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1.
RNA ; 2022 Jan 21.
Artigo em Inglês | MEDLINE | ID: mdl-35064043

RESUMO

Transposable elements (TEs) are genomic parasites that can propagate by inserting copies of themselves into host genomes. Mammalian genomes are typically dominated by LINE retrotransposons and their associated SINEs, and their mobilization in the germline is a challenge to genome integrity. There are genomic defenses against TE proliferation and the PIWI/piRNA defense is among the most well understood. However, the PIWI/piRNA system has been investigated largely in animals with abundant and actively mobilizing TEs and it is unclear how the PIWI/piRNA system functions in the absence of mobilizing TEs. The 13-lined ground squirrel provides an excellent opportunity to examine PIWI/piRNA and TE dynamics within the context of minimal, and possibly nonexistent, TE accumulation. We sequenced RNA and small RNAs pools from the testes of juvenile and adult squirrels and compared results to TE and PIWI/piRNA dynamics in the European rabbit and house mouse. Interestingly in squirrels, despite a lack of young insertions, TEs were still actively transcribed at higher levels compared to mouse and rabbit. All three Piwi genes were either not expressed, or only minimally expressed, prior to P8 in squirrel testis, but there was little TE expression change with the onset of Piwi expression. We also demonstrated there was not a major expression change in the two youngest squirrel LINE families in the transition from juvenile to adult testis in contrast to the youngest mouse and rabbit LINE families. These observations lead us to the conclusion that PIWI activity, as measured by the ping-pong cycle, was weaker for squirrel LINEs and SINEs and did not strongly reduce LINE and SINE transcription. We speculate that, although the PIWI/piRNA system is adaptable to novel TE threats, transcripts from TEs that are no longer threatening receive less attention from PIWI proteins.

2.
Genome Biol Evol ; 13(10)2021 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-34480557

RESUMO

Globin-X (GbX) is an enigmatic member of the vertebrate globin gene family with a wide phyletic distribution that spans protostomes and deuterostomes. Unlike canonical globins such as hemoglobins and myoglobins, functional data suggest that GbX does not have a primary respiratory function. Instead, evidence suggests that the monomeric, membrane-bound GbX may play a role in cellular signaling or protection against the oxidation of membrane lipids. Recently released genomes from key vertebrates provide an excellent opportunity to address questions about the early stages of the evolution of GbX in vertebrates. We integrate bioinformatics, synteny, and phylogenetic analyses to characterize the diversity of GbX genes in nonteleost ray-finned fishes, resolve relationships between the GbX genes of cartilaginous fish and bony vertebrates, and demonstrate that the GbX genes of cyclostomes and gnathostomes derive from independent duplications. Our study highlights the role that whole-genome duplications (WGDs) have played in expanding the repertoire of genes in vertebrate genomes. Our results indicate that GbX paralogs have a remarkably high rate of retention following WGDs relative to other globin genes and provide an evolutionary framework for interpreting results of experiments that examine functional properties of GbX and patterns of tissue-specific expression. By identifying GbX paralogs that are products of different WGDs, our results can guide the design of experimental work to explore whether gene duplicates that originate via WGDs have evolved novel functional properties or expression profiles relative to singleton or tandemly duplicated copies of GbX.

3.
Sci Rep ; 11(1): 12483, 2021 06 14.
Artigo em Inglês | MEDLINE | ID: mdl-34127736

RESUMO

Golgi phosphoprotein 3 (GOLPH3) was the first reported oncoprotein of the Golgi apparatus. It was identified as an evolutionarily conserved protein upon its discovery about 20 years ago, but its function remains puzzling in normal and cancer cells. The GOLPH3 gene is part of a group of genes that also includes the GOLPH3L gene. Because cancer has deep roots in multicellular evolution, studying the evolution of the GOLPH3 gene family in non-model species represents an opportunity to identify new model systems that could help better understand the biology behind this group of genes. The main goal of this study is to explore the evolution of the GOLPH3 gene family in birds as a starting point to understand the evolutionary history of this oncoprotein. We identified a repertoire of three GOLPH3 genes in birds. We found duplicated copies of the GOLPH3 gene in all main groups of birds other than paleognaths, and a single copy of the GOLPH3L gene. We suggest there were at least three independent origins for GOLPH3 duplicates. Amino acid divergence estimates show that most of the variation is located in the N-terminal region of the protein. Our transcript abundance estimations show that one paralog is highly and ubiquitously expressed, and the others were variable. Our results are an example of the significance of understanding the evolution of the GOLPH3 gene family, especially for unraveling its structural and functional attributes.


Assuntos
Aves/genética , Evolução Molecular , Complexo de Golgi/genética , Proteínas de Membrana/genética , Proteínas Oncogênicas/genética , Sequência de Aminoácidos/genética , Animais , Carcinogênese/genética , Duplicação Gênica , Humanos , Neoplasias/genética , Fosfoproteínas/genética , Alinhamento de Sequência
4.
Genome Biol Evol ; 12(8): 1419-1428, 2020 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-32697843

RESUMO

The leaf-nosed bats (Phyllostomidae) are outliers among chiropterans with respect to the unusually high diversity of dietary strategies within the family. Salivary glands, owing to their functions and high ultrastructural variability among lineages, are proposed to have played an important role during the phyllostomid radiation. To identify genes underlying salivary gland functional diversification, we sequenced submandibular gland transcriptomes from phyllostomid species representative of divergent dietary strategies. From the assembled transcriptomes, we performed an array of selection tests and gene expression analyses to identify signatures of adaptation. Overall, we identified an enrichment of immunity-related gene ontology terms among 53 genes evolving under positive selection. Lineage-specific selection tests revealed several endomembrane system genes under selection in the vampire bat. Many genes that respond to insulin were under selection and differentially expressed genes pointed to modifications of amino acid synthesis pathways in plant-visitors. Results indicate salivary glands have diversified in various ways across a functional diverse clade of mammals in response to niche specializations.


Assuntos
Adaptação Biológica/genética , Evolução Biológica , Quirópteros/genética , Seleção Genética , Glândula Submandibular/metabolismo , Animais , Quirópteros/metabolismo , Dieta , Comportamento Alimentar , Transcriptoma
5.
Anal Biochem ; 602: 113781, 2020 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-32485163

RESUMO

MicroRNAs (miRNAs) are 18-24 nucleotide regulatory RNAs. They are involved in the regulation of genetic and biological pathways through post transcriptional gene silencing and/or translational repression. Data suggests a slow evolutionary rate for the saltwater crocodile (Crocodylus porosus) over the past several million years when compared to birds, the closest extant relatives of crocodilians. Understanding gene regulation in the saltwater crocodile in the context of relatively slow genomic change thus holds potential for the investigation of genomics, evolution, and adaptation. Utilizing eleven tissue types and sixteen small RNA libraries, we report 644 miRNAs in the saltwater crocodile with >78% of miRNAs being novel to crocodilians. We also identified potential targets for the miRNAs and analyzed the relationship of the miRNA repertoire to transposable elements (TEs). Results suggest an increased association of DNA transposons with miRNAs when compared to retrotransposons. This work reports the first comprehensive analysis of miRNAs in Crocodylus porosus and addresses the potential impacts of miRNAs in regulating the genome in the saltwater crocodile. In addition, the data suggests a supporting role of TEs as a source for miRNAs, adding to the increasing evidence that TEs play a significant role in the evolution of gene regulation.


Assuntos
Elementos de DNA Transponíveis/genética , MicroRNAs/genética , Jacarés e Crocodilos , Animais , Biblioteca Gênica , Salinidade
6.
Sci Rep ; 10(1): 8684, 2020 05 26.
Artigo em Inglês | MEDLINE | ID: mdl-32457384

RESUMO

Essential for calcium homeostasis, TRPV5 and TRPV6 are calcium-selective channels belonging to the transient receptor potential (TRP) gene family. In this study, we investigated the evolutionary history of these channels to add an evolutionary context to the already available physiological information. Phylogenetic analyses revealed that paralogs found in mammals, sauropsids, amphibians, and chondrichthyes, are the product of independent duplication events in the ancestor of each group. Within amniotes, we identified a traceable signature of three amino acids located at the amino-terminal intracellular region. The signature correlates with both the duplication events and the phenotype of fast inactivation observed in mammalian TRPV6 channels. Electrophysiological recordings and mutagenesis revealed that the signature sequence modulates the phenotype of fast inactivation in all clades of vertebrates but reptiles. A transcriptome analysis showed a change in tissue expression from gills, in marine vertebrates, to kidneys in terrestrial vertebrates. Our results highlight a cytoplasmatic structural triad composed by the Helix-Loop-Helix domain, the S2-S3 linker, and the TRP domain helix that is important on modulating the activity of calcium-selective TRPV channels.


Assuntos
Cálcio/metabolismo , Evolução Molecular , Canais de Cátion TRPV/metabolismo , Sequência de Aminoácidos , Anfíbios/metabolismo , Animais , Aves/metabolismo , Brânquias/metabolismo , Células HEK293 , Sequências Hélice-Alça-Hélice , Humanos , Rim/metabolismo , Mamíferos/metabolismo , Mutagênese Sítio-Dirigida , Filogenia , Alinhamento de Sequência , Canais de Cátion TRPV/química , Canais de Cátion TRPV/classificação , Canais de Cátion TRPV/genética
7.
Nat Commun ; 9(1): 2774, 2018 07 17.
Artigo em Inglês | MEDLINE | ID: mdl-30018307

RESUMO

Broad paradigms of vertebrate genomic repeat element evolution have been largely shaped by analyses of mammalian and avian genomes. Here, based on analyses of genomes sequenced from over 60 squamate reptiles (lizards and snakes), we show that patterns of genomic repeat landscape evolution in squamates challenge such paradigms. Despite low variance in genome size, squamate genomes exhibit surprisingly high variation among species in abundance (ca. 25-73% of the genome) and composition of identifiable repeat elements. We also demonstrate that snake genomes have experienced microsatellite seeding by transposable elements at a scale unparalleled among eukaryotes, leading to some snake genomes containing the highest microsatellite content of any known eukaryote. Our analyses of transposable element evolution across squamates also suggest that lineage-specific variation in mechanisms of transposable element activity and silencing, rather than variation in species-specific demography, may play a dominant role in driving variation in repeat element landscapes across squamate phylogeny.


Assuntos
Variação Genética , Lagartos/genética , Repetições de Microssatélites , Filogenia , Serpentes/genética , Animais , Aves/classificação , Aves/genética , Elementos de DNA Transponíveis , Evolução Molecular , Tamanho do Genoma , Genômica , Lagartos/classificação , Mamíferos/classificação , Mamíferos/genética , Serpentes/classificação
8.
Genome Biol Evol ; 10(8): 2110-2129, 2018 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-30060036

RESUMO

Colubridae represents the most phenotypically diverse and speciose family of snakes, yet no well-assembled and annotated genome exists for this lineage. Here, we report and analyze the genome of the garter snake, Thamnophis sirtalis, a colubrid snake that is an important model species for research in evolutionary biology, physiology, genomics, behavior, and the evolution of toxin resistance. Using the garter snake genome, we show how snakes have evolved numerous adaptations for sensing and securing prey, and identify features of snake genome structure that provide insight into the evolution of amniote genomes. Analyses of the garter snake and other squamate reptile genomes highlight shifts in repeat element abundance and expansion within snakes, uncover evidence of genes under positive selection, and provide revised neutral substitution rate estimates for squamates. Our identification of Z and W sex chromosome-specific scaffolds provides evidence for multiple origins of sex chromosome systems in snakes and demonstrates the value of this genome for studying sex chromosome evolution. Analysis of gene duplication and loss in visual and olfactory gene families supports a dim-light ancestral condition in snakes and indicates that olfactory receptor repertoires underwent an expansion early in snake evolution. Additionally, we provide some of the first links between secreted venom proteins, the genes that encode them, and their evolutionary origins in a rear-fanged colubrid snake, together with new genomic insight into the coevolutionary arms race between garter snakes and highly toxic newt prey that led to toxin resistance in garter snakes.


Assuntos
Evolução Molecular , Genoma , Anotação de Sequência Molecular , Comportamento Predatório , Serpentes/genética , Adaptação Fisiológica , Animais , Feminino , Células Fotorreceptoras de Vertebrados , Receptores Odorantes/genética , Répteis/classificação , Répteis/genética , Pigmentos da Retina/genética , Seleção Genética , Serpentes/classificação , Serpentes/fisiologia , Peçonhas/genética , Canais de Sódio Disparados por Voltagem/genética
9.
Chromosome Res ; 26(1-2): 25-43, 2018 03.
Artigo em Inglês | MEDLINE | ID: mdl-29392473

RESUMO

Transposable elements (TEs) are genetic elements with the ability to mobilize and replicate themselves in a genome. Mammalian genomes are dominated by TEs, which can reach copy numbers in the hundreds of thousands. As a result, TEs have had significant impacts on mammalian evolution. Here we summarize the current understanding of TE content in mammal genomes and find that, with a few exceptions, most fall within a predictable range of observations. First, one third to one half of the genome is derived from TEs. Second, most mammalian genomes are dominated by LINE and SINE retrotransposons, more limited LTR retrotransposons, and minimal DNA transposon accumulation. Third, most mammal genome contains at least one family of actively accumulating retrotransposon. Finally, horizontal transfer of TEs among lineages is rare. TE exaptation events are being recognized with increasing frequency. Despite these beneficial aspects of TE content and activity, the majority of TE insertions are neutral or deleterious. To limit the deleterious effects of TE proliferation, the genome has evolved several defense mechanisms that act at the epigenetic, transcriptional, and post-transcriptional levels. The interaction between TEs and these defense mechanisms has led to an evolutionary arms race where TEs are suppressed, evolve to escape suppression, then are suppressed again as the defense mechanisms undergo compensatory change. The result is complex and constantly evolving interactions between TEs and host genomes.


Assuntos
Elementos de DNA Transponíveis/genética , Evolução Molecular , Genoma/genética , Mamíferos/genética , Animais , Humanos , Retroelementos
10.
Genome Biol Evol ; 10(1): 344-358, 2018 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-29340581

RESUMO

The genes that encode the α- and ß-chain subunits of vertebrate hemoglobin have served as a model system for elucidating general principles of gene family evolution, but little is known about patterns of evolution in amniotes other than mammals and birds. Here, we report a comparative genomic analysis of the α- and ß-globin gene clusters in sauropsids (archosaurs and nonavian reptiles). The objectives were to characterize changes in the size and membership composition of the α- and ß-globin gene families within and among the major sauropsid lineages, to reconstruct the evolutionary history of the sauropsid α- and ß-globin genes, to resolve orthologous relationships, and to reconstruct evolutionary changes in the developmental regulation of gene expression. Our comparisons revealed contrasting patterns of evolution in the unlinked α- and ß-globin gene clusters. In the α-globin gene cluster, which has remained in the ancestral chromosomal location, evolutionary changes in gene content are attributable to the differential retention of paralogous gene copies that were present in the common ancestor of tetrapods. In the ß-globin gene cluster, which was translocated to a new chromosomal location, evolutionary changes in gene content are attributable to differential gene gains (via lineage-specific duplication events) and gene losses (via lineage-specific deletions and inactivations). Consequently, all major groups of amniotes possess unique repertoires of embryonic and postnatally expressed ß-type globin genes that diversified independently in each lineage. These independently derived ß-type globins descend from a pair of tandemly linked paralogs in the most recent common ancestor of sauropsids.


Assuntos
Evolução Molecular , Família Multigênica , Filogenia , alfa-Globinas/genética , Globinas beta/genética , Animais , Duplicação Gênica , Genoma , Répteis/genética , Vertebrados/genética
11.
Syst Biol ; 67(2): 236-249, 2018 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-28945862

RESUMO

The rapid diversification of Myotis bats into more than 100 species is one of the most extensive mammalian radiations available for study. Efforts to understand relationships within Myotis have primarily utilized mitochondrial markers and trees inferred from nuclear markers lacked resolution. Our current understanding of relationships within Myotis is therefore biased towards a set of phylogenetic markers that may not reflect the history of the nuclear genome. To resolve this, we sequenced the full mitochondrial genomes of 37 representative Myotis, primarily from the New World, in conjunction with targeted sequencing of 3648 ultraconserved elements (UCEs). We inferred the phylogeny and explored the effects of concatenation and summary phylogenetic methods, as well as combinations of markers based on informativeness or levels of missing data, on our results. Of the 294 phylogenies generated from the nuclear UCE data, all are significantly different from phylogenies inferred using mitochondrial genomes. Even within the nuclear data, quartet frequencies indicate that around half of all UCE loci conflict with the estimated species tree. Several factors can drive such conflict, including incomplete lineage sorting, introgressive hybridization, or even phylogenetic error. Despite the degree of discordance between nuclear UCE loci and the mitochondrial genome and among UCE loci themselves, the most common nuclear topology is recovered in one quarter of all analyses with strong nodal support. Based on these results, we re-examine the evolutionary history of Myotis to better understand the phenomena driving their unique nuclear, mitochondrial, and biogeographic histories.


Assuntos
Quirópteros/classificação , Quirópteros/genética , Genoma Mitocondrial/genética , Genoma/genética , Filogenia , Animais
12.
Gen Comp Endocrinol ; 250: 85-94, 2017 09 01.
Artigo em Inglês | MEDLINE | ID: mdl-28622977

RESUMO

Evolutionary studies of genes that have been functionally characterized and whose variation has been associated with pathological conditions represent an opportunity to understand the genetic basis of pathologies. α2-Adrenoreceptors (ADRA2) are a class of G protein-coupled receptors that regulate several physiological processes including blood pressure, platelet aggregation, insulin secretion, lipolysis, and neurotransmitter release. This gene family has been extensively studied from a molecular/physiological perspective, yet much less is known about its evolutionary history. Accordingly, the goal of this study was to investigate the evolutionary history of α2-adrenoreceptors (ADRA2) in vertebrates. Our results show that in addition to the three well-recognized α2-adrenoreceptor genes (ADRA2A, ADRA2B and ADRA2C), we recovered a clade that corresponds to the fourth member of the α2-adrenoreceptor gene family (ADRA2D). We also recovered a clade that possesses two ADRA2 sequences found in two lamprey species. Furthermore, our results show that mammals and crocodiles are characterized by possessing three α2-adrenoreceptor genes, whereas all other vertebrate groups possess the full repertoire of α2-adrenoreceptor genes. Among vertebrates ADRA2D seems to be a dispensable gene, as it was lost two independent times during the evolutionary history of the group. Additionally, we found that most examined species possess the most common alleles described for humans; however, there are cases in which non-human mammals possess the alternative variant. Finally, transcript abundance profiles revealed that during the early evolutionary history of gnathostomes, the expression of ADRA2D in different taxonomic groups became specialized to different tissues, but in the ancestor of sarcopterygians this specialization would have been lost.


Assuntos
Jacarés e Crocodilos/genética , Evolução Molecular , Mamíferos/genética , Receptores Adrenérgicos alfa 2/genética , Animais , Sequência Conservada/genética , Funções Verossimilhança , Mamíferos/sangue , Filogenia , Polimorfismo Genético , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Sintenia/genética , Transcrição Genética
13.
Gen Comp Endocrinol ; 240: 129-137, 2017 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-27769631

RESUMO

The study of the evolutionary history of genes related to human disease lies at the interface of evolution and medicine. These studies provide the evolutionary context on which medical researchers should work, and are also useful in providing information to suggest further genetic experiments, especially in model species where genetic manipulations can be made. Here we studied the evolution of the ß-adrenoreceptor gene family in vertebrates with the aim of adding an evolutionary framework to the already abundant physiological information. Our results show that in addition to the three already described vertebrate ß-adrenoreceptor genes there is an additional group containing cyclostome sequences. We suggest that ß-adrenoreceptors diversified as a product of the two whole genome duplications that occurred in the ancestor of vertebrates. Gene expression patterns are in general consistent across species, suggesting that expression dynamics were established early in the evolutionary history of vertebrates, and have been maintained since then. Finally, amino acid polymorphisms that are associated to pathological conditions in humans appear to be common in non-human mammals, suggesting that the phenotypic effects of these mutations depend on epistatic interaction with other positions. The evolutionary analysis of the ß-adrenoreceptors delivers new insights about the diversity of these receptors in vertebrates, the evolution of the expression patterns and a comparative perspective regarding the polymorphisms that in humans are linked to pathological conditions.


Assuntos
Evolução Molecular , Receptores Adrenérgicos beta/genética , Vertebrados/genética , Animais , Duplicação Gênica , Genoma , Humanos , Filogenia
14.
Gene ; 591(1): 245-254, 2016 Oct 10.
Artigo em Inglês | MEDLINE | ID: mdl-27432065

RESUMO

Genes related to human diseases should be natural targets for evolutionary studies, since they could provide clues regarding the genetic bases of pathologies and potential treatments. Here we studied the evolution of the reprimo gene family, a group of tumor-suppressor genes that are implicated in p53-mediated cell cycle arrest. These genes, especially the reprimo duplicate located on human chromosome 2, have been associated with epigenetic modifications correlated with transcriptional silencing and cancer progression. We demonstrate the presence of a third reprimo lineage that, together with the reprimo and reprimo-like genes, appears to have been differentially retained during the evolutionary history of vertebrates. We present evidence that these reprimo lineages originated early in vertebrate evolution and expanded as a result of the two rounds of whole genome duplications that occurred in the last common ancestor of vertebrates. The reprimo gene has been lost in birds, and the third reprimo gene lineage has been retained in only a few distantly related species, such as coelacanth and gar. Expression analyses revealed that the reprimo paralogs are mainly expressed in the nervous system. Different vertebrate lineages have retained different reprimo paralogs, and even in species that have retained multiple copies, only one of them is heavily expressed.


Assuntos
Proteínas de Ciclo Celular/genética , Evolução Molecular , Genes Supressores de Tumor , Família Multigênica , Filogenia , Vertebrados/genética , Sequência de Aminoácidos , Animais , Duplicação Gênica , Humanos , Funções Verossimilhança , Alinhamento de Sequência , Sintenia/genética , Transcrição Genética , Proteína Supressora de Tumor p53/genética , Proteínas Supressoras de Tumor/química , Proteínas Supressoras de Tumor/genética
15.
Front Microbiol ; 7: 661, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27199976

RESUMO

Dietary shifts can result in changes to the gastrointestinal tract (GIT) microbiota, leading to negative outcomes for the host, including inflammation. Giant pandas (Ailuropoda melanoleuca) are physiologically classified as carnivores; however, they consume an herbivorous diet with dramatic seasonal dietary shifts and episodes of chronic GIT distress with symptoms including abdominal pain, loss of appetite and the excretion of mucous stools (mucoids). These episodes adversely affect the overall nutritional and health status of giant pandas. Here, we examined the fecal microbiota of two giant pandas' non-mucoid and mucoid stools and compared these to samples from a previous winter season that had historically few mucoid episodes. To identify the microbiota present, we isolated and sequenced the 16S rRNA using next-generation sequencing. Mucoids occurred following a seasonal feeding switch from predominately bamboo culm (stalk) to leaves. All fecal samples displayed low diversity and were dominated by bacteria in the phyla Firmicutes and to a lesser extent, Proteobacteria. Fecal samples immediately prior to mucoid episodes had lower microbial diversity as compared to mucoids. Mucoids were mostly comprised of common mucosal-associated taxa including Streptococcus and Leuconostoc species, and exhibited increased abundance for bacteria in the family Pasteurellaceae. Taken together, these findings indicate that mucoids may represent an expulsion of the mucosal lining that is driven by changes in diet. We suggest that these occurrences serve to reset their GIT microbiota following changes in bamboo part preference, as giant pandas have retained a carnivorous GIT anatomy while shifting to an herbivorous diet.

16.
Genome Biol Evol ; 8(5): 1327-37, 2016 05 09.
Artigo em Inglês | MEDLINE | ID: mdl-27060702

RESUMO

PIWI proteins and PIWI-interacting RNAs (piRNAs) are part of a cellular pathway that has evolved to protect genomes against the proliferation of transposable elements (TEs). PIWIs and piRNAs assemble into complexes that are involved in epigenetic and post-transcriptional repression of TEs. Most of our understanding of the mechanisms of piRNA-mediated TE silencing comes from fruit fly and mouse models. However, even in these well-studied animals it is unclear how piRNA responses relate to variable TE expression and whether the strength of the piRNA response affects TE content over time. Here, we assessed the evolutionary interactions between TE and piRNAs in a statistical framework using three nonmodel laurasiatherian mammals as a study system: dog, horse, and a vesper bat. These three species diverged ∼80 million years ago and have distinct genomic TE contents. By comparing species with distinct TE landscapes, we aimed to identify clear relationships among TE content, expression, and piRNAs. We found that the TE subfamilies that are the most transcribed appear to elicit the strongest "ping-pong" response. This was most evident among long interspersed elements, but the relationships between expression and ping-pong pilRNA (piRNA-like) expression were more complex among SINEs. SINE transcripts were equally abundant in the dog and horse yet new SINE insertions were relatively rare in the horse genome, where we identified a stronger piRNA response. Our analyses suggest that the piRNA response can have a strong impact on the TE composition of a genome. However, our results also suggest that the presence of a robust piRNA response is apparently not sufficient to stop TE mobilization and accumulation.


Assuntos
Elementos de DNA Transponíveis/genética , Evolução Molecular , Inativação Gênica , RNA Interferente Pequeno/genética , Seleção Genética , Animais , Quirópteros , Cães , Cavalos , Camundongos , Transcrição Genética
17.
Genome Biol Evol ; 8(3): 470-80, 2016 Feb 09.
Artigo em Inglês | MEDLINE | ID: mdl-26865070

RESUMO

Olfactory receptors (ORs) are membrane proteins that mediate the detection of odorants in the environment, and are the largest vertebrate gene family. Comparative studies of mammalian genomes indicate that OR repertoires vary widely, even between closely related lineages, as a consequence of frequent OR gains and losses. Several studies also suggest that mammalian OR repertoires are influenced by life history traits. Sauropsida is a diverse group of vertebrates group that is the sister group to mammals, and includes birds, testudines, squamates, and crocodilians, and represents a natural system to explore predictions derived from mammalian studies. In this study, we analyzed olfactory receptor (OR) repertoire variation among several representative species and found that the number of intact OR genes in sauropsid genomes analyzed ranged over an order of magnitude, from 108 in the green anole to over 1,000 in turtles. Our results suggest that different sauropsid lineages have highly divergent OR repertoire composition that derive from lineage-specific combinations of gene expansions, losses, and retentions of ancestral OR genes. These differences also suggest that varying degrees of adaption related to life history have shaped the unique OR repertoires observed across sauropsid lineages.


Assuntos
Evolução Molecular , Filogenia , Receptores Odorantes/genética , Jacarés e Crocodilos/genética , Animais , Aves , Lagartos/genética , Mamíferos , Odorantes/análise , Especificidade da Espécie , Tartarugas/genética
18.
Genome Biol Evol ; 7(11): 3009-21, 2015 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-26475318

RESUMO

The genes in the Myb superfamily encode for three related transcription factors in most vertebrates, A-, B-, and c-Myb, with functionally distinct roles, whereas most invertebrates have a single Myb. B-Myb plays an essential role in cell division and cell cycle progression, c-Myb is involved in hematopoiesis, and A-Myb is involved in spermatogenesis and regulating expression of pachytene PIWI interacting RNAs, a class of small RNAs involved in posttranscriptional gene regulation and the maintenance of reproductive tissues. Comparisons between teleost fish and tetrapods suggest that the emergence and functional divergence of the Myb genes were linked to the two rounds of whole-genome duplication early in vertebrate evolution. We combined phylogenetic, synteny, structural, and gene expression analyses of the Myb paralogs from elephant shark and lampreys with data from 12 bony vertebrates to reconstruct the early evolution of vertebrate Mybs. Phylogenetic and synteny analyses suggest that the elephant shark and Japanese lamprey have copies of the A-, B-, and c-Myb genes, implying their origin could be traced back to the common ancestor of lampreys and gnathostomes. However, structural and gene expression analyses suggest that their functional roles diverged between gnathostomes and cyclostomes. In particular, we did not detect A-Myb expression in testis suggesting that the involvement of A-Myb in the pachytene PIWI interacting RNA pathway is probably a gnathostome-specific innovation. We speculate that the secondary loss of a central domain in lamprey A-Myb underlies the functional differences between the cyclostome and gnathostome A-Myb proteins.


Assuntos
Evolução Biológica , Genes myb/genética , Lampreias/genética , Filogenia , Tubarões/genética , Sintenia , Sequência de Aminoácidos , Animais , Teorema de Bayes , Funções Verossimilhança , Dados de Sequência Molecular , Análise de Sequência de DNA , Vertebrados/genética
19.
Science ; 346(6215): 1254449, 2014 Dec 12.
Artigo em Inglês | MEDLINE | ID: mdl-25504731

RESUMO

To provide context for the diversification of archosaurs--the group that includes crocodilians, dinosaurs, and birds--we generated draft genomes of three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the comparatively rapid evolution is derived in birds. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs, thereby providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs.


Assuntos
Jacarés e Crocodilos/genética , Aves/genética , Dinossauros/genética , Evolução Molecular , Genoma , Jacarés e Crocodilos/classificação , Animais , Evolução Biológica , Aves/classificação , Sequência Conservada , Elementos de DNA Transponíveis , Dinossauros/classificação , Variação Genética , Anotação de Sequência Molecular , Dados de Sequência Molecular , Filogenia , Répteis/classificação , Répteis/genética , Alinhamento de Sequência , Análise de Sequência de DNA , Transcriptoma
20.
Mol Biol Evol ; 31(6): 1536-45, 2014 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-24692655

RESUMO

Vesper bats (family Vespertilionidae) experienced a rapid adaptive radiation beginning around 36 Ma that resulted in the second most species-rich mammalian family (>400 species). Coincident with that radiation was an initial burst of DNA transposon activity that has continued into the present in some species. Such extensive and recent DNA transposon activity has not been seen in any other extant mammal. Indeed, retrotransposon activity is much more common in all other sequenced mammal genomes. Deep sequencing of the small RNA fraction from a vespertilionid bat, Eptesicus fuscus, as well as a dog and horse revealed large numbers of 17-24 bp putative miRNAs (p/miRNAs). Although the origination rate of p/miRNAs is similar in all three taxa, 61.1% of postdivergence p/miRNAs in Eptesicus are derived from transposable elements (TEs) compared with only 23.9% and 16.5% in the dog and horse, respectively. Not surprisingly, given the retrotransposon bias of dog and horse, the majority of TE-derived p/miRNAs are associated with retrotransposons. In Eptesicus, however, 58.7% of the TE-derived and 35.9% of the total p/miRNAs arose not from retrotransposons but from bat-specific DNA transposons. Notably, we observe that the timing of the DNA transposon expansion and the resulting introduction of novel p/miRNAs coincide with the rapid diversification of the family Vespertilionidae. Furthermore, potential targets of the DNA transposon-derived p/miRNAs are identifiable and enriched for genes that are important for regulation of transcription. We propose that lineage-specific DNA transposon activity lead to the rapid and repeated introduction of novel p/miRNAs. Some of these p/miRNAs are likely functional miRNAs and potentially influenced the diversification of Vespertilionidae. Our observations suggest a mechanism for introducing functional genomic variation rapidly through the expansion of DNA transposons that fits within the TE-thrust hypothesis.


Assuntos
Quirópteros/classificação , Quirópteros/genética , Elementos de DNA Transponíveis , MicroRNAs/genética , Animais , Cães , Evolução Molecular , Frequência do Gene , Variação Genética , Genoma , Sequenciamento de Nucleotídeos em Larga Escala , Cavalos , Mamíferos/genética , Filogenia , Retroelementos
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