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1.
Genome Biol Evol ; 16(5)2024 05 02.
Article in English | MEDLINE | ID: mdl-38776329

ABSTRACT

We have sequenced, assembled, and analyzed the nuclear and mitochondrial genomes and transcriptomes of Potamopyrgus estuarinus and Potamopyrgus kaitunuparaoa, two prosobranch snail species native to New Zealand that together span the continuum from estuary to freshwater. These two species are the closest known relatives of the freshwater species Potamopyrgus antipodarum-a model for studying the evolution of sex, host-parasite coevolution, and biological invasiveness-and thus provide key evolutionary context for understanding its unusual biology. The P. estuarinus and P. kaitunuparaoa genomes are very similar in size and overall gene content. Comparative analyses of genome content indicate that these two species harbor a near-identical set of genes involved in meiosis and sperm functions, including seven genes with meiosis-specific functions. These results are consistent with obligate sexual reproduction in these two species and provide a framework for future analyses of P. antipodarum-a species comprising both obligately sexual and obligately asexual lineages, each separately derived from a sexual ancestor. Genome-wide multigene phylogenetic analyses indicate that P. kaitunuparaoa is likely the closest relative to P. antipodarum. We nevertheless show that there has been considerable introgression between P. estuarinus and P. kaitunuparaoa. That introgression does not extend to the mitochondrial genome, which appears to serve as a barrier to hybridization between P. estuarinus and P. kaitunuparaoa. Nuclear-encoded genes whose products function in joint mitochondrial-nuclear enzyme complexes exhibit similar patterns of nonintrogression, indicating that incompatibilities between the mitochondrial and the nuclear genome may have prevented more extensive gene flow between these two species.


Subject(s)
Phylogeny , Snails , Animals , Snails/genetics , New Zealand , Genetic Introgression , Evolution, Molecular , Genome, Mitochondrial , Genome
2.
Mol Biol Evol ; 40(1)2023 01 04.
Article in English | MEDLINE | ID: mdl-36625177

ABSTRACT

Recent advances in long-read sequencing technology have allowed for single-molecule sequencing of entire mitochondrial genomes, opening the door for direct investigation of the mitochondrial genome architecture and recombination. We used PacBio sequencing to reassemble mitochondrial genomes from two species of New Zealand freshwater snails, Potamopyrgus antipodarum and Potamopyrgus estuarinus. These assemblies revealed a ∼1.7 kb structure within the mitochondrial genomes of both species that was previously undetected by an assembly of short reads and likely corresponding to a large noncoding region commonly present in the mitochondrial genomes. The overall architecture of these Potamopyrgus mitochondrial genomes is reminiscent of the chloroplast genomes of land plants, harboring a large single-copy (LSC) region and a small single-copy (SSC) region separated by a pair of inverted repeats (IRa and IRb). Individual sequencing reads that spanned across the Potamopyrgus IRa-SSC-IRb structure revealed the occurrence of a "flip-flop" recombination. We also detected evidence for two distinct IR haplotypes and recombination between them in wild-caught P. estuarinus, as well as extensive intermolecular recombination between single-nucleotide polymorphisms in the LSC region. The chloroplast-like architecture and repeat-mediated mitochondrial recombination we describe here raise fundamental questions regarding the origins and commonness of inverted repeats in cytoplasmic genomes and their role in mitochondrial genome evolution.


Subject(s)
Genome, Chloroplast , Genome, Mitochondrial , Animals , Sequence Analysis, DNA , Recombination, Genetic , Chloroplasts , Phylogeny
3.
Mol Biol Evol ; 38(9): 3581-3592, 2021 08 23.
Article in English | MEDLINE | ID: mdl-33885820

ABSTRACT

How does asexual reproduction influence genome evolution? Although is it clear that genomic structural variation is common and important in natural populations, we know very little about how one of the most fundamental of eukaryotic traits-mode of genomic inheritance-influences genome structure. We address this question with the New Zealand freshwater snail Potamopyrgus antipodarum, which features multiple separately derived obligately asexual lineages that coexist and compete with otherwise similar sexual lineages. We used whole-genome sequencing reads from a diverse set of sexual and asexual individuals to analyze genomic abundance of a critically important gene family, rDNA (the genes encoding rRNAs), that is notable for dynamic and variable copy number. Our genomic survey of rDNA in P. antipodarum revealed two striking results. First, the core histone and 5S rRNA genes occur between tandem copies of the 18S-5.8S-28S gene cluster, a unique architecture for these crucial gene families. Second, asexual P. antipodarum harbor dramatically more rDNA-histone copies than sexuals, which we validated through molecular and cytogenetic analysis. The repeated expansion of this genomic region in asexual P. antipodarum lineages following distinct transitions to asexuality represents a dramatic genome structural change associated with asexual reproduction-with potential functional consequences related to the loss of sexual reproduction.


Subject(s)
Genome , Histones , Animals , Genomics , Histones/genetics , Humans , Reproduction, Asexual/genetics , Snails/genetics
4.
J Evol Biol ; 2020 Apr 17.
Article in English | MEDLINE | ID: mdl-32304112

ABSTRACT

How changes in selective regimes affect trait evolution is an important open biological question. We take advantage of naturally occurring and repeated transitions from sexual to asexual reproduction in a New Zealand freshwater snail species, Potamopyrgus antipodarum, to address how evolution in an asexual context-including the potential for relaxed selection on male-specific traits-influences sperm morphology. The occasional production of male offspring by the otherwise all-female asexual P. antipodarum lineages affords a unique and powerful opportunity to assess the fate of sperm traits in a context where males are exceedingly rare. These comparisons revealed that the sperm produced by 'asexual' males are markedly distinct from sexual counterparts. We also found that the asexual male sperm harboured markedly higher phenotypic variation and was much more likely to be morphologically abnormal. Together, these data suggest that transitions to asexual reproduction might be irreversible, at least in part because male function is likely to be compromised. These results are also consistent with a scenario where relaxed selection and/or mutation accumulation in the absence of sex translates into rapid trait degeneration.

5.
J Endod ; 46(3): 391-396, 2020 Mar.
Article in English | MEDLINE | ID: mdl-32029265

ABSTRACT

INTRODUCTION: Information is scarce regarding current usage practices of nickel-titanium (NiTi) engine-driven instruments in clinical practice. Therefore, the specific purpose of this survey was to assess trends among endodontists regarding the use and reuse of NiTi instruments. METHODS: A 16-question survey was sent by e-mail to about 4000 active members of the American Association of Endodontists. Data were collected over a 6-month period and compared using chi-square tests. RESULTS: A total of 957 surveys were collected (response rate = 23%). Of the respondents, 40.2% worked in solo practices; among them, there were significantly fewer recent graduates (<10 years) compared with those who graduated more than 10 years ago. Furthermore, 41.7% were in a group practice, 4.3% in corporate practice, 10.7% in university settings, and 3% in the military. Overall, 98.3% of respondents reported using NiTi instruments. Respondents who graduated less than 25 years ago use NiTi instruments significantly more (99%) than those who graduated more than 25 years ago (92.6%). Although 22.9% of respondents buy presterilized instruments, 41.6% sterilize them before use, and 35.5% do not sterilize new instruments before use; dental officers in the military reported that they use sterile new instruments in 100% of cases. NiTi instruments were reused by 74% of respondents. The 2 largest segments of the specialist endodontic instrument market belonged to Dentsply (York, PA; 56.9%) and EdgeEndo (Albuquerque, NM; 28.8%). CONCLUSIONS: There are significant differences in the use of NiTi instruments among types of practice and years since graduation. There were noticeable changes compared with findings reported about 10 years ago.


Subject(s)
Dental Alloys , Dental Instruments , Endodontists , Equipment Design , Humans , Nickel , Practice Patterns, Dentists' , Root Canal Preparation , Surveys and Questionnaires , Titanium , United States
6.
Genome Biol Evol ; 11(10): 2767-2773, 2019 10 01.
Article in English | MEDLINE | ID: mdl-31553440

ABSTRACT

Parasitoid wasps are among the most speciose animals, yet have relatively few available genomic resources. We report a draft genome assembly of the wasp Diachasma alloeum (Hymenoptera: Braconidae), a host-specific parasitoid of the apple maggot fly Rhagoletis pomonella (Diptera: Tephritidae), and a developing model for understanding how ecological speciation can "cascade" across trophic levels. Identification of gene content confirmed the overall quality of the draft genome, and we manually annotated ∼400 genes as part of this study, including those involved in oxidative phosphorylation, chemosensation, and reproduction. Through comparisons to model hymenopterans such as the European honeybee Apis mellifera and parasitoid wasp Nasonia vitripennis, as well as a more closely related braconid parasitoid Microplitis demolitor, we identified a proliferation of transposable elements in the genome, an expansion of chemosensory genes in parasitoid wasps, and the maintenance of several key genes with known roles in sexual reproduction and sex determination. The D. alloeum genome will provide a valuable resource for comparative genomics studies in Hymenoptera as well as specific investigations into the genomic changes associated with ecological speciation and transitions to asexuality.


Subject(s)
Genome, Insect , Wasps/genetics , Animals , Female , Genes, Insect , Genetic Speciation , Hymenoptera/genetics , Male , Models, Biological , Reproduction, Asexual/genetics , Sex Determination Processes
7.
BMC Genomics ; 20(1): 605, 2019 Jul 23.
Article in English | MEDLINE | ID: mdl-31337355

ABSTRACT

BACKGROUND: Lichens, encompassing 20,000 known species, are symbioses between specialized fungi (mycobionts), mostly ascomycetes, and unicellular green algae or cyanobacteria (photobionts). Here we describe the first parallel genomic analysis of the mycobiont Cladonia grayi and of its green algal photobiont Asterochloris glomerata. We focus on genes/predicted proteins of potential symbiotic significance, sought by surveying proteins differentially activated during early stages of mycobiont and photobiont interaction in coculture, expanded or contracted protein families, and proteins with differential rates of evolution. RESULTS: A) In coculture, the fungus upregulated small secreted proteins, membrane transport proteins, signal transduction components, extracellular hydrolases and, notably, a ribitol transporter and an ammonium transporter, and the alga activated DNA metabolism, signal transduction, and expression of flagellar components. B) Expanded fungal protein families include heterokaryon incompatibility proteins, polyketide synthases, and a unique set of G-protein α subunit paralogs. Expanded algal protein families include carbohydrate active enzymes and a specific subclass of cytoplasmic carbonic anhydrases. The alga also appears to have acquired by horizontal gene transfer from prokaryotes novel archaeal ATPases and Desiccation-Related Proteins. Expanded in both symbionts are signal transduction components, ankyrin domain proteins and transcription factors involved in chromatin remodeling and stress responses. The fungal transportome is contracted, as are algal nitrate assimilation genes. C) In the mycobiont, slow-evolving proteins were enriched for components involved in protein translation, translocation and sorting. CONCLUSIONS: The surveyed genes affect stress resistance, signaling, genome reprogramming, nutritional and structural interactions. The alga carries many genes likely transferred horizontally through viruses, yet we found no evidence of inter-symbiont gene transfer. The presence in the photobiont of meiosis-specific genes supports the notion that sexual reproduction occurs in Asterochloris while they are free-living, a phenomenon with implications for the adaptability of lichens and the persistent autonomy of the symbionts. The diversity of the genes affecting the symbiosis suggests that lichens evolved by accretion of many scattered regulatory and structural changes rather than through introduction of a few key innovations. This predicts that paths to lichenization were variable in different phyla, which is consistent with the emerging consensus that ascolichens could have had a few independent origins.


Subject(s)
Ascomycota/genetics , Chlorophyta/genetics , Lichens/genetics , Symbiosis/genetics , Gene Transfer, Horizontal , Genome, Fungal
8.
Curr Opin Insect Sci ; 31: 77-83, 2019 02.
Article in English | MEDLINE | ID: mdl-31109677

ABSTRACT

Boasting a staggering diversity of reproductive strategies, insects provide attractive models for the comparative study of the causes and consequences of transitions to asexuality. We provide an overview of some contemporary studies of reproductive systems in insects and compile an initial database of asexual insect genome resources. Insect systems have already yielded some important insights into various mechanisms by which sex is lost, including genetic, endosymbiont-mediated, and hybridization. Studies of mutation and substitution after loss of sex provide the strongest empirical support for hypothesized effects of asexuality, whereas there is mixed evidence for ecological hypotheses such as increased parasite load and altered niche breadth in asexuals. Most hypotheses have been explored in a select few taxa (e.g. stick insects, aphids), such that much of the great taxonomic breadth of insects remain understudied. Given the variation in the proximate causes of asexuality in insects, we argue for expanding the taxonomic breadth of study systems. Despite some challenges for investigating sex in insects, the increasing cost-effectiveness of genomic sequencing makes data generation for closely-related asexual and sexual lineages increasingly feasible.


Subject(s)
Insecta/genetics , Insecta/physiology , Reproduction, Asexual/genetics , Animals , Female , Hybridization, Genetic , Male , Parthenogenesis , Symbiosis
9.
Evolution ; 72(4): 808-824, 2018 04.
Article in English | MEDLINE | ID: mdl-29520921

ABSTRACT

Harmful mutations are ubiquitous and inevitable, and the rate at which these mutations are removed from populations is a critical determinant of evolutionary fate. Closely related sexual and asexual taxa provide a particularly powerful setting to study deleterious mutation elimination because sexual reproduction should facilitate mutational clearance by reducing selective interference between sites and by allowing the production of offspring with different mutational complements than their parents. Here, we compared the rate of removal of conservative (i.e., similar biochemical properties) and radical (i.e., distinct biochemical properties) nonsynonymous mutations from mitochondrial genomes of sexual versus asexual Potamopyrgus antipodarum, a New Zealand freshwater snail characterized by coexisting and ecologically similar sexual and asexual lineages. Our analyses revealed that radical nonsynonymous mutations are cleared at higher rates than conservative changes and that sexual lineages eliminate radical changes more rapidly than asexual counterparts. These results are consistent with reduced efficacy of purifying selection in asexual lineages allowing harmful mutations to remain polymorphic longer than in sexual lineages. Together, these data illuminate some of the population-level processes contributing to mitochondrial mutation accumulation and suggest that mutation accumulation could influence the outcome of competition between sexual and asexual lineages.


Subject(s)
Amino Acid Substitution , Amino Acids/genetics , Mutation , Reproduction, Asexual , Snails/physiology , Animals , Evolution, Molecular , Genome, Mitochondrial , New Zealand , Snails/genetics
10.
J Hered ; 108(7): 791-806, 2017 10 30.
Article in English | MEDLINE | ID: mdl-28992199

ABSTRACT

The cellular mechanisms of meiosis are critical for proper gamete formation in sexual organisms. Functional studies in model organisms have identified genes essential for meiosis, yet the extent to which this core meiotic machinery is conserved across non-model systems is not fully understood. Moreover, it is unclear whether deviation from canonical modes of sexual reproduction is accompanied by modifications in the genetic components involved in meiosis. We used a robust approach to identify and catalogue meiosis genes in Hymenoptera, an insect order typically characterized by haplodiploid reproduction. Using newly available genome data, we searched for 43 genes involved in meiosis in 18 diverse hymenopterans. Seven of eight genes with roles specific to meiosis were found across a majority of surveyed species, suggesting the preservation of core meiotic machinery in haplodiploid hymenopterans. Phylogenomic analyses of the inventory of meiosis genes and the identification of shared gene duplications and losses provided support for the grouping of species within Proctotrupomorpha, Ichneumonomorpha, and Aculeata clades, along with a paraphyletic Symphyta. The conservation of meiosis genes across Hymenoptera provides a framework for studying transitions between reproductive modes in this insect group.


Subject(s)
Genes, Insect , Hymenoptera/genetics , Meiosis/genetics , Animals , Evolution, Molecular , Gene Duplication , Phylogeny
11.
Mol Ecol ; 26(14): 3663-3675, 2017 Jul.
Article in English | MEDLINE | ID: mdl-28429458

ABSTRACT

Reciprocal co-evolving interactions between hosts and parasites are a primary source of strong selection that can promote rapid and often population- or genotype-specific evolutionary change. These host-parasite interactions are also a major source of disease. Despite their importance, very little is known about the genomic basis of co-evolving host-parasite interactions in natural populations, especially in animals. Here, we use gene expression and sequence evolution approaches to take critical steps towards characterizing the genomic basis of interactions between the freshwater snail Potamopyrgus antipodarum and its co-evolving sterilizing trematode parasite, Microphallus sp., a textbook example of natural coevolution. We found that Microphallus-infected P. antipodarum exhibit systematic downregulation of genes relative to uninfected P. antipodarum. The specific genes involved in parasite response differ markedly across lakes, consistent with a scenario where population-level co-evolution is leading to population-specific host-parasite interactions and evolutionary trajectories. We also used an FST -based approach to identify a set of loci that represent promising candidates for targets of parasite-mediated selection across lakes as well as within each lake population. These results constitute the first genomic evidence for population-specific responses to co-evolving infection in the P. antipodarum-Microphallus interaction and provide new insights into the genomic basis of co-evolutionary interactions in nature.


Subject(s)
Biological Coevolution , Genetics, Population , Host-Parasite Interactions/genetics , Snails/genetics , Snails/parasitology , Trematoda/pathogenicity , Animals , New Zealand
12.
Mol Biol Evol ; 31(3): 660-72, 2014 Mar.
Article in English | MEDLINE | ID: mdl-24336924

ABSTRACT

To establish which meiosis genes are present in ciliates, and to look for clues as to which recombination pathways may be treaded by them, four genomes were inventoried for 11 meiosis-specific and 40 meiosis-related genes. We found that the set of meiosis genes shared by Tetrahymena thermophila, Paramecium tetraurelia, Ichthyophthirius multifiliis, and Oxytricha trifallax is consistent with the prevalence of a Mus81-dependent class II crossover pathway that is considered secondary in most model eukaryotes. There is little evidence for a canonical class I crossover pathway that requires the formation of a synaptonemal complex (SC). This gene inventory suggests that meiotic processes in ciliates largely depend on mitotic repair proteins for executing meiotic recombination. We propose that class I crossovers and SCs were reduced sometime during the evolution of ciliates. Consistent with this reduction, we provide microscopic evidence for the presence only of degenerate SCs in Stylonychia mytilus. In addition, lower nonsynonymous to synonymous mutation rates of some of the meiosis genes suggest that, in contrast to most other nuclear genes analyzed so far, meiosis genes in ciliates are largely evolving at a slower rate than those genes in fungi and animals.


Subject(s)
Ciliophora/genetics , Crossing Over, Genetic , Genes, Protozoan/genetics , Meiosis/genetics , Synaptonemal Complex , Cell Nucleus/genetics , Cell Nucleus/ultrastructure , Ciliophora/ultrastructure , Likelihood Functions , Phylogeny , Synaptonemal Complex/genetics , Synaptonemal Complex/ultrastructure
14.
G3 (Bethesda) ; 3(11): 1927-43, 2013 Nov 06.
Article in English | MEDLINE | ID: mdl-24062528

ABSTRACT

Nbs1, a core component of the Mre11-Rad50-Nbs1 complex, plays an essential role in the cellular response to DNA double-strand breaks (DSBs) and poorly understood roles in meiosis. We used the basidiomycete Coprinus cinereus to examine the meiotic roles of Nbs1. We identified the C. cinereus nbs1 gene and demonstrated that it corresponds to a complementation group previously known as rad3. One allele, nbs1-2, harbors a point mutation in the Nbs1 FHA domain and has a mild spore viability defect, increased frequency of meiosis I nondisjunction, and an altered crossover distribution. The nbs1-2 strain enters meiosis with increased levels of phosphorylated H2AX, which we hypothesize represent unrepaired DSBs formed during premeiotic replication. In nbs1-2, there is no apparent induction of Spo11-dependent DSBs during prophase. We propose that replication-dependent DSBs, resulting from defective replication fork protection and processing by the Mre11-Rad50-Nbs1 complex, are competent to form meiotic crossovers in C. cinereus, and that these crossovers lead to high levels of faithful chromosome segregation. In addition, although crossover distribution is altered in nbs1-2, the majority of crossovers were found in subtelomeric regions, as in wild-type. Therefore, the location of crossovers in C. cinereus is maintained when DSBs are induced via a Spo11-independent mechanism.


Subject(s)
Coprinus/genetics , Endodeoxyribonucleases/genetics , Fungal Proteins/genetics , Nuclear Proteins/genetics , Alleles , Chromosome Segregation/genetics , Chromosomes/genetics , Chromosomes/metabolism , Coprinus/classification , Coprinus/physiology , DNA Breaks, Double-Stranded , DNA Repair , Endodeoxyribonucleases/chemistry , Endodeoxyribonucleases/metabolism , Fungal Proteins/chemistry , Fungal Proteins/metabolism , Genotype , Histones/genetics , Histones/metabolism , Meiosis , Mutation , Nuclear Proteins/chemistry , Nuclear Proteins/metabolism , Phosphorylation , Phylogeny , Polymorphism, Single Nucleotide , Recombination, Genetic , Spores, Fungal/cytology
15.
BMC Genomics ; 14: 412, 2013 Jun 19.
Article in English | MEDLINE | ID: mdl-23782598

ABSTRACT

BACKGROUND: Sexual reproduction is a widely studied biological process because it is critically important to the genetics, evolution, and ecology of eukaryotes. Despite decades of study on this topic, no comprehensive explanation has been accepted that explains the evolutionary forces underlying its prevalence and persistence in nature. Monogonont rotifers offer a useful system for experimental studies relating to the evolution of sexual reproduction due to their rapid reproductive rate and close relationship to the putatively ancient asexual bdelloid rotifers. However, little is known about the molecular underpinnings of sex in any rotifer species. RESULTS: We generated mRNA-seq libraries for obligate parthenogenetic (OP) and cyclical parthenogenetic (CP) strains of the monogonont rotifer, Brachionus calyciflorus, to identify genes specific to both modes of reproduction. Our differential expression analysis identified receptors with putative roles in signaling pathways responsible for the transition from asexual to sexual reproduction. Differential expression of a specific copy of the duplicated cell cycle regulatory gene CDC20 and specific copies of histone H2A suggest that such duplications may underlie the phenotypic plasticity required for reproductive mode switch in monogononts. We further identified differential expression of genes involved in the formation of resting eggs, a process linked exclusively to sex in this species. Finally, we identified transcripts from the bdelloid rotifer Adineta ricciae that have significant sequence similarity to genes with higher expression in CP strains of B. calyciflorus. CONCLUSIONS: Our analysis of global gene expression differences between facultatively sexual and exclusively asexual populations of B. calyciflorus provides insights into the molecular nature of sexual reproduction in rotifers. Furthermore, our results offer insight into the evolution of obligate asexuality in bdelloid rotifers and provide indicators important for the use of monogononts as a model system for investigating the evolution of sexual reproduction.


Subject(s)
Gene Expression Profiling , Ovum/physiology , Reproduction, Asexual/genetics , Rotifera/genetics , Rotifera/physiology , Animals , Cell Cycle Proteins/genetics , Cytoskeleton/genetics , DNA Transposable Elements/genetics , Gametogenesis/genetics , Histones/genetics , Meiosis/genetics , Recombination, Genetic/genetics , Rotifera/cytology , Rotifera/metabolism
16.
J Hered ; 104(3): 357-70, 2013.
Article in English | MEDLINE | ID: mdl-23487324

ABSTRACT

A long-standing question in evolutionary biology is how sexual reproduction has persisted in eukaryotic lineages. As cyclical parthenogens, monogonont rotifers are a powerful model for examining this question, yet the molecular nature of sexual reproduction in this lineage is currently understudied. To examine genes involved in meiosis, we generated partial genome assemblies for 2 distantly related monogonont species, Brachionus calyciflorus and B. manjavacas. Here we present an inventory of 89 meiotic genes, of which 80 homologs were identified and annotated from these assemblies. Using phylogenetic analysis, we show that several meiotic genes have undergone relatively recent duplication events that appear to be specific to the monogonont lineage. Further, we compare the expression of "meiosis-specific" genes involved in recombination and all annotated copies of the cell cycle regulatory gene CDC20 between obligate parthenogenetic (OP) and cyclical parthenogenetic (CP) strains of B. calyciflorus. We show that "meiosis-specific" genes are expressed in both CP and OP strains, whereas the expression of one of the CDC20 genes is specific to cyclical parthenogenesis. The data presented here provide insights into mechanisms of cyclical parthenogenesis and establish expectations for studies of obligate asexual relatives of monogononts, the bdelloid rotifer lineage.


Subject(s)
Meiosis/genetics , Parthenogenesis/genetics , Phylogeny , Rotifera/genetics , Animals , Cell Cycle Proteins/genetics , Chromosomes/genetics , DNA Replication , Expressed Sequence Tags , Gene Expression Regulation
17.
Mol Ecol Resour ; 13(2): 289-94, 2013 Mar.
Article in English | MEDLINE | ID: mdl-23280235

ABSTRACT

Understanding the evolution and maintenance of sexual reproduction is one of the central challenges of evolutionary biology, yet we know very little about how sex influences molecular evolution. The New Zealand freshwater snail Potamopyrgus antipodarum is ideally suited to address this knowledge gap because obligately sexual individuals often coexist with multiple independently derived obligately asexual lineages. This unusual situation allows direct comparisons both between sexual and asexual P. antipodarum and across populations that differ in the relative frequency of sexual individuals. As such, P. antipodarum has received a great deal of attention as a model system for the maintenance of sex in nature and is also used as a model for environmental toxicology and biological invasions. Molecular genetic resources for P. antipodarum will thus be useful to investigators in a variety of biological fields. We used 454 sequencing of cDNA libraries to generate transcriptomes from two sexual and two asexual P. antipodarum lineages. A de novo assembly of 116.7 Mb of sequence reads produced 41 396 contigs, and sequence similarity-based Gene Ontology annotations were obtained for 3740 contigs. We detected 408 315 SNP loci and 7315 microsatellite loci, which together represent the first genome-scale resource available for P. antipodarum. Raw 454 read sequences, contig sequences, annotation data and polymorphism data are publicly available in a searchable online database and for download at http://www.biology.uiowa.edu/neiman/transcriptome.php.


Subject(s)
Snails/classification , Snails/genetics , Transcriptome , Animals , Expressed Sequence Tags , Microsatellite Repeats , Phylogeny , Reproduction , Reproduction, Asexual , Sequence Analysis, DNA , Snails/physiology
18.
PLoS One ; 6(6): e20774, 2011.
Article in English | MEDLINE | ID: mdl-21695260

ABSTRACT

BACKGROUND: Parabasalia are single-celled eukaryotes (protists) that are mainly comprised of endosymbionts of termites and wood roaches, intestinal commensals, human or veterinary parasites, and free-living species. Phylogenetic comparisons of parabasalids are typically based upon morphological characters and 18S ribosomal RNA gene sequence data (rDNA), while biochemical or molecular studies of parabasalids are limited to a few axenically cultivable parasites. These previous analyses and other studies based on PCR amplification of duplicated protein-coding genes are unable to fully resolve the evolutionary relationships of parabasalids. As a result, genetic studies of Parabasalia lag behind other organisms. PRINCIPAL FINDINGS: Comparing parabasalid EF1α, α-tubulin, enolase and MDH protein-coding genes with information from the Trichomonas vaginalis genome reveals difficulty in resolving the history of species or isolates apart from duplicated genes. A conserved single-copy gene encodes the largest subunit of RNA polymerase II (Rpb1) in T. vaginalis and other eukaryotes. Here we directly sequenced Rpb1 degenerate PCR products from 10 parabasalid genera, including several T. vaginalis isolates and avian isolates, and compared these data by phylogenetic analyses. Rpb1 genes from parabasalids, diplomonads, Parabodo, Diplonema and Percolomonas were all intronless, unlike intron-rich homologs in Naegleria, Jakoba and Malawimonas. CONCLUSIONS/SIGNIFICANCE: The phylogeny of Rpb1 from parasitic and free-living parabasalids, and conserved Rpb1 insertions, support Trichomonadea, Tritrichomonadea, and Hypotrichomonadea as monophyletic groups. These results are consistent with prior analyses of rDNA and GAPDH sequences and ultrastructural data. The Rpb1 phylogenetic tree also resolves species- and isolate-level relationships. These findings, together with the relative ease of Rpb1 isolation, make it an attractive tool for evaluating more extensive relationships within Parabasalia.


Subject(s)
Gene Dosage/genetics , Genes, Protozoan/genetics , Parabasalidea/genetics , Parasites/genetics , Phylogeny , RNA Polymerase II/genetics , Animals , Genetic Markers , Glyceraldehyde-3-Phosphate Dehydrogenase (Phosphorylating)/genetics , Humans , Molecular Sequence Data , Open Reading Frames/genetics , Protozoan Proteins/genetics
20.
Curr Biol ; 20(24): R1078-9, 2010 Dec 21.
Article in English | MEDLINE | ID: mdl-21172628

ABSTRACT

Approximately half of all eukaryotic genes show signs of prokaryotic origin. Genes derived from eubacteria are more abundant than those from archaebacteria, but the latter are functionally more important. This supports archaebacteria as founding ancestors of the eukaryotic nucleus.


Subject(s)
Archaea/physiology , Biological Evolution , Eukaryotic Cells/physiology , Phylogeny , Symbiosis
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