Fine-Scale Characterization of Genomic Structural Variation in the Human Genome Reveals Adaptive and Biomedically Relevant Hotspots.

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：:Nemerteans are one of few animal groups that have evolved the ability to utilize toxins for both defense and subduing prey, but little is known about specific nemertean toxins. In particular, no study has identified specific toxin genes even though peptide toxins are known from some nemertean species. Information abou...

journal_title：Genome biology and evolution

authors： Whelan NV,Kocot KM,Santos SR,Halanych KM

更新日期：2014-11-27 00:00:00

abstract：:The Bateson-Dobzhansky-Muller (BDM) model of reproductive isolation by genetic incompatibility is a widely accepted model of speciation. Because of the exceptionally rich biological information about the budding yeast Saccharomyces cerevisiae, the identification of BDM incompatibilities in yeast would greatly deepen o...

journal_title：Genome biology and evolution

authors： Li C,Wang Z,Zhang J

更新日期：2013-01-01 00:00:00

abstract：:It has been estimated that the sister plant pathogenic fungal species Heterobasidion irregulare and Heterobasidion annosum may have been allopatrically isolated for 34-41 Myr. They are now sympatric due to the introduction of the first species from North America into Italy, where they freely hybridize. We used a compa...

journal_title：Genome biology and evolution

authors： Sillo F,Garbelotto M,Friedman M,Gonthier P

更新日期：2015-11-01 00:00:00

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...

journal_title：Genome biology and evolution

authors： Fares MA,Sabater-Muñoz B,Toft C

更新日期：2017-05-01 00:00:00

abstract：:Poaceae (grasses) is an agriculturally important and widely distributed family of plants with extraordinary phenotypic diversity, much of which was generated under recent lineage-specific evolution. Yet, little is known about the genes and functional modules involved in the lineage-specific divergence of grasses. Here...

journal_title：Genome biology and evolution

authors： Assis R

更新日期：2019-01-01 00:00:00

abstract：:Fish use olfaction to sense a variety of nonvolatile chemical signals in water. However, the evolutionary importance of olfaction in species-rich cichlids is controversial. Here, we determined an almost complete sequence of the vomeronasal type 2 receptor-like (OlfC: putative amino acids receptor in teleosts) gene clu...

journal_title：Genome biology and evolution

authors： Nikaido M,Suzuki H,Toyoda A,Fujiyama A,Hagino-Yamagishi K,Kocher TD,Carleton K,Okada N

更新日期：2013-01-01 00:00:00

abstract：:The Asian honey bee (Apis dorsata) is distinct from its more widely distributed cousin Apis mellifera by a few key characteristics. Most prominently, A. dorsata, nest in the open by forming a colony clustered around the honeycomb, whereas A. mellifera nest in concealed cavities. Additionally, the worker and reproducti...

journal_title：Genome biology and evolution

authors： Oppenheim S,Cao X,Rueppel O,Krongdang S,Phokasem P,DeSalle R,Goodwin S,Xing J,Chantawannakul P,Rosenfeld JA

更新日期：2020-01-01 00:00:00

abstract：:Acquisition of Elizabethkingia infections in intensive care units (ICUs) has risen in the past decade. Treatment of Elizabethkingia infections is challenging due to the lack of effective therapeutic regimens, leading to a high mortality rate. Elizabethkingia infections have long been attributed to Elizabethkingia meni...

journal_title：Genome biology and evolution

authors： Teo J,Tan SY,Liu Y,Tay M,Ding Y,Li Y,Kjelleberg S,Givskov M,Lin RT,Yang L

更新日期：2014-05-06 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：:In general, proteins do not work alone; they form macromolecular complexes to play fundamental roles in diverse cellular functions. On the basis of their iterative clustering procedure and frequency of occurrence in the macromolecular complexes, the protein subunits have been categorized as core and attachment. Core p...

journal_title：Genome biology and evolution

authors： Chakraborty S,Ghosh TC

更新日期：2013-01-01 00:00:00

abstract：:Nucleomorphs are the remnant nuclei of algal endosymbionts that were engulfed by nonphotosynthetic host eukaryotes. These peculiar organelles are found in cryptomonad and chlorarachniophyte algae, where they evolved from red and green algal endosymbionts, respectively. Despite their independent origins, cryptomonad an...

journal_title：Genome biology and evolution

authors： Tanifuji G,Onodera NT,Wheeler TJ,Dlutek M,Donaher N,Archibald JM

更新日期：2011-01-01 00:00:00

abstract：:MicroRNAs (miRNAs) are short endogenous RNA molecules that regulate gene expression at the posttranscriptional level and have been shown to play critical roles during animal development. The identification and comparison of miRNAs in metazoan species are therefore paramount for our understanding of the evolution of bo...

journal_title：Genome biology and evolution

authors： Marco A,Hui JH,Ronshaugen M,Griffiths-Jones S

更新日期：2010-01-01 00:00:00

abstract：:Recently, a new Chlamydia-related organism, Protochlamydia naegleriophila KNic, was discovered within a Naegleria amoeba. To decipher the mechanisms at play in the modeling of genomes from the Protochlamydia genus, we sequenced the full genome of Pr. naegleriophila, which includes a 2,885,090 bp chromosome and a 145,2...

journal_title：Genome biology and evolution

authors： Bertelli C,Cissé OH,Rusconi B,Kebbi-Beghdadi C,Croxatto A,Goesmann A,Collyn F,Greub G

更新日期：2016-08-25 00:00:00

abstract：:Human-specific small insertions and deletions (HS indels, with lengths <100 bp) are reported to be ubiquitous in the human genome. However, whether these indels contribute to human-specific traits remains unclear. Here we employ a modified McDonald-Kreitman (MK) test and a combinatorial population genetics approach to...

journal_title：Genome biology and evolution

authors： Chen CH,Chuang TJ,Liao BY,Chen FC

更新日期：2009-10-20 00:00:00

abstract：:Thousands of candidate human-specific regulatory sequences (HSRS) have been identified, supporting the hypothesis that unique to human phenotypes result from human-specific alterations of genomic regulatory networks. Collectively, a compendium of multiple diverse families of HSRS that are functionally and structurally...

journal_title：Genome biology and evolution

authors： Glinsky GV

更新日期：2016-09-19 00:00:00

abstract：:Primary metabolism is essential to plants for growth and development, and secondary metabolism helps plants to interact with the environment. Many plant metabolites are industrially important. These metabolites are produced by plants through complex metabolic pathways. Lack of knowledge about these pathways is hinderi...

journal_title：Genome biology and evolution

authors： Mukherjee D,Mukherjee A,Ghosh TC

更新日期：2015-11-10 00:00:00

abstract：:Bacterial degraders of chlorophenoxy herbicides have been isolated from various ecosystems, including pristine environments. Among these degraders, the sphingomonads constitute a prominent group that displays versatile xenobiotic-degradation capabilities. Four separate sequencing strategies were required to provide th...

journal_title：Genome biology and evolution

authors： Nielsen TK,Rasmussen M,Demanèche S,Cecillon S,Vogel TM,Hansen LH

更新日期：2017-09-01 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

authors： Yi M,Chen F,Luo M,Cheng Y,Zhao H,Cheng H,Zhou R

更新日期：2014-05-19 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：: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

authors： Guillory WX,Onyshchenko A,Ruck EC,Parks M,Nakov T,Wickett NJ,Alverson AJ

更新日期：2018-06-01 00:00:00

abstract：:In many species, spermatogenesis involves more cell divisions than oogenesis, and the male germline, therefore, accumulates more DNA replication errors, a phenomenon known as male mutation bias. The extent of male mutation bias (α) is estimated by comparing substitution rates of the X, Y, and autosomal chromosomes, as...

journal_title：Genome biology and evolution

authors： Link V,Aguilar-Gómez D,Ramírez-Suástegui C,Hurst LD,Cortez D

更新日期：2017-09-01 00:00:00

abstract：:Different genes and proteins evolve at very different rates. To identify the factors that explain these differences is an important aspect of research in molecular evolution. One such factor is the role a protein plays in a large molecular network. Here, we analyze the evolutionary rates of enzyme-coding genes in the ...

journal_title：Genome biology and evolution

authors： Aguilar-Rodríguez J,Wagner A

更新日期：2018-11-01 00:00:00

abstract：:Prokaryote genomes are the result of a dynamic flux of genes, with increases achieved via horizontal gene transfer and reductions occurring through gene loss. The ecological and selective forces that drive this genomic flexibility vary across species. Bacillus subtilis is a naturally competent bacterium that occupies ...

journal_title：Genome biology and evolution

authors： Brito PH,Chevreux B,Serra CR,Schyns G,Henriques AO,Pereira-Leal JB

更新日期：2018-01-01 00:00:00

abstract：:Ubiquinone (Q) is an isoprenoid quinone that functions as membrane electron carrier in mitochondria and bacterial organisms belonging to the alpha, beta, and gamma class of proteobacteria. The biosynthesis of Q follows various biochemical steps catalyzed by diverse proteins that are, in general, homologous in mitochon...

journal_title：Genome biology and evolution

authors： Degli Esposti M

更新日期：2017-11-01 00:00:00

abstract：:Developmental constraints on genome evolution have been suggested to follow either an early conservation model or an "hourglass" model. Both models agree that late development strongly diverges between species, but debate on which developmental period is the most conserved. Here, based on a modified "Transcriptome Age...

journal_title：Genome biology and evolution

authors： Liu J,Robinson-Rechavi M

更新日期：2018-09-01 00:00:00

abstract：:The ribonuclease (RNase) A superfamily is a vertebrate-specific gene family. Because of a massive expansion that occurred during the early mammalian evolution, extant mammals in general have much more RNase genes than nonmammalian vertebrates. Mammalian RNases have been associated with diverse physiological functions ...

journal_title：Genome biology and evolution

authors： Goo SM,Cho S

更新日期：2013-01-01 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：:"Candidatus Endomicrobium trichonymphae" (Bacteria; Elusimicrobia) is an obligate intracellular symbiont of the cellulolytic protist genus Trichonympha in the termite gut. A previous genome analysis of "Ca Endomicrobium trichonymphae" phylotype Rs-D17 (genomovar Ri2008), obtained from a Trichonympha agilis cell in the...

journal_title：Genome biology and evolution

authors： Izawa K,Kuwahara H,Kihara K,Yuki M,Lo N,Itoh T,Ohkuma M,Hongoh Y

更新日期：2016-10-13 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

authors： Wein T,Dagan T

更新日期：2019-11-01 00:00:00