Genome-Level Analysis of Selective Constraint without Apparent Sequence Conservation.

abstract：:The alphabaculovirus Anticarsia gemmatalis multiple nucleopolyhedrovirus (AgMNPV) is the world's most successful viral bioinsecticide. Through the 1980s and 1990s, this virus was extensively used for biological control of populations of Anticarsia gemmatalis (Velvetbean caterpillar) in soybean crops. During this perio...

journal_title：Genome biology and evolution

authors： Brito AF,Braconi CT,Weidmann M,Dilcher M,Alves JM,Gruber A,Zanotto PM

更新日期：2015-11-27 00:00:00

abstract：:Organisms show striking differences in genome structure; however, the functional implications and fundamental forces that govern these differences remain obscure. The intron-exon organization of nuclear genes is involved in a particularly large variety of structures and functional roles. We performed a 22-species stud...

journal_title：Genome biology and evolution

authors： Irimia M,Maeso I,Burguera D,Hidalgo-Sánchez M,Puelles L,Roy SW,Garcia-Fernàndez J,Ferran JL

更新日期：2011-01-01 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

authors： Taylor-Brown A,Pillonel T,Greub G,Vaughan L,Nowak B,Polkinghorne A

更新日期：2018-10-01 00:00:00

abstract：:The posttranslational modification of proteins by the ubiquitination pathway is an important regulatory mechanism in eukaryotes. To date, however, studies on the evolutionary history of the proteins involved in this pathway have been restricted to E1 and E2 enzymes, whereas E3 studies have been focused mainly in metaz...

journal_title：Genome biology and evolution

authors： Grau-Bové X,Sebé-Pedrós A,Ruiz-Trillo I

更新日期：2013-01-01 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

authors： Zhang F,Broughton RE

更新日期：2013-01-01 00:00:00

abstract：:Salmonella enterica subsp. enterica serovar Heidelberg (S. Heidelberg) is one of the top serovars causing human salmonellosis. Recently, an antibiotic-resistant strain of this serovar was implicated in a large 2011 multistate outbreak resulting from consumption of contaminated ground turkey that involved 136 confirmed...

journal_title：Genome biology and evolution

authors： Hoffmann M,Zhao S,Pettengill J,Luo Y,Monday SR,Abbott J,Ayers SL,Cinar HN,Muruvanda T,Li C,Allard MW,Whichard J,Meng J,Brown EW,McDermott PF

更新日期：2014-05-01 00:00:00

abstract：:Adaptive prediction is a capability of diverse organisms, including microbes, to sense a cue and prepare in advance to deal with a future environmental challenge. Here, we investigated the timeframe over which adaptive prediction emerges when an organism encounters an environment with novel structure. We subjected yea...

journal_title：Genome biology and evolution

authors： López García de Lomana A,Kaur A,Turkarslan S,Beer KD,Mast FD,Smith JJ,Aitchison JD,Baliga NS

更新日期：2017-06-01 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

authors： Gottlieb Y,Lalzar I,Klasson L

更新日期：2015-05-28 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：:Mitochondrial DNA (mtDNA) mutations underlie a variety of human genetic disorders and are associated with the aging process. mtDNA polymorphisms are widely used in a variety of evolutionary applications. Although mtDNA mutation spectra are known to differ between distantly related model organisms, the extent to which ...

journal_title：Genome biology and evolution

authors： Howe DK,Baer CF,Denver DR

更新日期：2009-12-23 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：:The study of microbe domestication has witnessed major advances that contribute to a better understanding of the emergence of artificially selected phenotypes and set the foundations of their rational improvement for biotechnology. Several features make Saccharomyces cerevisiae an ideal model for such a study, notably...

journal_title：Genome biology and evolution

authors： Barbosa R,Pontes A,Santos RO,Montandon GG,de Ponzzes-Gomes CM,Morais PB,Gonçalves P,Rosa CA,Sampaio JP

更新日期：2018-08-01 00:00:00

abstract：:Olfactory receptors (ORs) are membrane proteins that mediate the detection of odorants in the environment, and are the largest vertebrate gene family. Comparative studies of mammalian genomes indicate that OR repertoires vary widely, even between closely related lineages, as a consequence of frequent OR gains and loss...

journal_title：Genome biology and evolution

authors： Vandewege MW,Mangum SF,Gabaldón T,Castoe TA,Ray DA,Hoffmann FG

更新日期：2016-02-09 00:00:00

abstract：:This study investigated long-term substitution rate differences using three calibration points, divergences between lobe-finned vertebrates and ray-finned fish, between mammals and sauropsids, and between holosteans (gar and bowfin) and teleost fish with amino acid sequence data of 625 genes for 25 bony vertebrates. T...

journal_title：Genome biology and evolution

authors： Takezaki N

更新日期：2018-07-01 00:00:00

abstract：:Nematodes are highly abundant animals with diverse habitats and lifestyles. Some are free living whereas others parasitize animals or plants, and among the latter, infection abilities change across developmental stages to infect hosts and complete life cycles. To determine the relationship between transcriptome evolut...

journal_title：Genome biology and evolution

authors： Lu MR,Lai CK,Liao BY,Tsai IJ

更新日期：2020-07-01 00:00:00

abstract：:Retrotransposons, DNA sequences capable of creating copies of themselves, compose about half of the human genome and played a central role in the evolution of mammals. Their current position in the host genome is the result of the retrotranscription process and of the following host genome evolution. We apply a model ...

journal_title：Genome biology and evolution

authors： Riba A,Fumagalli MR,Caselle M,Osella M

更新日期：2020-11-03 00:00:00

abstract：:Horizontal gene transfer is a common mechanism in Bacteria that has contributed to the genomic content of existing organisms. Traditional methods for estimating bacterial phylogeny, however, assume only vertical inheritance in the evolution of homologous genes, which may result in errors in the estimated phylogenies. ...

journal_title：Genome biology and evolution

authors： Coimbra NDR,Goes-Neto A,Azevedo V,Ouangraoua A

更新日期：2020-04-01 00:00:00

abstract：:By comparing the patterns of evolution in the coding and upstream noncoding regions of yeast ribosomal protein (RP) genes duplicated in a genome duplication, we find that although nonsynonymous sites in the coding sequences show strong evidence for the fixation of recent gene conversion events, similar patterns are le...

journal_title：Genome biology and evolution

authors： Evangelisti AM,Conant GC

更新日期：2010-01-01 00:00:00

abstract：:The ability to obtain genome-wide sequences of very large numbers of individuals from natural populations raises questions about optimal sampling designs and the limits to extracting information on key population-genetic parameters from temporal-survey data. Methods are introduced for evaluating whether observed tempo...

journal_title：Genome biology and evolution

authors： Lynch M,Ho WC

更新日期：2020-04-01 00:00:00

abstract：:The Arabidopsis DA1 genes appear to have multiple functions in regulating organ size and abiotic stress response, but the biological roles of its closely related genes remain unknown. Evolutionary analyses might provide some clues to aid in an understanding of their functional diversification. In this work, we charact...

journal_title：Genome biology and evolution

authors： Zhao M,He L,Gu Y,Wang Y,Chen Q,He C

更新日期：2014-04-01 00:00:00

abstract：:Hemerythrins and hemocyanins are respiratory proteins present in some of the most ecologically diverse animal lineages; however, the precise evolutionary history of their enzymatic domains (hemerythrin, hemocyanin M, and tyrosinase) is still not well understood. We survey a wide dataset of prokaryote and eukaryote gen...

journal_title：Genome biology and evolution

authors： Martín-Durán JM,de Mendoza A,Sebé-Pedrós A,Ruiz-Trillo I,Hejnol A

更新日期：2013-01-01 00:00:00

abstract：:Mitochondrial ORFans (open reading frames having no detectable homology and with unknown function) were discovered in bivalve molluscs with doubly uniparental inheritance (DUI) of mitochondria. In these animals, two mitochondrial lineages are present, one transmitted through eggs (F-type), the other through sperm (M-t...

journal_title：Genome biology and evolution

authors： Milani L,Ghiselli F,Maurizii MG,Nuzhdin SV,Passamonti M

更新日期：2014-02-01 00:00:00

abstract：:Discoba (Excavata) is an evolutionarily important group of eukaryotes that includes Jakobida, with the most bacterial-like mitochondrial genomes known, and Euglenozoa, many of which have extensively fragmented mitochondrial genomes. However, little is known about the mitochondrial genomes of Heterolobosea, the third m...

journal_title：Genome biology and evolution

authors： Yang J,Harding T,Kamikawa R,Simpson AGB,Roger AJ

更新日期：2017-05-01 00:00:00

abstract：:SHORT VEGETATIVE PHASE (SVP) genes are members of the well-known MADS-box gene family that regulates vital developmental processes in plants. In Arabidopsis, there are two SVP paralogs, SVP/AGAMOUS-LIKE22 (SVP/AGL22) and AGL24. SVP protein suppresses the flowering process, whereas AGL24 acts as a flowering activator. ...

journal_title：Genome biology and evolution

authors： Liu X,Sun Z,Dong W,Wang Z,Zhang L

更新日期：2018-11-01 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

authors： Coronado-Zamora M,Salvador-Martínez I,Castellano D,Barbadilla A,Salazar-Ciudad I

更新日期：2019-05-01 00:00:00

abstract：:The effect of homologous recombination (HR) on the evolution of microbial genomes remains contentious as competing hypotheses seek to explain the evolutionary dynamics of microbial species. Evidence for HR between microbial genomes is widespread, and this process has been proposed to act as a cohesive force that can c...

journal_title：Genome biology and evolution

authors： Doroghazi JR,Buckley DH

更新日期：2011-01-01 00:00:00

abstract：:Gene duplications and novel genes have been shown to play a major role in helminth adaptation to a parasitic lifestyle because they provide the novelty necessary for adaptation to a changing environment, such as living in multiple hosts. Here we present the de novo sequenced and annotated genome of the parasitic trema...

journal_title：Genome biology and evolution

authors： Zajac N,Zoller S,Seppälä K,Moi D,Dessimoz C,Jokela J,Hartikainen H,Glover N

更新日期：2021-01-23 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

authors： Nozawa M,Ikeo K,Gojobori T

更新日期：2018-08-01 00:00:00

abstract：:Mitochondrial evolution has given rise to a complex array of organelles, ranging from classical aerobic mitochondria to mitochondrial remnants known as hydrogenosomes and mitosomes. The latter are found in anaerobic eukaryotes, and these highly derived organelles often retain only scant evidence of their mitochondrial...

journal_title：Genome biology and evolution

authors： Pérez-Brocal V,Shahar-Golan R,Clark CG

更新日期：2010-07-12 00:00:00

abstract：:One of the striking features of many eukaryotes is the apparent amount of redundancy in coding and non-coding elements of their genomes. Despite the possible evolutionary advantages, there are fewer examples of redundant sequences in viral genomes, particularly those with RNA genomes. The factors constraining the main...

journal_title：Genome biology and evolution

authors： Willemsen A,Zwart MP,Higueras P,Sardanyés J,Elena SF

更新日期：2016-10-12 00:00:00