当前位置： SCI文献检索 > MOLECULAR BIOLOGY AND EVOLUTION期刊下所有文献 > Comparative transcriptome analyses reveal core parasitism genes and suggest gene duplication and repurposing as sources of structural novelty.

Comparative transcriptome analyses reveal core parasitism genes and suggest gene duplication and repurposing as sources of structural novelty.

Abstract：

:The origin of novel traits is recognized as an important process underlying many major evolutionary radiations. We studied the genetic basis for the evolution of haustoria, the novel feeding organs of parasitic flowering plants, using comparative transcriptome sequencing in three species of Orobanchaceae. Around 180 genes are upregulated during haustorial development following host attachment in at least two species, and these are enriched in proteases, cell wall modifying enzymes, and extracellular secretion proteins. Additionally, about 100 shared genes are upregulated in response to haustorium inducing factors prior to host attachment. Collectively, we refer to these newly identified genes as putative "parasitism genes." Most of these parasitism genes are derived from gene duplications in a common ancestor of Orobanchaceae and Mimulus guttatus, a related nonparasitic plant. Additionally, the signature of relaxed purifying selection and/or adaptive evolution at specific sites was detected in many haustorial genes, and may play an important role in parasite evolution. Comparative analysis of gene expression patterns in parasitic and nonparasitic angiosperms suggests that parasitism genes are derived primarily from root and floral tissues, but with some genes co-opted from other tissues. Gene duplication, often taking place in a nonparasitic ancestor of Orobanchaceae, followed by regulatory neofunctionalization, was an important process in the origin of parasitic haustoria.

journal_name

Mol Biol Evol

journal_title

Molecular biology and evolution

authors

Yang Z,Wafula EK,Honaas LA,Zhang H,Das M,Fernandez-Aparicio M,Huang K,Bandaranayake PC,Wu B,Der JP,Clarke CR,Ralph PE,Landherr L,Altman NS,Timko MP,Yoder JI,Westwood JH,dePamphilis CW

doi

10.1093/molbev/msu343

subject

Has Abstract

pub_date

2015-03-01 00:00:00

pages

767-90

issue

3

eissn

0737-4038

issn

1537-1719

pii

msu343

journal_volume

32

pub_type

杂志文章

相关文献

MOLECULAR BIOLOGY AND EVOLUTION文献大全
  • Automated structural comparisons clarify the phylogeny of the right-hand-shaped polymerases.

    abstract：:Polymerases are essential for life, being responsible for replication, transcription, and the repair of nucleic acid molecules. Those that share a right-hand-shaped fold and catalytic site structurally similar to the DNA polymerase I of Escherichia coli may catalyze RNA- or DNA-dependent RNA polymerization, reverse tr...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/molbev/msu219

    authors： Mönttinen HA,Ravantti JJ,Stuart DI,Poranen MM

    更新日期：2014-10-01 00:00:00

  • Estimating gene gain and loss rates in the presence of error in genome assembly and annotation using CAFE 3.

    abstract：:Current sequencing methods produce large amounts of data, but genome assemblies constructed from these data are often fragmented and incomplete. Incomplete and error-filled assemblies result in many annotation errors, especially in the number of genes present in a genome. This means that methods attempting to estimate...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/molbev/mst100

    authors： Han MV,Thomas GW,Lugo-Martinez J,Hahn MW

    更新日期：2013-08-01 00:00:00

  • FUBAR: a fast, unconstrained bayesian approximation for inferring selection.

    abstract：:Model-based analyses of natural selection often categorize sites into a relatively small number of site classes. Forcing each site to belong to one of these classes places unrealistic constraints on the distribution of selection parameters, which can result in misleading inference due to model misspecification. We pre...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/molbev/mst030

    authors： Murrell B,Moola S,Mabona A,Weighill T,Sheward D,Kosakovsky Pond SL,Scheffler K

    更新日期：2013-05-01 00:00:00

  • Analysis of the overdispersed clock in the short-term evolution of hepatitis C virus: Using the E1/E2 gene sequences to infer infection dates in a single source outbreak.

    abstract：:The assumption of a molecular clock for dating events from sequence information is often frustrated by the presence of heterogeneity among evolutionary rates due, among other factors, to positively selected sites. In this work, our goal is to explore methods to estimate infection dates from sequence analysis. One such...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/molbev/msk012

    authors： Wróbel B,Torres-Puente M,Jiménez N,Bracho MA,García-Robles I,Moya A,González-Candelas F

    更新日期：2006-06-01 00:00:00

  • The shoot stem cell niche in angiosperms: expression patterns of WUS orthologues in rice and maize imply major modifications in the course of mono- and dicot evolution.

    abstract：:In Arabidopsis, stem cell homeostasis in the shoot apical meristem (SAM) is controlled by a feedback loop between WUS and CLV functions. We have identified WUS orthologues in maize and rice by a detailed phylogenetic analysis of the WOX gene family and subsequent cloning. A single WUS orthologue is present in the rice...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/molbev/msl125

    authors： Nardmann J,Werr W

    更新日期：2006-12-01 00:00:00

  • Molecular characteristics of diverse populations are consistent with the hypothesis of a recent invasion of Drosophila melanogaster by mobile P elements.

    abstract：:Approximately 100 strains derived from natural populations of Drosophila melanogaster were tested for the presence or absence of P-element sequences by using two molecular probes derived from internal regions of a full-sized P element. Strains that had been collected from several continents at varying times during the...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/oxfordjournals.molbev.a040491

    authors： Anxolabéhère D,Kidwell MG,Periquet G

    更新日期：1988-05-01 00:00:00

  • Interchromosomal exchange of genetic information between gene arrangements on the third chromosome of Drosophila pseudoobscura.

    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

    pub_type： 杂志文章

    doi：10.1093/oxfordjournals.molbev.a040271

    authors： Popadić A,Popadić D,Anderson WW

    更新日期：1995-09-01 00:00:00

  • Novel rearrangements of arthropod mitochondrial DNA detected with long-PCR: applications to arthropod phylogeny and evolution.

    abstract：:Rearrangements of mitochondrial DNA gene order have been suggested as a tool for defining the pattern of evolutionary divergence in arthropod taxa. We have employed a combination of highly conserved insect-based polymerase chain reaction (PCR) primers with long-PCR to survey 14 noninsect arthropods for mitochondrial g...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/oxfordjournals.molbev.a004141

    authors： Roehrdanz RL,Degrugillier ME,Black WC 4th

    更新日期：2002-06-01 00:00:00

  • Evolution of trypsinogen activation peptides.

    abstract：:The activation peptide of mammalian trypsinogens contains a highly conserved tetra-aspartate sequence (D19-D20-D21-D22) preceding the K23-I24 scissile peptide bond, which is hydrolyzed as the first step in the activation process. Here, we examined the evolution and function of trypsinogen activation peptides through i...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/molbev/msg183

    authors： Chen JM,Kukor Z,Le Maréchal C,Tóth M,Tsakiris L,Raguénès O,Férec C,Sahin-Tóth M

    更新日期：2003-11-01 00:00:00

  • Sequencing errors and molecular evolutionary analysis.

    abstract：:Heuristic approaches were used to quantify the influence that sequencing errors have on estimates of nucleotide diversity, substitution rate, and the construction of genealogies. Error rates of less than 1 nucleotide/kb probably have little affect on conclusions about the evolutionary history of highly polymorphic org...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/oxfordjournals.molbev.a040756

    authors： Clark AG,Whittam TS

    更新日期：1992-07-01 00:00:00

  • Molecular phylogeny, biogeography, and habitat preference evolution of marsupials.

    abstract：:Marsupials exhibit great diversity in ecology and morphology. However, compared with their sister group, the placental mammals, our understanding of many aspects of marsupial evolution remains limited. We use 101 mitochondrial genomes and data from 26 nuclear loci to reconstruct a dated phylogeny including 97% of exta...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/molbev/msu176

    authors： Mitchell KJ,Pratt RC,Watson LN,Gibb GC,Llamas B,Kasper M,Edson J,Hopwood B,Male D,Armstrong KN,Meyer M,Hofreiter M,Austin J,Donnellan SC,Lee MS,Phillips MJ,Cooper A

    更新日期：2014-09-01 00:00:00

  • Partitioning the variation in mammalian substitution rates.

    abstract：:We have used analysis of variance to partition the variation in synonymous and amino acid substitution rates between three effects (gene, lineage, and a gene-by-lineage interaction) in mammalian nuclear and mitochondrial genes. We find that gene effects are stronger for amino acid substitution rates than for synonymou...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/oxfordjournals.molbev.a004231

    authors： Smith NG,Eyre-Walker A

    更新日期：2003-01-01 00:00:00

  • 267 Spanish Exomes Reveal Population-Specific Differences in Disease-Related Genetic Variation.

    abstract：:Recent results from large-scale genomic projects suggest that allele frequencies, which are highly relevant for medical purposes, differ considerably across different populations. The need for a detailed catalog of local variability motivated the whole-exome sequencing of 267 unrelated individuals, representative of t...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/molbev/msw005

    authors： Dopazo J,Amadoz A,Bleda M,Garcia-Alonso L,Alemán A,García-García F,Rodriguez JA,Daub JT,Muntané G,Rueda A,Vela-Boza A,López-Domingo FJ,Florido JP,Arce P,Ruiz-Ferrer M,Méndez-Vidal C,Arnold TE,Spleiss O,Alvarez-Tejado

    更新日期：2016-05-01 00:00:00

  • Taxonomic congruence versus total evidence, and amniote phylogeny inferred from fossils, molecules, and morphology.

    abstract：:Taxonomic congruence and total evidence are competing paradigms in phylogenetic inference. Taxonomic congruence focuses on deriving a consensus from the results obtained from separately analyzed data sets, whereas total evidence uses character congruence in the search for the best-fitting hypothesis for all of the ava...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/oxfordjournals.molbev.a040071

    authors： Eernisse DJ,Kluge AG

    更新日期：1993-11-01 00:00:00

  • Nineteenth century seeds reveal the population genetics of landrace barley (Hordeum vulgare).

    abstract：:Barley (Hordeum vulgare) is a major crop, grown worldwide and in a wide range of climatic conditions. Despite its importance as a crop species, little is known about the population genetics of barley and the effects of bottlenecks, adaptation, and gene flow on genetic diversity within and between landrace populations....

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/molbev/msp308

    authors： Leino MW,Hagenblad J

    更新日期：2010-04-01 00:00:00

  • Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior.

    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

    pub_type： 杂志文章

    doi：10.1093/molbev/msh194

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

    更新日期：2004-09-01 00:00:00

  • The biochemical basis of life history adaptation: molecular and enzymological causes of NADP(+)-isocitrate dehydrogenase activity differences between morphs of Gryllus firmus that differ in lipid biosynthesis and life history.

    abstract：:Although whole-organism aspects of life-history physiology are well studied and molecular information (e.g., transcript abundance) on life-history variation is accumulating rapidly, much less information is available on the biochemical (enzymological) basis of life-history adaptation. The present study investigated th...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/molbev/msr171

    authors： Schilder RJ,Zera AJ,Black C,Hoidal M,Wehrkamp C

    更新日期：2011-12-01 00:00:00

  • Non-African populations of Drosophila melanogaster have a unique origin.

    abstract：:Drosophila melanogaster is widely used as a model in DNA variation studies. Patterns of polymorphism have, however, been affected by the history of this species, which is thought to have recently spread out of Africa to the rest of the world. We analyzed DNA sequence variation in 11 populations, including four contine...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/molbev/msh089

    authors： Baudry E,Viginier B,Veuille M

    更新日期：2004-08-01 00:00:00

  • Extensive Differential Splicing Underlies Phenotypically Plastic Aphid Morphs.

    abstract：:Phenotypic plasticity results in a diversity of phenotypes from a single genotype in response to environmental cues. To understand the molecular basis of phenotypic plasticity, studies have focused on differential gene expression levels between environmentally determined phenotypes. The extent of alternative splicing ...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/molbev/msy095

    authors： Grantham ME,Brisson JA

    更新日期：2018-08-01 00:00:00

  • Hyaloraphidium curvatum: a linear mitochondrial genome, tRNA editing, and an evolutionary link to lower fungi.

    abstract：:We have sequenced the mitochondrial DNA (mtDNA) of Hyaloraphidium curvatum, an organism previously classified as a colorless green alga but now recognized as a lower fungus based on molecular data. The 29.97-kbp mitochondrial chromosome is maintained as a monomeric, linear molecule with identical, inverted repeats (1....

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/oxfordjournals.molbev.a004084

    authors： Forget L,Ustinova J,Wang Z,Huss VA,Lang BF

    更新日期：2002-03-01 00:00:00

  • Multiple ribonuclease H-encoding genes in the Caenorhabditis elegans genome contrasts with the two typical ribonuclease H-encoding genes in the human genome.

    abstract：:Database searches of the Caenorhabditis elegans and human genomic DNA sequences revealed genes encoding ribonuclease H1 (RNase H1) and RNase H2 in each genome. The human genome contains a single copy of each gene, whereas C. elegans has four genes encoding RNase H1-related proteins and one gene for RNase H2. By analyz...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/oxfordjournals.molbev.a004015

    authors： Arudchandran A,Cerritelli SM,Bowen NJ,Chen X,Krause MW,Crouch RJ

    更新日期：2002-11-01 00:00:00

  • Divergence time of porcine reproductive and respiratory syndrome virus subtypes.

    abstract：:Porcine reproductive and respiratory syndrome virus (PRRSV) recently emerged in domestic pigs of Western Europe and North America. Although time of emergence was identical on the two continents, genetic composition was markedly different with a clear geographical subtype structure, indicating that subtypes diverged in...

    journal_title：Molecular biology and evolution

    pub_type： 评论,信件

    doi：10.1093/molbev/msi208

    authors： Forsberg R

    更新日期：2005-11-01 00:00:00

  • Neighboring genes show interchromosomal colocalization after their separation.

    abstract：:The order of genes on eukaryotic chromosomes is nonrandom. Some neighboring genes show order conservation among species, while some neighboring genes separate during evolution. Here, we investigated whether neighboring genes show interactions after their separation. We found that neighboring gene pairs tend to show in...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/molbev/msu065

    authors： Dai Z,Xiong Y,Dai X

    更新日期：2014-05-01 00:00:00

  • The problem of rooting rapid radiations.

    abstract：:There are many examples of groups (such as birds, bees, mammals, multicellular animals, and flowering plants) that have undergone a rapid radiation. In such cases, where there is a combination of short internal and long external branches, correctly estimating and rooting phylogenetic trees is known to be a difficult p...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/molbev/msm178

    authors： Shavit L,Penny D,Hendy MD,Holland BR

    更新日期：2007-11-01 00:00:00

  • Evolution of the Telomere-Associated Protein POT1a in Arabidopsis thaliana Is Characterized by Positive Selection to Reinforce Protein-Protein Interaction.

    abstract：:Gene duplication is a major driving force in genome evolution. Here, we explore the nature and origin of the POT1 gene duplication in Arabidopsis thaliana. Protection of Telomeres (POT1) is a conserved multifunctional protein that modulates telomerase activity and its engagement with telomeres. Arabidopsis thaliana en...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/molbev/msv025

    authors： Beilstein MA,Renfrew KB,Song X,Shakirov EV,Zanis MJ,Shippen DE

    更新日期：2015-05-01 00:00:00

  • Metabolic adaptation after whole genome duplication.

    abstract：:Whole genome duplications (WGDs) have been hypothesized to be responsible for major transitions in evolution. However, the effects of WGD and subsequent gene loss on cellular behavior and metabolism are still poorly understood. Here we develop a genome scale evolutionary model to study the dynamics of gene loss and me...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/molbev/msp160

    authors： van Hoek MJ,Hogeweg P

    更新日期：2009-11-01 00:00:00

  • Higher ribosomal RNA substitution rates in Bacillariophyceae and Dasycladales than in Mollusca, Echinodermata, and Actinistia-Tetrapoda.

    abstract：:Molecular evolutionary rates within two protistan and three metazoan taxa were estimated using divergence times derived from fossil records. The results indicate that the small-subunit rRNA sequences within Dasycladales (Chlorophyta) and Bacillariophyceae evolved at a rate approximately two to three times faster than ...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/oxfordjournals.molbev.a025653

    authors： Sorhannus U

    更新日期：1996-09-01 00:00:00

  • Lokiarchaeota Marks the Transition between the Archaeal and Eukaryotic Selenocysteine Encoding Systems.

    abstract：:Selenocysteine (Sec) is the 21st amino acid in the genetic code, inserted in response to UGA codons with the help of RNA structures, the SEC Insertion Sequence (SECIS) elements. The three domains of life feature distinct strategies for Sec insertion in proteins and its utilization. While bacteria and archaea possess s...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/molbev/msw122

    authors： Mariotti M,Lobanov AV,Manta B,Santesmasses D,Bofill A,Guigó R,Gabaldón T,Gladyshev VN

    更新日期：2016-09-01 00:00:00

  • Complete mtDNA sequence of the North American freshwater mussel, Lampsilis ornata (Unionidae): an examination of the evolution and phylogenetic utility of mitochondrial genome organization in Bivalvia (Mollusca).

    abstract：:Molluscs in general, and bivalves in particular, exhibit an extraordinary degree of mitochondrial gene order variation when compared with other metazoans. Two factors inhibiting our understanding the evolution of gene rearrangement in bivalves are inadequate taxonomic sampling and failure to examine gene order in a ph...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/molbev/msg218

    authors： Serb JM,Lydeard C

    更新日期：2003-11-01 00:00:00

  • Tracing the Archaeal Origins of Eukaryotic Membrane-Trafficking System Building Blocks.

    abstract：:In contrast to prokaryotes, eukaryotic cells are characterized by a complex set of internal membrane-bound compartments. A subset of these, and the protein machineries that move material between them, define the membrane-trafficking system (MTS), the emergence of which represents a landmark in eukaryotic evolution. Un...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/molbev/msw034

    authors： Klinger CM,Spang A,Dacks JB,Ettema TJ

    更新日期：2016-06-01 00:00:00