Transcriptome using Illumina sequencing reveals the traits of spermatogenesis and developing testes in Eriocheir sinensis

Transcriptome analysis of reproductive tract tissues of male river prawn Macrobrachium americanum

BACKGROUND

The river prawn, Macrobrachium americanum (M. americanum), is one of the largest prawns of the genus in Latin America and is an amphidromous species distributed along the Pacific coast of America. This prawn has commercial value due to its size and taste, making it a good option for aquaculture production. Its culture has been attempted in ponds and concrete tanks, but no successful technique can still support commercial production. Understanding the mechanisms that regulate reproduction at the molecular level is very important. This knowledge can provide tools for manipulating transcripts, which could increase the number or size of animals in the culture. Our understanding of the mechanism that regulates the reproduction of M. americanum at the molecular level is limited.

AIM

Perform and analyze the transcriptome assembly of the testes, vas deferens, and terminal ampulla of M. americanum. to provide new molecular information about its reproduction.

METHODS AND RESULTS

The cDNA library was constructed and sequenced for each tissue to identify novel transcripts. A combined transcriptome with the three tissues was assembled using Trinity software. Unigenes were annotated using BLASTx and BLAST2GO. The transcriptome assembly generated 1,059,447 unigenes, of which 7222 genes had significant hits (e-value < 1 × 10-5) when compared against the Swiss-Prot database. Around 75 genes were related to sex determination, testis development, spermatogenesis, spermiogenesis, fertilization, maturation of testicular cells, neuropeptides, hormones, hormone receptors, and/or embryogenesis.

CONCLUSIONS

These results provide new molecular information about M. americanum reproduction, representing a reference point for further genetic studies of this species.

Cell adhesion function was altered during the seasonal regression of the seminiferous epithelium in the mink species Neovison vison

Minks are seasonal breeders whose seminiferous epithelium undergoes regression through massive germ cell death, leaving only Sertoli cells and spermatogonial cells in the tubules. However, the molecular mechanisms that control this biological process remain largely unknown. This study describes a transcriptomic analysis of mink testes at various reproductive stages (active, regressing, and inactive). A comparison of seminiferous epithelium at different stages of reproduction shows that cell adhesion is altered during regression. In addition, genes and proteins involved in forming the blood-testis barrier (BTB) were examined in sexually active and inactive minks. The seminiferous epithelium in the testes of sexually inactive minks expressed occludin, but this expression was not discernibly observed in the testes of sexually active minks. There was no discernible expression of CX43 in the seminiferous epithelium in the testes of sexually inactive minks, but CX43 was expressed in the testes of sexually active minks. During the regression process, we observed a remarkable increase in the expression levels of Claudin-11, which is associated with Sertoli-germ cell junctions. In conclusion, these findings suggest a loss of Sertoli-germ cell adhesion, which may regulate postmeiotic cell shedding during testicular regression in mink.

Dietary Lasia spinosa Thw. improves reproductive performance of aged roosters

The application of artificial insemination is particularly, owing to which breeder animals are considered an important resource in breeding farms. However, the reproductive performance of roosters typically declines with age, and the economic loss experienced by breeders is attributable to this shortened reproductive lifespan. Lasia spinosa Thw. (LST) reportedly improved reproductive capacity in male rodents. The objective of this study was to investigate the effects of LST on the reproductive performance of aged roosters. Male Guangxi Partridge chicken (mean weight, 3032.41 ± 34.48 g; age, 500 days; n = 72) randomly received the following three dietary treatments: LST0 group (a basal diet), LST2 group (a basal diet with 2% LST powder), and LST4 group (a basal diet with 4% LST powder). Computer-aided sperm analysis revealed that dietary LST supplementation significantly improved semen volume, sperm motility, and concentration. Furthermore, the most potent effects were observed in the treatment group with the administration of 2% LST, which significantly improved the weight of the testes. Hematoxylin-eosin staining revealed the increase in diameter of the seminiferous tubule and height of the seminiferous tubule epithelium possibly caused as a result of LST treatment. A significant increase in fructose and glucose concentrations were observed in the testis and seminal plasma; in addition, a significant increase was observed in the α-glycosidase levels in the testis and spermatozoa. However, the monoaldehyde levels in the spermatozoa appeared to decline significantly. Additionally, the fertility rate increased significantly following 2% LST supplementation. RNA-seq analysis revealed that 34 and 16 unigenes were upregulated and downregulated, respectively, in testicular tissues from roosters that received dietary supplementation of 2% LST. The assigned functions of the unigenes revealed that LST primarily influenced the mechanisms underlying catalytic activity and cellular processes. Kyoto Encyclopedia of Genes and Genomes enrichment analysis suggested that spermatogenesis-related pathways were significantly enriched, including ABC transporters, ribosome biogenesis in eukaryotes, and VEGF, cAMP, and ErbB signaling pathways.

Metabolomics integrated with transcriptomics reveals the changes during developmental stages in Shiraia bambusicola

Shiraia bambusicola is a fungus with high economic value widely used in medicine, agriculture, and food. We wished to understand the genes and metabolites changes involved in the different developmental stages of S. bambusicola. So, to reveal key genes and metabolites in the main active metabolite, the  were analyzed in different developmental stages of S. bambusicola fruiting body. A total of 29,137 Unigenes were annotated. In the whole growth process, differentially expressed genes were involved in the pathways of cytochrome P450, transcription factors, transporters, and so on, while in the early stage of growth, genes enriching to synthesis pathways of basic substances. In the middle stage of growth, genes with more prominent changes were involved in the pathways of the cell cycle, cancer mechanisms, and aminobenzoate degradation; in the later stage of growth, differentially expressed genes that enriched synthesis pathways of secondary metabolites. A total of 612 metabolites were detected from different growth stages of S. bambusicola. Among them, coumarins, alkaloids, rutin, liquiritigenin, quercetin, and other medically relevant metabolites were detected for the first time. We have identified 31 secondary metabolites,  relevantly only accumulated in the early and middle stage, but not detected in the later stage, such as flavonols, coumarins, nucleotides and its derivates and hydroxycinnamoyl derivatives. The differential genes and metabolites of the same group were enriched in 127 pathways, and more significantly in ubiquinone and other terpenoid quinone biosynthesis, phenylalanine metabolism, phenylalanine, tyrosine and tryptophan biosynthesis, and phenylpropanoid biosynthesis. The correlation networks of several significantly enriched pathways were analyzed, and the relationships within and between these pathways, genes, and metabolites, were analyzed. The synthetic pathway of hypocrellin has been speculated upon. We believe that hypocrellin is synthesized in S. bambusicola via the shikimic acid pathway followed by phenylalanine, tyrosine, and tryptophan biosynthesis pathway, then the ubiquinone and other terpenoid quinone biosynthesis pathway, and finally a series of polymerization and modification reactions. Several genes and metabolites involved in the biosynthesis of hypocrellin have been identified. This study provides a reference for further research on S. bambusicola, by providing a basis for its use and development.

Identification of Key Genes Related to Postnatal Testicular Development Based on Transcriptomic Data of Testis in Hu Sheep

The selection of testis size can improve the reproductive capacity of livestock used for artificial insemination and has been considered as an important strategy for accelerating the breeding process. Although much work has been done to investigate the mechanisms of testis development in various species, there is little information available in regard to the differences in transcriptomic profiling of sheep testes at different developmental stages. In this work, we aimed to identify differentially expressed genes (DEGs) by RNA-Seq in sheep during different growth stages, including 0 month old (infant, M0), 3 months old (puberty, M3), 6 months old (sexual maturity, M6) and 12 months old (body maturity, M12). A total of 4,606 (2,381 up and 2,225 down), 7,500 (4,368 up and 3,132 down), 15 (8 up and seven down) DEGs were identified in M3_vs_M0, M6_vs_M3, and M12_vs_M6 comparison, respectively. Of which, a number of genes were continuously up-regulated and down-regulated with testicular development, including ODF3, ZPBP1, PKDREJ, MYBL1, PDGFA, IGF1, LH, INSL3, VIM, AMH, INHBA, COL1A1, COL1A2, and INHA. GO analysis illustrated that DEGs were mainly involved in testis development and spermatogenesis. KEGG analysis identified several important pathways and verified several reproduction-associated DEGs such as COL1A1, COL1A2, PDGFA, and IGF1. In addition, two gene modules highly associated with testis development and core genes with testis size were identified using weighted gene co-expression network analysis (WGCNA), including hub genes positively associated with testis size such as RANBP9, DNAH17, SPATA4, CIB4 and SPEM1, and those negatively associated with testis size such as CD81, CSK, PDGFA, VIM, and INHBA. This study comprehensively identified key genes related to sheep testicular development, which may provide potential insights for understanding male fertility and better guide in animal breeding.

Characterization of the foxl2 gene involved in the vtg expression in mud crab (Scylla paramamosain)

Forkhead box protein L2 (Foxl2) is involved in multiple physiological processes, such as ovarian development, granulosa cell differentiation, ovarian follicle development, and oocyte growth. In this study, a Spfoxl2 gene encoded 530 amino acid protein with characteristic forkhead (FH) domain was identified from transcriptome data of mud crab Scylla paramamosain and validated the accuracy by PCR technology. Meanwhile, the orthologues of the Spfoxl2 gene in other 14 crustacean species were identified with the same method. Further multiple sequence alignment analysis revealed the Foxl2 was highly conserved, especially in the FH domain, even completely identical in several species. Besides, the semi-quantitative PCR (Sq-PCR) result showed Spfoxl2 gene was mainly expressed in the gonad (testis and ovary). Further quantitative real-time PCR (qRT-PCR) result demonstrated its expression level in the testis was significantly higher than that in the ovary (p < 0.01). In addition, the qRT-PCR result showed that in zoea V, megalopa, and larval I, the expression level of Spfoxl2 in megalopa is the highest. In addition, a putative Foxl2 binding site was identified on the promoter region of Spvtg, and knockdown of Spfoxl2 mediated by RNAi technology increased the expression of Spvtg in the ovary, suggesting Spfoxl2 might be the upstream negative regulator of Spvtg. Overall, this study provided new insights into the role of Spfoxl2 in ovary development through regulating Spvtg expression in S. paramamosain.

RNA binding proteins involved in regulation of protein synthesis to initiate biogenesis of secondary tumor in hepatocellular carcinoma in mice

Background

The tumor microenvironment (TM) in close contact with cancer cells is highly related to tumor growth and cancer metastasis. This study is to explore the biogenesis mechanism of a secondary hepatocellular carcinoma (HCC) based on the function of RNA binding proteins (RBPs)-encoding genes in the physiological microenvironment (PM).

Methods

The healthy and HCC mice were used to isolate the PM, pre-tumor microenvironment (PTM), and TM. The samples were analyzed using the technology of RNA-seq and bioinformatics. The differentially expressed RBPs-encoding genes (DERs) and differentially expressed DERs-associated genes (DEDs) were screened to undergo GO and KEGG analysis.

Results

18 DERs and DEDs were identified in the PTM vs. PM, 87 in the TM vs. PTM, and 87 in the TM vs. PM. Those DERs and DEDs participated in the regulation of gene expression at the levels of chromatin conformation, gene activation and silencing, splicing and degradation of mRNA, biogenesis of piRNA and miRNA, ribosome assemble, and translation of proteins.

Conclusion

The genes encoding RBPs and the relevant genes are involved in the transformation from PM to PTM, then constructing the TM by regulating protein synthesis. This regulation included whole process of biological genetic information transmission from chromatin conformation to gene activation and silencing to mRNA splicing to ribosome assemble to translation of proteins and degradation of mRNA. The abnormality of those functions in the organic microenvironments promoted the metastasis of HCC and initiated the biogenesis of a secondary HCC in a PM when the PM encountered the invasion of cancer cells.

Photoperiodic effect on the testicular transcriptome in broiler roosters

Information about the effects of photoperiod on the testicular transcriptome of broiler roosters is limited. The aim of the present study was to explore the effect of different photoperiodic regimes on gene expression in the testes of broiler breeder roosters. One hundred and twenty Arbor Acres broiler breeder roosters aged 20 weeks were assigned to one of three groups (n = 40) and subjected to different photoperiodic regimes: control (CTR; 12.5 L:11.5 D), short day (SD; 8 L:16 D) and long day (LD; 16 L:8 D). After 4 weeks, the testes of 10 randomly selected birds from each group were dissected, sliced and haematoxylin-eosin stained. The testicular transcriptome of roosters from the SD and LD groups was determined by RNA sequencing (RNA-Seq), and the results were confirmed using quantitative real-time PCR. The seminiferous tubule area and sperm count increased significantly with the prolongation of photoperiod (p < .01). Additionally, the RNA-Seq results indicated that 387 genes were upregulated and 1,052 genes were downregulated in the LD group compared with those in the SD group. Several crucial genes involved in rooster testicular development and reproduction were also screened, including heat shock proteins 90, extracellular regulated protein kinases 1, phosphatidylinositol 3-kinase, adenosine 5'-monophosphate -activated protein kinase, BCL-6 and Smad3. The differentially expressed genes were enriched in the mammalian targets of rapamycin (mTOR), forkhead box (FoxO), transforming growth factor beta (TGF-β) and insulin signalling pathway. In conclusion, a 16 hr photoperiod for 4 weeks increased the seminiferous tubule duct area and promoted spermatogenesis in the rooster's testicles, and the mTOR, FoxO, TGF-β and insulin signalling pathways may be involved.

Transcriptome profiling of laser-captured germ cells and functional characterization of zbtb40 during 17alpha-methyltestosterone-induced spermatogenesis in orange-spotted grouper (Epinephelus coioides)

BACKGROUND

Spermatogenesis is an intricate process regulated by a finely organized network. The orange-spotted grouper (Epinephelus coioides) is a protogynous hermaphroditic fish, but the regulatory mechanism of its spermatogenesis is not well-understood. In the present study, transcriptome sequencing of the male germ cells isolated from orange-spotted grouper was performed to explore the molecular mechanism underlying spermatogenesis.

RESULTS

In this study, the orange-spotted grouper was induced to change sex from female to male by 17alpha-methyltestosterone (MT) implantation. During the spermatogenesis, male germ cells (spermatogonia, spermatocytes, spermatids, and spermatozoa) were isolated by laser capture microdissection. Transcriptomic analysis for the isolated cells was performed. A total of 244,984,338 clean reads were generated from four cDNA libraries. Real-time PCR results of 13 genes related to sex differentiation and hormone metabolism indicated that transcriptome data are reliable. RNA-seq data showed that the female-related genes and genes involved in hormone metabolism were highly expressed in spermatogonia and spermatozoa, suggesting that these genes participate in the spermatogenesis. Interestingly, the expression of zbtb family genes showed significantly changes in the RNA-seq data, and their expression patterns were further examined during spermatogenesis. The analysis of cellular localization of Eczbtb40 and the co-localization of Eczbtb40 and Eccyp17a1 in different gonadal stages suggested that Eczbtb40 might interact with Eccyp17a1 during spermatogenesis.

CONCLUSIONS

Our study, for the first time, investigated the transcriptome of the male germ cells from orange-spotted grouper, and identified functional genes, GO terms, and KEGG pathways involved in spermatogenesis. Furthermore, Eczbtb40 was first characterized and its role during spermatogenesis was predicted. These data will contribute to future studies on the molecular mechanism of spermatogenesis in teleosts.

The Single-molecule long-read sequencing of Scylla paramamosain

Scylla paramamosain is an important aquaculture crab, which has great economical and nutritional value. To the best of our knowledge, few full-length crab transcriptomes are available. In this study, a library composed of 12 different tissues including gill, hepatopancreas, muscle, cerebral ganglion, eyestalk, thoracic ganglia, intestine, heart, testis, ovary, sperm reservoir, and hemocyte was constructed and sequenced using Pacific Biosciences single-molecule real-time (SMRT) long-read sequencing technology. A total of 284803 full-length non-chimeric reads were obtained, from which 79005 high-quality unique transcripts were obtained after error correction and sequence clustering and redundant. Additionally, a total of 52544 transcripts were annotated against protein database (NCBI nonredundant, Swiss-Prot, KOG, and KEGG database). A total of 23644 long non-coding RNAs (lncRNAs) and 131561 simple sequence repeats (SSRs) were identified. Meanwhile, the isoforms of many genes were also identified in this study. Our study provides a rich set of full-length cDNA sequences for S. paramamosain, which will greatly facilitate S. paramamosain research.

RNA-seq data reveals a coordinated regulation mechanism of multigenes involved in the high accumulation of palmitoleic acid and oil in sea buckthorn berry pulp

BACKGROUND

Sea buckthorn is a woody oil crop in which palmitoleic acid (C16:1n7, an omega-7 fatty acid (FA)) contributes approximately 40% of the total FA content in berry pulp (non-seed tissue). However, the molecular mechanisms contributing to the high accumulation of C16:1n7 in developing sea buckthorn berry pulp (SBP) remain poorly understood.

RESULTS

We identified 1737 unigenes associated with lipid metabolism through RNA-sequencing analysis of the four developmental stages of berry pulp in two sea buckthorn lines, 'Za56' and 'TF2-36'; 139 differentially expressed genes were detected between the different berry pulp developmental stages in the two lines. Analyses of the FA composition showed that the C16:1n7 contents were significantly higher in line 'Za56' than in line 'TF2-36' in the mid-late developmental stages of SBP. Additionally, qRT-PCR analyses of 15 genes involved in FA and triacylglycerol (TAG) biosynthesis in both lines revealed that delta9-ACP-desaturase (ACP-Δ9D) competed with 3-ketoacyl-ACP-synthase II (KASII) for the substrate C16:0-ACP and that ACP-Δ9D and delta9-CoA-desaturase (CoA-Δ9D) gene expression positively correlated with C16:1n7 content; KASII and fatty acid elongation 1 (FAE1) gene expression positively correlated with C18:0 content in developing SBP. Specifically, the abundance of ACP-Δ9D and CoA-Δ9D transcripts in line 'Za56', which had a higher C16:1n7 content than line 'TF2-36', suggests that these two genes play an important role in C16:1n7 biosynthesis. Furthermore, the high expressions of the glycerol-3-phosphate dehydrogenase (GPD1) gene and the WRINKLED1 (WRI1) transcription factor contributed to increased biosynthesis of TAG precursor and FAs, respectively, in the early developmental stages of SBP, and the high expression of the diacylglycerol O-acyltransferase 1 (DGAT1) gene increased TAG assembly in the later developmental stages of SBP. Overall, we concluded that increased ACP-Δ9D and CoA-Δ9D levels coupled with decreased KASII and FAE1 activity is a critical event for high C16:1n7 accumulation and that the coordinated high expression of WRI1, GPD1, and DGAT1 genes resulted in high oil accumulation in SBP.

CONCLUSION

Our results provide a scientific basis for understanding the mechanism of high C16:1n7 accumulation in berry pulp (non-seed tissue) and are valuable to the genetic breeding programme for achieving a high quality and yield of SBP oil.

Transcriptomic Analysis Reveals Insights on Male Infertility in Octopus maya Under Chronic Thermal Stress

Octopus maya endemic to the Yucatan Peninsula, Mexico, is an ectotherm organism particularly temperature-sensitive. Studies in O. maya females show that temperatures above 27°C reduce the number of eggs per spawn, fertilization rate and the viability of embryos. High temperatures also reduce the male reproductive performance and success. However, the molecular mechanisms are still unknown. The transcriptomic profiles of testes from thermally stressed (30°C) and not stressed (24°C) adult male octopuses were compared, before and after mating to understand the molecular bases involved in the low reproductive performance at high temperature. The testis paired-end cDNA libraries were sequenced using the Illumina MiSeq platform. Then, the transcriptome was assembled de novo using Trinity software. A total of 53,214,611 high-quality paired reads were used to reconstruct 85,249 transcripts and 77,661 unigenes with an N50 of 889 bp length. Later, 13,154 transcripts were annotated implementing Blastx searches in the UniProt database. Differential expression analysis revealed 1,881 transcripts with significant difference among treatments. Functional annotation and pathway mapping of differential expressed transcripts revealed significant enrichment for biological processes involved in spermatogenesis, gamete generation, germ cell development, spermatid development and differentiation, response to stress, inflammatory response and apoptosis. Remarkably, the transcripts encoding genes such as ZMYND15, KLHL10, TDRD1, TSSK2 and DNAJB13, which are linked to male infertility in other species, were differentially expressed among the treatments. The expression levels of these key genes, involved in sperm motility and spermatogenesis were validated by quantitative real-time PCR. The results suggest that the reduction in male fertility at high temperature can be related to alterations in spermatozoa development and motility.

Transcriptome Dynamics During Turbot Spermatogenesis Predicting the Potential Key Genes Regulating Male Germ Cell Proliferation and Maturation

Spermatogenesis is a dynamic developmental process in which spermatogonial stem cells proliferate, differentiate and mature into functional spermatozoa. These processes require an accurate gene regulation network. Here, we investigated the dynamic changes that occur during spermatogenesis through a combination of histological and transcriptome analyses of different developmental stages of the testis. We constructed 18 testis transcriptome libraries, and the average length, N50, and GC content of the unigenes were 1,795 bp; 3,240 bp and 49.25%, respectively. Differentially expressed genes (DEGs) that were related to germ cell proliferation and maturation, such as NANOS3, RARs, KIFs, steroid hormone synthesis-related genes and receptor genes, were identified between pairs of testis at different developmental stages. Gene ontology annotation and pathway analyses were conducted on DEGs with specific expression patterns involved in the regulation of spermatogenesis. Nine important pathways such as steroid hormone biosynthesis related to spermatogenesis were identified. A total of 21 modules that ranged from 49 to 7,448 genes were designed by a weighted gene co-expression network analysis. Furthermore, a total of 83 candidate miRNA were identified by computational methods. Our study provides the first transcriptomic evidence for differences in gene expression between different developmental stages of spermatogenesis in turbot (Scophthalmus maximus).

Molecular characterization of putative neuropeptide, amine, diffusible gas and small molecule transmitter biosynthetic enzymes in the eyestalk ganglia of the American lobster, Homarus americanus

The American lobster, Homarus americanus, is a model for investigating the neuromodulatory control of physiology and behavior. Prior studies have shown that multiple classes of chemicals serve as locally released/circulating neuromodulators/neurotransmitters in this species. Interestingly, while many neuroactive compounds are known from Homarus, little work has focused on identifying/characterizing the enzymes responsible for their biosynthesis, despite the fact that these enzymes are key components for regulating neuromodulation/neurotransmission. Here, an eyestalk ganglia-specific transcriptome was mined for transcripts encoding enzymes involved in neuropeptide, amine, diffusible gas and small molecule transmitter biosynthesis. Using known Drosophila melanogaster proteins as templates, transcripts encoding putative Homarus homologs of peptide precursor processing (signal peptide peptidase, prohormone processing protease and carboxypeptidase) and immature peptide modifying (glutaminyl cyclase, tyrosylprotein sulfotransferase, protein disulfide isomerase, peptidylglycine-α-hydroxylating monooxygenase and peptidyl-α-hydroxyglycine-α-amidating lyase) enzymes were identified in the eyestalk assembly. Similarly, transcripts encoding full complements of the enzymes responsible for dopamine [tryptophan-phenylalanine hydroxylase (TPH), tyrosine hydroxylase and DOPA decarboxylase (DDC)], octopamine (TPH, tyrosine decarboxylase and tyramine β-hydroxylase), serotonin (TPH or tryptophan hydroxylase and DDC) and histamine (histidine decarboxylase) biosynthesis were identified from the eyestalk ganglia, as were those responsible for the generation of the gases nitric oxide (nitric oxide synthase) and carbon monoxide (heme oxygenase), and the small molecule transmitters acetylcholine (choline acetyltransferase), glutamate (glutaminase) and GABA (glutamic acid decarboxylase). The presence and identity of the transcriptome-derived transcripts were confirmed using RT-PCR. The data presented here provide a foundation for future gene-based studies of neuromodulatory control at the level of neurotransmitter/modulator biosynthesis in Homarus.