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1.
Gene ; 766: 145144, 2021 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-32916248

RESUMO

The elongases of very long-chain fatty acids (Elovls) are involved in the rate-limiting of the carbon chain elongation reaction in fatty acid (FA) biosynthesis in vertebrates. One member of the Elovls family, Elovl4, has been regarded as a critical enzyme involved in the biosynthesis pathway of polyunsaturated fatty acids (PUFAs). To explore the role of Elovl4 in PUFA synthesis in Trachinotus ovatus, the cDNA of the Elovl4b gene is cloned from T. ovatus (ToElovl4b). The ORF of ToElovl4b was 918 bp and encoded 305 amino acid (aa) protein sequences. Sequence alignment showed that the deduced amino acids contained significant structural features of the Elovl4 family, such as a histidine box motif (HXXHH), multiple transmembrane domains and an endoplasmic reticulum (ER) retention signal. Moreover, phylogenetic analysis revealed that ToElovl4b was highly conserved with that of Rachycentron canadum Elovl4b. Moreover, heterologous expression in yeast demonstrated that ToElovl4b could efficiently elongate 18:2n-6, 18:3n-6 and 20:5n-3 FAs up to 20:2n-6, 20:3n-6 and 22:5n-3, respectively. Furthermore, the tissue expression profile indicated that mRNA expression of ToElovl4b was higher in the gonads and brain than in other tissues. Additionally, nutritional regulation suggested the highest mRNA levels of ToElovl4b in liver and brain were under feeding with 1:1 FO-SO (fish oil, FO; soybean oil, SO) and 1:1 FO-CO (corn oil, CO)), respectively. These new insights were useful for understanding the molecular basis and regulation of LC-PUFA biosynthesis in fish.


Assuntos
Proteínas de Peixes/genética , Peixes/genética , Peixes/metabolismo , Distribuição Tecidual/genética , Sequência de Aminoácidos , Animais , Sequência de Bases , Encéfalo/metabolismo , Elongases de Ácidos Graxos/genética , Ácidos Graxos Insaturados/genética , Feminino , Fígado/metabolismo , Masculino , Filogenia , RNA Mensageiro/genética , Alinhamento de Sequência
2.
PLoS One ; 15(10): e0231127, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33022692

RESUMO

Biodiversity is an important parameter for the evaluation of the extant environmental conditions. Here, we used environmental DNA (eDNA) metabarcoding to investigate fish biodiversity in five different estuaries in Japan. Water samples for eDNA were collected from river mouths and adjacent coastal areas of two estuaries with high degrees of development (the Tama and Miya Rivers) and three estuaries with relatively low degrees of development (the Aka, Takatsu, and Sendai Rivers). A total of 182 fish species across 67 families were detected. Among them, 11 species occurred in all the rivers studied. Rare fishes including endangered species were successfully detected in rich natural rivers. Biodiversity was the highest in the Sendai River and lowest in the Tama River, reflecting the degree of human development along each river. Even though nutrient concentration was low in both the Aka and Sendai Rivers, the latter exhibited greater diversity, including many tropical or subtropical species, owing to its more southern location. Species composition detected by eDNA varied among rivers, reflecting the distribution and migration of fishes. Our results are in accordance with the ecology of each fish species and environmental conditions of each river.


Assuntos
Código de Barras de DNA Taxonômico/métodos , DNA Ambiental/análise , Peixes/classificação , Animais , Biodiversidade , Monitoramento Ambiental/métodos , Estuários , Peixes/genética , Atividades Humanas , Japão , Filogenia , Rios
3.
PLoS One ; 15(8): e0237111, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32750100

RESUMO

Animal Tubulin-Based-Polymorphism (aTBP), an intron length polymorphism method recently developed for vertebrate genotyping, has been successfully applied to the identification of several fish species. Here, we report data that demonstrate the ability of the aTBP method to assign a specific profile to fish species, each characterized by the presence of commonly shared amplicons together with additional intraspecific polymorphisms. Within each aTBP profile, some fragments are also recognized that can be attributed to taxonomic ranks higher than species, e.g. genus and family. Versatility of application across different taxonomic ranks combined with the presence of a significant number of DNA polymorphisms, makes the aTBP method an additional and useful tool for fish genotyping, suitable for different purposes such as species authentication, parental recognition and detection of allele variations in response to environmental changes.


Assuntos
Proteínas de Peixes/genética , Peixes/genética , Técnicas de Genotipagem/métodos , Polimorfismo Genético , Tubulina (Proteína)/genética , Animais
4.
Proc Natl Acad Sci U S A ; 117(29): 17112-17121, 2020 07 21.
Artigo em Inglês | MEDLINE | ID: mdl-32647058

RESUMO

Resilience to environmental stressors due to climate warming is influenced by local adaptations, including plastic responses. The recent literature has focused on genomic signatures of climatic adaptation, but little is known about how plastic capacity may be influenced by biogeographic and evolutionary processes. We investigate phenotypic plasticity as a target of climatic selection, hypothesizing that lineages that evolved in warmer climates will exhibit greater plastic adaptive resilience to upper thermal stress. This was experimentally tested by comparing transcriptomic responses within and among temperate, subtropical, and desert ecotypes of Australian rainbowfish subjected to contemporary and projected summer temperatures. Critical thermal maxima were estimated, and ecological niches delineated using bioclimatic modeling. A comparative phylogenetic expression variance and evolution model was used to assess plastic and evolved changes in gene expression. Although 82% of all expressed genes were found in the three ecotypes, they shared expression patterns in only 5 out of 236 genes that responded to the climate change experiment. A total of 532 genes showed signals of adaptive (i.e., genetic-based) plasticity due to ecotype-specific directional selection, and 23 of those responded to projected summer temperatures. Network analyses demonstrated centrality of these genes in thermal response pathways. The greatest adaptive resilience to upper thermal stress was shown by the subtropical ecotype, followed by the desert and temperate ecotypes. Our findings indicate that vulnerability to climate change will be highly influenced by biogeographic factors, emphasizing the value of integrative assessments of climatic adaptive traits for accurate estimation of population and ecosystem responses.


Assuntos
Adaptação Fisiológica/genética , Mudança Climática , Ecossistema , Temperatura Alta , Animais , Austrália , Clima Desértico , Ecótipo , Peixes/genética , Peixes/fisiologia , Genômica , Transcriptoma/genética
5.
PLoS One ; 15(7): e0236427, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32702074

RESUMO

Many parts of Asia, including Taiwan, have suffered severely from freshwater fish invasions. However, few studies using an assemblage approach have been conducted in the region so far that would help to prioritize suitable preventive actions. In this study, we focused on the invasion process from the import stage to the establishment stage, and defined establishment success as the success during this predefined process. We used datasets of freshwater fish assemblages in Taiwan to (1) compare established versus non-established alien species to distinguish the determinants of establishment success, and (2) to use these determinants to test a life history hypothesis which predicts that the magnitudes of the determinants should be significantly different between established alien species and native species. We collated a dataset for freshwater fish species which were imported into Taiwan (n = 118) of which some successfully established (n = 26), and another dataset for freshwater fish species native to Taiwan (n = 77). For each imported species, we collected data for 17 variables, including two phylogenetic, two human-use, two invasion history, and 11 life history variables. We then used decision tree methods, which have advantages in analyzing datasets with many variables of mixed types without the need to make assumptions about data distributions and input data for missing values. Our results showed that aquaculture use and maximum body length were the most important determinants for predicting establishment success of alien freshwater fish in Taiwan. Comparing five important determinants between established alien versus native species showed that the established alien species were significantly more often used in aquaculture, were associated with a higher number of established countries, and had a larger body length and greater highest water temperature tolerance than the native species. We thus conclude that our results provided evidence to support our stated hypothesis. We suggest that aquaculture use, measures of body size, and the number of previously invaded countries may alert researchers and conservation managers to species with a high establishment potential, especially for countries with similar conditions as those in Taiwan.


Assuntos
Ecossistema , Peixes/fisiologia , Biologia de Ecossistemas de Água Doce , Espécies Introduzidas , Animais , Aquicultura , Tamanho Corporal/fisiologia , Peixes/genética , Água Doce , Humanos , Filogenia , Taiwan
7.
Nat Commun ; 11(1): 2772, 2020 06 02.
Artigo em Inglês | MEDLINE | ID: mdl-32487986

RESUMO

Vestigial structures are key indicators of evolutionary descent, but the mechanisms underlying their development are poorly understood. This study examines vestigial eye formation in the teleost Astyanax mexicanus, which consists of a sighted surface-dwelling morph and multiple populations of blind cave morphs. Cavefish embryos initially develop eyes, but they subsequently degenerate and become vestigial structures embedded in the head. The mutated genes involved in cavefish vestigial eye formation have not been characterized. Here we identify cystathionine ß-synthase a (cbsa), which encodes the key enzyme of the transsulfuration pathway, as one of the mutated genes responsible for eye degeneration in multiple cavefish populations. The inactivation of cbsa affects eye development by increasing the transsulfuration intermediate homocysteine and inducing defects in optic vasculature, which result in aneurysms and eye hemorrhages. Our findings suggest that localized modifications in the circulatory system may have contributed to the evolution of vestigial eyes in cavefish.


Assuntos
Cistationina beta-Sintase/genética , Cistationina/metabolismo , Olho/embriologia , Olho/metabolismo , Peixes/fisiologia , Animais , Apoptose , Evolução Biológica , Encéfalo/embriologia , Sistema Cardiovascular , Cistationina beta-Sintase/metabolismo , Biologia do Desenvolvimento , Olho/citologia , Olho/crescimento & desenvolvimento , Feminino , Peixes/embriologia , Peixes/genética , Regulação da Expressão Gênica no Desenvolvimento/genética , Técnicas de Silenciamento de Genes , Cabeça , Cristalino/citologia , Cristalino/metabolismo , Masculino , Modelos Animais
8.
Proc Biol Sci ; 287(1928): 20200468, 2020 06 10.
Artigo em Inglês | MEDLINE | ID: mdl-32486985

RESUMO

The rise of the southern Andes and the Quaternary glacial cycles influenced the landscape of Patagonia, affecting the phylogeographic and biogeographic patterns of its flora and fauna. Here, we examine the phylogeography of the freshwater fish, Percichthys trucha, using 53 sequenced microsatellite DNA markers. Fish (n = 835) were collected from 16 river systems (46 locations) spanning the species range on both sides of the Andes. Eleven watersheds drain to the Pacific, five of which are trans-Andean (headwaters east of Andes). The remaining five drainages empty into the Atlantic. Three analytical approaches (neighbour-joining tree, hierarchical AMOVAs, Structure) revealed evidence of historic drainage reversals: fish from four of the five trans-Andean systems (Puelo, Futalaufquen/Yelcho, Baker, Pascua) exhibited greater genetic similarity with Atlantic draining systems than with Pacific systems with headwaters west of Andes. Present-day drainage (Pacific versus Atlantic) explained only 5% of total genetic variance, while ancestral drainage explained nearly 27% of total variance. Thus, the phylogeographic structure of P. trucha is consistent with episodes of drainage reversal in multiple systems and suggests a major role for deglaciation in the genetic and indeed the geographical distribution of P. trucha in Patagonia. The study emphasizes the significant role of historical processes in the current pattern of genetic diversity and differentiation in a fish from a southern temperate region.


Assuntos
Peixes/genética , Repetições de Microssatélites , Refúgio de Vida Selvagem , Animais , DNA Mitocondrial , Variação Genética , Genética Populacional , Filogeografia
9.
Gene ; 754: 144860, 2020 Sep 05.
Artigo em Inglês | MEDLINE | ID: mdl-32531457

RESUMO

Arunachal Pradesh, the largest state of North-East India covers almost 60.93% of the Eastern Himalayan hotspot. Fish diversity and species identification is utmost important for fisheries management. But, in some cases morphological characteristics based identification is difficult for a non-specialist to perform. In view of the above, the present study emphasized on the assessment of DNA barcoding, phylogenetics and genetic diversity of fish species in the Ranganadi River, Arunachal Pradesh, India. India. Arunachal Pradesh, the largest state of North-East India covers almost 60.93% of the Eastern Himalayan hotspot. Altogether 114 specimens, representing 22 species, belonging to 3 orders and 5 families were successfully barcoded and found to be 98-100% identical from both GenBank and BOLD databases. Out of these 22 fish species, it was found that one species assessed was Endangered, three species as Near Threatened and one species as Vulnerable. A Neighbour Joining (NJ) tree was constructed using Rstudio for the purpose of a phylogenetic analysis of the identified species. The barcoding gap analysis using K2P, P-distance and Jukes-Cantor was done to detect the presence of cryptic species and barcoding success. The nucleotide base composition and genetic distance analysis were also performed, using MEGA 6.0. DNA Sequence Polymorphism v6.12.03 analysis revealed the nucleotide diversity (p) and haplotype diversity (Hd). The Hd for the whole dataset was found to be 0.975, which showed high genetic diversity in the Ranganadi River. Both morphological key identifying characters and molecular data corroborated the phylogenetic analysis. This COI barcode library, generated in the present study, not only helped in species identification and molecular study, but also in cryptic species identification.


Assuntos
Biodiversidade , Código de Barras de DNA Taxonômico , DNA/análise , Peixes/classificação , Peixes/genética , Variação Genética , Filogenia , Animais , DNA/genética , Água Doce , Rios
10.
PLoS One ; 15(5): e0233081, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32463827

RESUMO

ZMAT2 is among the least-studied of mammalian proteins and genes, even though it is the ortholog of Snu23, a protein involved in pre-mRNA splicing in yeast. Here we have used data from genomic and gene expression repositories to examine the Zmat2 gene and locus in 8 terrestrial vertebrates, 10 ray-finned fish, and 1 lobe-finned fish representing > 500 million years of evolutionary diversification. The analyses revealed that vertebrate Zmat2 genes are similar to their mammalian counterparts, as in 16/19 species studied they contain 6 exons, and in 18/19 encode a single conserved protein. However, unlike in mammals, no Zmat2 pseudogenes were identified in these vertebrates, although an expressed Zmat2 paralog was characterized in flycatcher that resembled a DNA copy of a processed and retro-transposed mRNA, and thus could be a proto-pseudogene captured during its evolutionary journey from active to inert. The Zmat2 locus in terrestrial vertebrates, and in spotted gar and coelacanth, also shares additional genes with its mammalian counterparts, including Histidyl-tRNA synthetase (Hars), Hars2, and others, but these are absent from the Zmat2 locus in teleost fish, in which Stem-loop-binding protein 2 (Slbp2) and Lymphocyte cytosolic protein 2a (Lcp2a) are present instead. Taken together, these observations argue that a recognizable Zmat2 was present in the earliest vertebrate ancestors, and postulate that during chromosomal tetraploidization and subsequent re-diploidization during modern teleost evolution, the duplicated Zmat2 gene was retained and the original lost. This study also highlights how information from genomic resources can be leveraged to reveal new biologically significant insights.


Assuntos
Proteínas de Peixes/genética , Peixes/classificação , Sequência de Aminoácidos , Animais , Sequência Conservada , Evolução Molecular , Proteínas de Peixes/química , Peixes/genética , Duplicação Gênica , Filogenia , Dedos de Zinco
11.
BMC Bioinformatics ; 21(1): 174, 2020 May 04.
Artigo em Inglês | MEDLINE | ID: mdl-32366294

RESUMO

BACKGROUND: Transcriptome analysis by next-generation sequencing has become a popular technique in recent years. This approach is quite suitable for non-model organism study, as de novo assembly is independent of prior genomic sequences of organisms. De novo sequencing has benefited many studies on commercially important fish species. However, to understand the functions of these assembled sequences, they still need to be annotated with existing sequence databases. By combining Basic Local Alignment Search Tool (BLAST) and Gene Ontology analysis, we were able to identify homologous sequences of assembled sequences and describe their characteristics using pre-defined tags for each gene, though the above conventional annotation results obtained for non-model assembled sequences was still associated with a lack of pre-defined tags and poorly documented records in the database. RESULTS: We introduced Blast2Fish, a novel approach for performing functional enrichment analysis on non-model teleost fish transcriptome data. The Blast2Fish pipeline was designed to be a reference-based enrichment method. Instead of annotating the BLAST single top hit by a pre-defined gene-to-tag database, we included 500 hits to search related PubMed articles and parse biological terms. These descriptive terms were then sorted and recorded as annotations for the query. The results showed that Blast2Fish was capable of providing meaningful annotations on immunology topics for non-model fish transcriptome analysis. CONCLUSION: Blast2Fish provides a novel approach for annotating sequences of non-model fish. The reference-based strategy allows annotation to be performed without pre-defined tags for each gene. This method strongly benefits non-model teleost fish studies for gene functional enrichment analysis.


Assuntos
Biologia Computacional/métodos , Proteínas de Peixes/genética , Peixes/genética , Anotação de Sequência Molecular/métodos , Animais , Bases de Dados de Ácidos Nucleicos , Proteínas de Peixes/química , Proteínas de Peixes/metabolismo , Peixes/metabolismo , Perfilação da Expressão Gênica , Genômica , Sequenciamento de Nucleotídeos em Larga Escala , Internet , Software , Transcriptoma
12.
Cell Mol Life Sci ; 77(21): 4223-4236, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-32367192

RESUMO

The determination of sex is an important hallmark in the life cycle of organisms, in which the fate of gonads and then the individual sex are defined. In gonochoristic teleost fish, this process is characterized by a high plasticity, considering that in spite of genotypic sex many environmental factors can cause shifts from one to another molecular pathway, resulting in organisms with mismatching genotypic and phenotypic sexes. Interestingly, in most instances, both female-to-male or male-to-female sex-reversed individuals develop functional gonads with normal gametogenesis and respective progenies with full viability. The study of these mechanisms is being spread to other non-model species or to those inhabiting more extreme environmental conditions. Although water temperature is an important mechanism involved in sex determination, there are other environmental stressors affected by the climate change which are also implicated in stress response-induced masculinization in fish. In this regard, the brain has emerged as the transducer of the environment input that can influence the gonadal fate. Furthermore, the evaluation of other environmental stressors or their synergic effect on sex determination at conditions that simulate the natural environments is growing gradually. Within such scope, the concerns related to climate change impacts rely on the fact that many of biotic and abiotic parameters reported to affect sex ratios are expected to increase concomitantly as a result of increased greenhouse gas emissions and, particularly worrying, many of them are related to male bias in the populations, such as high temperature, hypoxia, and acidity. These environmental changes can also generate epigenetic changes in sex-related genes affecting their expression, with implications on sex differentiation not only of exposed individuals but also in following generations. The co-analysis of multi-stressors with potential inter- and transgenerational effects is essential to allow researchers to perform long-term predictions on climate change impacts in wild populations and for establishing highly accurate monitoring tools and suitable mitigation strategies.


Assuntos
Peixes/fisiologia , Processos de Determinação Sexual , Animais , Mudança Climática , Meio Ambiente , Epigênese Genética , Feminino , Peixes/genética , Regulação da Expressão Gênica no Desenvolvimento , Masculino , Diferenciação Sexual , Estresse Fisiológico
13.
Nat Commun ; 11(1): 2669, 2020 05 29.
Artigo em Inglês | MEDLINE | ID: mdl-32472063

RESUMO

Reef fishes are an exceptionally speciose vertebrate assemblage, yet the main drivers of their diversification remain unclear. It has been suggested that Miocene reef rearrangements promoted opportunities for lineage diversification, however, the specific mechanisms are not well understood. Here, we assemble near-complete reef fish phylogenies to assess the importance of ecological and geographical factors in explaining lineage origination patterns. We reveal that reef fish diversification is strongly associated with species' trophic identity and body size. Large-bodied herbivorous fishes outpace all other trophic groups in recent diversification rates, a pattern that is consistent through time. Additionally, we show that omnivory acts as an intermediate evolutionary step between higher and lower trophic levels, while planktivory represents a common transition destination. Overall, these results suggest that Miocene changes in reef configurations were likely driven by, and subsequently promoted, trophic innovations. This highlights trophic evolution as a key element in enhancing reef fish diversification.


Assuntos
Biodiversidade , Evolução Biológica , Peixes/classificação , Especiação Genética , Animais , Coevolução Biológica , Tamanho Corporal , Recifes de Corais , Peixes/genética , Geografia , Herbivoria , Filogenia
14.
PLoS Genet ; 16(4): e1008658, 2020 04.
Artigo em Inglês | MEDLINE | ID: mdl-32302300

RESUMO

Understanding the extent to which ecological divergence is repeatable is essential for predicting responses of biodiversity to environmental change. Here we test the predictability of evolution, from genotype to phenotype, by studying parallel evolution in a salmonid fish, Arctic charr (Salvelinus alpinus), across eleven replicate sympatric ecotype pairs (benthivorous-planktivorous and planktivorous-piscivorous) and two evolutionary lineages. We found considerable variability in eco-morphological divergence, with several traits related to foraging (eye diameter, pectoral fin length) being highly parallel even across lineages. This suggests repeated and predictable adaptation to environment. Consistent with ancestral genetic variation, hundreds of loci were associated with ecotype divergence within lineages of which eight were shared across lineages. This shared genetic variation was maintained despite variation in evolutionary histories, ranging from postglacial divergence in sympatry (ca. 10-15kya) to pre-glacial divergence (ca. 20-40kya) with postglacial secondary contact. Transcriptome-wide gene expression (44,102 genes) was highly parallel across replicates, involved biological processes characteristic of ecotype morphology and physiology, and revealed parallelism at the level of regulatory networks. This expression divergence was not only plastic but in part genetically controlled by parallel cis-eQTL. Lastly, we found that the magnitude of phenotypic divergence was largely correlated with the genetic differentiation and gene expression divergence. In contrast, the direction of phenotypic change was mostly determined by the interplay of adaptive genetic variation, gene expression, and ecosystem size. Ecosystem size further explained variation in putatively adaptive, ecotype-associated genomic patterns within and across lineages, highlighting the role of environmental variation and stochasticity in parallel evolution. Together, our findings demonstrate the parallel evolution of eco-morphology and gene expression within and across evolutionary lineages, which is controlled by the interplay of environmental stochasticity and evolutionary contingencies, largely overcoming variable evolutionary histories and genomic backgrounds.


Assuntos
Ecótipo , Evolução Molecular , Peixes/anatomia & histologia , Peixes/genética , Expressão Gênica , Variação Genética , Genoma/genética , Animais , Ecologia , Feminino , Deriva Genética , Especiação Genética , Genética Populacional , Genômica , Masculino , Simpatria
15.
BMC Genomics ; 21(1): 278, 2020 Apr 03.
Artigo em Inglês | MEDLINE | ID: mdl-32245399

RESUMO

BACKGROUND: Scatophagus argus is a popular farmed fish in several countries of Southeast Asia, including China. Although S. argus has a highly promising economic value, a significant lag of breeding research severely obstructs the sustainable development of aquaculture industry. As one of the most important economic traits, growth traits are controlled by multiple gene loci called quantitative trait loci (QTLs). It is urgently needed to launch a marker assisted selection (MAS) breeding program to improve growth and other pivotal traits. Thus a high-density genetic linkage map is necessary for the fine mapping of QTLs associated with target traits. RESULTS: Using restriction site-associated DNA sequencing, 6196 single nucleotide polymorphism (SNP) markers were developed from a full-sib mapping population for genetic map construction. A total of 6193 SNPs were grouped into 24 linkage groups (LGs), and the total length reached 2191.65 cM with an average marker interval of 0.35 cM. Comparative genome mapping revealed 23 one-to-one and 1 one-to-two syntenic relationships between S. argus LGs and Larimichthys crocea chromosomes. Based on the high-quality linkage map, a total of 44 QTLs associated with growth-related traits were identified on 11 LGs. Of which, 19 significant QTLs for body weight were detected on 9 LGs, explaining 8.8-19.6% of phenotypic variances. Within genomic regions flanking the SNP markers in QTL intervals, we predicted 15 candidate genes showing potential relationships with growth, such as Hbp1, Vgll4 and Pim3, which merit further functional exploration. CONCLUSIONS: The first SNP genetic map with a fine resolution of 0.35 cM for S. argus has been developed, which shows a high level of syntenic relationship with L. crocea genomes. This map can provide valuable information for future genetic, genomic and evolutionary studies. The QTLs and SNP markers significantly associated with growth-related traits will act as useful tools in gene mapping, map-based cloning and MAS breeding to speed up the genetic improvement in important traits of S. argus. The interesting candidate genes are promising for further investigations and have the potential to provide deeper insights into growth regulation in the future.


Assuntos
Mapeamento Cromossômico/métodos , Peixes/crescimento & desenvolvimento , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas , Mapeamento por Restrição/métodos , Animais , Cruzamento , China , Cromossomos/genética , Pesqueiros , Peixes/genética , Marcadores Genéticos , Genótipo , Fenótipo , Sintenia
16.
PLoS One ; 15(4): e0231356, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32298330

RESUMO

The ancestor of most teleost fishes underwent a whole-genome duplication event three hundred million years ago. Despite its antiquity, the effects of this event are evident both in the structure of teleost genomes and in how the surviving duplicated genes still operate to drive form and function. I inferred a set of shared syntenic regions that survive from the teleost genome duplication (TGD) using eight teleost genomes and the outgroup gar genome (which lacks the TGD). I then phylogenetically modeled the TGD's resolution via shared and independent gene losses and applied a new simulation-based statistical test for the presence of bias toward the preservation of genes from one parental subgenome. On the basis of that test, I argue that the TGD was likely an allopolyploidy. I find that duplicate genes surviving from this duplication in zebrafish are less likely to function in early embryo development than are genes that have returned to single copy at some point in this species' history. The tissues these ohnologs are expressed in, as well as their biological functions, lend support to recent suggestions that the TGD was the source of a morphological innovation in the structure of the teleost retina. Surviving duplicates also appear less likely to be essential than singletons, despite the fact that their single-copy orthologs in mouse are no less essential than other genes.


Assuntos
Evolução Molecular , Peixes/genética , Poliploidia , Animais , Peixes/classificação , Genoma , Filogenia
17.
Cytogenet Genome Res ; 160(3): 148-155, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32272470

RESUMO

Transposable elements have driven genome evolution and plasticity in many ways across a range of organisms. Different types of biotic and abiotic stresses can stimulate the expression or transposition of these mobile elements. Here, we cytogenetically analyzed natural fish populations of the same species living under different environmental conditions to test the influence and organization of transposable elements in their genome. Differential behavior was observed for the markers Rex 1, Rex 3, and Rex 6 in the chromosomes of individuals of the same species but coming from different environments (polluted and unpolluted). An increase in the number of Rex transposable elements in the chromosomes and their influence on the genome of populations living in a polluted environment indicates that they must be under constant adaptive evolution.


Assuntos
Adaptação Fisiológica/genética , Elementos de DNA Transponíveis/genética , Evolução Molecular , Peixes/genética , Animais , Cromossomos/genética , Genoma/genética , Rios , Estresse Fisiológico/genética
18.
PLoS One ; 15(4): e0231718, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32310994

RESUMO

Water sampling and filtration of environmental DNA (eDNA) analysis have been performed by several different methods, and each method may yield a different species composition or eDNA concentration. Here, we investigated the eDNA of seawater samples directly collected by SCUBA to compare two widely used filtration methods: open filtration with a glass filter (GF/F) and enclosed filtration (Sterivex). We referred to biomass based on visual observation data collected simultaneously to clarify the difference between organism groups. Water samples were collected at two points in the Sea of Japan in May, September and December 2018. The respective samples were filtered through GF/F and Sterivex for eDNA extraction. We quantified the eDNA concentration of five fish and two cnidarian species by quantitative polymerase chain reaction (qPCR) using species-specific primers/probe sets. A strong correlation of eDNA concentration was obtained between GF/F and Sterivex; the intercepts and slopes of the linear regression lines were slightly different in fish and jellyfish. The amount of eDNA detected using the GF/F filtration method was higher than that detected using Sterivex when the eDNA concentration was high; the opposite trend was observed when the eDNA concentration was relatively low. The concentration of eDNA correlated with visually estimated biomass; eDNA concentration per biomass in jellyfish was approximately 700 times greater than that in fish. We conclude that GF/F provides an advantage in collecting a large amount of eDNA, whereas Sterivex offers superior eDNA sensitivity. Both filtration methods are effective in estimating the spatiotemporal biomass size of target marine species.


Assuntos
Cnidários/genética , DNA Ambiental/genética , Filtração/instrumentação , Peixes/genética , Água do Mar/análise , Animais , DNA Ambiental/análise , DNA Ambiental/isolamento & purificação , Desenho de Equipamento , Cifozoários/genética
19.
Nat Ecol Evol ; 4(6): 841-852, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32231327

RESUMO

Sturgeons seem to be frozen in time. The archaic characteristics of this ancient fish lineage place it in a key phylogenetic position at the base of the ~30,000 modern teleost fish species. Moreover, sturgeons are notoriously polyploid, providing unique opportunities to investigate the evolution of polyploid genomes. We assembled a high-quality chromosome-level reference genome for the sterlet, Acipenser ruthenus. Our analysis revealed a very low protein evolution rate that is at least as slow as in other deep branches of the vertebrate tree, such as that of the coelacanth. We uncovered a whole-genome duplication that occurred in the Jurassic, early in the evolution of the entire sturgeon lineage. Following this polyploidization, the rediploidization of the genome included the loss of whole chromosomes in a segmental deduplication process. While known adaptive processes helped conserve a high degree of structural and functional tetraploidy over more than 180 million years, the reduction of redundancy of the polyploid genome seems to have been remarkably random.


Assuntos
Peixes/genética , Genoma , Animais , Cromossomos , Filogenia , Poliploidia
20.
BMC Genomics ; 21(1): 223, 2020 Mar 11.
Artigo em Inglês | MEDLINE | ID: mdl-32160866

RESUMO

BACKGROUND: Based on an initial collecting of database sequences from the gap junction protein gene family (also called connexin genes) in a few teleosts, the naming of these sequences appeared variable. The reasons could be (i) that the structure in this family is variable across teleosts, or (ii) unfortunate naming. Rather clear rules for the naming of genes in fish and mammals have been outlined by nomenclature committees, including the naming of orthologous and ohnologous genes. We therefore analyzed the connexin gene family in teleosts in more detail. We covered the range of divergence times in teleosts (eel, Atlantic herring, zebrafish, Atlantic cod, three-spined stickleback, Japanese pufferfish and spotted pufferfish; listed from early divergence to late divergence). RESULTS: The gene family pattern of connexin genes is similar across the analyzed teleosts. However, (i) several nomenclature systems are used, (ii) specific orthologous groups contain genes that are named differently in different species, (iii) several distinct genes have the same name in a species, and (iv) some genes have incorrect names. The latter includes a human connexin pseudogene, claimed as GJA4P, but which in reality is Cx39.2P (a delta subfamily gene often called GJD2like). We point out the ohnologous pairs of genes in teleosts, and we suggest a more consistent nomenclature following the outlined rules from the nomenclature committees. We further show that connexin sequences can indicate some errors in two high-quality chromosome assemblies that became available very recently. CONCLUSIONS: Minimal consistency exists in the present practice of naming teleost connexin genes. A consistent and unified nomenclature would be an advantage for future automatic annotations and would make various types of subsequent genetic analyses easier. Additionally, roughly 5% of the connexin sequences point out misassemblies in the new high-quality chromosome assemblies from herring and cod.


Assuntos
Conexinas/genética , Peixes/genética , Análise de Sequência de DNA/métodos , Animais , Proteínas de Peixes/genética , Família Multigênica , Filogenia , Terminologia como Assunto
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