Gonadal transcriptomic analysis of yellow catfish (Pelteobagrus fulvidraco): identification of sex-related genes and genetic markers

2014 ◽  
Vol 46 (21) ◽  
pp. 798-807 ◽  
Author(s):  
Jianguo Lu ◽  
Peixian Luan ◽  
Xiaofeng Zhang ◽  
Shuqun Xue ◽  
Lina Peng ◽  
...  
Keyword(s):  
Sex Determination ◽  
De Novo ◽  
High Reliability ◽  
Expression Patterns ◽  
Pelteobagrus Fulvidraco ◽  
Yellow Catfish ◽  
Gonad Tissue ◽  
Freshwater Aquaculture ◽  
East And Southeast Asia ◽  
Molecular Marker Development

Yellow catfish ( Pelteobagrus fulvidraco) has been recognized as a vital freshwater aquaculture species in East and Southeast Asia. In addition to its commercial interest, it is also attracted much attention because of its value in studying sex-determination mechanisms. A comprehensive gonadal transcriptome analysis is believed to provide a resource for genome annotation, candidate gene identification, and molecular marker development. Herein, we performed a de novo assembly of yellow catfish gonad transcriptome by high-throughput Illumina sequencing. A total of 82,123 contigs were obtained, ranging from 351 to 21,268 bp, and N50 of 2,329 bp. Unigenes of 21,869 in total were identified. Of these, 229 and 1,188 genes were found to be specifically expressed in XY gonad tissue for 1 yr and 2 yr old yellow catfish, respectively; correspondingly, 51 and 40 genes were identified in XX gonad tissue at those two stages. Gene ontology and KEGG analysis were conducted and classified all contigs into different categories. A large number of unigenes involved in sex determination were identified, as well as microsatellites and SNP variants. The expression patterns of sex-related genes were then validated by quantitative real-time PCR (qRT-PCR) suggesting the high reliability of RNA-Seq results. In this study, the transcriptome of yellow catfish gonad was first sequenced, assembled, and characterized; it provides a valuable genomic resource for better understanding of yellow catfish sex determination as well as development of molecular markers, thereby assisting in the production of monosex yellow catfish for aquaculture.

scholarly journals Molecular Cloning and Expression Analysis of Interleukin-8 and -10 in Yellow Catfish and in Response to Bacterial Pathogen Infection

2019 ◽  
Vol 2019 ◽  
pp. 1-9 ◽  
Author(s):  
Yingping Xiao ◽  
Lintian Yu ◽  
Guohong Gui ◽  
Yujie Gong ◽  
Xueting Wen ◽  
...  
Keyword(s):  
Intestinal Inflammation ◽  
Expression Patterns ◽  
Bacterial Pathogen ◽  
Interleukin 8 ◽  
Cloning And Expression ◽  
Pelteobagrus Fulvidraco ◽  
Yellow Catfish ◽  
Pathogen Infection ◽  
Feed Supplementation ◽  
Freshwater Aquaculture

The yellow catfish (Pelteobagrus fulvidraco) is an important economic freshwater aquaculture species in Asia. However, little is known about its immune response to bacterial pathogen infection. Here, two cytokines, the proinflammatory cytokine interleukin-8 (IL-8) and the anti-inflammatory cytokine interleukin-10 (IL-10), were identified and characterized in the yellow catfish for the first time. We found that the full length of the IL-8 cDNA was 784 bp and contained an open reading frame (ORF) of 336 bp, while the IL-10 gene was 973 bp in length with a 549 bp of ORF. In addition, both the IL-8 and the IL-10 had similar tissue-specific expression patterns. They were more abundant in the spleen and lowest expressed in the liver. Furthermore, IL-10 but not IL-8 was significantly upregulated in the intestine of yellow catfish by feed supplementation ofClostridium butyricum(CB).More importantly, the expression levels of intestinal IL-10 and IL-8 were up- and downregulated by pathogenAeromonas punctatastimuli with the presence of CB, respectively. Collectively, these results suggest that IL-10 and IL-8 mediate important roles in the immunity of yellow catfish, and feed supplementation of CB may able to reduce the intestinal inflammation caused by bacteria infections through regulating the expression of IL-10 and IL-8.

scholarly journals Effects of Microplastics on Immune Responses of the Yellow Catfish Pelteobagrus fulvidraco Under Hypoxia

2021 ◽  
Vol 12 ◽  
Author(s):  
Li'ang Li ◽  
Ran Xu ◽  
Lingfeng Jiang ◽  
Elvis Genbo Xu ◽  
Man Wang ◽  
...  
Keyword(s):  
Hypoxia Inducible Factor ◽  
Aquatic Organisms ◽  
Freshwater Ecosystem ◽  
Pelteobagrus Fulvidraco ◽  
Yellow Catfish ◽  
High Concentration ◽  
Negative Effects ◽  
Freshwater Organisms ◽  
Freshwater Aquaculture ◽  
Tnf Α

Compared with marine organisms, research on microplastics (MPs) in freshwater organisms is still less although MPs have been widely found in the freshwater ecosystem. Hypoxia is a ubiquitous issue in freshwater aquaculture, and under such scenarios, the toxic effects of MPs on typical aquaculture fish need to be clarified. In this study, we studied the effects of MPs (polystyrene) on specific growth rate (SGR), hypoxia-inducible factor-1α (HIF-1α), tumor necrosis factor-α (TNF-α), interleukin-8 (IL-8), and interferon (IFN) in the yellow catfish (Pelteobagrus fulvidraco) under hypoxic conditions. After 15 days of exposure, the SGR was not affected by MPs or hypoxia. MPs significantly increased the expressions of HIF-1α and TNF-α but inhibited the expression of IFN at high concentration MPs under normoxia. However, hypoxia significantly inhibited the expression of IL-8 and TNF-α under high MP concentration and low MP concentration, respectively. In addition, MPs had significant concentration-dependent inhibitory effects on IFN under hypoxia. Surprisingly, a positive correction between HIF-1α and TNF-α was found in fish. Although hypoxia might alleviate the effects of MPs with low concentrations, the interaction of hypoxia and MPs aggravated the negative effects of MPs on immune factors at high concentration MPs. This study provided new insight into the complex effects of hypoxia and MPs on aquatic organisms, and future studies should focus on the cellular pathways of immune cells in fish. Given that MPs could induce the immune response in fish, considerations should be paid to the impacts of MPs on freshwater aquaculture, and hypoxia should be taken into consideration when evaluating the effects of MPs.

scholarly journals Inferring the genetic basis of sex determination from the genome of a dioecious nightshade

2020 ◽  
Author(s):  
Meng Wu ◽  
Gregory J. Anderson ◽  
Matthew W. Hahn ◽  
Leonie C. Moyle ◽  
Rafael F. Guerrero
Keyword(s):  
Sex Determination ◽  
Genetic Basis ◽  
De Novo ◽  
Expression Patterns ◽  
Gene Family Evolution ◽  
Genetic Mechanisms ◽  
Determination System ◽  
Heterogametic Sex ◽  
Sex Determination System ◽  
Evolution Of Dioecy

ABSTRACTDissecting the genetic mechanisms underlying dioecy (i.e. separate female and male individuals) is critical for understanding the evolution of this pervasive reproductive strategy. Nonetheless, the genetic basis of sex determination remains unclear in many cases, especially in systems where dioecy has arisen recently. Within the economically important plant genus Solanum (∼2000 species), dioecy is thought to have evolved independently at least 4 times across roughly 20 species. Here, we generate the first genome sequence of a dioecious Solanum and use it to ascertain the genetic basis of sex determination in this species. We de novo assembled and annotated the genome of S. appendiculatum (assembly size: ∼750 Mb; scaffold N50: 0.92 Mb; ∼35,000 genes), identified sex-specific sequences and their locations in the genome, and inferred that males in this species are the heterogametic sex. We also analyzed gene expression patterns in floral tissues of males and females, finding ∼100 genes that are differentially expressed between the sexes. These analyses, together with observed patterns of gene-family evolution specific to S. appendiculatum, consistently implicate a suite of genes from the regulatory network controlling pectin degradation and modification in the expression of sex. Furthermore, the genome of a species with a relatively young sex determination system provides the foundational resources for future studies on the independent evolution of dioecy in this speciose clade.

Effects of replacing fish meal with maggot meal on meat quality of yellow catfish (Pelteobagrus fulvidraco)

2013 ◽  
Vol 20 (2) ◽  
pp. 392-401
Author(s):  
Yanhua HUANG ◽  
Yuanhong WEN ◽  
Junming CAO ◽  
Guoxia WANG ◽  
Wenyan MO ◽  
...  
Keyword(s):  
Meat Quality ◽  
Fish Meal ◽  
Pelteobagrus Fulvidraco ◽  
Yellow Catfish

scholarly journals Dissecting the chromosome-level genome of the Asian Clam (Corbicula fluminea)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tongqing Zhang ◽  
Jiawen Yin ◽  
Shengkai Tang ◽  
Daming Li ◽  
Xiankun Gu ◽  
...  
Keyword(s):  
De Novo ◽  
Corbicula Fluminea ◽  
Gene Families ◽  
Ruditapes Philippinarum ◽  
Genomic Sequences ◽  
Future Research ◽  
Asian Clam ◽  
Sequencing Technologies ◽  
East And Southeast Asia ◽  
Clam Corbicula

AbstractThe Asian Clam (Corbicula fluminea) is a valuable commercial and medicinal bivalve, which is widely distributed in East and Southeast Asia. As a natural nutrient source, the clam is rich in protein, amino acids, and microelements. The genome of C. fluminea has not yet been characterized; therefore, genome-assisted breeding and improvements cannot yet be implemented. In this work, we present a de novo chromosome-scale genome assembly of C. fluminea using PacBio and Hi-C sequencing technologies. The assembled genome comprised 4728 contigs, with a contig N50 of 521.06 Kb, and 1,215 scaffolds with a scaffold N50 of 70.62 Mb. More than 1.51 Gb (99.17%) of genomic sequences were anchored to 18 chromosomes, of which 1.40 Gb (92.81%) of genomic sequences were ordered and oriented. The genome contains 38,841 coding genes, 32,591 (83.91%) of which were annotated in at least one functional database. Compared with related species, C. fluminea had 851 expanded gene families and 191 contracted gene families. The phylogenetic tree showed that C. fluminea diverged from Ruditapes philippinarum, ~ 228.89 million years ago (Mya), and the genomes of C. fluminea and R. philippinarum shared 244 syntenic blocks. Additionally, we identified 2 MITF members and 99 NLRP members in C. fluminea genome. The high-quality and chromosomal Asian Clam genome will be a valuable resource for a range of development and breeding studies of C. fluminea in future research.

scholarly journals Sequencing an F1 hybrid of Silurus asotus and S. meridionalis enabled the assembly of high-quality parental genomes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Weitao Chen ◽  
Ming Zou ◽  
Yuefei Li ◽  
Shuli Zhu ◽  
Xinhui Li ◽  
...  
Keyword(s):  
De Novo ◽  
Parental Species ◽  
F1 Hybrids ◽  
Pelteobagrus Fulvidraco ◽  
F1 Hybrid ◽  
Short Reads ◽  
Final Assembly ◽  
Genome Complexity ◽  
Hybrid Genome ◽  
Silurus Asotus

AbstractGenome complexity such as heterozygosity may heavily influence its de novo assembly. Sequencing somatic cells of the F1 hybrids harboring two sets of genetic materials from both of the paternal and maternal species may avoid alleles discrimination during assembly. However, the feasibility of this strategy needs further assessments. We sequenced and assembled the genome of an F1 hybrid between Silurus asotus and S. meridionalis using the SequelII platform and Hi-C scaffolding technologies. More than 300 Gb raw data were generated, and the final assembly obtained 2344 scaffolds composed of 3017 contigs. The N50 length of scaffolds and contigs was 28.55 Mb and 7.49 Mb, respectively. Based on the mapping results of short reads generated for the paternal and maternal species, each of the 29 chromosomes originating from S. asotus and S. meridionalis was recognized. We recovered nearly 94% and 96% of the total length of S. asotus and S. meridionalis. BUSCO assessments and mapping analyses suggested that both genomes had high completeness and accuracy. Further analyses demonstrated the high collinearity between S. asotus, S. meridionalis, and the related Pelteobagrus fulvidraco. Comparison of the two genomes with that assembled only using the short reads from non-hybrid parental species detected a small portion of sequences that may be incorrectly assigned to the different species. We supposed that at least part of these situations may have resulted from mitotic recombination. The strategy of sequencing the F1 hybrid genome can recover the vast majority of the parental genomes and may improve the assembly of complex genomes.

Anaesthetic effects of eugenol on preservation and transportation of yellow catfish ( Pelteobagrus fulvidraco )

2021 ◽  
Author(s):  
Jian‐he Xu ◽  
Yi Liu ◽  
Xin‐wei Zhou ◽  
Hao‐tian Ding ◽  
Xiu‐jin Dong ◽  
...  
Keyword(s):  
Pelteobagrus Fulvidraco ◽  
Yellow Catfish
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