Abstract:
:DNA cytosine methylation is central to many biological processes, including regulation of gene expression, cellular differentiation, and development. This DNA modification is conserved across animals, having been found in representatives of sponges, ctenophores, cnidarians, and bilaterians, and with very few known instances of secondary loss in animals. Myxozoans are a group of microscopic, obligate endoparasitic cnidarians that have lost many genes over the course of their evolution from free-living ancestors. Here, we investigated the evolution of the key enzymes involved in DNA cytosine methylation in 29 cnidarians and found that these enzymes were lost in an ancestor of Myxosporea (the most speciose class of Myxozoa). Additionally, using whole-genome bisulfite sequencing, we confirmed that the genomes of two distant species of myxosporeans, Ceratonova shasta and Henneguya salminicola, completely lack DNA cytosine methylation. Our results add a notable and novel taxonomic group, the Myxosporea, to the very short list of animal taxa lacking DNA cytosine methylation, further illuminating the complex evolutionary history of this epigenetic regulatory mechanism.
journal_name
Mol Biol Evoljournal_title
Molecular biology and evolutionauthors
Kyger R,Luzuriaga-Neira A,Layman T,Milkewitz Sandberg TO,Singh D,Huchon D,Peri S,Atkinson SD,Bartholomew JL,Yi SV,Alvarez-Ponce Ddoi
10.1093/molbev/msaa214subject
Has Abstractpub_date
2021-01-23 00:00:00pages
393-404issue
2eissn
0737-4038issn
1537-1719pii
5902833journal_volume
38pub_type
杂志文章abstract::We investigated diverse genomic selections using high-density single nucleotide polymorphism data of five distinct cattle breeds. Based on allele frequency differences, we detected hundreds of candidate regions under positive selection across Holstein, Angus, Charolais, Brahman, and N'Dama. In addition to well-known g...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msu333
更新日期:2015-03-01 00:00:00
abstract::Interbreeding between hatchery-reared and wild fish, through deliberate stocking or escapes from fish farms, can result in rapid phenotypic and gene expression changes in hybrids, but the underlying mechanisms are unknown. We assessed if one generation of captive breeding was sufficient to generate inter- and/or trans...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msz135
更新日期:2019-10-01 00:00:00
abstract::At present there is tremendous interest in characterizing the magnitude and distribution of linkage disequilibrium (LD) throughout the human genome, which will provide the necessary foundation for genome-wide LD analyses and facilitate detailed evolutionary studies. To this end, a human high-density single-nucleotide ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msg032
更新日期:2003-02-01 00:00:00
abstract::Partial 18S rRNA sequence of the nemertine Cerebratulus lacteus was obtained and compared with those of coelomate metazoans and acoelomate platyhelminths to test whether nemertines share a most recent common ancestor with the platyhelminths, as traditionally has been implied, or whether nemertines lie within a protost...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040716
更新日期:1992-03-01 00:00:00
abstract::The functionality of long noncoding RNAs (lncRNAs) is disputed. In general, lncRNAs are under weak selective pressures, suggesting that the majority of lncRNAs may be nonfunctional. However, although some surveys showed negligible phenotypic effects upon lncRNA perturbation, key biological roles were demonstrated for ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msz212
更新日期:2020-01-01 00:00:00
abstract::For populations to maintain optimal fitness, harmful mutations must be efficiently purged from the genome. Yet, under circumstances that diminish the effectiveness of natural selection, such as the process of plant and animal domestication, deleterious mutations are predicted to accumulate. Here, we compared the load ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msv106
更新日期:2015-09-01 00:00:00
abstract::The apparent stasis in the evolution of avian chromosomes suggests that birds may have experienced relatively low rates of gene gain and loss in multigene families. To investigate this possibility and to explore the phenotypic consequences of variation in gene copy number, we examined evolutionary changes in the famil...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msu341
更新日期:2015-04-01 00:00:00
abstract::Protein-protein interaction networks have evolved mainly through connectivity rewiring and gene duplication. However, how protein function influences these processes and how a network grows in time have not been well studied. Using protein-protein interaction data and genomic data from the budding yeast, we first exam...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msi249
更新日期:2006-01-01 00:00:00
abstract::The mitoribosome, as known from studies in model organisms, deviates considerably from its ancestor, the bacterial ribosome. Deviations include substantial reduction of the mitochondrial ribosomal RNA (mt-rRNA) structure and acquisition of numerous mitochondrion-specific (M) mitoribosomal proteins (mtRPs). A broadly a...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msaa223
更新日期:2020-09-04 00:00:00
abstract::Enzyme function is strongly affected by temperature, and orthologs from species adapted to different thermal environments often show temperature compensation in kinetic properties. Antarctic notothenioid fishes live in a habitat of constant, extreme cold (-1.86 +/- 2 degrees C), and orthologs of the enzyme A4-lactate ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msh237
更新日期:2004-12-01 00:00:00
abstract::Detecting selection on codon usage (CU) is a difficult task, since CU can be shaped by both the mutational process and selective constraints operating at the DNA, RNA, and protein levels. Yang and Nielsen (2008) developed a test (which we call CUYN) for detecting selection on CU using two competing mutation-selection ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msy047
更新日期:2018-06-01 00:00:00
abstract::The nuclear large subunit (LSU) rRNA gene is a rich source of phylogenetic characters because of its large size, mosaic of slowly and rapidly evolving regions, and complex secondary structure variation. Nevertheless, many studies have indicated that inconsistency, bias, and gene-specific error (e.g., within-individual...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a003767
更新日期:2001-12-01 00:00:00
abstract::The protein tyrosine phosphatase (PTP) family plays a central role in signal transduction pathways by controlling the phosphorylation state of serine, threonine, and tyrosine residues. PTPs can be divided into dual specificity phosphatases and the classical PTPs, which can comprise of one or two phosphatase domains. W...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msh055
更新日期:2004-04-01 00:00:00
abstract::During the course of a random sequencing project of the genome of the dimorphic yeast Yarrowia lipolytica, we have identified sequences that were repeated in the genome and that matched the reverse transcriptase (RT) sequence of non-long terminal repeat (non-LTR) retrotransposons. Extension of sequencing on each side ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a004125
更新日期:2002-05-01 00:00:00
abstract::Polytoma obtusum and Polytoma uvella are members of a clade of nonphotosynthetic chlorophyte algae closely related to Chlamydomonas humicola and other photosynthetic members of the Chlamydomonadaceae. Descended from a nonphotosynthetic mutant, these obligate heterotrophs retain a plastid (leucoplast) with a functional...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a003968
更新日期:2001-09-01 00:00:00
abstract::Sponges (Porifera) are among the simplest living and the earliest branching metazoans. They hold a pivotal role for studying genome evolution of the entire metazoan branch, both as an outgroup to Eumetazoa and as the closest branching phylum to the common ancestor of all multicellular animals (Urmetazoa). In order to ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq174
更新日期:2010-12-01 00:00:00
abstract::Recently, Lee et al. (Lee JH, Silhavy JL, Lee JE, et al. (30 co-authors). 2012. Evolutionarily assembled cis-regulatory module at a human ciliopathy locus. Science (335:966-969.) demonstrated that mutation in either of the transmembrane protein encoding genes, TMEM138 or TMEM216, causes phenotypically indistinguishabl...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mss215
更新日期:2013-01-01 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
pub_type: 杂志文章
doi:10.1093/molbev/msh194
更新日期:2004-09-01 00:00:00
abstract::This study examines molecular relationships across a wide range of species in the mass spawning scleractinian coral genus Acropora. Molecular phylogenies were obtained for 28 species using DNA sequence analyses of two independent markers, a nuclear intron and the mtDNA putative control region. Although the composition...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a003916
更新日期:2001-07-01 00:00:00
abstract::Homologues of glucosephosphate isomerase (GPI, EC 5.3.1.9) were purified to homogeneity and kinetically characterized from Mytilus edulis and Isognomon alatus, two bivalve molluscs experiencing contrasting thermal environments. The enzyme isolated from I. alatus functions at warmer temperatures (25-35 C) than GPI from...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040346
更新日期:1985-05-01 00:00:00
abstract::The organization of the mitochondrial genome is generally very conserved among vertebrates. Because of this, examination of the rare rearrangements which do occur has been suggested as offering a powerful alternative to phylogenetic analyses of mitochondrial DNA sequences. Here, we report on an avian mitochondrial rea...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026223
更新日期:2000-01-01 00:00:00
abstract::The plant pathogen Phytophthora infestans emerged in Europe in 1845, triggering the Irish potato famine and massive European potato crop losses that continued until effective fungicides were widely employed in the 20th century. Today the pathogen is ubiquitous, with more aggressive and virulent strains surfacing in re...
journal_title:Molecular biology and evolution
pub_type: 历史文章,信件
doi:10.1093/molbev/msu086
更新日期:2014-06-01 00:00:00
abstract::Until recently, phylogenetic analyses have been routinely based on homologous sequences of a single gene. Given the vast number of gene sequences now available, phylogenetic studies are now based on the analysis of multiple genes. Thus, it has become necessary to devise statistical methods to combine multiple molecula...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a004053
更新日期:2002-12-01 00:00:00
abstract::The T1 family of retrotransposable elements is interspersed and moderately repeated in five member species of the Anopheles gambiae sibling-species complex and has diverged little since the radiation of the complex. T1 includes two closely related but independent subfamilies, defined by the presence or absence of link...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040599
更新日期:1990-05-01 00:00:00
abstract::We describe a stochastic birth-and-death model of evolution of horizontally transferred genes in microbial populations. The model is a generalization of the stochastic model described by Berg and Kurland and includes five parameters: the rate of mutational inactivation, selection coefficient, invasion rate (i.e., rate...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msi167
更新日期:2005-08-01 00:00:00
abstract::Based on previous observations that newly inserted LINEs and SINEs have particularly long 3' A-tails, which shorten rapidly during evolutionary time, we have analyzed the rat and mouse genomes for evidence of recently inserted SINEs and LINEs. We find that the youngest predicted subfamilies of rodent identifier (ID) e...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msh225
更新日期:2004-11-01 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
pub_type: 杂志文章
doi:10.1093/molbev/msp120
更新日期:2009-09-01 00:00:00
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
更新日期:2007-11-01 00:00:00
abstract::Most phenotypic traits are controlled by many genes, but a global picture of the genotype-phenotype map (GPM) is lacking. For example, in no species do we know generally how many genes affect a trait and how large these effects are. It is also unclear to what extent GPMs are shaped by natural selection. Here we addres...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msu131
更新日期:2014-06-01 00:00:00
abstract::Knowledge of mutation rates is crucial for calibrating population genetics models of demographic history in units of years. However, mutation rates remain challenging to estimate because of the need to identify extremely rare events. We estimated the nuclear mutation rate in wolves by identifying de novo mutations in ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msz159
更新日期:2019-07-12 00:00:00