scholarly journals Comparison of Myosepta Development and Transcriptome Profiling between Blunt Snout Bream with and Tilapia without Intermuscular Bones

Biology ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 1311
Author(s):  
Jia-Jia Zhou ◽  
Yong-Jie Chang ◽  
Yu-Long Chen ◽  
Xu-Dong Wang ◽  
Qing Liao ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Economic Value ◽  
Transcriptome Profiling ◽  
Abdominal Muscle ◽  
Megalobrama Amblycephala ◽  
Formation Mechanisms ◽  
Blunt Snout Bream ◽  
Expression Levels ◽  
Significant Expression

Intermuscular bones (IBs) are small spicule-like bones located in the myosepta of basal teleosts, which negatively affect the edibleness and economic value of fish. Blunt snout bream (Megalobrama amblycephala, with epineural and epipleural IBs) and tilapia (Oreochromis niloticus, without epineural and epipleural IBs) are two major aquaculture species and ideal models for studying the formation mechanisms of fish IBs. Here, we compared myosepta development between M. amblycephala and O. niloticus, based on histological analysis, transcriptome profiling, and expression analysis of bone-related genes. The histological results showed that dye condensation began to appear in the myosepta 20 days post hatching (dph) in M. amblycephala, and IBs could be clearly observed 50 dph in the myosepta, based on different staining methods. However, in O. niloticus, dye condensation was not observed in the myosepta from 10 to 60 dph. Differentially expressed genes (DEGs) at different developmental stages were screened by comparing the transcriptomes of M. amblycephala and O. niloticus, and KEGG analysis demonstrated that these DEGs were enriched in many bone-related pathways, such as focal adhesion, calcium, and Wnt signaling pathways. Quantitative PCR was performed to further compare the expression levels of some bone-related genes (scxa, scxb, runx2a, runx2b, bgp, sp7, col1a2, entpd5a, entpd5b, phex, alpl, and fgf23). All the tested genes (except for alpl) exhibited higher expression levels in M. amblycephala than in O. niloticus. A comparison of the dorsal and abdominal muscle tissues between the two species also revealed significant expression differences for most of the tested genes. The results suggest that scxa, scxb, runx2a, runx2b, entpd5a, col1a2, and bgp may play important roles in IB development. Our findings provide some insights into the molecular mechanisms of IB formation, as well as clues for further functional analysis of the identified genes to better understand the development of IBs.

scholarly journals Threonine affects digestion capacity and hepatopancreatic gene expression of juvenile blunt snout bream (Megalobrama amblycephala)

2015 ◽  
Vol 114 (4) ◽  
pp. 533-543 ◽  
Author(s):  
Habte-Michael Habte-Tsion ◽  
Mingchun Ren ◽  
Bo Liu ◽  
Jun Xie ◽  
Xianping Ge ◽  
...  
Keyword(s):  
Gene Expression ◽  
Protein Content ◽  
Translation Initiation Factor ◽  
Megalobrama Amblycephala ◽  
Relative Gene Expression ◽  
Feeding Trial ◽  
Blunt Snout Bream ◽  
Expression Levels ◽  
Relative Gene ◽  
Gene Expression Levels

The present study conducted a 9-week feeding trial to investigate the effects of threonine (Thr) on the digestion capacity and hepatopancreas gene expression of juvenile blunt snout bream (Megalobrama amblycephala). For this purpose, three tanks (300 litres/tank) were randomly arranged and assigned to each experimental diet. Juvenile fish were fed with diets containing graded Thr levels (0·58, 1·08, 1·58, 2·08 or 2·58 % of the diet) to apparent satiation four times daily. At the end of the feeding trial, the results indicated that hepatopancreas weight, hepatosomatic index, hepatopancreatic protein content, intestinal weight, intestosomatic index and intestinal protein content increased with increasing dietary Thr levels up to 1·58 % and thereafter decreased (P< 0·05). The activities of chymotrypsin, trypsin, amylase and lipase elevated as dietary Thr levels increased up to 1·58 % (P< 0·05), while these activities decreased in most cases after 1·58 % dietary Thr except for chymotrypsin and trypsin in the hepatopancreas (plateau 1·58–2·08 % Thr). The relative gene expression levels of chymotrypsin, trypsin, amylase, lipase, target of rapamycin and insulin-like growth factor-I were up-regulated, and the highest values were observed with 1·58 % dietary Thr or 1·58 and 2·08 % dietary Thr, whereas the relative gene expression levels of eukaryotic translation initiation factor 4E-binding protein 2 gradually decreased (P< 0·10) as dietary Thr levels increased up to 1·58 % and thereafter significantly increased (P< 0·05), which could explain that about 1·58 % dietary Thr could improve the growth and development of digestive organs and activities of digestive enzymes of juvenile blunt snout bream.

scholarly journals Nepenthes × ventrata Transcriptome Profiling Reveals a Similarity Between the Evolutionary Origins of Carnivorous Traps and Floral Organs

2021 ◽  
Vol 12 ◽  
Author(s):  
Anna V. Shchennikova ◽  
Alexey V. Beletsky ◽  
Mikhail A. Filyushin ◽  
Maria A. Slugina ◽  
Eugeny V. Gruzdev ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
De Novo ◽  
Transcriptome Profiling ◽  
Mads Box ◽  
Mads Box Genes ◽  
Evolutionary Origins ◽  
Novel Structure ◽  
Genes Encoding

The emergence of the carnivory syndrome and traps in plants is one of the most intriguing questions in evolutionary biology. In the present study, we addressed it by comparative transcriptomics analysis of leaves and leaf-derived pitcher traps from a predatory plant Nepenthes ventricosa × Nepenthes alata. Pitchers were collected at three stages of development and a total of 12 transcriptomes were sequenced and assembled de novo. In comparison with leaves, pitchers at all developmental stages were found to be highly enriched with upregulated genes involved in stress response, specification of shoot apical meristem, biosynthesis of sucrose, wax/cutin, anthocyanins, and alkaloids, genes encoding digestive enzymes (proteases and oligosaccharide hydrolases), and flowering-related MADS-box genes. At the same time, photosynthesis-related genes in pitchers were transcriptionally downregulated. As the MADS-box genes are thought to be associated with the origin of flower organs from leaves, we suggest that Nepenthes species could have employed a similar pathway involving highly conserved MADS-domain transcription factors to develop a novel structure, pitcher-like trap, for capture and digestion of animal prey during the evolutionary transition to carnivory. The data obtained should clarify the molecular mechanisms of trap initiation and development and may contribute to solving the problem of its emergence in plants.

Transcriptome profiling towards understanding of the morphogenesis in the scale development of blunt snout bream (Megalobrama amblycephala)

Genomics ◽  
2021 ◽  
Vol 113 (3) ◽  
pp. 983-991
Author(s):  
Zhiqiang Wang ◽  
Yongyi Jia ◽  
Xin Huang ◽  
Dongmei Zhu ◽  
Han Liu ◽  
...  
Keyword(s):  
Scale Development ◽  
Transcriptome Profiling ◽  
Megalobrama Amblycephala ◽  
Blunt Snout Bream

scholarly journals YAP/TEAD1 Complex Is a Default Repressor of Cardiac Toll-Like Receptor Genes

2021 ◽  
Vol 22 (13) ◽  
pp. 6649
Author(s):  
Yunan Gao ◽  
Yan Sun ◽  
Adife Gulhan Ercan-Sencicek ◽  
Justin S. King ◽  
Brynn N. Akerberg ◽  
...  
Keyword(s):  
Heart Development ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Heart Diseases ◽  
Luciferase Reporter ◽  
Binding Motif ◽  
Expression Levels ◽  
Genomic Regions

Toll-like receptors (TLRs) are a family of pattern recognition receptors (PRRs) that modulate innate immune responses and play essential roles in the pathogenesis of heart diseases. Although important, the molecular mechanisms controlling cardiac TLR genes expression have not been clearly addressed. This study examined the expression pattern of Tlr1, Tlr2, Tlr3, Tlr4, Tlr5, Tlr6, Tlr7, Tlr8, and Tlr9 in normal and disease-stressed mouse hearts. Our results demonstrated that the expression levels of cardiac Tlr3, Tlr7, Tlr8, and Tlr9 increased with age between neonatal and adult developmental stages, whereas the expression of Tlr5 decreased with age. Furthermore, pathological stress increased the expression levels of Tlr2, Tlr4, Tlr5, Tlr7, Tlr8, and Tlr9. Hippo-YAP signaling is essential for heart development and homeostasis maintenance, and YAP/TEAD1 complex is the terminal effector of this pathway. Here we found that TEAD1 directly bound genomic regions adjacent to Tlr1, Tlr2, Tlr3, Tlr4, Tlr5, Tlr6, Tlr7, and Tlr9. In vitro, luciferase reporter data suggest that YAP/TEAD1 repression of Tlr4 depends on a conserved TEAD1 binding motif near Tlr4 transcription start site. In vivo, cardiomyocyte-specific YAP depletion increased the expression of most examined TLR genes, activated the synthesis of pro-inflammatory cytokines, and predisposed the heart to lipopolysaccharide stress. In conclusion, our data indicate that the expression of cardiac TLR genes is associated with age and activated by pathological stress and suggest that YAP/TEAD1 complex is a default repressor of cardiac TLR genes.

scholarly journals Development of Teleost Intermuscular Bones Undergoing Intramembranous Ossification Based on Histological-Transcriptomic-Proteomic Data

2019 ◽  
Vol 20 (19) ◽  
pp. 4698 ◽  
Author(s):  
Chun-Hong Nie ◽  
Shi-Ming Wan ◽  
Yu-Long Liu ◽  
Han Liu ◽  
Wei-Min Wang ◽  
...  
Keyword(s):  
Bone Formation ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Critical Role ◽  
Megalobrama Amblycephala ◽  
Histological Structure ◽  
Intramembranous Ossification ◽  
Absolute Quantitation ◽  
Alizarin Red ◽  
Tail Part

Intermuscular bones (IBs) specially exist in lower teleost fish and the molecular mechanism for its development remains to be clarified. In this study, different staining methods and comparative proteomics were conducted to investigate the histological structure and proteome of IB development in Megalobrama amblycephala, including four key IB developmental stages (S1—IBs have not emerged in the tail part; S2—several small IBs started to ossify in the tail part; S3—IBs appeared rapidly; S4—all the IBs appeared with mature morphology). Alcian blue and alizarin red S stained results indicated that IBs were gradually formed from S2 to S4, undergoing intramembranous ossification without a cartilaginous phase. A total of 3368 proteins were identified by using the isobaric tags for relative and absolute quantitation (iTRAQ) approach. Functional annotation showed that proteins which were differentially expressed among stages were involved in calcium, MAPK, Wnt, TGF-β, and osteoclast pathways which played a critical role in bone formation and differentiation. Three proteins (collagen9α1, stat1, tnc) associated with chondrocytes did not exhibit significant changes through S2 to S4; however, proteins (entpd5, casq1a, pvalb, anxa2a, anxa5) which associated with osteoblasts and bone formation and differentiation showed significantly a higher expression level from S1 to S2, as well as to S3 and S4. These further demonstrated that development of IBs did not go through a cartilaginous phase. The inhibitors of TGF-β and Wnt pathways were tested on zebrafish (sp7/eGFP) and the results indicated that both inhibitors significantly delayed IB development. This study provides a comprehensive understanding of the IB ossification pattern, which will help further elucidate the molecular mechanisms for IB development in teleosts.

scholarly journals Identification and Characterization of Dimorphic Expression of Sex-Related Genes in Rock Bream, a Fish With Multiple Sex Chromosomes

2021 ◽  
Vol 12 ◽  
Author(s):  
Huan Li ◽  
Qihui Zhu ◽  
Ruiyi Chen ◽  
Mingtao Liu ◽  
Dongdong Xu
Keyword(s):  
Sex Determination ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Sex Chromosome ◽  
Expression Profiles ◽  
Transcriptional Analysis ◽  
Oplegnathus Fasciatus ◽  
Expression Levels ◽  
Rock Bream ◽  
Dimorphic Expression

The rock bream (Oplegnathus fasciatus) is a typical fish with a unique multiple sex chromosome system. In this study, we investigated the gene expression profiling in the gonads and brains of both males and females using RNA-Seq to identify sex-related genes and pathways. In accordance with the dimorphic expression profiles, combined with Gene ontology and KEGG enrichment analyses, a number of potential genes and pathways associated with sex determination were obtained from transcriptional analysis, especially some sex-biased genes and pathways. Next, we selected 18 candidate genes and analyzed their expression in different tissues and developmental stages. We found that the expression levels of Amh, Dmrt1, Sox9, Dmrtb1, and Nanos2 were significantly higher in the testis than those in the ovary or other tissues, whereas the expression levels of ZP4, Bouncer, RNF208, FoxH1, and TOB were significantly higher in the ovary than those in the testis. Furthermore, the expression levels of these genes in different developmental stages of gonads also showed sexually dimorphic patterns, suggesting that they might play important roles during gonadal development. These genes are useful markers for investigating sex determination and differentiation in rock bream. The findings of this study can provide insights into the molecular mechanisms of sex determination and differentiation in fish with multiple sex chromosome systems.

scholarly journals Wood Transcriptome Profiling Identifies Critical Pathway Genes of Secondary Wall Biosynthesis and Novel Regulators for Vascular Cambium Development in Populus

Genes ◽  
2019 ◽  
Vol 10 (9) ◽  
pp. 690 ◽  
Author(s):  
Min-Ha Kim ◽  
Jin-Seong Cho ◽  
Hyung-Woo Jeon ◽  
Kanidta Sangsawang ◽  
Donghwan Shim ◽  
...  
Keyword(s):  
Secondary Wall ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Hybrid Poplar ◽  
Secondary Growth ◽  
Leaf Tissue ◽  
Transcriptome Profiling ◽  
Wood Formation ◽  
Vascular Cambium ◽  
Critical Pathway

Wood, the most abundant biomass on Earth, is composed of secondary xylem differentiated from vascular cambium. However, the underlying molecular mechanisms of wood formation remain largely unclear. To gain insight into wood formation, we performed a series of wood-forming tissue-specific transcriptome analyses from a hybrid poplar (Populus alba × P. glandulosa, clone BH) using RNA-seq. Together with shoot apex and leaf tissue, cambium and xylem tissues were isolated from vertical stem segments representing a gradient of secondary growth developmental stages (i.e., immature, intermediate, and mature stem). In a comparative transcriptome analysis of the ‘developing xylem’ and ‘leaf’ tissue, we could identify critical players catalyzing each biosynthetic step of secondary wall components (e.g., cellulose, xylan, and lignin). Several candidate genes involved in the initiation of vascular cambium formation were found via a co-expression network analysis using abundantly expressed genes in the ‘intermediate stem-derived cambium’ tissue. We found that transgenic Arabidopsis plants overexpressing the PtrHAM4-1, a GRAS family transcription factor, resulted in a significant increase of vascular cambium development. This phenotype was successfully reproduced in the transgenic poplars overexpressing the PtrHAM4-1. Taken together, our results may serve as a springboard for further research to unravel the molecular mechanism of wood formation, one of the most important biological processes on this planet.

scholarly journals Integrated transcriptomic and proteomic analysis reveals the complex molecular mechanisms underlying stone cell formation in Korla pear

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Aisajan Mamat ◽  
Kuerban Tusong ◽  
Juan Xu ◽  
Peng Yan ◽  
Chuang Mei ◽  
...  
Keyword(s):  
Cell Differentiation ◽  
Proteomic Analysis ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Cell Formation ◽  
Parenchyma Cell ◽  
Lignin Biosynthesis ◽  
Cell Content ◽  
Stone Cell ◽  
Fruit Samples

AbstractKorla pear (Pyrus sinkiangensis Yü) is a landrace selected from a hybrid pear species in the Xinjiang Autonomous Region in China. In recent years, pericarp roughening has been one of the major factors that adversely affects fruit quality. Compared with regular fruits, rough-skin fruits have a greater stone cell content. Stone cells compose sclerenchyma tissue that is formed by secondary thickening of parenchyma cell walls. In this work, we determined the main components of stone cells by isolating them from the pulp of rough-skin fruits at the ripening stage. Stone cell staining and apoptosis detection were then performed on fruit samples that were collected at three different developmental stages (20, 50 and 80 days after flowering (DAF)) representing the prime, late and stationary stages of stone cell differentiation, respectively. The same batches of samples were used for parallel transcriptomic and proteomic analysis to identify candidate genes and proteins that are related to SCW biogenesis in Korla pear fruits. The results showed that stone cells are mainly composed of cellulose (52%), hemicellulose (23%), lignin (20%) and a small amount of polysaccharides (3%). The periods of stone cell differentiation and cell apoptosis were synchronous and primarily occurred from 0 to 50 DAF. The stone cell components increased abundantly at 20 DAF but then decreased gradually. A total of 24,268 differentially expressed genes (DEGs) and 1011 differentially accumulated proteins (DAPs) were identified from the transcriptomic and proteomic data, respectively. We screened the DEGs and DAPs that were enriched in SCW-related pathways, including those associated with lignin biosynthesis (94 DEGs and 31 DAPs), cellulose and xylan biosynthesis (46 DEGs and 18 DAPs), S-adenosylmethionine (SAM) metabolic processes (10 DEGs and 3 DAPs), apoplastic ROS production (16 DEGs and 2 DAPs), and cell death (14 DEGs and 6 DAPs). Among the identified DEGs and DAPs, 63 significantly changed at both the transcript and protein levels during the experimental periods. In addition, the majority of these identified genes and proteins were expressed the most at the prime stage of stone cell differentiation, but their levels gradually decreased at the later stages.

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