Parallel evolution of nacre building gene sets in molluscs.

Abstract:

:The capacity to biomineralize is closely linked to the rapid expansion of animal life during the early Cambrian, with many skeletonized phyla first appearing in the fossil record at this time. The appearance of disparate molluscan forms during this period leaves open the possibility that shells evolved independently and in parallel in at least some groups. To test this proposition and gain insight into the evolution of structural genes that contribute to shell fabrication, we compared genes expressed in nacre (mother-of-pearl) forming cells in the mantle of the bivalve Pinctada maxima and the gastropod Haliotis asinina. Despite both species having highly lustrous nacre, we find extensive differences in these expressed gene sets. Following the removal of housekeeping genes, less than 10% of all gene clusters are shared between these molluscs, with some being conserved biomineralization genes that are also found in deuterostomes. These differences extend to secreted proteins that may localize to the organic shell matrix, with less than 15% of this secretome being shared. Despite these differences, H. asinina and P. maxima both secrete proteins with repetitive low-complexity domains (RLCDs). Pinctada maxima RLCD proteins-for example, the shematrins-are predominated by silk/fibroin-like domains, which are absent from the H. asinina data set. Comparisons of shematrin genes across three species of Pinctada indicate that this gene family has undergone extensive divergent evolution within pearl oysters. We also detect fundamental bivalve-gastropod differences in extracellular matrix proteins involved in mollusc-shell formation. Pinctada maxima expresses a chitin synthase at high levels and several chitin deacetylation genes, whereas only one protein involved in chitin interactions is present in the H. asinina data set, suggesting that the organic matrix on which calcification proceeds differs fundamentally between these species. Large-scale differences in genes expressed in nacre-forming cells of Pinctada and Haliotis are compatible with the hypothesis that gastropod and bivalve nacre is the result of convergent evolution. The expression of novel biomineralizing RLCD proteins in each of these two molluscs and, interestingly, sea urchins suggests that the evolution of such structural proteins has occurred independently multiple times in the Metazoa.

journal_name

Mol Biol Evol

authors

Jackson DJ,McDougall C,Woodcroft B,Moase P,Rose RA,Kube M,Reinhardt R,Rokhsar DS,Montagnani C,Joubert C,Piquemal D,Degnan BM

doi

10.1093/molbev/msp278

subject

Has Abstract

pub_date

2010-03-01 00:00:00

pages

591-608

issue

3

eissn

0737-4038

issn

1537-1719

pii

msp278

journal_volume

27

pub_type

杂志文章
  • HLA Heterozygote Advantage against HIV-1 Is Driven by Quantitative and Qualitative Differences in HLA Allele-Specific Peptide Presentation.

    abstract::Pathogen-mediated balancing selection is regarded as a key driver of host immunogenetic diversity. A hallmark for balancing selection in humans is the heterozygote advantage at genes of the human leukocyte antigen (HLA), resulting in improved HIV-1 control. However, the actual mechanism of the observed heterozygote ad...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msz249

    authors: Arora J,Pierini F,McLaren PJ,Carrington M,Fellay J,Lenz TL

    更新日期:2020-03-01 00:00:00

  • Rare variation facilitates inferences of fine-scale population structure in humans.

    abstract::Understanding the genetic structure of human populations has important implications for the design and interpretation of disease mapping studies and reconstructing human evolutionary history. To date, inferences of human population structure have primarily been made with common variants. However, recent large-scale re...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msu326

    authors: O'Connor TD,Fu W,NHLBI GO Exome Sequencing Project.,ESP Population Genetics and Statistical Analysis Working Group, Emily Turner.,Mychaleckyj JC,Logsdon B,Auer P,Carlson CS,Leal SM,Smith JD,Rieder MJ,Bamshad MJ,Nickerson DA,Ake

    更新日期:2015-03-01 00:00:00

  • Bidirectional genetic control of phenotypic heterogeneity and its implication for cancer drug resistance.

    abstract::Negative genetic regulators of phenotypic heterogeneity, or phenotypic capacitors/stabilizers, elevate population-average fitness by limiting deviation from the optimal phenotype and increase the efficacy of natural selection by enhancing the phenotypic differences among genotypes. Stabilizers can presumably be switch...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msaa332

    authors: Mo N,Zhang X,Shi W,Yu G,Chen X,Yang JR

    更新日期:2020-12-23 00:00:00

  • DNA sequence variation in the mitochondrial control region of red-backed voles (Clethrionomys).

    abstract::The complete mitochondrial DNA (mtDNA) control region was sequenced for 71 individuals from five species of the rodent genus Clethrionomys both to understand patterns of variation and to explore the existence of previously described domains and other elements. Among species, the control region ranged from 942 to 971 b...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.molbev.a003935

    authors: Matson CW,Baker RJ

    更新日期:2001-08-01 00:00:00

  • Alu monomer revisited: recent generation of Alu monomers.

    abstract::Alu is a predominant short interspersed element (SINE) family in the human genome and consists of two monomer units connected by an A-rich linker. At present, dimeric Alu elements are active in humans, but Alu monomers are present as fossilized sequences. A comparative genome analysis of human and chimpanzee genomes r...

    journal_title:Molecular biology and evolution

    pub_type: 信件

    doi:10.1093/molbev/msq218

    authors: Kojima KK

    更新日期:2011-01-01 00:00:00

  • Phylogenomic analysis supports the monophyly of cryptophytes and haptophytes and the association of rhizaria with chromalveolates.

    abstract::Here we use phylogenomics with expressed sequence tag (EST) data from the ecologically important coccolithophore-forming alga Emiliania huxleyi and the plastid-lacking cryptophyte Goniomonas cf. pacifica to establish their phylogenetic positions in the eukaryotic tree. Haptophytes and cryptophytes are members of the p...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msm089

    authors: Hackett JD,Yoon HS,Li S,Reyes-Prieto A,Rümmele SE,Bhattacharya D

    更新日期:2007-08-01 00:00:00

  • Probabilities of Unranked and Ranked Anomaly Zones under Birth-Death Models.

    abstract::A labeled gene tree topology that is more probable than the labeled gene tree topology matching a species tree is called "anomalous." Species trees that can generate such anomalous gene trees are said to be in the "anomaly zone." Here, probabilities of "unranked" and "ranked" gene tree topologies under the multispecie...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msz305

    authors: Kim A,Rosenberg NA,Degnan JH

    更新日期:2020-05-01 00:00:00

  • The Influence of Polyploidy on the Evolution of Yeast Grown in a Sub-Optimal Carbon Source.

    abstract::Polyploidization events have occurred during the evolution of many fungi, plant, and animal species and are thought to contribute to speciation and tumorigenesis, however little is known about how ploidy level contributes to adaptation at the molecular level. Here we integrate whole genome sequencing, RNA expression a...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msx205

    authors: Scott AL,Richmond PA,Dowell RD,Selmecki AM

    更新日期:2017-10-01 00:00:00

  • Comparisons of the molecular evolutionary process at rbcL and ndhF in the grass family (Poaceae).

    abstract::We examine rate heterogeneity among evolutionary lineages of the grass family at two plasmid loci, ndhF and rbcL, and we introduce a method to determine whether patterns of rate heterogeneity are correlated between loci. We show both that rates of synonymous evolution are heterogeneous among grass lineages and that ar...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.molbev.a025817

    authors: Gaut BS,Clark LG,Wendel JF,Muse SV

    更新日期:1997-07-01 00:00:00

  • A graphical method for detecting recombination in phylogenetic data sets.

    abstract::Current phylogenetic tree reconstruction methods assume that there is a single underlying tree topology for all sites along the sequence. The presence of mosaic sequences due to recombination violates this assumption and will cause phylogenetic methods to give misleading results due to the imposition of a single tree ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.molbev.a025722

    authors: McGuire G,Wright F,Prentice MJ

    更新日期:1997-11-01 00:00:00

  • Evolution of paralogous genes: Reconstruction of genome rearrangements through comparison of multiple genomes within Staphylococcus aureus.

    abstract::Analysis of evolution of paralogous genes in a genome is central to our understanding of genome evolution. Comparison of closely related bacterial genomes, which has provided clues as to how genome sequences evolve under natural conditions, would help in such an analysis. With species Staphylococcus aureus, whole-geno...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msk013

    authors: Tsuru T,Kawai M,Mizutani-Ui Y,Uchiyama I,Kobayashi I

    更新日期:2006-06-01 00:00:00

  • Origin and Evolution of Water Oxidation before the Last Common Ancestor of the Cyanobacteria.

    abstract::Photosystem II, the water oxidizing enzyme, altered the course of evolution by filling the atmosphere with oxygen. Here, we reconstruct the origin and evolution of water oxidation at an unprecedented level of detail by studying the phylogeny of all D1 subunits, the main protein coordinating the water oxidizing cluster...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msv024

    authors: Cardona T,Murray JW,Rutherford AW

    更新日期:2015-05-01 00:00:00

  • Complex evolution of light-dependent protochlorophyllide oxidoreductases in aerobic anoxygenic phototrophs: origin, phylogeny and function.

    abstract::Light-dependent and dark-operative protochlorophyllide oxidoreductases (LPORs and DPORs) are evolutionary and structurally distinct enzymes that are essential for the synthesis of (bacterio)chlorophyll, the primary pigment needed for both anoxygenic and oxygenic photosynthesis. In contrast to the long-held hypothesis ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msaa234

    authors: Chernomor O,Peters L,Schneidewind J,Loeschcke A,Knieps-Grünhagen E,Schmitz F,von Lieres E,Kutta RJ,Svensson V,Jaeger KE,Drepper T,von Haeseler A,Krauss U

    更新日期:2020-09-15 00:00:00

  • Population structure in the American oyster as inferred by nuclear gene genealogies.

    abstract::Multiple haplotypes from each of three nuclear loci were isolated and sequenced from geographic populations of the American oyster, Crassostrea virginica. In tests of alternative phylogeographic hypotheses for this species, nuclear gene genealogies constructed for these haplotypes were compared to one another, to a mi...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.molbev.a025908

    authors: Hare MP,Avise JC

    更新日期:1998-02-01 00:00:00

  • The phylogenetic position of Rhopalura ophiocomae (Orthonectida) based on 18S ribosomal DNA sequence analysis.

    abstract::The Orthonectida is a small, poorly known phylum of parasites of marine invertebrates. Their phylogenetic placement is obscure; they have been considered to be multicellular protozoans, primitive animals at a "mesozoan" grade of organization, or secondarily simplified flatworm-like organisms. The best known species in...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.molbev.a025683

    authors: Hanelt B,Van Schyndel D,Adema CM,Lewis LA,Loker ES

    更新日期:1996-11-01 00:00:00

  • "Patchy-tachy" leads to false positives for recombination.

    abstract::Indirect tests have detected recombination in mitochondrial DNA (mtDNA) from many animal lineages, including mammals. However, it is possible that features of the molecular evolutionary process without recombination could be incorrectly inferred by indirect tests as being due to recombination. We have identified one s...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msr076

    authors: Sun S,Evans BJ,Golding GB

    更新日期:2011-09-01 00:00:00

  • Evolution of primate ABO blood group genes and their homologous genes.

    abstract::There are three common alleles (A, B, and O) at the human ABO blood group locus. We compared nucleotide sequences of these alleles, and relatively large numbers of nucleotide differences were found among them. These differences correspond to the divergence time of at least a few million years, which is unusually large...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.molbev.a025776

    authors: Saitou N,Yamamoto F

    更新日期:1997-04-01 00:00:00

  • From DNA to fitness differences: sequences and structures of adaptive variants of Colias phosphoglucose isomerase (PGI).

    abstract::Colias eurytheme butterflies display extensive allozyme polymorphism in the enzyme phosphoglucose isomerase (PGI). Earlier studies on biochemical and fitness effects of these genotypes found evidence of strong natural selection maintaining this polymorphism in the wild. Here we analyze the molecular features of this p...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msj062

    authors: Wheat CW,Watt WB,Pollock DD,Schulte PM

    更新日期:2006-03-01 00:00:00

  • Homologs of mitochondrial transcription factor B, sparsely distributed within the eukaryotic radiation, are likely derived from the dimethyladenosine methyltransferase of the mitochondrial endosymbiont.

    abstract::Mitochondrial transcription factor B (mtTFB), an essential component in regulating the expression of mitochondrial DNA-encoded genes in both yeast and humans, is a dimethyladenosine methyltransferase (DMT) that has acquired a secondary role in mitochondrial transcription. So far, mtTFB has only been well studied in Op...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msk001

    authors: Shutt TE,Gray MW

    更新日期:2006-06-01 00:00:00

  • Molecular evolution of the ligands of the insulin-signaling pathway: dilp genes in the genus Drosophila.

    abstract::Drosophila melanogaster, unlike mammals, has seven insulin-like peptides (DILPS). In Drosophila, all seven genes (dilp1-7) are single copy in the 12 species studied, except for D. grimshawi with two tandem copies of dilp2. Our comparative analysis revealed that genes dilp1-dilp7 exhibit differential functional constra...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msq353

    authors: Guirao-Rico S,Aguadé M

    更新日期:2011-05-01 00:00:00

  • Alu and LINE1 distributions in the human chromosomes: evidence of global genomic organization expressed in the form of power laws.

    abstract::Spatial distribution and clustering of repetitive elements are extensively studied during the last years, as well as their colocalization with other genomic components. Here we investigate the large-scale features of Alu and LINE1 spatial arrangement in the human genome by studying the size distribution of interrepeat...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msm181

    authors: Sellis D,Provata A,Almirantis Y

    更新日期:2007-11-01 00:00:00

  • A Highly Specific Genome-Wide Association Study Integrated with Transcriptome Data Reveals the Contribution of Copy Number Variations to Specialized Metabolites in Arabidopsis thaliana Accessions.

    abstract::Lineage-specific gene duplications contribute to a large variation in specialized metabolites among different plant species. There is also considerable variability in the specialized metabolites within a single plant species. However, it is unclear whether copy number variations (CNVs) derived from gene duplication ev...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msx234

    authors: Shirai K,Matsuda F,Nakabayashi R,Okamoto M,Tanaka M,Fujimoto A,Shimizu M,Shinozaki K,Seki M,Saito K,Hanada K

    更新日期:2017-12-01 00:00:00

  • Evolution of immunoglobulin VH pseudogenes in chickens.

    abstract::In chickens, there is a single functional gene (VH1) coding for the heavy chain variable region of immunoglobulins, and immunoglobulin diversity is generated by gene conversion of the VH1 gene by many variable region pseudogenes (psi VH's) that exist on the 5' side of the VH1 gene. To understand the evolution of this ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.molbev.a040194

    authors: Ota T,Nei M

    更新日期:1995-01-01 00:00:00

  • Asymmetric evolution in two fish-specifically duplicated receptor tyrosine kinase paralogons involved in teleost coloration.

    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

    pub_type: 杂志文章

    doi:10.1093/molbev/msk003

    authors: Braasch I,Salzburger W,Meyer A

    更新日期:2006-06-01 00:00:00

  • Visualizing and assessing phylogenetic congruence of core gene sets: a case study of the gamma-proteobacteria.

    abstract::Here, we address a much-debated topic: is there or is there not an organismal tree of gamma-proteobacteria that can be unambiguously inferred from a core of shared genes? We apply several recently developed analytical methods to this problem, for the first time. Our heat map analyses of P values and of bootstrap bipar...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msj113

    authors: Susko E,Leigh J,Doolittle WF,Bapteste E

    更新日期:2006-05-01 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

  • Sequenceserver: A Modern Graphical User Interface for Custom BLAST Databases.

    abstract::Comparing newly obtained and previously known nucleotide and amino-acid sequences underpins modern biological research. BLAST is a well-established tool for such comparisons but is challenging to use on new data sets. We combined a user-centric design philosophy with sustainable software development approaches to crea...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msz185

    authors: Priyam A,Woodcroft BJ,Rai V,Moghul I,Munagala A,Ter F,Chowdhary H,Pieniak I,Maynard LJ,Gibbins MA,Moon H,Davis-Richardson A,Uludag M,Watson-Haigh NS,Challis R,Nakamura H,Favreau E,Gómez EA,Pluskal T,Leonard G,Rump

    更新日期:2019-12-01 00:00:00

  • Functional compensation of primary and secondary metabolites by duplicate genes in Arabidopsis thaliana.

    abstract::It is well known that knocking out a gene in an organism often causes no phenotypic effect. One possible explanation is the existence of duplicate genes; that is, the effect of knocking out a gene is compensated by a duplicate copy. Another explanation is the existence of alternative pathways. In terms of metabolic pr...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msq204

    authors: Hanada K,Sawada Y,Kuromori T,Klausnitzer R,Saito K,Toyoda T,Shinozaki K,Li WH,Hirai MY

    更新日期:2011-01-01 00:00:00

  • Evolutionary origins of human herpes simplex viruses 1 and 2.

    abstract::Herpesviruses have been infecting and codiverging with their vertebrate hosts for hundreds of millions of years. The primate simplex viruses exemplify this pattern of virus-host codivergence, at a minimum, as far back as the most recent common ancestor of New World monkeys, Old World monkeys, and apes. Humans are the ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msu185

    authors: Wertheim JO,Smith MD,Smith DM,Scheffler K,Kosakovsky Pond SL

    更新日期:2014-09-01 00:00:00

  • CCA Addition gone wild: Unusual Occurrence and Phylogeny of four different tRNA Nucleotidyltransferases in Acanthamoeba castellanii.

    abstract::tRNAs are important players in the protein synthesis machinery, where they act as adapter molecules for translating the mRNA codons into the corresponding amino acid sequence. In a series of highly conserved maturation steps, the primary transcripts are converted into mature tRNAs. In the amoebozoan Acanthamoeba caste...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msaa270

    authors: Erber L,Betat H,Mörl M

    更新日期:2020-10-23 00:00:00