Full-Length Gonad Transcriptome Analysis of Amur Sturgeon Dmrt Family Genes: Identification, Characterization and Expression Patterns During Gonadal Differentiation

Abstract The regulatory mechanisms that govern sex differentiation in sturgeon are still poorly understood. The doublesex and Mab-3-related transcription factor (Dmrt) gene family is known for its extensive roles in sex determination and differentiation across vertebrates. This study aimed to identify new members of sturgeon Dmrt family genes and core actors in the gonadal differentiation of Amur sturgeon. A full-length gonad transcriptome database was exploited to identify Dmrt gene orthologs. Analyses of phylogenetic relationships and selection pressure were performed, and tissue expression profiles and spatiotemporal expression patterns in gonads were then analyzed using real-time PCR. In total, five Dmrt family genes were identified from the full-length gonad transcriptome, including Dmrt2, DmrtA1, DmrtA2, DmrtB1a and DmrtB1b. Phylogenetic analysis showed that these genes were clustered into clades corresponding to the doublesex/Mav-3 (DM) genes of vertebrates. Furthermore, the analysis of evolutionary selective pressure indicated that DmrtB1a and DmrtB1b were subject to positive selection, suggesting the existence of adaptive evolution in sturgeon. The extensive tissues expression profiling of each Dmrt family gene revealed typical characteristics. Remarkably, according to a spatiotemporal expression pattern analysis, DmrtA1 and DmrtA2 were predominantly distributed in undifferentiated gonads (UGs) and developing ovaries, whereas DmrtB1b showed the lowest expression in UGs. In later stages, DmrtB1b expression continuously increased in testes and was significantly higher in testes than in ovaries at 24 months after hatching (M) and 36M, which strongly suggests that DmrtB1b is a core regulatory factor involved in sexual differentiation in sturgeon. This study provides a genetic resource of full-length Dmrt family genes and increases the understanding of Dmrt functions in sex differentiation in sturgeon.

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Comparative analysis of miR-155 tissue expression profiles of different breeds of chicken

10.1101/409623 ◽

2018 ◽

Author(s):

Sifan Xu ◽

Yang Chang ◽

Guanxian Wu ◽

Wanting Zhang ◽

Chaolai Man

Keyword(s):

Skeletal Muscle ◽

Muscle Development ◽

Expression Profiles ◽

Expression Patterns ◽

Tissue Expression ◽

Stem Loop ◽

Factors Affecting ◽

Spatiotemporal Expression ◽

Expression Activity ◽

Chicken Breeds

AbstractmiR-155 is an important microRNA which has multiple functions in many physiological and pathological processes. In this study, partial pri-miR-155 sequences were cloned from AA+ broiler, Sanhuang broiler and Hi-Line Brown layer, respectively. Stem-loop RT-qPCR was performed to detect the miR-155 spatiotemporal expression profiles of each chicken breed. The results showed that the partial pri-miR-155 sequences of different breeds of chicken were high conserved. The expression patterns of miR-155 between broiler and layer were basically similar, and miR-155 is expressed highly in immune related tissues. Interestingly, miR-155 expression activity had higher level in fat tissue of the three chicken breeds (14-day-old), but it decreased significantly in fat of the Hi-Line Brown layer (10-month-old and 24-month-old). In addition, the expression activities of miR-155 in 14-day-old broilers (AA+ broiler and Sanhuang broiler) were significantly lower than that of Hi-Line Brown layer (14-day-old) (P<0.05). Moreover, miR-155 expression activities in skeletal muscle of 14-day-old and 10-month-old Hi-Line Brown layer were also significantly lower than that of 24-month-old layer (P<0.05). The results indicated that miR-155 might be one of the important factors affecting the differences in skeletal muscle development and adipogenesis between different chicken breeds. These data can serve as a foundation for further study the functions and mechanisms of miR-155 in the physiological and pathological contexts.

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MicroRNA-1 Expression and Function in Hyalomma Anatolicum anatolicum (Acari: Ixodidae) Ticks

Frontiers in Physiology ◽

10.3389/fphys.2021.596289 ◽

2021 ◽

Vol 12 ◽

Author(s):

Jin Luo ◽

Qiaoyun Ren ◽

Wenge Liu ◽

Xiaofei Qiu ◽

Gaofeng Zhang ◽

...

Keyword(s):

High Throughput Sequencing ◽

Gene Selection ◽

Developmental Stages ◽

Expression Profiles ◽

Expression Patterns ◽

Tissue Expression ◽

Hyalomma Anatolicum ◽

Internal Reference ◽

Hyalomma Anatolicum Anatolicum ◽

Significant Difference

MicroRNAs act as mRNA post-transcriptional regulators, playing important roles in cell differentiation, transcriptional regulation, growth, and development. In this study, microRNA expression profiles of Hyalomma anatolicum anatolicum ticks at different developmental stages were detected by high-throughput sequencing and functionally assessed. In total, 2,585,169, 1,252,678, 1,558,217, and 1,155,283 unique reads were obtained from eggs, larvae, nymphs, and adults, respectively, with 42, 46, 45, and 41 conserved microRNAs in these stages, respectively. Using eggs as a control, 48, 43, and 39 microRNAs were upregulated, and 3, 10, and 9 were downregulated in larvae, nymphs, and adults, respectively. MicroRNA-1 (miR-1) was expressed in high abundance throughout Ha. anatolicum development, with an average of nearly one million transcripts, and it is highly conserved among tick species. Quantitative real-time PCR (qPCR) showed that miR-1 expression gradually increased with tick development, reaching the highest level at engorgement. Differential tissue expression was detected, with significantly higher levels in the salivary glands and epidermis than in the midgut. Inhibition assays showed no significant change in body weight or spawning time or amount between experimental and control groups, but there was a significant difference (p < 0.01) in engorgement time. With miR-1 inhibition, ticks displayed obvious deformities during later development. To more fully explain the microRNA mechanism of action, the miR-1 cluster was analyzed according to the target gene; members that jointly act on Hsp60 include miR-5, miR-994, miR-969, and miR-1011. Therefore, microRNAs are critical for normal tick development, and the primary structure of the mature sequence of miR-1 is highly conserved. Nonetheless, different developmental stages and tissues show different expression patterns, with a certain role in prolonging feeding. miR-1, together with other cluster members, regulates mRNA function and may be used as a molecular marker for species origin, evolution analysis, and internal reference gene selection.

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Molecular cloning and expression profile of β-ketoacyl-acp synthase gene from tung tree (Vernicia fordii Hemsl.)

Genetika ◽

10.2298/gensr1501143l ◽

2015 ◽

Vol 47 (1) ◽

pp. 143-159 ◽

Cited By ~ 4

Author(s):

Hongxu Long ◽

Xiaofeng Tan ◽

Fangfang Yan ◽

Lin Zhang ◽

Ze Li ◽

...

Keyword(s):

Fatty Acid ◽

Expression Profiles ◽

Expression Patterns ◽

Full Length ◽

Cloning And Expression ◽

Tung Tree ◽

Degenerate Primers ◽

Expression Levels ◽

Full Length Cdna ◽

Vernicia Fordii

Tung tree (Vernicia fordii) is an important woody oil tree. Tung tree seeds contain 50-60% oil with approximately 80 mole ?-eleostearic acid (9 cis, 11 trans, 13 trans octadecatrienoic acid). Fatty acid synthesis is catalyzed by the concerted action of acetyl-CoA carboxylase and fatty acid synthase, a multienzyme complex including ?-ketoacyl-acyl-carrier-protein synthase (KAS). Little is known about KAS in tung tree. The objective of this study was to clone KAS genes and analyze their expression profiles in tung tree. A full-length cDNA encoding KAS III and a partial cDNA encoding KAS II were isolated from tung tree by PCR cloning using degenerate primers and rapid amplification of cDNA ends system. The full-length cDNA of VfKAS III was 1881 bp in length with an open reading frame of 1212 bp. VfKAS III genomic DNA was also isolated and sequenced, which contained 8 exons in 5403 bp length. The deduced VfKAS III protein shared approximately 80% identity with homologous KAS IIIs from other plants. Quantitative PCR analysis revealed that KAS II and KAS III were expressed in all of the tissues and organs tested but exhibited different expression patterns in tung tree. The expression levels of KAS II in young tissues were much lower than those in mature tissues, whereas the highest expression levels of KAS III were observed in young stem and young leaf. These results should facilitate further studies on the regulation of tung oil biosynthesis by KAS in tung tree.

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Genome-Wide Identification and Characterization of Fox Genes in the Honeybee, Apis cerana, and Comparative Analysis with Other Bee Fox Genes

International Journal of Genomics ◽

10.1155/2018/5702061 ◽

2018 ◽

Vol 2018 ◽

pp. 1-12

Author(s):

Hongyi Nie ◽

Haiyang Geng ◽

Yan Lin ◽

Shupeng Xu ◽

Zhiguo Li ◽

...

Keyword(s):

Gene Family ◽

Bombus Terrestris ◽

Expression Profiles ◽

Phylogenetic Analyses ◽

Expression Patterns ◽

Apis Cerana ◽

Tissue Expression ◽

Genome Wide ◽

Fox Genes

The forkhead box (Fox) gene family, one of the most important families of transcription factors, participates in various biological processes. However, Fox genes in Hymenoptera are still poorly known. In this study, 14 Fox genes were identified in the genome of Apis cerana. In addition, 16 (Apis mellifera), 13 (Apis dorsata), 16 (Apis florea), 17 (Bombus terrestris), 16 (Bombus impatiens), and 18 (Megachile rotundata) Fox genes were identified in their genomes, respectively. Phylogenetic analyses suggest that FoxA is absent in the genome of A. dorsata genome. Similarly, FoxG is missing in the genomes A. cerana and A. dorsata. Temporal expression profiles obtained by quantitative real-time PCR revealed that Fox genes have distinct expression patterns in A. cerana, especially for three genes ACSNU03719T0 (AcFoxN4), ACSNU05765T0 (AcFoxB), and ACSNU07465T0 (AcFoxL2), which displayed high expression at the egg stage. Tissue expression patterns showed that FoxJ1 is significantly higher in the antennae of A. cerana and A. mellifera compared to other tissues. These results may facilitate a better understanding of the potential physiological functions of the Fox gene family in A. cerana and provide valuable information for a comprehensive functional analysis of the Fox gene family in Hymenopterans.

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Primordial Germ Cell Migration and Histological and Molecular Characterization of Gonadal Differentiation in Pachón Cavefish Astyanax mexicanus

Sexual Development ◽

10.1159/000513378 ◽

2021 ◽

pp. 1-18

Author(s):

Boudjema Imarazene ◽

Séverine Beille ◽

Elodie Jouanno ◽

Adéle Branthonne ◽

Violette Thermes ◽

...

Keyword(s):

Germ Cell ◽

Regulatory Network ◽

Sex Differentiation ◽

Expression Patterns ◽

Primordial Germ Cells ◽

Primordial Germ Cell ◽

Gonadal Development ◽

Individual Variability ◽

Gonadal Differentiation ◽

Astyanax Mexicanus

The genetic regulatory network governing vertebrate gonadal differentiation appears less conserved than previously thought. Here, we investigated the gonadal development of Astyanax mexicanus Pachón cavefish by looking at primordial germ cells (PGCs) migration and proliferation, gonad histology, and gene expression patterns. We showed that PGCs are first detected at the 80% epiboly stage and then reach the gonadal primordium at 1 day post-fertilization (dpf). However, in contrast to the generally described absence of PGCs proliferation during their migration phase, PGCs number in cavefish doubles between early neurula and 8–9 somites stages. Combining both gonadal histology and vasa (germ cell marker) expression patterns, we observed that ovarian and testicular differentiation occurs around 65 dpf in females and 90 dpf in males, respectively, with an important inter-individual variability. The expression patterns of dmrt1, gsdf, and amh revealed a conserved predominant male expression during cavefish gonadal development, but none of the ovarian differentiation genes, i. e., foxl2a, cyp19a1a, and wnt4b displayed an early sexually dimorphic expression, and surprisingly all these genes exhibited predominant expression in adult testes. Altogether, our results lay the foundation for further research on sex determination and differentiation in A. mexicanus and contribute to the emerging picture that the vertebrate sex differentiation downstream regulatory network is less conserved than previously thought, at least in teleost fishes.

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A re-assessment of gene-tag classification approaches for describing var gene expression patterns during human Plasmodium falciparum malaria parasite infections

Wellcome Open Research ◽

10.12688/wellcomeopenres.12053.1 ◽

2017 ◽

Vol 2 ◽

pp. 86 ◽

Cited By ~ 6

Author(s):

George Githinji ◽

Peter C. Bull

Keyword(s):

Gene Expression ◽

Plasmodium Falciparum ◽

Severe Malaria ◽

Expression Profiles ◽

Expression Patterns ◽

Full Length ◽

Endothelial Protein C Receptor ◽

Gene Sequences ◽

Sequence Features ◽

Var Gene

PfEMP1 are variant parasite antigens that are inserted on the surface of Plasmodium falciparum infected erythrocytes (IE). Through interactions with various host molecules, PfEMP1 mediate IE sequestration in tissues and play a key role in the pathology of severe malaria. PfEMP1 is encoded by a diverse multi-gene family called var. Previous studies have shown that that expression of specific subsets of var genes are associated with low levels of host immunity and severe malaria. However, in most clinical studies to date, full-length var gene sequences were unavailable and various approaches have been used to make comparisons between var gene expression profiles in different parasite isolates using limited information. Several studies have relied on the classification of a 300 – 500 base-pair “DBLα tag” region in the DBLα domain located at the 5’ end of most var genes. We assessed the relationship between various DBLα tag classification methods, and sequence features that are only fully assessable through full-length var gene sequences. We compared these different sequence features in full-length var gene from six fully sequenced laboratory isolates. These comparisons show that despite a long history of recombination, DBLα sequence tag classification can provide functional information on important features of full-length var genes. Notably, a specific subset of DBLα tags previously defined as “group A-like” is associated with CIDRα1 domains proposed to bind to endothelial protein C receptor. This analysis helps to bring together different sources of data that have been used to assess var gene expression in clinical parasite isolates.

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Sexual Development of the Hermaphroditic Scallop Argopecten irradians Revealed by Morphological, Endocrine and Molecular Analysis

Frontiers in Cell and Developmental Biology ◽

10.3389/fcell.2021.646754 ◽

2021 ◽

Vol 9 ◽

Author(s):

Huilan Wei ◽

Wanru Li ◽

Tian Liu ◽

Yajuan Li ◽

Liangjie Liu ◽

...

Keyword(s):

Sexual Development ◽

Sex Differentiation ◽

Expression Patterns ◽

Molecular Study ◽

Gonadal Development ◽

Argopecten Irradians ◽

Whole Process ◽

Spatiotemporal Expression ◽

Key Driver ◽

Dimorphic Expression

Simultaneous or functional hermaphrodites possessing both ovary and testis at the same time are good materials for studying sexual development. However, previous research on sex determination and differentiation was mainly conducted in gonochoristic species and studies on simultaneous hermaphrodites are still limited. In this study, we conducted a combined morphological, endocrine and molecular study on the gonadal development of a hermaphroditic scallop Argopecten irradians aged 2–10 month old. Morphological analysis showed that sex differentiation occurred at 6 months of age. By examining the dynamic changes of progesterone, testosterone and estradiol, we found testosterone and estradiol were significantly different between the ovaries and testes almost throughout the whole process, suggesting the two hormones may be involved in scallop sex differentiation. In addition, we identified two critical sex-related genes FoxL2 and Dmrt1L, and investigated their spatiotemporal expression patterns. Results showed that FoxL2 and Dmrt1L were female- and male-biased, respectively, and mainly localized in the germ cells and follicular cells, indicating their feasibility as molecular markers for early identification of sex. Further analysis on the changes of FoxL2 and Dmrt1L expression in juveniles showed that significant sexual dimorphic expression of FoxL2 occurred at 2 months of age, earlier than that of Dmrt1L. Moreover, FoxL2 expression was significantly correlated with estradiol/testosterone ratio (E2/T). All these results indicated that molecular sex differentiation occurs earlier than morphological sex differentiation, and FoxL2 may be a key driver that functions through regulating sex steroid hormones in the scallop. This study will deepen our understanding of the molecular mechanism underlying sex differentiation and development in spiralians.

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Characterization and expression analysis of the SPL gene family during floral development and abiotic stress in pecan (Carya illinoinensis)

PeerJ ◽

10.7717/peerj.12490 ◽

2021 ◽

Vol 9 ◽

pp. e12490

Author(s):

Min Wang ◽

Zhenghai Mo ◽

Ruozhu Lin ◽

Cancan Zhu

Keyword(s):

Fruit Development ◽

Expression Profiles ◽

Expression Patterns ◽

Element Analysis ◽

Systematic Analysis ◽

Cis Element ◽

Gene Pairs ◽

Spatiotemporal Expression ◽

Squamosa Promoter Binding Protein ◽

Flower And Fruit Development

SQUAMOSA promoter binding protein-like (SPL) genes are a type of plant-specific transcription factors that play crucial roles in the regulation of phase transition, floral transformation, fruit development, and various stresses. Although SPLs have been characterized in several model species, no systematic analysis has been studied in pecans, an important woody oil tree species. In this study, a total of 32 SPL genes (CiSPLs) were identified in the pecan genome. After conducting phylogenetic analysis of the conserved SBP proteins from Arabidopsis, rice, and poplar, the CiSPLs were separated into eight subgroups. The CiSPL genes within the same subgroup contained very similar exon-intron structures and conserved motifs. Nine segmentally duplicated gene pairs in the pecan genome and 16 collinear gene pairs between the CiSPL and AtSPL genes were identified. Cis-element analysis showed that CiSPL genes may regulate plant meristem differentiation and seed development, participate in various biological processes, and respond to plant hormones and environmental stresses. Therefore, we focused our study on the expression profiles of CiSPL genes during flower and fruit development. Most of the CiSPL genes were predominantly expressed in buds and/or female flowers. Additionally, quantitative real time PCR (qRT-PCR) analyses confirmed that CiSPL genes showed distinct spatiotemporal expression patterns in response to drought and salt treatments. The study provides foundation for the further exploration of the function and evolution of SPL genes in pecan.

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Sexually dimorphic gene expression patterns during gonadal differentiation in olive flounder, Paralichthys olivaceus

Animal Biology ◽

10.1163/15707563-00002470 ◽

2015 ◽

Vol 65 (3-4) ◽

pp. 193-207 ◽

Cited By ~ 7

Author(s):

Aiyun Wen ◽

Feng You ◽

Peng Sun ◽

Jun Li ◽

Dongdong Xu ◽

...

Keyword(s):

Gene Expression ◽

Transcription Factor ◽

Synergistic Effects ◽

Paralichthys Olivaceus ◽

Expression Patterns ◽

Olive Flounder ◽

Gene Expression Patterns ◽

Gonadal Differentiation ◽

Rt Pcr ◽

Related Transcription Factor

The present study aims to elucidate the different expression patterns and possible roles of Doublesex and Mab-3-related transcription factor 1 (dmrt1), dmrt4, SRY-related transcription factor 9 (sox9) and cytochrome P450 aromatase 19a (cyp19a) during gonadal differentiation in olive flounder, Paralichthys olivaceus. We first analyzed the gene expression patterns in tissues using RT-PCR, which indicated dmrt1, sox9 and cyp19a were sex-related genes with sexual dimorphic expression. The quantitative expression changes of these three genes together with dmrt4 during gonadal differentiation were further examined using real-time RT-PCR. The results showed that dmrt1 was scarcely expressed in the primitive gonad and during following periods of gonadal differentiation. Its expression increased rapidly in the differentiating testis. Dmrt4 was strongly expressed in primitive gonads and much less expressed during following periods of gonadal differentiation. Its expression became strong in differentiating testes. While sox9 was highly expressed in the primitive gonad, it was expressed with fluctuations during following periods of gonadal differentiation. Cyp19a started expressing in primitive gonads, and its expression quantity fluctuated during latter periods of gonadal differentiation, but was strongly expressed in the early stage of differentiating ovaries. Results of in situ hybridization showed that dmrt4 and sox9 transcripts were both mainly localized in spermatocytes and our results suggested these four sex-related genes might be involved in gonadal differentiation through their synergistic effects in flounder.

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Candidate Serum Biomarkers for Prostate Adenocarcinoma Identified by mRNA Differences in Prostate Tissue and Verified with Protein Measurements in Tissue and Blood

Clinical Chemistry ◽

10.1373/clinchem.2011.171637 ◽

2012 ◽

Vol 58 (3) ◽

pp. 599-609 ◽

Cited By ~ 41

Author(s):

Eric W Klee ◽

Olga P Bondar ◽

Marcia K Goodmanson ◽

Roy B Dyer ◽

Sibel Erdogan ◽

...

Keyword(s):

Gene Expression ◽

Prostate Cancer ◽

Matrix Protein ◽

Expression Profiles ◽

Expression Patterns ◽

Tissue Expression ◽

Prostate Adenocarcinoma ◽

Prostate Tissue ◽

Blood Concentrations ◽

Tissue Extracts

Abstract BACKGROUND Improved tests are needed for detection and management of prostate cancer. We hypothesized that differential gene expression in prostate tissue could help identify candidate blood biomarkers for prostate cancer and that blood from men with advanced prostate disease could be used to verify the biomarkers presence in circulation. METHODS We identified candidate markers using mRNA expression patterns from laser-capture microdissected prostate tissue and confirmed tissue expression using immunohistochemistry (IHC) for the subset of candidates having commercial antisera. We analyzed tissue extracts with tandem mass spectrometry (MS/MS) and measured blood concentrations using immunoassays and MS/MS of trypsin-digested, immunoextracted peptides. RESULTS We selected 35 novel candidate prostate adenocarcinoma biomarkers. For all 13 markers having commercial antisera for IHC, tissue expression was confirmed; 6 showed statistical discrimination between nondiseased and malignant tissue, and only 5 were detected in tissue extracts by MS/MS. Sixteen of the 35 candidate markers were successfully assayed in blood. Four of 8 biomarkers measured by ELISA and 3 of 10 measured by targeted MS showed statistically significant increases in blood concentrations of advanced prostate cancer cases, compared with controls. CONCLUSIONS Seven novel biomarkers identified by gene expression profiles in prostate tissue were shown to have statistically significant increased concentrations in blood from men with advanced prostate adenocarcinoma compared with controls: apolipoprotein C1, asporin, cartilage oligomeric matrix protein, chemokine (C-X-C motif) ligand 11 (CXCL11), CXCL9, coagulation factor V, and proprotein convertase subtilisin/kexin 6.

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