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1.
Genomics ; 116(1): 110757, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-38061482

RESUMO

To understand the environmental adaptations among sessile bivalves lacking adaptive immunity, a series of analyses were conducted, with special emphasis on the widely distributed C. ariakensis. Employing Pacbio sequencing and Hi-C technologies, whole genome for each of a C. ariakensis (southern China) and C. hongkongensis individual was generated, with the contig N50 reaching 6.2 and 13.0 Mb, respectively. Each genome harbored over 30,000 protein-coding genes, with approximately half of each genome consisting of repeats. Genome alignment suggested possible introgression between C. gigas and C. ariakensis (northern China), and re-sequencing data corroborated this result and indicated significant gene flow between C. gigas and C. ariakensis. These introgressed candidates, well-represented by genes related to immunity and osmotic pressure, may be associated with environmental stresses. Gene family dynamics modeling suggested immune-related genes were well represented among the expanded genes in C. ariakensis. These outcomes could be attributed to the spread of C. ariakensis.


Assuntos
Crassostrea , Animais , Crassostrea/genética , Sequenciamento Completo do Genoma , China
2.
Environ Res ; 259: 119561, 2024 Jul 06.
Artigo em Inglês | MEDLINE | ID: mdl-38972345

RESUMO

Due to rapid urbanization, the Beibu Gulf, a semi-closed gulf in the northwestern South China Sea, faces escalating ecological and environmental threats. Understanding the assembly mechanisms and driving factors of bacterioplankton in the Beibu Gulf is crucial for preserving its ecological functions and services. In the present study, we investigated the spatiotemporal dynamics of bacterioplankton communities and their assembly mechanisms in the Beibu Gulf based on the high-throughput sequencing of the bacterial 16 S rRNA gene. Results showed significantly higher bacterioplankton diversity during the wet season compared to the dry season. Additionally, distinct seasonal variations in bacterioplankton composition were observed, characterized by an increase in Cyanobacteria and Thermoplasmatota and a decrease in Proteobacteria and Bacteroidota during the wet season. Null model analysis revealed that stochastic processes governed bacterioplankton community assembly in the Beibu Gulf, with drift and homogenizing dispersal dominating during the dry and wet seasons, respectively. Enhanced deterministic assembly of bacterioplankton was also observed during the wet season. Redundancy and random forest model analyses identified the physical properties (e.g., temperature) and nutrient content (e.g., nitrate) of water as primary environmental drivers influencing bacterioplankton dynamics. Moreover, variation partitioning and distance-decay of similarity revealed that environmental filtering played a significant role in shaping bacterioplankton variations in this rapidly developed coastal ecosystem. These findings advance our understanding of bacterioplankton assembly in coastal ecosystems and establish a theoretical basis for effective ecological health management amidst ongoing global changes.

3.
Environ Res ; 257: 119298, 2024 Sep 15.
Artigo em Inglês | MEDLINE | ID: mdl-38823616

RESUMO

Antibiotic resistance poses a considerable global public health concern, leading to heightened rates of illness and mortality. However, the impact of seasonal variations and environmental factors on the health risks associated with antibiotic resistance genes (ARGs) and their assembly mechanisms is not fully understood. Based on metagenomic sequencing, this study investigated the antibiotic resistome, mobile genetic elements (MGEs), and microbiomes in a subtropical coastal ecosystem of the Beibu Gulf, China, over autumn and winter, and explored the factors influencing seasonal changes in ARG and MGE abundance and diversity. Results indicated that ARG abundance and diversity were higher in winter than in autumn, with beta-lactam and multidrug resistance genes being the most diverse and abundant, respectively. Similarly, MGE abundance and diversity increased in winter and were strongly correlated with ARGs. In contrast, more pronounced associations between microbial communities, especially archaea, and the antibiotic resistome were observed in autumn than in winter. The co-occurrence network identified multiple interactions between MGEs and various multidrug efflux pumps in winter, suggesting a potential for ARG dissemination. Multivariate correlation analyses and path modeling indicated that environmental factors driving microbial community changes predominantly influenced antibiotic resistome assembly in autumn, while the relative importance of MGEs increased significantly in winter. These findings suggest an elevated health risk associated with antimicrobial resistance in the Beibu Gulf during winter, attributed to the dissemination of ARGs by horizontal gene transfer. The observed seasonal variations highlight the dynamic nature of antibiotic resistance dissemination in coastal ecosystems, emphasizing the need for comprehensive surveillance and management measures to address the growing threat of antimicrobial resistance in vulnerable environments.


Assuntos
Resistência Microbiana a Medicamentos , Ecossistema , Estações do Ano , China , Resistência Microbiana a Medicamentos/genética , Sequências Repetitivas Dispersas , Saúde Ambiental , Microbiota/efeitos dos fármacos , Antibacterianos/farmacologia
4.
Fish Shellfish Immunol ; 73: 42-49, 2018 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-29208497

RESUMO

Antimicrobial peptides (AMPs) are the most important players in the innate immune system, providing a principal first-line of defense against the invading pathogens. Crustin, a type of whey acidic protein (WAP) domain-containing and cationic cysteine-rich AMP, can function in a protease inhibition or an effector molecule manner. In the present study, a new Crustin was cloned and identified from Pacific white shrimp Litopenaeus vannamei and designated as LvCrustinA. The full-length cDNA of LvCrustinA was 687 bp, with a 519 bp open reading frame (ORF) that encoded a peptide of 172 amino acids. Domain analysis indicated that LvCrustinA contained a Glycine-rich region in the N-terminal and a single WAP domain within eight cysteines in the C-terminal. The 5' upstream regulatory sequence of 1249 bp (promoter) was obtained using a genome walking method, and it contained several conserved transcription factors binding motifs including NF-κB, AP-1 and STAT (Signal transducers and activators of transcription). Dual-reporter assay showed that NF-κB transcription factors LvDorsal and LvRelish, and AP-1 transcription factor Lvc-Jun could up-regulate the promoter activity of LvCrustinA, suggesting that NF-κB and JNK-c-Jun pathways could be involved in regulating the expression of LvCrustinA. Moreover, LvCrustinA was abundantly expressed in immune related tissues such as gill, hemocyte and epithelium, and its expression was up-regulated in response to Vibrio parahaemolyticus and White spot syndrome virus (WSSV) challenges in gill tissue, suggesting that LvCrustinA could be involved in the host defense against bacterial and viral infection. Additionally, RNAi mediated knockdown of LvCrustinA resulted in shrimps with the higher cumulative mortality during V. parahaemolyticus and WSSV infection. Taken together, these results provided some insight into the expression and transcriptional regulatory role of LvCrustinA, and its defensive role against pathogenic infection.


Assuntos
Peptídeos Catiônicos Antimicrobianos/genética , Peptídeos Catiônicos Antimicrobianos/imunologia , Regulação da Expressão Gênica/imunologia , Imunidade Inata/genética , Penaeidae/genética , Penaeidae/imunologia , Vibrio parahaemolyticus/fisiologia , Vírus da Síndrome da Mancha Branca 1/fisiologia , Sequência de Aminoácidos , Animais , Peptídeos Catiônicos Antimicrobianos/química , Proteínas de Artrópodes/química , Proteínas de Artrópodes/genética , Proteínas de Artrópodes/imunologia , Sequência de Bases , Perfilação da Expressão Gênica , Filogenia , Regiões Promotoras Genéticas , Alinhamento de Sequência
5.
BMC Genomics ; 16: 1006, 2015 Nov 25.
Artigo em Inglês | MEDLINE | ID: mdl-26607692

RESUMO

BACKGROUND: The Pacific white shrimp (Litopenaeus vannamei) is the world's most prevalent cultured crustacean species. However, the supply of high-quality broodstocks is limited and baseline information related to its reproductive activity and molecular issues related to gonad development are scarce. In this study, we performed transcriptome sequencing on the gonads of adult male and female L. vannamei to identify sex-related genes. RESULTS: A total of 25.16 gigabases (Gb) of sequences were generated from four L. vannamei gonadal tissue libraries. After quality control, 24.11 Gb of clean reads were selected from the gonadal libraries. De-novo assembly of all the clean reads generated a total of 65,218 unigenes with a mean size of 1021 bp and a N50 of 2000 bp. A search of all-unigene against Nr, SwissProt, KEGG, COG and NT databases resulted in 26,482, 23,062, 20,659, 11,935 and 14,626 annotations, respectively, providing a total of 30,304 annotated unigenes. Among annotated unigenes, 12,320 unigenes were assigned to gene ontology categories and 20,659 unigenes were mapped to 258 KEGG pathways. By comparing the ovary and testis libraries, 19,279 testicular up-regulated and 3,529 ovarian up-regulated unigenes were identified. Enrichment analysis of differentially expressed unigenes resulted in 1060 significantly enriched GO terms and 34 significantly enriched KEGG pathways. Nine ovary-specific, 6 testis-specific, 45 testicular up-regulated and 39 ovarian up-regulated unigenes were then confirmed by semi-quantitative PCR and quantitative real-time PCR. In addition, using all-unigenes as a reference, a total of 13,233 simple sequence repeats (SSRs) were identified in 10,411 unigene sequences. CONCLUSIONS: The present study depicts the first large-scale RNA sequencing of shrimp gonads. We have identified many important sex-related functional genes, GO terms and pathways, all of which will facilitate future research into the reproductive biology of shrimp. We expect that the SSRs detected in this study can then be used as genetic markers for germplasm evaluation of breeding and imported populations.


Assuntos
Perfilação da Expressão Gênica , Ovário/metabolismo , Penaeidae/genética , Testículo/metabolismo , Transcriptoma , Animais , Biologia Computacional/métodos , Feminino , Regulação da Expressão Gênica , Sequenciamento de Nucleotídeos em Larga Escala , Masculino , Repetições de Microssatélites , Anotação de Sequência Molecular , Especificidade de Órgãos/genética , Processos de Determinação Sexual/genética
6.
Gene ; 924: 148555, 2024 Oct 05.
Artigo em Inglês | MEDLINE | ID: mdl-38772515

RESUMO

The Hong Kong oyster, Crassostrea hongkongensis, is a significant bivalve species with economic importance. It primarily inhabits the estuarine intertidal zones in southern China, making it susceptible to salinity fluctuations. Consequently, investigating the molecular mechanisms governing salinity regulation in C. hongkongensis is essential. In this study, we conducted miRNA-seq on C. hongkongensis to compare miRNA expression differences under varying salinities (5‰, 25‰, and 35‰). The miRNA sequencing revealed 51 known miRNAs and 95 novel miRNAs across nine small RNA libraries (S5, S25, and S35). Among these miRNAs, we identified 6 down-regulated differentially expressed (DE) miRNAs in response to hypo-salinity stress (5‰), while 1 up-regulated DE miRNA and 5 down-regulated DE miRNAs were associated with hyper-salinity stress (35‰). Additionally, we predicted 931 and 768 potential target genes for hypo- and hyper-salinity stress, respectively. Functional gene annotation indicated that the target genes under hypo-salinity stress were linked to vesicle-mediated transport and metal ion binding. Conversely, those under hyper-salinity stress were primarily involved in signal transduction and metabolic processes. These findings have provided insights into the regulatory role of miRNAs, their potential target genes and associated pathways in oyster hypo- and hyper-salinity stress, which establish a foundation for future studies on the roles of miRNAs in salinity acclimation mechanisms in C. hongkongensis.


Assuntos
Crassostrea , MicroRNAs , Salinidade , Animais , Crassostrea/genética , MicroRNAs/genética , Aclimatação/genética , Estresse Salino/genética , Anotação de Sequência Molecular , Perfilação da Expressão Gênica/métodos , RNA-Seq/métodos
7.
Artigo em Inglês | MEDLINE | ID: mdl-38246111

RESUMO

Salinity, a key limiting factor, affects the distribution and survival of marine species. The Hong Kong oyster (Crassostrea hongkongensis), a euryhaline species found along the coast of the South China Sea, has become a major aquaculture bivalve species. To determine the molecular mechanism by which oysters respond to coastal waters with varying salinity levels, we used RNA-seq to sequence the gill samples of oysters exposed to normal (25 ‰, S25), low (5 ‰, S5) and high (35 ‰, S35) salinity conditions for one month. The results revealed different expression transcriptome levels among oysters living under low and high salinity conditions. Using high-throughput sequencing, we identified 811 up-regulated genes and 769 down-regulated genes. As determined by KEGG pathway mapping, the differentially expressed genes (DEGs) were significantly enriched in the prion diseases, histidine metabolism, arginine and proline metabolism, and beta-alanine metabolism pathways in both the S5 vs. S25 and S35 vs. S25 group comparison. Several DEGs including heat shock 70 kDa protein 12B-like, poly (ADP-ribose) polymerase (PARP), and tripartite motif-containing protein 2 (TRIM2), and low-density lipoprotein receptor-like, as well as KEGG pathways, including arginine and proline metabolism, apoptosis, PPAR signaling pathway, the thyroid hormone signaling pathway, were concerning response to salinity stress. Additionally, eight DEGs involved in salinity adaptation were selected for RT-qPCR validation, and the results confirmed the credibility of the transcriptome sequencing data. Overall, we designed a one-month, medium-term experiment to examine the responses of C. hongkongensis exposed to different levels of salinity stress and performed transcriptome analysis using high-throughput sequencing. Our results enhance current understanding of the molecular mechanisms of salinity stress responses in C. hongkongensis and provided insights into the osmotic biology of oysters.


Assuntos
Crassostrea , Animais , Crassostrea/metabolismo , Transcriptoma , Estresse Salino , Arginina/genética , Arginina/metabolismo , Prolina/genética , Prolina/metabolismo , Salinidade
8.
PLoS One ; 19(6): e0305197, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38917086

RESUMO

Bellamya purificata is an important medicinal value and economically farmed species in China. However, because little is known about the genetic characteristics of this species, the utilization of high-quality germplasm resources is hindered. The study examined the genetic differentiation between, and the structure of 12 B. purificata populations in Guangxi using 7 microsatellite DNA markers. High genetic diversity occurred in each population, with mean observed heterozygosity 0.655 and a mean expected heterozygosity 0.832. Analysis of molecular variance reveals genetic diversity to be greater within (95.2%) than among populations (4.8%). Genetic differentiation between populations is weak (Fst = 0.048, P < 0.001), with mixing of genetic clusters prevalent at the level of the individual. Genetic flow exists between populations (Nm = 3.084-11.778), with Longshui and Guilin populations exchanging frequently. A Mantel test reveals a low correlation between geographic and genetic distances (r = 0.2482, P < 0.071), suggesting that dispersal between neighboring populations facilitates population exchange. No significant heterozygosity excess was observed for any population (P > 0.05), indicating a lack of recent genetic bottlenecks. The results provide important genetic information for B. purificata, and data for potential germplasm discovery and aquaculture development.


Assuntos
Variação Genética , Repetições de Microssatélites , China , Repetições de Microssatélites/genética , Genética Populacional , Fluxo Gênico , Filogenia
9.
Mar Environ Res ; 187: 105948, 2023 May.
Artigo em Inglês | MEDLINE | ID: mdl-36931046

RESUMO

The South American mussel, Mytella strigata, is a highly invasive fouling species of great concern along intertidal shores in East and Southeast Asia, posing serious threats to native biodiversity and ecosystems. Intertidal areas, being increasingly attacked by heatwaves over the last decade, are among the most thermally challenging habitats, yet the fate of this highly invasive mussel under scenarios of hotter heatwaves remains unknown. Here, we investigated how M. strigata responded to intensifying heatwaves frequently occurring in the South China Sea. Over 97% of individuals survived the five-day-lasting heatwaves, suggesting their high ability to cope with short-term heatwaves. Virtually unaffected clearance rate and absorption efficiency throughout the course of heatwaves indicate the maintenance of energy acquisition, and significantly decreased respiration rate implies the depression of energy metabolism, generating significant decreases in the O:N ratio when heatwaves occurred. Scope for growth of heatwaves-stressed mussels significantly decreased during initial exposure and then increased over time. These findings indicate the remarkable ability of M. strigata to cope with heatwaves recorded in its invasive habitats and call the attention for the rapid spread of this highly invasive fouling species in the context of climate change.


Assuntos
Ecossistema , Espécies Introduzidas , Mytilidae , Animais , Humanos , Mudança Climática , Metabolismo Energético , Temperatura Alta , Adaptação Fisiológica
10.
J Adv Res ; 2023 Dec 02.
Artigo em Inglês | MEDLINE | ID: mdl-38043610

RESUMO

INTRODUCTION: Golden pompano (Trachinotus ovatus) is economically significant important for offshore cage aquaculture in China and Southeast Asian countries. Lack of high-quality genomic data and accurate gene annotations greatly restricts its genetic breeding progress. OBJECTIVES: To decode the mechanisms of sex determination and rapid growth in golden pompano and facilitate the sex- and growth-aimed genetic breeding. METHODS: Genome assemblies of male and female golden pompano were generated using Illumina, PacBio, BioNano, genetic maps and Hi-C sequencing data. Genomic comparisons, whole genome re-sequencing of 202 F1 individuals, QTL mapping and gonadal transcriptomes were used to analyze the sex determining region, sex chromosome evolution, SNP loci, and growth candidate genes. Zebrafish model was used to investigate the functions of growth candidate gene. RESULTS: Female (644.45 Mb) and male (652.12 Mb) genomes of golden pompano were assembled and annotated at the chromosome level. Both genomes are highly conserved and no new or highly differentiated sex chromosomes occur. A 3.5 Mb sex determining region on LG15 was identified, where Hsd17b1, Micall2 and Lmx1a were putative candidates for sex determination. Three SNP loci significantly linked to growth were pinpointed, and a growth-linked gene gpsstr1 was identified by locus BSNP1369 (G â†’ C, 17489695, Chr23). Loss of sstr1a (homologue of gpsstr1) in zebrafish caused growth retardation. CONCLUSION: This study provides insights into sex chromosome evolution, sex determination and rapid growth of golden pompano.

11.
Gene ; 809: 146026, 2022 Jan 30.
Artigo em Inglês | MEDLINE | ID: mdl-34687789

RESUMO

It is difficult to distinguish the sexes of Trachinotus ovatus based on appearance, and little data about sex-determining genes are available for this species. Here, we generated 200 F2 individuals using the parents R404 and R403. DNA samples were collected from 50 individuals of each sex and aggregated into sex-specific DNA pools. Specific-locus amplified fragment sequencing was integrated with bulked segregant analysis to detect candidate sex-associated genes. Approximately 3,153,153 high-quality single-nucleotide polymorphism (SNP) markers and 135,363 high-quality insertion-deletion (Indel) markers were generated. Six candidate regions within chromosome 14, encompassing 132 candidate genes, were identified as closely related to sex. Based on annotations, six genes (EVM0019817, EVM0004192, EVM0001445, EVM0005260, EVM0014734, and EVM0009626) were predicted to be closely associated with sex. These results present an efficient genetic mapping approach that lays a foundation for molecular sex discrimination in T. ovatus.


Assuntos
Proteínas de Peixes/genética , Peixes/genética , Polimorfismo de Nucleotídeo Único , Análise para Determinação do Sexo/métodos , Animais , Mapeamento Cromossômico/métodos , Feminino , Mutação INDEL , Masculino , Análise de Sequência de DNA
12.
Mar Environ Res ; 179: 105705, 2022 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-35863129

RESUMO

Intertidal and estuarine bivalves are adapted to fluctuating environmental conditions but the cellular adaptive mechanisms under combined stress scenarios are not well understood. The Hong Kong oysters Crassostrea hongkongensis experience periodic hypoxia/reoxygenation and salinity fluctuations during tidal cycles and extreme weather, which can negatively affect the respiratory organs (gills) involved in oxygen uptake and transport. We determined the effects of periodic hypoxia under different salinities on the oxidative stress response in Hong Kong oysters. Oxidative stress parameters (activities of superoxide dismutase (SOD), and catalase (CAT), tissue levels of malondialdehyde (MDA) and protein carbonyl content (PCC)) were determined in the gills of oysters exposed to diel-cycling hypoxia (hypoxia at night: 12h at 2 mg/L, reoxygenation: 12h at 6 mg/L) and normal dissolved oxygen (DO) (6 mg/L) under three salinities (10, 25, and 35‰) for 28 days. Oxygen regime in combination with salinity changes had significant interactive effects on all studied parameters except SOD. Salinity, DO and their interactions increased PCC after 14 and 28 days of exposure, and the combination of hypoxia/reoxygenation and decreased salinity showed the most severe effect. MDA content of the gills increased only after the long-term (28 days) exposure in decreased or increased salinity under normal DO treatments, showing PCC was more sensitive than MDA as biomarker of oxidative stress. Low salinity suppressed SOD activity regardless of the DO, whereas hypoxia induced SOD responses. CAT activities decreased significantly under high salinity with hypoxia/reoxygenation conditions. Our findings highlighted that periodic hypoxia/reoxygenation with salinity change induced antioxidant responses, which can impact the health of Hong Kong oyster C. hongkongensis and prolonged salinity stress may be one reason for the mortality during its aquaculture process.


Assuntos
Crassostrea , Poluentes Químicos da Água , Animais , Antioxidantes , Crassostrea/metabolismo , Brânquias , Hipóxia/metabolismo , Oxigênio/metabolismo , Carbonilação Proteica , Salinidade , Superóxido Dismutase/metabolismo , Poluentes Químicos da Água/metabolismo
13.
Yi Chuan ; 33(2): 168-74, 2011 Feb.
Artigo em Zh | MEDLINE | ID: mdl-21377974

RESUMO

To study the molecular mechanism of cold tolerance, we cloned TCP-1-eta homolog gene from Litopenaeus vannamei and studied its relationship with cold tolerance. Based on the sequence from electronic cloning, a pair of primers were designed, and a 1 705 bp cDNA was obtained by RT-PCR. The cDNA contains 1 629 bp ORF, which encodes a peptide of 542 aa. Tissue expression pattern by real-time PCR analysis revealed that TCP-1-eta mRNA mainly existed in muscle tissue. Cold induction by different temperatures revealed that TCP-1-eta mRNA expression started to increase after treatment at 15°C for 36 h, and the increase was remarkable after treatment at 13°C. As for treatment at 13°C for different times, the expression pattern was almost not changed during the first 36 h, but significantly increased after 36 h of treatment. A SNP (single nucleotide polymorphism) site was found in 731 bp of ORF, and the genotypes of 216 Litopenaeus vannamei were determined by PCR-RFLP. Variance analysis indicated that the SNP genotype was significantly related with cold tolerance parameter Cooling-Degree Hours (CDH), and CDH for CC type of Litopenaeus vannamei was longer than TT type.


Assuntos
Chaperonina 60/genética , Chaperonina 60/metabolismo , Clonagem Molecular , Penaeidae/fisiologia , Sequência de Aminoácidos , Animais , Sequência de Bases , Temperatura Baixa , Dados de Sequência Molecular , Penaeidae/genética
14.
Mar Pollut Bull ; 167: 112282, 2021 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-33780757

RESUMO

Ocean acidification and hypoxia have become increasingly severe in coastal areas, and their co-occurrence poses emerging threats to coastal ecosystems. Here, we investigated the combined effects of ocean acidification and hypoxia on the reproductive capacity of the thick-shelled mussel Mytilus coruscus. Our results demonstrated low pH but not low oxygen induced decreased gonadosomatic index (GSI) in mussels. Male mussels had a lower level of sex steroids (estradiol, testosterone, and progesterone) when kept at low pH. Expression of genes related to reproduction were also impacted by low pH with a downregulation of genes involved in gonad development in males (ß-catenin and Wnt-7b involved in males) and an upregulation of testosterone synthesis inhibition-related gene (Wnt-4) in females. Overall, our results suggest that ocean acidification has an impact on the gonadal development through an alternation of gene expression and level of steroids while hypoxia had no significant effect.


Assuntos
Mytilus , Animais , Ecossistema , Gônadas , Concentração de Íons de Hidrogênio , Hipóxia , Masculino , Oceanos e Mares , Água do Mar
15.
Gene ; 764: 145090, 2021 Jan 05.
Artigo em Inglês | MEDLINE | ID: mdl-32861880

RESUMO

Litopenaeus vannamei (L. vannamei) is one of the most widely cultured shrimp species in the world. The species often suffers from cold stress. To understand the molecular mechanism of cold tolerance, we performed transcriptomic analysis on two contrasting cultivars of L. vannamei, namely, cold-tolerant Guihai 2 (GH2) and cold-sensitive Guihai1 (GH1), under a control temperature (28 °C), cold stress (16 °C), and recovery to 28 °C. A total of 84.5 Gb of sequences were generated from 12 L. vannamei hepatopancreas libraries. The de-novo assembly generated a total of 143,029 unigenes with a mean size of 1,052 bp and an N50 of 2,604 bp, of which 34.08% were annotated in the Nr database. We analyzed the differentially expressed genes (DEGs) between nine comparison groups and detected a total of 21,026 DEGs. KEGG pathways, including lysosome, sphingolipid metabolism and nitrogen metabolism, were significantly enriched by DEGs between different temperatures in GH2. Furthermore, eight of the most significantly DEGs under cold stress from the transcriptomic analysis were selected for quantitative real-time PCR (qPCR) validation. Overall, we compared gene expression changes under cold stress in cold-tolerant and cold-sensitive L. vannamei for the first time. The results may further extend our understanding of the cold stress-response mechanism in L. vannamei.


Assuntos
Aclimatação/genética , Resposta ao Choque Frio/genética , Hepatopâncreas/metabolismo , Penaeidae/fisiologia , Frutos do Mar , Animais , Aquicultura , China , Temperatura Baixa/efeitos adversos , Regulação da Expressão Gênica/fisiologia , Anotação de Sequência Molecular , RNA-Seq , Reação em Cadeia da Polimerase em Tempo Real , Transcriptoma/genética
16.
Int J Nanomedicine ; 15: 6409-6420, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32922008

RESUMO

AIM: Tumor cell-derived microparticles (MP) can function as a targeted delivery carrier for anti-tumor drugs. Here, we aimed to generate paclitaxel-loaded microparticles (MP-PTX) from HeLa cells and examined its therapeutic potential on human cervical carcinoma. METHODS: MP-PTX was generated from HeLa cells by ultraviolet radiation and subsequent centrifugation. The particle size, drug loading rate, and stability of MP-PTX were examined in vitro. Flow cytometry and the MTT assay were performed to test the inhibitory effect of MP-PTX using different cell lines. Immunodeficient mice bearing HeLa cervical carcinoma were treated with 0.9% normal saline, MP, paclitaxel (PTX) (2.5 mg/kg), or MP-PTX (PTX content identical to PTX group) every day for 6 consecutive days. Tumor volume and animal survival were observed. Micro 18F-FDG PET/CT was performed to monitor the therapeutic efficacy. The proliferation activity of cells and microvessel density in tumor tissues were determined by immunohistochemical staining using Ki-67 and CD31, respectively. RESULTS: Dynamic laser scattering measurements showed that the particle size of MP-PTX was 285.58 ± 2.95 nm and the polydispersity index was 0.104 ± 0.106. And the particle size of MP-PTX was not change at 4°C for at least one week. More than 1% of PTX in the medium could be successfully encapsulated into HeLa cell-derived MP. When compared with PTX, MP-PTX treatment significantly increased apoptosis of tumor cells and reduced their proliferation. In addition, MP-PTX showed lower toxicity to normal human umbilical vein endothelial cells (HUVEC) than PTX. In vivo studies further demonstrated that MP-PTX treatment significantly inhibited the growth of cervical carcinoma, prolonged the survival of tumor-bearing mice, and reduced the toxicity of PTX. Immunohistochemical staining revealed that MP-PTX treatment led to decreased Ki-67 positive tumor cells and decreased microvessel density in tumor tissues. CONCLUSION: Our results demonstrated that HeLa-derived MP-PTX significantly enhanced the anti-cancer effects of PTX with reduced toxicity, which may provide a novel strategy for the treatment of cervical carcinoma.


Assuntos
Micropartículas Derivadas de Células/metabolismo , Paclitaxel/uso terapêutico , Neoplasias do Colo do Útero/tratamento farmacológico , Neoplasias do Colo do Útero/patologia , Animais , Antineoplásicos/farmacologia , Antineoplásicos/uso terapêutico , Linhagem Celular Tumoral , Proliferação de Células/efeitos dos fármacos , Micropartículas Derivadas de Células/efeitos dos fármacos , Portadores de Fármacos/química , Células Endoteliais/efeitos dos fármacos , Feminino , Células HeLa , Humanos , Rim/efeitos dos fármacos , Rim/metabolismo , Fígado/efeitos dos fármacos , Fígado/metabolismo , Camundongos Endogâmicos BALB C , Camundongos Nus , Neovascularização Fisiológica/efeitos dos fármacos , Paclitaxel/farmacologia , Tamanho da Partícula
17.
Mol Ecol Resour ; 20(4): 980-994, 2020 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-32198971

RESUMO

Crassostrea hongkongensis is a popular and important native oyster species that is cultured mainly along the coast of the South China Sea. However, the absence of a reference genome has restricted genetic studies and the development of molecular breeding schemes for this species. Here, we combined PacBio and 10 × Genomics technologies to create a C. hongkongensis genome assembly, which has a size of 610 Mb, and is close to that estimated by flow cytometry (~650 Mb). Contig and scaffold N50 are 2.57 and 4.99 Mb, respectively, and BUSCO analysis indicates that 95.8% of metazoan conserved genes are completely represented. Using a high-density linkage map of its closest related species, C. gigas, a total of 521 Mb (85.4%) was anchored to 10 haploid chromosomes. Comparative genomic analyses with other molluscs reveal that several immune- or stress response-related genes extensively expanded in bivalves by tandem duplication, including C1q, Toll-like receptors and Hsp70, which are associated with their adaptation to filter-feeding and sessile lifestyles in shallow sea and/or deep-sea ecosystems. Through transcriptome sequencing, potential genes and pathways related to sex determination and gonad development were identified. The genome and transcriptome of C. hongkongensis provide valuable resources for future molecular studies, genetic improvement and genome-assisted breeding of oysters.


Assuntos
Cromossomos/genética , Crassostrea/genética , Genoma/genética , Adaptação Fisiológica/genética , Animais , China , Mapeamento Cromossômico/métodos , Ecossistema , Genômica/métodos , Análise de Sequência de DNA , Transcriptoma/genética
18.
J Exp Zool B Mol Dev Evol ; 312(8): 855-71, 2009 Dec 15.
Artigo em Inglês | MEDLINE | ID: mdl-19504540

RESUMO

To investigate germline development and germ cell specification, we identified a Dazl homolog (CagDazl) from gynogenetic gibel carp (Carassius auratus gibelio). Its cDNA sequence and BAC clone sequence analyses revealed the genomic organization conservation and conserved synteny of the Dazl family members and their neighborhood genes among vertebrates, especially in fish. Moreover, a polyclonal antibody specific to CagDazl was produced and used to examine its expression and distribution throughout germline development at protein level. Firstly, ovary-specific expression pattern of CagDazl was confirmed in adult tissues by RT-PCR and Western blot. In addition, in situ hybridization and immunofluorescence localization demonstrated its specific expression in germ cells, and both its transcript and protein were localized to germ plasm. Then, co-localization of CagDazl and mitochondrial cloud was found, confirming that CagDazl transcript and its protein are germ plasm component and move via METRO pathway during oogenesis. Furthermore, the CagDazl is abundant and continuous throughout germline development and germ cell specification including primordial germ cell (PGC) formation, oogonium differentiation, oocyte development, and embryogenesis, and the dynamic distribution occurs at different development stages. The data suggest that maternal CagDazl might play an important role in gibel carp PGC formation. Therefore, CagDazl is a useful and specific marker for tracing germ plasm and germ cell development in the gynogenetic gibel carp. In addition, in comparison with previous studies in sexual reproduction species, the continuous and dynamic distribution of CagDazl protein in the germ plasm throughout the life cycle seems to have significant implication in sex evolution of vertebrates.


Assuntos
Carpas/embriologia , Evolução Molecular , Células Germinativas , Proteínas de Ligação a RNA/genética , Sequência de Aminoácidos , Animais , Sequência de Bases , Western Blotting , Carpas/genética , Primers do DNA , Imunofluorescência , Hibridização In Situ , Dados de Sequência Molecular , Proteínas de Ligação a RNA/química , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Homologia de Sequência de Aminoácidos
19.
Artigo em Inglês | MEDLINE | ID: mdl-31029056

RESUMO

The Trachinotus ovatus (T. ovatus) reach sexual maturity as late as 4-5 years, and there are no obvious morphology differences between males and females, even at maturity, making the selection of male and female parents for selective breeding difficult. To examine the potential regulatory mechanism of sexual differentiation, we conducted a microRNAs (miRNAs) analysis on the ovaries and testes of T. ovatus. A total of 13,423,691 and 11,734,953 raw reads, representing 91,883,908 and 86,879,726 unique sequences of 18-35 nt length obtained from the ovaries and testes, respectively. After mapping to the T. ovatus transcriptome reference sequence (unpublished data), and comparing the miRNA sequences with the miRBase database, 179 known mature miRNAs and 100 novel miRNAs were identified. Expression analysis showed that, 165 miRNAs were differentially expressed between the ovary and testis. To validate the Illumina results, the expression patterns of the nine most differently expressed miRNAs (dre-miR-7a, dre-miR-7b, dre-miR-153a-3p, dre-miR-144-3p, dre-miR-301a, dre-miR-92a-3p, dre-miR-727-5p, Novel 124, and Novel 190, as well as those of five miRNAs that may relate to gonad development (dre-miR-143, dre-miR-101a, dre-miR-202-5p, dre-let-7c-5p, and dre-miR-181a-5p), were assayed with RT-qPCR. The expression trends for all the miRNAs validated with RT-qPCR were consistent with the next-generation sequencing data. The identification and characterization of the miRNAs differentially expressed between the ovary and the testis of the T. ovatus will increase our understanding of the role of miRNAs in gonad differentiation. These data also facilitate studies on miRNA regulation of teleost reproduction.


Assuntos
Peixes/genética , MicroRNAs/genética , Animais , Feminino , Peixes/crescimento & desenvolvimento , Perfilação da Expressão Gênica , Regulação da Expressão Gênica no Desenvolvimento , Sequenciamento de Nucleotídeos em Larga Escala , Masculino , Ovário/metabolismo , Ovário/ultraestrutura , Diferenciação Sexual , Testículo/metabolismo , Testículo/ultraestrutura , Transcriptoma
20.
Artigo em Inglês | MEDLINE | ID: mdl-30785072

RESUMO

The rice flower carp (Cyprinus carpio var. Quanzhounensis) is a bony fish (superclass Osteichthyes), with very soft bones that is a significant feature unlike the other carp species. In this study, we analyzed the mRNA and microRNA (miRNA) transcriptomes in the intermuscular bones of rice flower carp and Jian carp (Cyprinus carpio var. Jian) (a typical member of common carp in China), using Illumina RNA sequencing. We identified 55,340 genes (including 47,541 known genes and 8231 predicted new genes) and 662 miRNAs (including 595 known miRNAs and 67 novel miRNAs) in the two species. By comparing the transcriptomes of the two species, we identified 1523 differentially expressed genes (DEGs) (including 576 up - and 947 downregulated DEGs) and 352 differentially expressed miRNAs (DEMs) (including 85 up- and 267 downregulated DEMs). According to the Gene Ontology (GO) annotation, 7 DEGs and 12 DEMs were found to be involved in the regulation of bone mineralization. The results of this study improve our understanding of the mRNA and miRNA profiles of carp bones, particularly those of the rice flower carp.


Assuntos
Carpas/genética , MicroRNAs/genética , RNA Mensageiro/genética , Transcriptoma , Animais , Feminino , Regulação da Expressão Gênica , Masculino , Anotação de Sequência Molecular , Especificidade da Espécie
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