Deletion rate evolution and its effect on genome size and coding density.

abstract：:A recent investigation found evidence that the transition of Arabidopsis thaliana from ancestral self-incompatibility (SI) to full self-compatibility occurred very recently and suggested that this occurred through a selective fixation of a nonfunctional allele (PsiSCR1) at the SCR gene, which determines pollen specifi...

journal_title：Molecular biology and evolution

authors： Bechsgaard JS,Castric V,Charlesworth D,Vekemans X,Schierup MH

更新日期：2006-09-01 00:00:00

abstract：:Microbial species play important roles in different environments and the production of high-quality genomes from metagenome data sets represents a major obstacle to understanding their ecological and evolutionary dynamics. Metagenome-Assembled Genomes Orchestra (MAGO) is a computational framework that integrates and s...

journal_title：Molecular biology and evolution

authors： Murovec B,Deutsch L,Stres B

更新日期：2020-02-01 00:00:00

abstract：:In a series of highly influential publications, Cavalli-Sforza and colleagues used principal component (PC) analysis to produce maps depicting how human genetic diversity varies across geographic space. Within Europe, the first axis of variation (PC1) was interpreted as evidence for the demic diffusion model of agricu...

journal_title：Molecular biology and evolution

authors： François O,Currat M,Ray N,Han E,Excoffier L,Novembre J

更新日期：2010-06-01 00:00:00

abstract：:Several new families of DNA transposons were identified by computer-assisted searches in a wide range of animal species that includes nematodes, flat worms, mosquitoes, sea squirt, zebrafish, and humans. Many of these elements have coding capacity for transposases, which are related to each other and to those encoded ...

journal_title：Molecular biology and evolution

authors： Feschotte C

更新日期：2004-09-01 00:00:00

abstract：:It is well known that molecular data "saturates" with increasing sequence divergence (thereby losing phylogenetic information) and that in addition the accumulation of misleading information due to chance similarities or to systematic bias may accompany saturation as well. Exploratory data analysis methods that can qu...

journal_title：Molecular biology and evolution

authors： White WT,Hills SF,Gaddam R,Holland BR,Penny D

更新日期：2007-09-01 00:00:00

abstract：:We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the...

journal_title：Molecular biology and evolution

authors： Katoh K,Standley DM

更新日期：2013-04-01 00:00:00

abstract：:To investigate DNA variation in natural plant populations, a 1.8-kb region of the acidic chitinase locus (ChiA)was analyzed for 17 ecotypes of Arabidopsis thaliana sampled worldwide and 3 Arabis species in Japan. As in the Adh region, dimorphism was detected throughout the investigated ChiA region, suggesting the poss...

journal_title：Molecular biology and evolution

authors： Kawabe A,Innan H,Terauchi R,Miyashita NT

更新日期：1997-12-01 00:00:00

abstract：:DNA supercoiling is the master function that interconnects chromosome structure and global gene transcription. This function has recently been shown to be under strong selection in Escherichia coli. During the evolution of 12 initially identical populations propagated in a defined environment for 20,000 generations, p...

journal_title：Molecular biology and evolution

authors： Crozat E,Winkworth C,Gaffé J,Hallin PF,Riley MA,Lenski RE,Schneider D

更新日期：2010-09-01 00:00:00

abstract：:The Mlc1 gene of Drosophila melanogaster encodes two MLC1 isoforms via developmentally regulated alternative pre-mRNA splicing. In larval muscle and tubular and abdominal muscles of adults, all of the six exons are included in the spliced mRNA, whereas, in the fibrillar indirect flight muscle of adult, exon 5 is exclu...

journal_title：Molecular biology and evolution

authors： Leicht BG,Lyckegaard EM,Benedict CM,Clark AG

更新日期：1993-07-01 00:00:00

abstract：:The ancestral homeland of Australian dingoes and Pacific dogs is proposed to be in South China. However, the location and timing of their dispersal and relationship to dog domestication is unclear. Here, we sequenced 7,000- to 2,000-year-old complete mitochondrial DNA (mtDNA) genomes of 27 ancient canids (one gray wol...

journal_title：Molecular biology and evolution

authors： Zhang M,Sun G,Ren L,Yuan H,Dong G,Zhang L,Liu F,Cao P,Ko AM,Yang MA,Hu S,Wang GD,Fu Q

更新日期：2020-05-01 00:00:00

abstract：:Long noncoding RNAs (lncRNAs) do not code for proteins but function as RNAs. Because the functions of an RNA rely on either its sequence or secondary structure, lncRNAs should be folded at least as strongly as messenger RNAs (mRNAs), which serve as messengers for translation and are generally thought to lack secondary...

journal_title：Molecular biology and evolution

authors： Yang JR,Zhang J

更新日期：2015-04-01 00:00:00

abstract：:Protein interactions are central to most biological processes. We investigated the dynamics of emergence of the protein interaction network of Saccharomyces cerevisiae by mapping origins of proteins on an evolutionary tree. We demonstrate that evolutionary periods are characterized by distinct connectivity levels of t...

journal_title：Molecular biology and evolution

authors： Kunin V,Pereira-Leal JB,Ouzounis CA

更新日期：2004-07-01 00:00:00

abstract：:The adaptive radiation of cichlid fishes in East African Lake Malawi encompasses over 500 species that are believed to have evolved within the last 800,000 years from a common founder population. It has been proposed that hybridization between ancestral lineages can provide the genetic raw material to fuel such except...

journal_title：Molecular biology and evolution

authors： Svardal H,Quah FX,Malinsky M,Ngatunga BP,Miska EA,Salzburger W,Genner MJ,Turner GF,Durbin R

更新日期：2020-04-01 00:00:00

abstract：:The degree to which an amino acid site is free to vary is strongly dependent on its structural and functional importance. An amino acid that plays an essential role is unlikely to change over evolutionary time. Hence, the evolutionary rate at an amino acid site is indicative of how conserved this site is and, in turn,...

journal_title：Molecular biology and evolution

authors： Mayrose I,Graur D,Ben-Tal N,Pupko T

更新日期：2004-09-01 00:00:00

abstract：:Whether higher-order chromatin organization is related to genome stability over evolutionary time remains elusive. We find that regions of conserved gene order across the genus Drosophila are larger if they harbor genes bound by B-type lamin (Lam) and Suppressor of Under-Replication (SUUR), two proteins located at the...

journal_title：Molecular biology and evolution

authors： Ranz JM,Díaz-Castillo C,Petersen R

更新日期：2012-01-01 00:00:00

abstract：:Past analyses of the genome of the yeast Saccharomyces cerevisiae have revealed substantial regional variation in G+C content. Important questions remain, though, as to the origin, nature, significance, and generality of this variation. We conducted an extensive analysis of the yeast genome to try to answer these ques...

journal_title：Molecular biology and evolution

authors： Bradnam KR,Seoighe C,Sharp PM,Wolfe KH

更新日期：1999-05-01 00:00:00

abstract：:Diverging from the classic paradigm of random gene order in eukaryotes, gene proximity can be leveraged to systematically identify functionally related gene neighborhoods in eukaryotes, utilizing techniques pioneered in bacteria. Current methods of identifying gene neighborhoods typically rely on sequence similarity t...

journal_title：Molecular biology and evolution

authors： Foflonker F,Blaby-Haas CE

更新日期：2021-01-23 00:00:00

abstract：:Ribosomal DNA (rDNA) is one of the most conserved genes in eukaryotes. The multiples copies of rDNA in the genome evolve in a concerted manner, through unequal crossing over and/or gene conversion, two mechanisms related to homologous recombination. Recombination increases local GC content in several organisms through...

journal_title：Molecular biology and evolution

authors： Escobar JS,Glémin S,Galtier N

更新日期：2011-09-01 00:00:00

abstract：:There is increasing evidence that X chromosomes have an unusual complement of genes, especially genes that have sex-specific expression. However, whereas in worm and fly the X chromosome has a dearth of male-specific genes, in mice genes that are uniquely expressed in spermatogonia are especially abundant on the X chr...

journal_title：Molecular biology and evolution

authors： Lercher MJ,Urrutia AO,Hurst LD

更新日期：2003-07-01 00:00:00

abstract：:Endogenous retroviruses are genomic elements formed by germline infiltration by originally exogenous viruses. These molecular fossils provide valuable information about the evolution of the retroviral family. Lentiviruses are an extensively studied genus of retroviruses infecting a broad range of mammals. Despite a we...

journal_title：Molecular biology and evolution

authors： Hron T,Farkašová H,Padhi A,Pačes J,Elleder D

更新日期：2016-10-01 00:00:00

abstract：:The Malagasy have been shown to be a genetically admixed population combining parental lineages with African and South East Asian ancestry. In the present paper, we fit the Malagasy admixture history in a highly resolved phylogeographic framework by typing a large set of mitochondrial DNA and Y DNA markers in unrelate...

journal_title：Molecular biology and evolution

authors： Tofanelli S,Bertoncini S,Castrì L,Luiselli D,Calafell F,Donati G,Paoli G

更新日期：2009-09-01 00:00:00

abstract：:Spinocerebellar ataxia type 10 is caused by ATTCT repeat expansion in the ATXN10 gene in humans. We studied the evolutionary history of the human genome to determine the time and mechanism of the acquisition of unstable ATTCT repeats in the genome. We found that long interspersed element-1 (LINE-1) was inserted into A...

journal_title：Molecular biology and evolution

authors： Kurosaki T,Matsuura T,Ohno K,Ueda S

更新日期：2009-11-01 00:00:00

abstract：:The occurrence of a fish-specific genome duplication (FSGD) in the lineage leading to teleost fishes is widely accepted, but the consequences of this event remain elusive. Teleosts, and the cichlid fishes from the species flocks in the East African Great Lakes in particular, evolved a unique complexity and diversity o...

journal_title：Molecular biology and evolution

authors： Braasch I,Salzburger W,Meyer A

更新日期：2006-06-01 00:00:00

abstract：:Inaccurate inference of positional homologies in multiple sequence alignments and systematic errors introduced by alignment heuristics obfuscate phylogenetic inference. Alignment masking, the elimination of phylogenetically uninformative or misleading sites from an alignment before phylogenetic analysis, is a common p...

journal_title：Molecular biology and evolution

authors： Rajan V

更新日期：2013-03-01 00:00:00

abstract：:We propose an improved version of the neighbor-joining (NJ) algorithm of Saitou and Nei. This new algorithm, BIONJ, follows the same agglomerative scheme as NJ, which consists of iteratively picking a pair of taxa, creating a new mode which represents the cluster of these taxa, and reducing the distance matrix by repl...

journal_title：Molecular biology and evolution

authors： Gascuel O

更新日期：1997-07-01 00:00:00

abstract：:To investigate the potential importance of gene duplication in D. melanogaster accessory gland protein (Acp) gene evolution we carried out a computational analysis comparing annotated D. melanogaster Acp genes to the entire D. melanogaster genome. We found that two known Acp genes are actually members of small multige...

journal_title：Molecular biology and evolution

authors： Holloway AK,Begun DJ

更新日期：2004-09-01 00:00:00

abstract：:During the last 60 years, the inversion polymorphism on the third chromosome of Drosophila pseudoobscura has become a case study of the evolution of linked blocks of genes, isolated from each other by the suppression of recombination in heterozygotes for different inversions. Due to its location within inverted region...

journal_title：Molecular biology and evolution

authors： Popadić A,Popadić D,Anderson WW

更新日期：1995-09-01 00:00:00

abstract：:Horizontal gene transfer (HGT) has been described as a common mechanism of transferring genetic material between prokaryotes, whereas genetic transfers from eukaryotes to prokaryotes have been rarely documented. Here we report a rare case of HGT in which plant expansin genes that code for plant cell-wall loosening pro...

journal_title：Molecular biology and evolution

authors： Nikolaidis N,Doran N,Cosgrove DJ

更新日期：2014-02-01 00:00:00

abstract：:Large-scale variation in chromosome size was analyzed in 35 natural isolates of Escherichia coli by physical mapping with a restriction enzyme whose sites are restricted to rDNA operons. Although the genetic maps and chromosome lengths of the laboratory strains E. coli K12 and Salmonella enterica sv. Typhimurium LT2 a...

journal_title：Molecular biology and evolution

authors： Bergthorsson U,Ochman H

更新日期：1998-01-01 00:00:00

abstract：:While it is widely accepted that most animals (Metazoa) do not have endogenous cellulases, relying instead on intestinal symbionts for cellulose digestion, the glycosyl hydrolase family 9 (GHF9) cellulases found in the genomes of termites, abalone, and sea squirts could be an exception. Using information from expresse...

journal_title：Molecular biology and evolution

authors： Davison A,Blaxter M

更新日期：2005-05-01 00:00:00