scholarly journals Comparative transcriptomic analysis of gonadal development and renewal in the ovoviviparous black rockfish (Sebastes schlegelii)

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Jianshuang Li ◽  
Likang Lyu ◽  
Haishen Wen ◽  
Yun Li ◽  
Xiaojie Wang ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Gonadal Development ◽  
Mature Stage ◽  
Reproductive Pattern ◽  
Cell Renewal ◽  
Rna Seq ◽  
Intercellular Interaction ◽  
Down Regulation ◽  
Black Rockfish ◽  
Sebastes Schlegelii

Abstract Background The black rockfish (Sebastes schlegelii) has an ovoviviparous reproductive pattern and long-term sperm storage, resulting in asynchronous gonadal development between the sexes. However, the comprehensive understanding of gonadal development in black rockfish has not yet been achieved. Here, we studied gonadal development and germ cell renewal using histology and RNA-seq. Results In this study, RNA-seq was performed on testes and ovaries to characterize key pathways and genes that are active during development and gamete maturation in black rockfish. Differentially expressed genes (DEGs) were identified and annotated in 4 comparisons (F_III vs. F_IV, F_IV vs. F_V, M_III vs. M_IV and M_IV vs. M_V). Based on analysis of DEGs enriched in the testis, 11 and 14 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were mapped to the M_III vs. M_IV group and the M_IV vs. M_V group, respectively. DEGs in ovarian development were also classified into 10 groups according to their biological functions. The expression patterns of the selected genes determined by qPCR were significantly correlated with the RNA-Seq results, supporting the reliability and accuracy of the RNA-Seq analysis. E2 levels showed down regulation from previtellogenesis to mature stage in female and T level showed down regulation from spermatogenesis to regressed stage in the male. Conclusions The categories “intercellular interaction and cytoskeleton”, “molecule amplification” and “repair in the cell cycle” were revealed to be crucial in testis development and spermatogenesis, as was the biosynthesis of a series of metabolites. Our results provide comprehensive insight into black rockfish gonadal development and provide a basis for further study of reproductive physiology and molecular biology in ovoviviparity teleosts.

Comparative Transcriptomic Analysis of Gonad Development and Renewal of Ovoviviparous Black Rockfish (Sebastes Schlegelii)

2020 ◽  
Author(s):  
Jianshaung Li ◽  
Haishen Wen ◽  
Likang Lyu ◽  
Yun Li ◽  
Xiaojie Wang ◽  
...  
Keyword(s):  
Gonad Development ◽  
Gonadal Development ◽  
Ovary Development ◽  
Reproductive Pattern ◽  
Cell Renewal ◽  
Rna Seq ◽  
Intercellular Interaction ◽  
Black Rockfish ◽  
Kegg Pathways ◽  
Sebastes Schlegelii

Abstract Background: Black rockfish (Sebastes schlegelii) has an ovoviviparous reproductive pattern and long-term sperm storage, which resulting in asynchronous gonadal development between the sexes. While the comprehensive understanding of gonad development of black rockfish has not been well studied. Here, we study the gonad development and germ cell renewal by histology and RNA-seq.Results: In this study, RNA-seq was performed on both testis and ovary to characterize key pathways and genes during development and gamete maturation in black rockfish. Different expression genes (DEGs) were identified and annotated in 4 comparisons (F_III vs F_IV, F_IV vs F_V, M_III vs M_IV and M_IV vs M_V). Based on enriched analysis of DEGs in testis, 11 and 14 significantly enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were mapped in M_III vs M_IV group and M_IV vs M_V group, respectively. And DEGs in ovary development periods were also classified into 10 biological function group. The results of the q-PCR expression pattern of the selected genes was significantly correlated with the RNA-Seq results, implying the reliability and accuracy of the RNA-Seq analysis.Conclusion: The categories intercellular interaction and cytoskeleton, molecule amplification and repairment in cell cycle were revealed to be crucial in testis development and spermatogenesis along with a series of metabolite biosynthesis. Our results provided a comprehensive insight into the black rockfish gonad development for further study of reproductive physiology and molecular biology in ovoviviparity.

scholarly journals De novo gonad transcriptome analysis of the common littoral shrimp Palaemon serratus: novel insights into sex-related genes

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Inés González-Castellano ◽  
Chiara Manfrin ◽  
Alberto Pallavicini ◽  
Andrés Martínez-Lage
Keyword(s):  
Transcriptome Analysis ◽  
De Novo ◽  
Expression Patterns ◽  
Gonadal Development ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Illumina Hiseq ◽  
Specific Expression ◽  
Development Processes ◽  
The Common

Abstract Background The common littoral shrimp Palaemon serratus is an economically important decapod resource in some European communities. Aquaculture practices prevent the genetic deterioration of wild stocks caused by overfishing and at the same time enhance the production. The biotechnological manipulation of sex-related genes has the proved potential to improve the aquaculture production but the scarcity of genomic data about P. serratus hinders these applications. RNA-Seq analysis has been performed on ovary and testis samples to generate a reference gonadal transcriptome. Differential expression analyses were conducted between three ovary and three testis samples sequenced by Illumina HiSeq 4000 PE100 to reveal sex-related genes with sex-biased or sex-specific expression patterns. Results A total of 224.5 and 281.1 million paired-end reads were produced from ovary and testis samples, respectively. De novo assembly of ovary and testis trimmed reads yielded a transcriptome with 39,186 transcripts. The 29.57% of the transcriptome retrieved at least one annotation and 11,087 differentially expressed genes (DEGs) were detected between ovary and testis replicates. Six thousand two hundred seven genes were up-regulated in ovaries meanwhile 4880 genes were up-regulated in testes. Candidate genes to be involved in sexual development and gonadal development processes were retrieved from the transcriptome. These sex-related genes were discussed taking into account whether they were up-regulated in ovary, up-regulated in testis or not differentially expressed between gonads and in the framework of previous findings in other crustacean species. Conclusions This is the first transcriptome analysis of P. serratus gonads using RNA-Seq technology. Interesting findings about sex-related genes from an evolutionary perspective (such as Dmrt1) and for putative future aquaculture applications (Iag or vitellogenesis genes) are reported here. We provide a valuable dataset that will facilitate further research into the reproductive biology of this shrimp.

scholarly journals RNA-Seq Implies Divergent Regulation Patterns of LincRNA on Spermatogenesis and Testis Growth in Goats

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 625
Author(s):  
Dongdong Bo ◽  
Xunping Jiang ◽  
Guiqiong Liu ◽  
Ruixue Hu ◽  
Yuqing Chong
Keyword(s):  
Target Genes ◽  
Expression Patterns ◽  
Testicular Development ◽  
Related Protein ◽  
Rna Seq ◽  
Down Regulation ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Regulation Of Growth ◽  
Fresh Insight

Long intergenic non-coding RNAs (lincRNAs) regulate testicular development by acting on protein-coding genes. However, little is known about whether lincRNAs and protein-coding genes exhibit the same expression pattern in the same phase of postnatal testicular development in goats. Therefore, this study aimed to demonstrate the expression patterns and roles of lincRNAs during the postnatal development of the goat testis. Herein, the testes of Yiling goats with average ages of 0, 30, 60, 90, 120, 150, and 180 days postnatal (DP) were used for RNA-seq. In total, 20,269 lincRNAs were identified, including 16,931 novel lincRNAs. We identified seven time-specifically diverse lincRNA modules and six mRNA modules by weighted gene co-expression network analysis (WGCNA). Interestingly, the down-regulation of growth-related lincRNAs was nearly one month earlier than the up-regulation of spermatogenesis-related lincRNAs, while the down-regulation of growth-related protein-coding genes and the correspondent up-regulation of spermatogenesis-related protein-coding genes occurred at the same age. Then, potential lincRNA target genes were predicted. Moreover, the co-expression network of lincRNAs demonstrated that ENSCHIT00000000777, ENSCHIT00000002069, and ENSCHIT00000005076 were the key lincRNAs in the process of testis development. Our study discovered the divergent regulation patterns of lincRNA on spermatogenesis and testis growth, providing a fresh insight into age-biased changes in lincRNA expression in the goat testis.

scholarly journals Genome-Wide Identification, Characterization and Expression Profiling of myosin Family Genes in Sebastes schlegelii

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 808
Author(s):  
Chaofan Jin ◽  
Mengya Wang ◽  
Weihao Song ◽  
Xiangfu Kong ◽  
Fengyan Zhang ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Muscle Growth ◽  
Myoblast Differentiation ◽  
Growth Stages ◽  
Marine Teleost ◽  
Black Rockfish ◽  
Skeletal Muscle Growth ◽  
Sebastes Schlegelii

Myosins are important eukaryotic motor proteins that bind actin and utilize the energy of ATP hydrolysis to perform a broad range of functions such as muscle contraction, cell migration, cytokinesis, and intracellular trafficking. However, the characterization and function of myosin is poorly studied in teleost fish. In this study, we identified 60 myosin family genes in a marine teleost, black rockfish (Sebastes schlegelii), and further characterized their expression patterns. myosin showed divergent expression patterns in adult tissues, indicating they are involved in different types and compositions of muscle fibers. Among 12 subfamilies, S. schlegelii myo2 subfamily was significantly expanded, which was driven by tandem duplication events. The up-regulation of five representative genes of myo2 in the skeletal muscle during fast-growth stages of juvenile and adult S. schlegelii revealed their active role in skeletal muscle fiber synthesis. Moreover, the expression regulation of myosin during the process of myoblast differentiation in vitro suggested that they contribute to skeletal muscle growth by involvement of both myoblast proliferation and differentiation. Taken together, our work characterized myosin genes systemically and demonstrated their diverse functions in a marine teleost species. This lays foundation for the further studies of muscle growth regulation and molecular mechanisms of indeterminate skeletal muscle growth of large teleost fishes.

scholarly journals Identification of Antimicrobial Peptide Genes in Black Rockfish Sebastes schlegelii and Their Responsive Mechanisms to Edwardsiella tarda Infection

Biology ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 1015
Author(s):  
Min Zhang ◽  
Min Cao ◽  
Yunji Xiu ◽  
Qiang Fu ◽  
Ning Yang ◽  
...  
Keyword(s):  
Antimicrobial Peptide ◽  
Single Molecule ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Amino Acid Sequences ◽  
Edwardsiella Tarda ◽  
Economic Losses ◽  
Dominant Type ◽  
Black Rockfish ◽  
Sebastes Schlegelii

The black rockfish, Sebastes schlegelii, is a typical viviparous teleost, which belongs to the family Scorpaenidae. Due to its high economic and ecological values, S. schlegelii has been widely cultured in East Asian countries. With the enlargement of cultivation scale, bacterial and viral diseases have become the main threats to the farming industry of S. schlegelii, which have resulted in significant economic losses. In this study, Illumina shotgun sequencing, single-molecule real-time (SMRT) sequencing, 10x genomics and high-throughput chromosome conformation capture (Hi-C) technologies were collectively applied to assemble the genome of S. schlegelii. Then, we identified the antimicrobial peptide genes (AMPs) in the S. schlegelii genome. In total, 214 AMPs were identified in the S. schlegelii genome, which can be divided into 33 classes according to the annotation and cataloging of the Antimicrobial Peptides Database (APD3). Among these AMPs, thrombin-derived C-terminal peptide (TCP) was the dominant type, followed by RegIIIgamma and chemokine. The amino acid sequences of the TCP, cgUbiquitin, RegIIIalpha, RegIIIgamma, chemokine shared 32.55%, 42.63%, 29.87%, 28.09%, and 32.15% similarities among the same type in S. schlegelii. Meanwhile, the expression patterns of these AMPs in nine healthy tissues and at different infection time points in intestine were investigated. The results showed that the numbers and types of AMPs that responded to Edwardsiella tarda infection gradually increased as the infection progressed. In addition, we analyzed the phylogenetic relationships of hepcidins in teleost. The identification of AMPs based on the whole genome could provide a comprehensive database of potential AMPs, and benefit for the understanding of the molecular mechanisms of immune responses to E. tarda infection in S. schlegelii. This would further offer insights into an accurate and effective design and development of AMP for aquaculture therapy in the future.

scholarly journals A chromosome-level genome of black rockfish, Sebastes schlegelii, provides insights into the evolution of live birth

2019 ◽  
Author(s):  
Yan He ◽  
Yue Chang ◽  
Lisui Bao ◽  
Mengjun Yu ◽  
Rui Li ◽  
...  
Keyword(s):  
Live Birth ◽  
Life History Strategy ◽  
Similar Function ◽  
Rna Seq ◽  
Black Rockfish ◽  
Sebastes Schlegelii ◽  
Ovarian Wall ◽  
Sound Foundation ◽  
Chromosome Level

Black rockfish (Sebastes schlegelii) is a teleost species where eggs are fertilized internally and retained in the maternal reproductive system, where they undergo development until live birth (termed viviparity). In the present study, we report a chromosome-level black rockfish genome assembly. High-throughput transcriptome analysis (RNA-seq and ATAC-seq), coupled with in situ hybridization (ISH) and immunofluorescence, identify several candidate genes for maternal preparation, sperm storage and release, and hatching. We propose that zona pellucida (ZP) genes retain sperm at the oocyte envelope, while genes in two distinct astacin metalloproteinase subfamilies serve to release sperm from the ZP and free the embryo from chorion at pre-hatching stage. Finally, we present a model of black rockfish reproduction, and propose that the rockfish ovarian wall has a similar function to uterus of mammals. Taken together, these genomic data reveal unprecedented insights into the evolution of an unusual teleost life history strategy, and provide a sound foundation for studying viviparity in non-mammalian vertebrates and an invaluable resource for rockfish ecology and evolution research.

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