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.

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

2019 ◽  
Vol 19 (5) ◽  
pp. 1309-1321 ◽  
Author(s):  
Yan He ◽  
Yue Chang ◽  
Lisui Bao ◽  
Mengjun Yu ◽  
Rui Li ◽  
...  
Keyword(s):  
Live Birth ◽  
Black Rockfish ◽  
Sebastes Schlegelii ◽  
Chromosome Level

scholarly journals The Bdkrb2 gene family provides a novel view of viviparity adaptation in Sebastes schlegelii

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jingjing Niu ◽  
Weihao Song ◽  
Rui Li ◽  
Haiyang Yu ◽  
Jian Guan ◽  
...  
Keyword(s):  
Protein Structure ◽  
Vascular System ◽  
Critical Role ◽  
Future Research ◽  
Breeding Cycle ◽  
Exterior Surface ◽  
Black Rockfish ◽  
Vascular Regulation ◽  
Sebastes Schlegelii ◽  
Ovarian Wall

Abstract Background Black rockfish (Sebastes schlegelii) is a viviparous teleost. We proposed that the rockfish ovarian wall had a similar function to the uterus of mammals previously. In the present study, the well-developed vascular system was observed in the ovarian wall and the exterior surface of the egg membrane. In gestation, adaptation of the ovary vasculature to the rising needs of the embryos occurs through both vasodilation and neovascularization. Bdkrb2, encoding a receptor for bradykinin, plays a critical role in the control of vasodilatation by regulating nitric oxide production. Results Eight Bdkrb2 genes were identified in the black rockfish genome. These genes were located on chromosome 14, which are arranged in a tandem array, forming a gene cluster spanning 50 kb. Protein structure prediction, phylogenetic analysis, and transcriptome analysis showed that eight Bdkrb2 genes evolved two kinds of protein structure and three types of tissue expression pattern. Overexpression of two Bdkrb2 genes in zebrafish indicated a role of them in blood vessel formation or remodeling, which is an important procedure for the viviparous rockfish getting prepared for fertilization and embryos implantation. Conclusions Our study characterizes eight Bdrkb2 genes in the black rockfish, which may contribute to preparation for fertilization and embryo implantation. This research provides a novel view of viviparity adaptation and lays the groundwork for future research into vascular regulation of ovarian tissue in the breeding cycle in black rockfish.

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.

scholarly journals The Bdkrb2 Gene Family Provides a Novel View of Viviparity Adaption in Sebastes schlegelii

2020 ◽  
Author(s):  
Jingjing Niu ◽  
Weihao Song ◽  
Rui Li ◽  
Haiyang Yu ◽  
Jian Guan ◽  
...  
Keyword(s):  
Protein Structure ◽  
Expression Pattern ◽  
Tissue Expression ◽  
No Production ◽  
Tissue Expression Pattern ◽  
Exterior Surface ◽  
Black Rockfish ◽  
Vascular Regulation ◽  
Sebastes Schlegelii ◽  
Ovarian Wall

Abstract Background: Black rockfish ( Sebastes schlegelii ) is a viviparous teleost . In the prior study, we reported a chromosome-level black rockfish genome assembly and proposed that the rockfish ovarian wall has a similar function to the uterus of mammals. In the present study, the well-developed vascular system was observed in the ovary wall and the exterior surface of the egg membrane. Adaptation of the ovary vasculature to the rising needs of the embryos occurs through both vasodilation and neovascularization. Bdkrb2 encodes a receptor for bradykinin. The two play a critical role in the control of vasodilatation by regulating NO production. Results: Eight Bdkrb2 genes were identified in the black rockfish genome. These genes are located on chromosome 14, which are arranged in a tandem array, forming a gene cluster spanning 50 kb. Protein structure prediction, phylogenetic analysis, and tissue expression pattern analysis was done to clarify the relationship of the Bdkrb2 genes and a preliminary exploration of function was conducted. The results show that the eight Bdkrb2 genes evolved two kinds of protein structure and three kinds of tissue expression pattern. Furthermore, some have a relatively high expression in ovarian wall, especially in stages of pre-fertilization and pre-hatching. Conclusions: Our study characterizes eight Bdkrb2 genes in the black rockfish, which have a regulatory role in the preparation for fertilization and hatching. This research provides a novel view of viviparity adaption and lays the groundwork for future research into vascular regulation of ovarian in the breeding cycle in black rockfish.

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 Role of the lncRNA BACE1-AS in shared disease mechanisms between heart failure and Alzheimer's disease

2020 ◽  
Vol 41 (Supplement_2) ◽  
Author(s):  
S Greco ◽  
A Made' ◽  
A.S Tascini ◽  
J Garcia Manteiga ◽  
S Castelvecchio ◽  
...  
Keyword(s):  
Heart Failure ◽  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
In Situ Hybridization ◽  
Cell Apoptosis ◽  
Common Disease ◽  
Funding Source ◽  
Mrna Levels ◽  
Rna Seq

Abstract Background BACE1 encodes for β-secretase, the key enzyme involved in β-amyloid (βA) generation, a peptide well known for its involvement in Alzheimer's disease (AD). Of note, heart failure (HF) and AD share several risk factors and effectors. We recently showed that, in the heart of ischemic HF patients, the levels of both BACE1, its antisense RNA BACE1-AS and βA are all increased. BACE1-AS positively regulates the expression of BACE1, triggering βA intracellular accumulation, and its overexpression or βA administration induce cardiovascular-cell apoptosis. Aim To characterize the transcripts of the BACE1 locus and to investigate the molecular mechanisms underpinning BACE1-AS regulation of cell vitality. Methods By PCR and sequencing, we studied in the heart the expression of a variety of antisense BACE1 transcripts predicted by FANTOM CAT Epigenome. We studied BACE1 RNA stability by BrdU pulse chase experiments (BRIC assay). The cellular localization of BACE1-AS RNA was investigated by in situ hybridization assay. BACE1-AS binding RNAs were evaluated by BACE1-AS-MS2-Tag pull-down in AC16 cardiomyocytes followed by RNA-seq. Enriched RNAs were validated by qPCR and analysed by bioinformatics comparison with publicly available gene expression datasets of AD brains. Results We readily detected several antisense BACE1 transcripts expressed in AC16 cardiomyocytes; however, only BACE1-AS RNAs overlapping exon 6 of BACE1 positively regulated BACE1 mRNA levels, acting by increasing its stability. BACE1 silencing reverted cell apoptosis induced by BACE1-AS expression, indicating that BACE1 is a functional target of BACE1-AS. However, in situ hybridization experiments indicated a mainly nuclear localization for BACE1-AS, which displayed a punctuated distribution, compatible with chromatin association and indicative of potential additional targets. To identify other BACE1-AS binding RNAs, a BACE1-AS-MS2-tag pull-down was performed and RNA-seq of the enriched RNAs identified 698 BACE1-AS interacting RNAs in cardiomyocytes. Gene ontology of the BACE1-AS binding RNAs identified categories of relevance for cardiovascular or neurological diseases, such as dopaminergic synapse, glutamatergic synapse, calcium signalling pathway and voltage-gated channel activity. In spite of the differences between brain and heart transcriptomes, BACE1-AS-interacting RNAs identified in cardiomyocytes were significantly enriched in transcripts differentially expressed in AD brains as well as in RNAs expressed by enhancer genomic regions that are significantly hypomethylated in AD brains. Conclusions These data shed a new light on the complexity of BACE1-AS locus and on the existence of RNAs interacting with BACE1-AS with a potential as enhancer-RNAs. Moreover, the dysregulation of the BACE1-AS/BACE1/βA pathway may be a common disease mechanism shared by cardiovascular and neurological degenerative diseases. Funding Acknowledgement Type of funding source: Public grant(s) – National budget only. Main funding source(s): Italian Health Ministery_Ricerca Corrente 2020

scholarly journals Loss of Wnt16 Leads to Skeletal Deformities and Downregulation of Bone Developmental Pathway in Zebrafish

2021 ◽  
Vol 22 (13) ◽  
pp. 6673
Author(s):  
Xiaochao Qu ◽  
Mei Liao ◽  
Weiwei Liu ◽  
Yisheng Cai ◽  
Qiaorong Yi ◽  
...  
Keyword(s):  
Gene Knockout ◽  
Integration Site ◽  
Skeletal Development ◽  
Rna Seq ◽  
Developmental Pathway ◽  
Mineral Density ◽  
Zebrafish Model ◽  
Protein Protein Interaction ◽  
Ct Analysis

Wingless-type MMTV integration site family, member 16 (wnt16), is a wnt ligand that participates in the regulation of vertebrate skeletal development. Studies have shown that wnt16 can regulate bone metabolism, but its molecular mechanism remains largely undefined. We obtained the wnt16-/- zebrafish model using the CRISPR-Cas9-mediated gene knockout screen with 11 bp deletion in wnt16, which led to the premature termination of amino acid translation and significantly reduced wnt16 expression, thus obtaining the wnt16-/- zebrafish model. The expression of wnt16 in bone-related parts was detected via in situ hybridization. The head, spine, and tail exhibited significant deformities, and the bone mineral density and trabecular bone decreased in wnt16-/- using light microscopy and micro-CT analysis. RNA sequencing was performed to explore the differentially expressed genes (DEGs). Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis found that the down-regulated DEGs are mainly concentrated in mTOR, FoxO, and VEGF pathways. Protein–protein interaction (PPI) network analysis was performed with the detected DEGs. Eight down-regulated DEGs including akt1, bnip4, ptena, vegfaa, twsg1b, prkab1a, prkab1b, and pla2g4f.2 were validated by qRT-PCR and the results were consistent with the RNA-seq data. Overall, our work provides key insights into the influence of wnt16 gene on skeletal development.

scholarly journals In situ RNA-seq

2013 ◽  
Vol 14 (9) ◽  
pp. 596-596 ◽  
Author(s):  
Hannah Stower
Keyword(s):  
Rna Seq

scholarly journals Effects of Food Deprivation Duration on the Behavior and Metabolism of Black Rockfish (Sebastes schlegelii)

Fishes ◽  
2021 ◽  
Vol 6 (4) ◽  
pp. 58
Author(s):  
Fengyuan Shen ◽  
Zonghang Zhang ◽  
Yiqiu Fu ◽  
Zhen Zhang ◽  
Xin Sun ◽  
...  
Keyword(s):  
Food Deprivation ◽  
Personality Assessment ◽  
Behavioral Assessment ◽  
Standard Metabolic Rate ◽  
Control Group ◽  
Black Rockfish ◽  
Swimming Time ◽  
Sebastes Schlegelii ◽  
Food Shortages

Fish often undergo food shortages in nature, especially for juveniles that are relatively vulnerable in most aspects. Therefore, the effects of food deprivation on fish behavior and physiology are worth exploring. Here, we investigated the behavioral and metabolic adaptations of the juvenile black rockfish Sebastes schlegelii to different durations of food deprivation. In this study, three treatments were set: control group, short-term food deprivation (STFD) group, and long-term food deprivation (LTFD) group. The rearing lasted for six weeks. During this period, videos were recorded three times per week to assess the locomotor activity and aggression. After this, the fishes’ boldness, neophobia, and aggressiveness were assessed using different behavioral assessment devices, while the standard metabolic rate (SMR) was measured by flow-type respirometry. In general, the values of the four indicators (swimming time, the number of turns, movement number, and attack number) for the STFD group were significantly higher than those for the control and LTFD group during the same period of rearing. In a subsequent personality assessment, the STFD group was observed to be significantly bolder in an assessment measuring boldness than the control and LTFD group (indicated by time in the circle, swimming time, number of times through the circle, and frequency in the circle). The LTFD group was observed to be more exploratory in the assessment of neophobia (indicated by duration in the exploratory area, distance from novelty item, and frequency of stay in the exploratory area). Indeed, the LTFD group was observed to be significantly less aggressive in the assessment of aggressiveness than the control and STFD group (indicated by attack number, attack range frequency, first attack, and winner). SMR was noted to be significantly higher in the STFD group than in the control and LTFD group. In conclusion, this study firstly reported the effects of food deprivation duration on the personalities of black rockfish, as well as the behavioral and physiological mechanisms. Thus, we hope to provide insights into the work of stock enhancement.

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