scholarly journals Transcriptome profiling of developing testes and spermatogenesis in Mongolian horse

2019 ◽  
Author(s):  
Bei LI ◽  
Xiaolong He ◽  
Yiping Zhao ◽  
Dongyi Bai ◽  
Ming Du ◽  
...  
Keyword(s):  
Developmental Stages ◽  
Male Gamete ◽  
Transcriptome Profiling ◽  
Testicular Development ◽  
Testis Development ◽  
Physiological Processes ◽  
Oocyte Meiosis ◽  
Mongolian Horse ◽  
Pathway Analyses ◽  
Upregulated Genes

Abstract Introduction: The development of horse testis and spermatogenesis is a complex physiological process. Methods: To study those physiological processes, 3 immature and 3 mature testes of Mongolian horse were collected, and six libraries were established using a high-throughput RNA sequencing technology (RNA-Seq) to screen for genes that were related to Mongolian horse testis development and spermatogenesis.Results & Discussion: A total of 16,237 upregulated genes and 8,641 downregulated genes in the testis of Mongolian horse were detected. These genes play important roles in different developmental stages of spermatogenesis and testicular development. Five alternative splicing (AS) event genes were detected, and different AS events can also influence both spermatogenesis and developing of testis. GO (Gene ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analyses were performed for functional annotation of the differentially expressed genes during testis development and spermatogenesis. For example, oocyte meiosis pathways were significantly involved in different stages of testis development and spermatogenesis.Conclusion: These genes were associated with spermatogenesis, male gamete generation, spermatid development, and oocyte meiosis.The finding that gene is a vital element in horse testis development improves our understanding of horse testis development and spermatogenesis.

scholarly journals Transcriptome profiling of developing testes and spermatogenesis in the Mongolian horse

2020 ◽  
Author(s):  
Bei LI ◽  
Xiaolong He ◽  
Yiping Zhao ◽  
Dongyi Bai ◽  
Ming Du ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Developmental Stages ◽  
Male Gamete ◽  
Transcriptome Profiling ◽  
Differentially Expressed ◽  
Testicular Development ◽  
Testis Development ◽  
Oocyte Meiosis ◽  
Alternative Splicing Events ◽  
Mongolian Horse

Abstract Background: Horse testis development and spermatogenesis are complex physiological processes. Methods: To study these processes, three immature and three mature testes were collected from the Mongolian horse, and six libraries were established using high-throughput RNA sequencing technology (RNA-Seq) to screen for genes related to testis development and spermatogenesis. Results: A total of 16,237 upregulated genes and 8,641 downregulated genes were detected in the testis of the Mongolian horse. These genes play important roles in different developmental stages of spermatogenesis and testicular development. Five genes with alternative splicing events that may influence spermatogenesis and development of the testis were detected. GO (Gene ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analyses were performed for functional annotation of the differentially expressed genes. Pathways related to “spermatogenesis,” male gamete generation,” “spermatid development” and “oocyte meiosis” were significantly involved in different stages of testis development and spermatogenesis. Conclusion: Genes, pathways and alternative splicing events were identified with inferred functions in the process of spermatogenesis in the Mongolian horse. The identification of these differentially expressed genetic signatures improves our understanding of horse testis development and spermatogenesis.

scholarly journals Transcriptome profiling of developing testes and spermatogenesis in the Mongolian horse

2020 ◽  
Author(s):  
Bei LI ◽  
Xiaolong He ◽  
Yiping Zhao ◽  
Dongyi Bai ◽  
Ming Du ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Developmental Stages ◽  
Male Gamete ◽  
Transcriptome Profiling ◽  
Differentially Expressed ◽  
Testicular Development ◽  
Testis Development ◽  
Oocyte Meiosis ◽  
Alternative Splicing Events ◽  
Mongolian Horse

Abstract Background: Horse testis development and spermatogenesis are complex physiological processes. Methods: To study these processes, three immature and three mature testes were collected from the Mongolian horse, and six libraries were established using high-throughput RNA sequencing technology (RNA-Seq) to screen for genes related to testis development and spermatogenesis. Results: A total of 16,237 upregulated genes and 8,641 downregulated genes were detected in the testis of the Mongolian horse. These genes play important roles in different developmental stages of spermatogenesis and testicular development. Five genes with alternative splicing events that may influence spermatogenesis and development of the testis were detected. GO (Gene ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analyses were performed for functional annotation of the differentially expressed genes. Pathways related to “spermatogenesis,” male gamete generation,” “spermatid development” and “oocyte meiosis” were significantly involved in different stages of testis development and spermatogenesis. Conclusion: Genes, pathways and alternative splicing events were identified with inferred functions in the process of spermatogenesis in the Mongolian horse. The identification of these differentially expressed genetic signatures improves our understanding of horse testis development and spermatogenesis.

scholarly journals Transcriptome profiling of developing testes and spermatogenesis in the Mongolian horse

2020 ◽  
Author(s):  
Bei LI ◽  
Xiaolong He ◽  
Yiping Zhao ◽  
Dongyi Bai ◽  
Ming Du ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Developmental Stages ◽  
Male Gamete ◽  
Transcriptome Profiling ◽  
Differentially Expressed ◽  
Testicular Development ◽  
Testis Development ◽  
Oocyte Meiosis ◽  
Alternative Splicing Events ◽  
Mongolian Horse

Abstract Background: Horse testis development and spermatogenesis are complex physiological processes. Methods: To study these processes, three immature and three mature testes were collected from the Mongolian horse, and six libraries were established using high-throughput RNA sequencing technology (RNA-Seq) to screen for genes related to testis development and spermatogenesis. Results: A total of 16,237 upregulated genes and 8,641 downregulated genes were detected in the testis of the Mongolian horse. These genes play important roles in different developmental stages of spermatogenesis and testicular development. Five genes with alternative splicing events that may influence spermatogenesis and development of the testis were detected. GO (Gene ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analyses were performed for functional annotation of the differentially expressed genes. Pathways related to “spermatogenesis,” male gamete generation,” “spermatid development” and “oocyte meiosis” were significantly involved in different stages of testis development and spermatogenesis. Conclusion: Genes, pathways and alternative splicing events were identified with inferred functions in the process of spermatogenesis in the Mongolian horse. The identification of these differentially expressed genetic signatures improves our understanding of horse testis development and spermatogenesis.

scholarly journals Absence of S100A4 in the mouse lens induces an aberrant retina-specific differentiation program and cataract

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Rupalatha Maddala ◽  
Junyuan Gao ◽  
Richard T. Mathias ◽  
Tylor R. Lewis ◽  
Vadim Y. Arshavsky ◽  
...  
Keyword(s):  
Calcium Binding ◽  
Late Onset ◽  
Cpg Islands ◽  
Transcriptome Profiling ◽  
Specific Gene ◽  
Pathway Network ◽  
S100a4 Expression ◽  
Histone H3k27 ◽  
Pathway Analyses ◽  
Upregulated Genes

AbstractS100A4, a member of the S100 family of multifunctional calcium-binding proteins, participates in several physiological and pathological processes. In this study, we demonstrate that S100A4 expression is robustly induced in differentiating fiber cells of the ocular lens and that S100A4(−/−) knockout mice develop late-onset cortical cataracts. Transcriptome profiling of lenses from S100A4(−/−) mice revealed a robust increase in the expression of multiple photoreceptor- and Müller glia-specific genes, as well as the olfactory sensory neuron-specific gene, S100A5. This aberrant transcriptional profile is characterized by corresponding increases in the levels of proteins encoded by the aberrantly upregulated genes. Ingenuity pathway network and curated pathway analyses of differentially expressed genes in S100A4(−/−) lenses identified Crx and Nrl transcription factors as the most significant upstream regulators, and revealed that many of the upregulated genes possess promoters containing a high-density of CpG islands bearing trimethylation marks at histone H3K27 and/or H3K4, respectively. In support of this finding, we further documented that S100A4(−/−) knockout lenses have altered levels of trimethylated H3K27 and H3K4. Taken together, our findings suggest that S100A4 suppresses the expression of retinal genes during lens differentiation plausibly via a mechanism involving changes in histone methylation.

scholarly journals Transcriptomic Analysis of the Anthocyanin Biosynthetic Pathway Reveals the Molecular Mechanism Associated with Purple Color Formation in Dendrobium Nestor

Life ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 113
Author(s):  
Xueqiang Cui ◽  
Jieling Deng ◽  
Changyan Huang ◽  
Xuan Tang ◽  
Xianmin Li ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Developmental Stages ◽  
Anthocyanin Biosynthesis ◽  
Transcriptome Profiling ◽  
Flower Color ◽  
Flower Bud ◽  
Color Formation ◽  
Color Development ◽  
Purple Coloration ◽  
Purple Color

Dendrobium nestor is a famous orchid species in the Orchidaceae family. There is a diversity of flower colorations in the Dendrobium species, but knowledge of the genes involved and molecular mechanism underlying the flower color formation in D. nestor is less studied. Therefore, we performed transcriptome profiling using Illumina sequencing to facilitate thorough studies of the purple color formation in petal samples collected at three developmental stages, namely—flower bud stage (F), half bloom stage (H), and full bloom stage (B) in D. nestor. In addition, we identified key genes and their biosynthetic pathways as well as the transcription factors (TFs) associated with purple flower color formation. We found that the phenylpropanoid–flavonoid–anthocyanin biosynthesis genes such as phenylalanine ammonia lyase, chalcone synthase, anthocyanidin synthase, and UDP-flavonoid glucosyl transferase, were largely up-regulated in the H and B samples as compared to the F samples. This upregulation might partly account for the accumulation of anthocyanins, which confer the purple coloration in these samples. We further identified several differentially expressed genes related to phytohormones such as auxin, ethylene, cytokinins, salicylic acid, brassinosteroid, and abscisic acid, as well as TFs such as MYB and bHLH, which might play important roles in color formation in D. nestor flower. Sturdy upregulation of anthocyanin biosynthetic structural genes might be a potential regulatory mechanism in purple color formation in D. nestor flowers. Several TFs were predicted to regulate the anthocyanin genes through a K-mean clustering analysis. Our study provides valuable resource for future studies to expand our understanding of flower color development mechanisms in D. nestor.

scholarly journals Identification, Expression and Evolution of Short-Chain Dehydrogenases/Reductases in Nile Tilapia (Oreochromis niloticus)

2021 ◽  
Vol 22 (8) ◽  
pp. 4201
Author(s):  
Shuai Zhang ◽  
Lang Xie ◽  
Shuqing Zheng ◽  
Baoyue Lu ◽  
Wenjing Tao ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Tandem Duplication ◽  
Developmental Stages ◽  
Short Chain ◽  
Sexually Dimorphic ◽  
Physiological Processes ◽  
Genome Wide ◽  
Nile Tilapia Oreochromis Niloticus ◽  
Tandem Duplications

The short-chain dehydrogenases/reductases (SDR) superfamily is involved in multiple physiological processes. In this study, genome-wide identification and comprehensive analysis of SDR superfamily were carried out in 29 animal species based on the latest genome databases. Overall, the number of SDR genes in animals increased with whole genome duplication (WGD), suggesting the expansion of SDRs during evolution, especially in 3R-WGD and polyploidization of teleosts. Phylogenetic analysis indicated that vertebrates SDRs were clustered into five categories: classical, extended, undefined, atypical, and complex. Moreover, tandem duplication of hpgd-a, rdh8b and dhrs13 was observed in teleosts analyzed. Additionally, tandem duplications of dhrs11-a, dhrs7a, hsd11b1b, and cbr1-a were observed in all cichlids analyzed, and tandem duplication of rdh10-b was observed in tilapiines. Transcriptome analysis of adult fish revealed that 93 SDRs were expressed in more than one tissue and 5 in one tissue only. Transcriptome analysis of gonads from different developmental stages showed that expression of 17 SDRs were sexually dimorphic with 11 higher in ovary and 6 higher in testis. The sexually dimorphic expressions of these SDRs were confirmed by in situ hybridization (ISH) and qPCR, indicating their possible roles in steroidogenesis and gonadal differentiation. Taken together, the identification and the expression data obtained in this study contribute to a better understanding of SDR superfamily evolution and functions in teleosts.

Ultrastructural Localization of Intracellular Calcium During Spermatogenesis of Sterlet (Acipenser ruthenus)

2016 ◽  
Vol 22 (6) ◽  
pp. 1155-1161 ◽  
Author(s):  
Amin Golpour ◽  
Martin Pšenička ◽  
Hamid Niksirat
Keyword(s):  
Intracellular Calcium ◽  
Developmental Stages ◽  
Physiological Function ◽  
Male Gamete ◽  
Ultrastructural Localization ◽  
Acrosomal Vesicle ◽  
Acipenser Ruthenus ◽  
Calcium Deposits ◽  
Late Stages ◽  
Sterlet Acipenser Ruthenus

AbstractCalcium regulates many intracellular events such as growth and differentiation during different stages of gamete development. The aim of this study was to localize and quantify the intracellular distribution of calcium during different developmental stages of spermatogenesis in sterlet, Acipenser ruthenus, using a combined oxalate–pyroantimonate technique. The distribution of calcium was described in spermatogonium, spermatocyte, spermatid, and spermatozoon stages. In the spermatogonium and spermatocyte, calcium deposits were mainly localized in the nucleus and cytoplasm. The spermatid had calcium in the nucleus, developing acrosomal vesicle, and cytoplasm. Intracellular calcium transformed from scattered deposits in spermatogonia and spermatocyte stages into an unbound form in spermatid and the spermatozoon. The proportion of area covered by calcium increased significantly (p<0.05) from early to late stages of spermatogenesis. The largest proportion of area covered by calcium was observed in the nucleus of the spermatozoon. In conclusion, although most of the intracellular calcium is deposited in limited areas of the spermatogonium and spermatocyte, it is present an unbound form in the larger area of spermatids and spermatozoa which probably reflects changes in its physiological function and homeostasis during the process of male gamete production in spermatogenesis.

scholarly journals Comprehensive analysis of miRNA-mRNA/lncRNA during gonadal development of triploid female rainbow trout (Oncorhynchus mykiss)

2020 ◽  
Author(s):  
Tianqing Huang ◽  
Wei Gu ◽  
Enhui Liu ◽  
Xiulan Shi ◽  
Bingqian Wang ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
High Throughput Sequencing ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Noncoding Rnas ◽  
Gonadal Development ◽  
Differentially Expressed ◽  
Rainbow Trout Oncorhynchus Mykiss ◽  
Oocyte Meiosis ◽  
Non Coding Rna

Abstract Background: Chromosomal ploidy manipulation is one of the means to create excellent germplasm. Triploid fish could provide an ideal sterile model for the mechanism research of abnormality in meiosis. The complete understanding of the coding and noncoding RNAs regulating sterility caused by meiosis abnormality is still not well understood.Results: By high-throughput sequencing, we compared the expression profiles of gonadal mRNA, long non-coding RNA (lncRNA), and microRNA (miRNA) at different developmental stages [65 days post fertilisation (dpf), 180 dpf, and 600 dpf] between the diploid (XX) and triploid (XXX) female rainbow trout. A majority of differentially expressed (DE) RNAs were identified, and 22 DE mRNAs related to oocyte meiosis and homologous recombination were characterized. The predicted miRNA-mRNA/lncRNA networks of 3 developmental stages were constructed based on the target pairs of DE lncRNA-miRNA and DE mRNA-miRNA. According to the networks, meiosis-related gene of ccne1 was targeted by dre-miR-15a-5p_R+1, and 6 targeted DE lncRNAs were identified. Also, RT-qPCR was performed to validate the credibility of the network.Conclusions: This study explored the potential interplay between coding and noncoding RNAs during the gonadal development of polyploid fish. It provides full insights into polyploidy-associated effects on fertility of fish. These differentially expressed coding and noncoding RNAs provide a novel resource for studying genome diversity of polyploid induction.

Evaluation of Appropriate Reference Genes For Investigating Gene Expression in Chlorops oryzae (Diptera: Chloropidae)

2019 ◽  
Vol 112 (5) ◽  
pp. 2207-2214 ◽  
Author(s):  
Ping Tian ◽  
Lin Qiu ◽  
Ailin Zhou ◽  
Guo Chen ◽  
Hualiang He ◽  
...  
Keyword(s):  
Gene Expression ◽  
Ribosomal Protein ◽  
Reference Genes ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Quantitative Polymerase Chain Reaction ◽  
Housekeeping Genes ◽  
Future Research ◽  
Economic Damage ◽  
Physiological Processes

Abstract Reverse transcription quantitative polymerase chain reaction (PCR) has become an invaluable technique for analyzing gene expression in many insects. However, this approach requires the use of stable reference genes to normalize the data. Chlorops oryzae causes significant economic damage to rice crops throughout Asia. The lack of suitable reference genes has hindered research on the molecular mechanisms underlying many physiological processes of this species. In this study, we used quantitative real-time PCR to evaluate the expression of eight C. oryzae housekeeping genes glyceraldehyde-3-phosphate dehydrogenase (GAPDH), β-actin (βACT), beta-tubulin (βTUB), Delta Elongation factor-1 (EF1δ), ribosomal protein S11 (RPS11), RPS15, C-terminal-Binding Protein (CtBP), and ribosomal protein 49 (RP49) in different developmental stages and tissues in both larvae and adults. We analyzed the data with four different software packages: geNorm, NormFinder, BestKeeper, and RefFinder and compared the results obtained with each method. The results indicate that PRS15 and RP49 can be used as stable reference genes for quantifying gene expression in different developmental stages and larval tissues. GAPDH and βACT, which have been considered stable reference genes by previous studies, were the least stable of the candidate genes with respect to larval tissues. GAPDH was, however, the most stable reference gene for adult tissues. We verified the candidate reference genes identified and found that the expression levels of Cadherins (Cads) changed when different reference genes were used to normalize gene expression. This study provides a valuable foundation for future research on gene function, and investigating the molecular basis of physiological processes, in C. oryzae.

Sign in / Sign up

Export Citation Format

Share Document