome biology and evolution

authors： R Marcelino V,Cremen MC,Jackson CJ,Larkum AA,Verbruggen H

更新日期：2016-10-05 00:00:00

abstract：:Although pooled-population sequencing has become a widely used approach for estimating allele frequencies, most work has proceeded in the absence of a proper statistical framework. We introduce a self-sufficient, closed-form, maximum-likelihood estimator for allele frequencies that accounts for errors associated with ...

journal_title：Genome biology and evolution

authors： Lynch M,Bost D,Wilson S,Maruki T,Harrison S

更新日期：2014-04-30 00:00:00

abstract：:Taeniid cestodes (including the human parasites Echinococcus spp. and Taenia solium) have very few mobile genetic elements (MGEs) in their genome, despite lacking a canonical PIWI pathway. The MGEs of these parasites are virtually unexplored, and nothing is known about their expression and silencing. In this work, we ...

journal_title：Genome biology and evolution

authors： Koziol U,Radio S,Smircich P,Zarowiecki M,Fernández C,Brehm K

更新日期：2015-07-01 00:00:00

abstract：:Neotropical primates (NP) are presently distributed in the New World from Mexico to northern Argentina, comprising three large families, Cebidae, Atelidae, and Pitheciidae, consequently to their diversification following their separation from Old World anthropoids near the Eocene/Oligocene boundary, some 40 Ma. The ev...

journal_title：Genome biology and evolution

authors： Schrago CG,Menezes AN,Furtado C,Bonvicino CR,Seuanez HN

更新日期：2014-11-05 00:00:00

abstract：:Throughout the animal kingdom chemical senses are one of the primary means by which organisms make sense of their environment. To achieve perception of complex chemosensory stimuli large repertoires of olfactory and gustatory receptors are employed in bony vertebrates, which are characterized by high evolutionary dyna...

journal_title：Genome biology and evolution

authors： Sharma K,Syed AS,Ferrando S,Mazan S,Korsching SI

更新日期：2019-02-01 00:00:00

abstract：:The large repABC plasmids of the order Rhizobiales with Class I quorum-regulated conjugative transfer systems often define the nature of the bacterium that harbors them. These otherwise diverse plasmids contain a core of highly conserved genes for replication and conjugation raising the question of their evolutionary ...

journal_title：Genome biology and evolution

authors： Wetzel ME,Olsen GJ,Chakravartty V,Farrand SK

更新日期：2015-11-19 00:00:00

abstract：:Theory suggests that biological modularity and robustness allow for maintenance of fitness under mutational change, and when this change is adaptive, for evolvability. Empirical demonstrations that these traits promote evolvability in nature remain scant however. This is in part because modularity, robustness, and evo...

journal_title：Genome biology and evolution

authors： Rorick MM,Wagner GP

更新日期：2011-01-01 00:00:00

abstract：:Allopolyploidization plays an important role in speciation, and some natural or synthetic allopolyploid fishes have been extensively applied to aquaculture. Although genetic and epigenetic inheritance and variation associated with plant allopolyploids have been well documented, the relative research in allopolyploid a...

journal_title：Genome biology and evolution

authors： Shao GM,Li XY,Wang Y,Wang ZW,Li Z,Zhang XJ,Zhou L,Gui JF

更新日期：2018-09-01 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

authors： Narechania A,Baker RH,Sit R,Kolokotronis SO,DeSalle R,Planet PJ

更新日期：2012-01-01 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

authors： Davis AC,Greenwold MJ,Sawyer RH

更新日期：2019-03-01 00:00:00

abstract：:Analyses of genomic diversity along the X chromosome and of its correlation with autosomal diversity can facilitate understanding of evolutionary forces in shaping sex-linked genomic architecture. Strong selective sweeps and accelerated genetic drift on the X-chromosome have been inferred in primates and other model s...

journal_title：Genome biology and evolution

authors： Chen ZH,Zhang M,Lv FH,Ren X,Li WR,Liu MJ,Nam K,Bruford MW,Li MH

更新日期：2018-04-01 00:00:00

abstract：:Positive selection and purifying selection reduce levels of variation at linked neutral loci. One consequence of these processes is that the amount of neutral diversity and the meiotic recombination rate are predicted to be positively correlated across the genome-a prediction met in some species but not others. To bet...

journal_title：Genome biology and evolution

authors： Kartje ME,Jing P,Payseur BA

更新日期：2020-04-01 00:00:00

abstract：:The selective pressures acting on viruses that replicate under enhanced mutation rates are largely unknown. Here, we describe resistance of foot-and-mouth disease virus to the mutagen 5-fluorouracil (FU) through a single polymerase substitution that prevents an excess of A to G and U to C transitions evoked by FU on t...

journal_title：Genome biology and evolution

authors： de la Higuera I,Ferrer-Orta C,de Ávila AI,Perales C,Sierra M,Singh K,Sarafianos SG,Dehouck Y,Bastolla U,Verdaguer N,Domingo E

更新日期：2017-05-01 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

authors： Carretero-Paulet L,Chang TH,Librado P,Ibarra-Laclette E,Herrera-Estrella L,Rozas J,Albert VA

更新日期：2015-01-09 00:00:00

abstract：:The mechanistic basis of regulatory variation and the prevailing evolutionary forces shaping that variation are known to differ between sexes and between chromosomes. Regulatory variation of gene expression can be due to functional changes within a gene itself (cis) or in other genes elsewhere in the genome (trans). T...

journal_title：Genome biology and evolution

authors： Graze RM,McIntyre LM,Morse AM,Boyd BM,Nuzhdin SV,Wayne ML

更新日期：2014-04-01 00:00:00

abstract：:Only few studies on snake venoms were dedicated to deeply characterize the toxin secretion of animals from the Colubridae family, despite the fact that they represent the majority of snake diversity. As a consequence, some evolutionary trends observed in venom proteins that underpinned the evolutionary histories of sn...

journal_title：Genome biology and evolution

authors： Campos PF,Andrade-Silva D,Zelanis A,Paes Leme AF,Rocha MM,Menezes MC,Serrano SM,Junqueira-de-Azevedo Ide L

更新日期：2016-08-16 00:00:00

abstract：:A major mode of gene expression evolution is based on changes in cis-regulatory elements (CREs) whose function critically depends on the presence of transcription factor-binding sites (TFBS). Because CREs experience extensive TFBS turnover even with conserved function, alignment-based studies of CRE sequence evolution...

journal_title：Genome biology and evolution

authors： Otto W,Stadler PF,López-Giraldéz F,Townsend JP,Lynch VJ,Wagner GP

更新日期：2009-05-25 00:00:00

abstract：:Natural products from microbes have provided humans with beneficial antibiotics for millennia. However, a decline in the pace of antibiotic discovery exerts pressure on human health as antibiotic resistance spreads, a challenge that may better faced by unveiling chemical diversity produced by microbes. Current microbi...

journal_title：Genome biology and evolution

authors： Cruz-Morales P,Kopp JF,Martínez-Guerrero C,Yáñez-Guerra LA,Selem-Mojica N,Ramos-Aboites H,Feldmann J,Barona-Gómez F

更新日期：2016-07-02 00:00:00

abstract：:Aspergillus ochraceoroseus and Aspergillus rambellii were isolated from soil detritus in Taï National Park, Ivory Coast, Africa. The Type strain for each species happens to be the only representative ever sampled. Both species secrete copious amounts of aflatoxin B1 and sterigmatocystin, because each of their genomes ...

journal_title：Genome biology and evolution

authors： Moore GG,Mack BM,Beltz SB

更新日期：2015-12-03 00:00:00