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1.
Genes (Basel) ; 10(9)2019 09 13.
Artigo em Inglês | MEDLINE | ID: mdl-31540274

RESUMO

The pikeperch (Sander lucioperca) is a fresh and brackish water Percid fish natively inhabiting the northern hemisphere. This species is emerging as a promising candidate for intensive aquaculture production in Europe. Specific traits like cannibalism, growth rate and meat quality require genomics based understanding, for an optimal husbandry and domestication process. Still, the aquaculture community is lacking an annotated genome sequence to facilitate genome-wide studies on pikeperch. Here, we report the first highly contiguous draft genome assembly of Sander lucioperca. In total, 413 and 66 giga base pairs of DNA sequencing raw data were generated with the Illumina platform and PacBio Sequel System, respectively. The PacBio data were assembled into a final assembly size of ~900 Mb covering 89% of the 1,014 Mb estimated genome size. The draft genome consisted of 1966 contigs ordered into 1,313 scaffolds. The contig and scaffold N50 lengths are 3.0 Mb and 4.9 Mb, respectively. The identified repetitive structures accounted for 39% of the genome. We utilized homologies to other ray-finned fishes, and ab initio gene prediction methods to predict 21,249 protein-coding genes in the Sander lucioperca genome, of which 88% were functionally annotated by either sequence homology or protein domains and signatures search. The assembled genome spans 97.6% and 96.3% of Vertebrate and Actinopterygii single-copy orthologs, respectively. The outstanding mapping rate (99.9%) of genomic PE-reads on the assembly suggests an accurate and nearly complete genome reconstruction. This draft genome sequence is the first genomic resource for this promising aquaculture species. It will provide an impetus for genomic-based breeding studies targeting phenotypic and performance traits of captive pikeperch.


Assuntos
Genoma , Percas/genética , Animais , Proteínas de Peixes/genética , Anotação de Sequência Molecular , Percas/classificação , Filogenia , Sequenciamento Completo do Genoma
2.
Int J Mol Sci ; 20(17)2019 Aug 30.
Artigo em Inglês | MEDLINE | ID: mdl-31480228

RESUMO

Karyotypic data from Australian native freshwater fishes are scarce, having been described from relatively few species. Golden perch (Macquaria ambigua) and Murray cod (Maccullochella peelii) are two large-bodied freshwater fish species native to Australia with significant indigenous, cultural, recreational and commercial value. The arid landscape over much of these fishes' range, coupled with the boom and bust hydrology of their habitat, means that these species have potential to provide useful evolutionary insights, such as karyotypes and sex chromosome evolution in vertebrates. Here we applied standard and molecular cytogenetic techniques to characterise karyotypes for golden perch and Murray cod. Both species have a diploid chromosome number 2n = 48 and a male heterogametic sex chromosome system (XX/XY). While the karyotype of golden perch is composed exclusively of acrocentric chromosomes, the karyotype of Murray cod consists of two submetacentric and 46 subtelocentric/acrocentric chromosomes. We have identified variable accumulation of repetitive sequences (AAT)10 and (CGG)10 along with diverse methylation patterns, especially on the sex chromosomes in both species. Our study provides a baseline for future cytogenetic analyses of other Australian freshwater fishes, especially species from the family Percichthyidae, to better understand their genome and sex chromosome evolution.


Assuntos
Água Doce , Cariótipo , Percas/genética , Perciformes/genética , Cromossomos Sexuais/genética , Animais , Bandeamento Cromossômico , Metilação de DNA/genética , Feminino , Geografia , Masculino , Metáfase , Repetições de Microssatélites/genética , Filogenia , Especificidade da Espécie , Telômero/genética
3.
Ecotoxicol Environ Saf ; 181: 130-137, 2019 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-31176247

RESUMO

The pikeperch Sander lucioperca is an economically important freshwater species that is currently threatened by higher summer temperatures caused by global warming. To clarify the physiological state of pikeperch reared under relatively high temperatures and to acquire valuable biomarkers to monitor heat stress in this species, 100 fish were subjected to five different temperature treatments, ranging from 23 °C (control) to 36 °C. The physiological and biochemical indexes of liver and blood were determined, and heat-shock cognate 70 kDa protein (Hsc70) mRNA expression profiles were analyzed. The results showed that the activities of superoxide dismutase, catalase, and glutathione peroxidase in heat-stressed pikeperch first increased and then decreased, exhibiting peaks at 34 °C, 28 °C, and 28 °C, respectively. The level of thiobarbituric acid-reactive substances (TBARS) in all experimental groups was significantly higher than that of the control. The numbers of red blood cells, the packed-cell volume, and the contents of hemoglobin were significantly higher in the 34 °C and 36 °C treatment groups. Under heat stress, the albumin, cholesterol, and triglycerides contents decreased with increasing temperatures. Real-time fluorescence-based quantitative RT-PCR showed that Hsc70 mRNA levels increased in all eight of the tested tissues under heat stress. Expression reached maximum levels at 34 °C in the muscle, heart and gill tissues, and at 36 °C in the other five tissues. These results demonstrate that several physiological and biochemical phenotypes, such as oxidative stress, antioxidant enzymes and molecular chaperones, could be important biomarkers of heat stress in pikeperch, and are potentially valuable to uncover the mechanisms of heat-stress responses in fish.


Assuntos
Proteínas de Peixes/metabolismo , Proteínas de Choque Térmico HSC70/metabolismo , Resposta ao Choque Térmico , Percas/metabolismo , Animais , Antioxidantes/metabolismo , Catalase/metabolismo , Contagem de Eritrócitos , Proteínas de Peixes/genética , Glutationa Peroxidase/metabolismo , Proteínas de Choque Térmico HSC70/genética , Resposta ao Choque Térmico/genética , Hemoglobinas/análise , Fígado/enzimologia , Fígado/metabolismo , Estresse Oxidativo , Percas/genética , Superóxido Dismutase/metabolismo , Substâncias Reativas com Ácido Tiobarbitúrico/metabolismo
4.
PLoS One ; 14(5): e0215933, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31063465

RESUMO

Considering the divergent temperature habitats and morphological traits of four Percidae species: yellow perch (Perca flavescens), Eurasian perch (Perca fluviatilis), pike perch (Sander lucioperca), and ruffe (Gymnocephalus cernua), we stepped into the transcriptome level to discover genes and mechanisms that drive adaptation to different temperature environments and evolution in body shape. Based on 93,566 to 181,246 annotated unigenes of the four species, we identified 1,117 one-to-one orthologous genes and subsequently constructed the phylogenetic trees that are consistent with previous studies. Together with the tree, the ratios of nonsynonymous to synonymous substitutions presented decreased evolutionary rates from the D. rerio branch to the sub-branch clustered by P. flavescens and P. fluviatilis. The specific 93 fast-evolving genes and 57 positively selected genes in P. flavescens, compared with 22 shared fast-evolving genes among P. fluviatilis, G. cernua, and S. lucioperca, showed an intrinsic foundation that ensure its adaptation to the warmer Great Lakes and farther south, especially in functional terms like "Cul4-RING E3 ubiquitin ligase complex." Meanwhile, the specific 78 fast-evolving genes and 41 positively selected genes in S. lucioperca drew a clear picture of how it evolved to a large and elongated body with camera-type eyes and muscle strength so that it could occupy the highest position in the food web. Overall, our results uncover genetic basis that support evolutionary adaptation of temperature and body shape in four Percid species, and could furthermore assist studies on environmental adaptation in fishes.


Assuntos
Adaptação Fisiológica/genética , Evolução Molecular , Perfilação da Expressão Gênica , Percas/genética , Percas/fisiologia , Temperatura Ambiente , Animais , Anotação de Sequência Molecular , Percas/anatomia & histologia
5.
Genes (Basel) ; 10(2)2019 02 25.
Artigo em Inglês | MEDLINE | ID: mdl-30823620

RESUMO

Olfaction, which is mediated by olfactory receptor (OR) genes, is essential in the daily life of fish, especially in foraging. However, Chinese perch (Siniperca chuatsi) is believed to prey with reliance on vision and lateral sensation, but not on olfaction. Therefore, understanding the evolutionary dynamics of the Chinese perch OR repertoire could provide insights into genetic evidence for adapting to a decreasing reliance on olfaction. Here, we reported a whole-genome analysis of the Chinese perch OR repertoire. Our analysis identified a total of 152 OR genes, including 123 functional genes and 29 pseudogenes, and showed their genomic organization. A phylogenetic tree was constructed, and the phylogenetic relationships of teleosts ORs was illustrated. The dN/dS (global ratios of non-synonymous to synonymous) analysis demonstrated that OR groups all appeared to be under purifying selection. Among the five Percomorpha fishes, Chinese perch only had 22 subfamilies, suggesting a decrease in OR diversities. The species-specific loss of subfamily 56 and 66 in Chinese perch, of which the genes belonged to subfamily 66, were orthologs of OR51E2, which recognized the plant odorant ß-ionone, indicating that extremely piscivorous fish which might lose those receptors responded to plant-related odors. Finally, the expression profiles of OR genes in the olfactory epithelium at different developmental stages were investigated using RNA-seq data. From the aforementioned results, the evolution of the OR repertoire may be shaped by the adaption of vision-dependent specializations for foraging in Chinese perch. The first systematic study of OR genes in Chinese perch could provide valuable genomic resources for the further investigation of olfactory function in teleosts.


Assuntos
Proteínas de Peixes/genética , Percas/genética , Receptores Odorantes/genética , Motivos de Aminoácidos , Animais , Evolução Molecular , Proteínas de Peixes/química , Proteínas de Peixes/metabolismo , Mucosa Olfatória/metabolismo , Percas/classificação , Percas/fisiologia , Filogenia , Polimorfismo Genético , Receptores Odorantes/química , Receptores Odorantes/metabolismo , Seleção Genética
6.
Syst Biol ; 68(2): 329-346, 2019 03 01.
Artigo em Inglês | MEDLINE | ID: mdl-30395332

RESUMO

Evolutionary history is typically portrayed as a branching phylogenetic tree, yet not all evolution proceeds in a purely bifurcating manner. Introgressive hybridization is one process that results in reticulate evolution. Most known examples of genome-wide introgression occur among closely related species with relatively recent common ancestry; however, we present evidence for ancient hybridization and genome-wide introgression between major stem lineages of darters, a species-rich clade of North American freshwater fishes. Previous attempts to resolve the relationships of darters have been confounded by the uncertain phylogenetic resolution of the lineage Allohistium. In this study, we investigate the phylogenomics of darters, specifically the relationships of Allohistium, through analyses of approximately 30,000 RADseq loci sampled from 112 species. Our phylogenetic inferences are based on traditional approaches in combination with strategies that accommodate reticulate evolution. These analyses result in a novel phylogenetic hypothesis for darters that includes ancient introgression between Allohistium and other two major darter lineages, minimally occurring 20 million years ago. Darters offer a compelling case for the necessity of incorporating phylogenetic networks in reconstructing the evolutionary history of diversification in species-rich lineages. We anticipate that the growing wealth of genomic data for clades of non-model organisms will reveal more examples of ancient hybridization, eventually requiring a re-evaluation of how evolutionary history is visualized and utilized in macroevolutonary investigations.


Assuntos
Percas/classificação , Filogenia , Animais , Variação Genética , Genoma/genética , América do Norte , Percas/genética
7.
Physiol Biochem Zool ; 91(6): 1115-1128, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-30295572

RESUMO

The pace-of-life syndrome (POLS) concept predicts that individuals with high baseline metabolic rates demonstrate high boldness, aggressiveness, and activity, especially in food acquisition, with associated relatively greater energy requirements. In fishes, these behaviors may increase individual vulnerability to angling. To test the predictions of the POLS concept, we quantified individual standard metabolic rate (SMR) and boldness in both wild-caught and hatchery-reared Eurasian perch (Perca fluviatilis). We found both SMR and boldness to be repeatable traits but detected no correlation between them. Individual vulnerability to angling was assessed in the hatchery-reared perch, but we found no difference in boldness or SMR between vulnerable and nonvulnerable perch. Wild-caught perch were ice fished using either natural or artificial bait, and we observed no differences in boldness or SMR with respect to bait type or capture order. Our findings do not support the predictions of the POLS concept and, consistent with earlier studies in perch, suggest that angling may not drive selection against boldness in this species.


Assuntos
Agressão , Metabolismo Basal , Pesqueiros , Percas/fisiologia , Tiroxina/sangue , Animais , Comportamento Alimentar , Finlândia , Percas/genética , Fenótipo
8.
G3 (Bethesda) ; 8(12): 3737-3743, 2018 12 10.
Artigo em Inglês | MEDLINE | ID: mdl-30355765

RESUMO

The Eurasian perch (Perca fluviatilis) is the most common fish of the Percidae family and is widely distributed across Eurasia. Perch is a popular target for professional and recreational fisheries, and a promising freshwater aquaculture species in Europe. However, despite its high ecological, economical and societal importance, the available genomic resources for P. fluviatilis are rather limited. In this work, we report de novo assembly and annotation of the whole genome sequence of perch. The linked-read based technology with 10X Genomics Chromium chemistry and Supernova assembler produced a draft perch genome ∼1.0 Gbp assembly (scaffold N 50 = 6.3 Mb; the longest individual scaffold of 29.3 Mb; BUSCO completeness of 88.0%), which included 281.6 Mb of putative repeated sequences. The perch genome assembly presented here, generated from small amount of starting material (0.75 ng) and a single linked-read library, is highly continuous and considerably more complete than the currently available draft of P. fluviatilis genome. A total of 23,397 protein-coding genes were predicted, 23,171 (99%) of which were annotated functionally from either sequence homology or protein signature searches. Linked-read technology enables fast, accurate and cost-effective de novo assembly of large non-model eukaryote genomes. The highly continuous assembly of the Eurasian perch genome presented in this study will be an invaluable resource for a range of genetic, ecological, physiological, ecotoxicological, functional and comparative genomic studies in perch and other fish species of the Percidae family.


Assuntos
Proteínas de Peixes/genética , Genoma/genética , Percas/genética , Animais , Sequenciamento de Nucleotídeos em Larga Escala
9.
Environ Pollut ; 243(Pt B): 1657-1668, 2018 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-30296762

RESUMO

This study aimed to better understand in situ cumulative effects of anthropogenic stressors on the health of St. Lawrence River (QC, Canada) yellow perch populations using high-throughput transcriptomics and a multi-biological level approach. Fish were collected in the upstream fluvial Lake Saint-François (LSF) with low degree of environmental perturbations; Lake Saint-Louis (LSL) considered having a moderate degree of anthropogenic stressors, and Lake Saint-Pierre (LSP) a sector where the perch population has been severely declining. Morphometric results indicated that fish from the downstream LSP showed lower body condition compared to LSF and LSL. Liver transcriptomic responses were assessed by RNA-sequencing. Two hundred and eighty genes were over-transcribed in LSP perch while 200 genes were under-transcribed compared to LSF and LSL. In LSP fish, genes transcripts related to reproduction, retinol, iron, thyroid hormones, oxidative stress, lipid metabolism and immune functions were among the most abundant suggesting that multiple metabolic and physiological pathways were impacted by environmental stressors at this site. Inhibition of liver superoxide dismutase, catalase and glutathione S-transferase activities were also observed at the cellular level. Overall, identified impacted biological pathways in perch from LSP may help understand the precarious state of this population and identify the factors inhibiting its recovery.


Assuntos
Fígado/metabolismo , Estresse Oxidativo/efeitos dos fármacos , Percas/genética , Percas/fisiologia , Poluentes Químicos da Água/análise , Poluentes Químicos da Água/toxicidade , Animais , Canadá , Catalase/antagonistas & inibidores , Catalase/genética , Catalase/metabolismo , Perfilação da Expressão Gênica , Glutationa Transferase/antagonistas & inibidores , Sequenciamento de Nucleotídeos em Larga Escala , Lagos , Metabolismo dos Lipídeos/genética , RNA/genética , Rios , Superóxido Dismutase/antagonistas & inibidores , Hormônios Tireóideos/genética , Vitamina A/genética , Vitamina A/metabolismo
10.
Proc Biol Sci ; 285(1884)2018 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-30068684

RESUMO

Agonistic character displacement (ACD) occurs when selection to avoid maladaptive interspecific aggression leads to the evolution of agonistic signals and/or associated behavioural biases in sympatry. Here, we test for a pattern consistent with ACD in male colour pattern in darters (Percidae: Etheostoma). Male colour pattern has been shown to function in male-male competition rather than female mating preferences in several darter species. Additionally, males bias their aggression towards conspecific over heterospecific males in sympatry but not in allopatry, consistent with divergent ACD in male behavioural biases. We use a common garden approach to show that differences in male colour pattern among four closely related darter species are genetically based. Additionally, we demonstrate that some aspects of male colour pattern exhibit enhanced differences in sympatric compared to allopatric populations of two darter species, consistent with ACD. However, other male colour traits are more similar between species in sympatry compared with allopatry, indicating that not all signal components are under strong divergent selection in sympatry. This study provides evidence that interspecific male-male aggressive interactions alone can promote elaborate male signal evolution both between and within species. We discuss the implications this has for male-driven ACD and cascade ACD.


Assuntos
Comportamento Animal , Cor , Percas/genética , Agressão , Animais , Feminino , Masculino , Percas/anatomia & histologia , Percas/fisiologia , Fenótipo , Especificidade da Espécie , Simpatria
11.
PLoS One ; 13(7): e0200001, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29995906

RESUMO

BACKGROUND: Geological evolution of the African continent has been subject to complex processes including uplift, volcanism, desert formation and tectonic rifting. This complex geology has created substantial biogeographical barriers, and coupled with anthropogenic introductions of freshwater fishes, has influenced the genetic diversity, connectivity and sub-structuring of the teleost fauna. Nile perch, Lates niloticus, is an iconic fish in Africa and is of high commercial importance, both in the species' native range and where it has been translocated. However, the species is in decline and there is a need to understand its population genetic structure to facilitate sustainable management of the fishery and aquaculture development. METHODOLOGY: Nile perch tissue samples were acquired from two West and four East (Lakes; Albert, Kyoga, Victoria and Turkana) African locations. Nineteen polymorphic microsatellite loci were used to study the genetic variation among populations across regions (West and East Africa), as well as between native and introduced environments within East Africa. PRINCIPAL FINDINGS AND THEIR SIGNIFICANCE: Results revealed strong and significant genetic structuring among populations across the sampled distribution (divergence across regions, FCT = 0.26, P = 0.000). STRUCTURE analysis at a broad scale revealed K = 2 clusters, the West African individuals were assigned to one cluster, while all individuals from the East African region, regardless of whether native or introduced, were assigned to another cluster. The distinct genetic clusters identified in the current study between the West and East African Nile perch, appear to have been maintained by presence of biogeographic barriers and restricted gene flow between the two regions. Therefore, any translocations of Nile perch should be carefully considered across the regions of West and East Africa. Further analysis at a regional scale revealed further structuring of up to K = 3 genetic clusters in East African Nile perch. Significantly (P < 0.05) lower genetic diversity based on analysis of allelic richness (AR) was obtained for the two translocated populations of Lake Kyoga (AR = 3.61) and Lake Victoria (AR = 3.52), compared to Nile perch populations from their putative origins of Lakes Albert (AR = 4.12) and Turkana (AR = 4.43). The lower genetic diversity in the translocated populations may be an indication of previous bottlenecks and may also indicate a difficulty for these populations to persist and adapt to climatic changes and anthropogenic pressures that are currently present in the East African region.


Assuntos
Fluxo Gênico , Lagos , Percas/genética , Rios , África , Migração Animal , Animais , Variação Genética , Técnicas de Genotipagem
12.
J Fish Biol ; 92(4): 1090-1109, 2018 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-29479689

RESUMO

Headwater-resident fishes may be prone to a high rate of isolation and a pronounced hierarchical genetic structure due to a combination of niche preference and dendritic effects of river networks. Genetic isolation patterns were compared using microsatellites in six headwater fishes, Fundulus olivaceus, Semotilus atromaculatus, Erimyzon claviformis, Etheostoma artesiae, Etheostoma whipplei and Etheostoma parvipinne, in three geographic regions that included drainages of small, medium and large sizes in the southern United States. All species showed hierarchical nesting of genetic populations and there were clear and mostly consistent differences between species and regions that were identified through summary statistics derived from two independent analyses. For species comparisons, a high isolation grouping (increased number of isolated genetic clusters or sites within regions) and a low-isolation grouping (decreased number of clusters or sites) were identified. Species group placement was related to niche breadth along the river continuum and presumed abundance and variability of preferred microhabitats, with increased headwater specialization among species being associated with placement in the high-isolation grouping. There was a weakly significant positive effect of drainage size on the number of isolated clusters or sites across all species. Regional patterns were shared in two species, with the region containing the smallest drainages having lower rates of isolation in both datasets. This study shows the effects of regional and species characteristics on genetic isolation for headwater species, which are especially prone to isolation due to spatial, dendritic effects of river networks.


Assuntos
Fundulidae/genética , Genética Populacional , Percas/genética , Isolamento Reprodutivo , Animais , Ecossistema , Geografia , Repetições de Microssatélites , Rios , Estados Unidos
13.
J Fish Biol ; 92(1): 94-104, 2018 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-29124770

RESUMO

This study characterized the gastrointestinal microbiome of nine juvenile farmed pikeperch Sander lucioperca using a metagenomics approach based on bacterial 16S rRNA gene sequencing. Potential changes in the gut microbiota during 2 months of S. lucioperca juvenile life were investigated. Results revealed that gut microbiota was dominated by Proteobacteria (95-92%), while other phyla Firmicutes (1-1·5%) and Actinobacteria (0·9-1·5%) were less abundant. At the family level, fish-gut microbiota were dominated by Enterobacteriaceae, which constituted c. 83% of all DNA sequence reads. Such a situation was present in all of the examined fish except one, which showed a different proportion of particular microbial taxa than the other fish. In this fish, a higher relative abundance (%) of Fusobacteria (21·0%), Bacteroidetes (9·5%) and Firmicutes (7·5%) was observed. There were no significant differences in the gut microbiome structure at different stages of development in the examined fish. This may indicate that Proteobacteria inhabiting the gut microbiota at an early stage of life are a necessary component of the pikeperch microbiome that may support proper nutrition of the fish. The information obtained on the gut microbiome could be useful in determining juvenile S. lucioperca health and improving rearing conditions by welfare monitoring in aquaculture.


Assuntos
Microbioma Gastrointestinal , Percas/microbiologia , Animais , Aquicultura , DNA Bacteriano/química , Metagenômica , Percas/genética , Percas/crescimento & desenvolvimento , Proteobactérias , RNA Ribossômico 16S/genética
14.
Genome ; 61(1): 1-6, 2018 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-28950069

RESUMO

The ribosomal intergenic spacer (IGS), responsible for the rate of transcription of rRNA genes, is associated with the growth and fecundity of individuals. A previous study of IGS length variants in a yellow perch (Perca flavescens) population revealed the presence of two predominant alleles differing by 1 kb due to variation in the number of repeat units. This study aims to assess whether length variation of IGS is the result of selection in natural populations. Length variation of IGS and 11 neutral microsatellite loci were assessed in geographically distant yellow perch populations. Most populations displayed the very same IGS alleles; they did not differ in frequencies among populations and the FST was not significantly different from zero. In contrast, diversity at microsatellite loci was high and differed among populations (FST = 0.18). Selection test based on FST identified IGS as a significant outlier from neutral expectations for population differentiation. Heterozygote excess was also detected in one specific cohort, suggesting temporal variation in the selection regime. While the exact mechanism remains to be specified, together the results of this study support the contention that balancing selection is acting to maintain two distinct IGS alleles in natural fish populations.


Assuntos
DNA Espaçador Ribossômico/química , Percas/genética , Seleção Genética , Sequências de Repetição em Tandem , Animais , Repetições de Microssatélites
15.
Mol Ecol ; 27(1): 196-215, 2018 01.
Artigo em Inglês | MEDLINE | ID: mdl-29165848

RESUMO

Populations that are adaptively divergent but maintain high gene flow may have greater resilience to environmental change as gene flow allows the spread of alleles that have already been tested elsewhere. In addition, populations naturally subjected to ecological disturbance may already hold resilience to future environmental change. Confirming this necessitates ecological genomic studies of high dispersal, generalist species. Here we perform one such study on golden perch (Macquaria ambigua) in the Murray-Darling Basin (MDB), Australia, using a genome-wide SNP data set. The MDB spans across arid to wet and temperate to subtropical environments, with low to high ecological disturbance in the form of low to high hydrological variability. We found high gene flow across the basin and three populations with low neutral differentiation. Genotype-environment association analyses detected adaptive divergence predominantly linked to an arid region with highly variable riverine flow, and candidate loci included functions related to fat storage, stress and molecular or tissue repair. The high connectivity of golden perch in the MDB will likely allow locally adaptive traits in its most arid and hydrologically variable environment to spread and be selected in localities that are predicted to become arid and hydrologically variable in future climates. High connectivity in golden perch is likely due to their generalist life history and efforts of fisheries management. Our study adds to growing evidence of adaptation in the face of gene flow and highlights the importance of considering ecological disturbance and adaptive divergence in biodiversity management.


Assuntos
Adaptação Fisiológica/genética , Biodiversidade , Mudança Climática , Fluxo Gênico , Percas/genética , Percas/fisiologia , Animais , Austrália , Análise por Conglomerados , Frequência do Gene/genética , Loci Gênicos , Geografia , Polimorfismo de Nucleotídeo Único/genética , Análise de Componente Principal
16.
Sci Rep ; 7(1): 16498, 2017 11 28.
Artigo em Inglês | MEDLINE | ID: mdl-29184116

RESUMO

Fish myotomes are comprised of anatomically segregated fast and slow muscle fibers that possess different metabolic and contractile properties. Although the expression profile properties in fast and slow muscle fibers had been investigated at the mRNA levels, a comprehensive analysis at proteomic and microRNA transcriptomic levels is limited. In the present study, we first systematically compared the proteomic and microRNA transcriptome of the slow and fast muscles of Chinese perch (Siniperca chuatsi). Total of 2102 proteins were identified in muscle tissues. Among them, 99 proteins were differentially up-regulated and 400 were down-regulated in the fast muscle compared with slow muscle. MiRNA microarrays revealed that 199 miRNAs identified in the two types of muscle fibers. Compared with the fast muscle, the 32 miRNAs was up-regulated and 27 down-regulated in the slow muscle. Specifically, expression of miR-103 and miR-144 was negatively correlated with SmyD1a and SmyD1b expression in fast and slow muscles, respectively. The luciferase reporter assay further verified that the miR-103 and miR-144 directly regulated the SmyD1a and SmyD1b expression by targeting their 3'-UTR. The constructed miRNA-SmyD1 interaction network might play an important role in controlling the development and performance of different muscle fiber types in Chinese perch.


Assuntos
Perfilação da Expressão Gênica , Fibras Musculares Esqueléticas/metabolismo , Percas/genética , Percas/metabolismo , Proteoma , Proteômica , Transcriptoma , Regiões 3' não Traduzidas , Animais , Biologia Computacional/métodos , Perfilação da Expressão Gênica/métodos , Regulação da Expressão Gênica , MicroRNAs/genética , Modelos Biológicos , Fibras Musculares de Contração Rápida/metabolismo , Fibras Musculares de Contração Lenta/metabolismo , Proteômica/métodos , Interferência de RNA , RNA Mensageiro/genética
17.
J Fish Biol ; 91(5): 1407-1418, 2017 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-28913865

RESUMO

Here the transcriptome and differential gene expression in the adult brain and gonads of the Chinese sea perch Lateolabrax maculatus were reported. A total of 78 256 909 clean reads were generated from the adult brain, ovary and testis by using the Illumina HiSeq2000 platform and assembled into 274 909 contigs. A total of 31 683 unigenes were annotated based on sequence similarity and 20 702 unigenes were found to exhibit 8237 gene ontology terms and 3888 signal pathways. Transcripts of 26 623 unigenes were present in all of the tissues, whereas pairwise comparisons revealed that 671/367, 496/315 and 1668/580 unigenes were up-down regulated by at least two-fold between the brain and ovary, ovary and testis and brain and testis, respectively. Homology search led to the identification of reproduction-associated genes of the brain-gonad axis, including those involved in sex differentiation and maintenance. The data provided an integrated and comprehensive transcriptome resource for L. maculatus, which could be used for further research on hypothalamus-pituitary-gonad axis gene function, reproduction regulation and sex-biased gene expression.


Assuntos
Regulação da Expressão Gênica , Sistema Hipotálamo-Hipofisário/metabolismo , Percas/genética , Transcriptoma , Animais , Feminino , Perfilação da Expressão Gênica , Masculino , Ovário/metabolismo , Percas/metabolismo , Diferenciação Sexual/genética , Testículo/metabolismo
18.
Fish Shellfish Immunol ; 70: 185-194, 2017 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-28860076

RESUMO

Heat shock protein 27 (HSP27), functioning as a stress induced protective protein, has been reported to participate in various biological processes, including apoptosis, thermal protection, and virus infection. In this study, a HSP27-like gene from the seawater fish sea perch, designated as LjHSP27, was characterized. The 1361 bp full-length cDNA of LjHSP27 encoded a 221 amino acid protein containing a conserved α-crystallin domain, two variable amino- and carboxy-terminal extensions, a WD/EPF motif, two serine phosphorylation sites, and two putative actin binding regions. Phylogenetic analysis showed that LjHSP27 shared the closest genetic relationship with HSP27 of the Asian seabass Lates calcarifer. LjHSP27 mRNA was ubiquitously expressed in all tissues examined, but significantly up-regulated in spleen and kidney and down-regulated in brain post red spotted grouper nervous necrosis virus (RGNNV) infection. In vitro, LjHSP27 transcript was remarkably reduced post RGNNV infection, but rapidly increased after polyinosinic-polycytidylic acid treatment. Up-regulation and down-regulation of LjHSP27 inhibited and promoted RGNNV replication in cultured LJB cells, respectively. Luciferase assay indicated that LjHSP27 could enhance the promoter activities of zebrafish interferon (IFN)1 and IFN3, suggesting its potential role in innate immune responses. Moreover, overexpression of LjHSP27 inhibited RGNNV-induced apoptosis, as indicated by the up-regulation of anti-apoptotic genes and down-regulation of pro-apoptotic genes, while KNK437 caused down-regulation of LjHSP27 dramatically led to opposite results, suggesting that LjHSP27 might exert its anti-RGNNV activities by regulating the apoptosis signaling pathway. Our results would provide a new insight into the underlying molecular mechanism of HSP and RGNNV interaction.


Assuntos
Doenças dos Peixes/imunologia , Regulação da Expressão Gênica/imunologia , Proteínas de Choque Térmico HSP27/genética , Proteínas de Choque Térmico HSP27/imunologia , Imunidade Inata/genética , Percas/genética , Percas/imunologia , Sequência de Aminoácidos , Animais , Sequência de Bases , Biologia Computacional , Proteínas de Peixes/química , Proteínas de Peixes/genética , Proteínas de Peixes/imunologia , Perfilação da Expressão Gênica/veterinária , Proteínas de Choque Térmico HSP27/química , Nodaviridae/fisiologia , Filogenia , Infecções por Vírus de RNA/imunologia , Alinhamento de Sequência/veterinária
19.
BMC Genomics ; 18(1): 489, 2017 06 28.
Artigo em Inglês | MEDLINE | ID: mdl-28659132

RESUMO

BACKGROUND: MicroRNAs (miRNAs) are endogenous small non-coding RNAs that play important roles in the regulation of diverse biological processes in eukaryotes. Chinese perch (Siniperca chuatsi) is one of the most economically important fish species widely cultured in China. Growth is an extremely important characteristic in fish. Individual differences in body size are common in Siniperca chuatsi, which significantly influence the aquaculture production of Siniperca chuatsi. However, the underline growth-related regulatory factors, such as miRNAs, are still unknown. RESULTS: To investigate the growth-related miRNAs in Siniperca chuatsi, two RNA libraries from four growth-related tissues (brain, pituitary, liver, and muscle) of Siniperca chuatsi at 6-month stage with relatively high or low growth rates (big-size group or small-size group) were obtained and sequenced using Solexa sequencing. A total of 252 known miRNAs and 12 novel miRNAs were identified. The expression patterns of these miRNAs in big-size group and small-size group were compared, and the results showed that 31 known and 5 novel miRNAs were differently expressed (DE). Furthermore, to verify the Solexa sequencing, five DE miRNAs were randomly selected and quantified by quantitative reverse transcription polymerase chain reaction (qRT-PCR). The results showed that their expression patterns were consistent with those of Solexa sequencing. In addition, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of target genes of DE miRNAs was performed. It showed that the target genes were involved in multiple biological processes including metabolic process, suggesting that metabolic process played an important role in growth of fish. CONCLUSIONS: Siniperca chuatsi is a popular and economically important species in aquaculture. In this study, miRNAs in Siniperca chuatsi with different growth rates were identified, and their expression profiles were compared. The data provides the first large-scale miRNA profiles related to growth of Siniperca chuatsi, which is expected to contribute to a better understanding of the role of miRNAs in regulating the biological processes of growth and possibly useful for Siniperca chuatsi breeding.


Assuntos
MicroRNAs/genética , Percas/crescimento & desenvolvimento , Percas/genética , Análise de Sequência de RNA , Animais , Especificidade de Órgãos
20.
PLoS One ; 12(4): e0176459, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28441436

RESUMO

Sauger (Sander canadensis) and walleye (S. vitreus) are percid fishes that naturally co-occur throughout much of the eastern United States. The native range of sauger extends into the upper Missouri River drainage where walleye did not historically occur, but have been stocked as a sport fish. Sauger populations have been declining due to habitat loss, fragmentation, and competition with non-native species, such as walleye. To effectively manage sauger populations, it is necessary to identify areas where sauger occur, and particularly where they co-occur with walleye. We developed quantitative PCR assays that can detect sauger and walleye DNA in filtered water samples. Each assay efficiently detected low quantities of target DNA and failed to detect DNA of non-target species with which they commonly co-occur.


Assuntos
Conservação dos Recursos Naturais/métodos , Ecossistema , Percas/genética , Reação em Cadeia da Polimerase em Tempo Real , Rios , Animais , Percas/metabolismo , Estados Unidos
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