Time-Course Transcriptome Analysis Reveals Global Gene Expression Profiling and Dynamic Developmental Signatures across Complete Life Cycle of Bombyx mori

Background: The silkworm (Bombyx mori) is an important lepidopteran model insect worldwide which undergoes a complete metamorphosis developmental process. Although genome sequencing has been long performed, no transcriptome data covering the complete life cycle are available. Methods: Herein, a total of 10 samples were collected consecutively at four different developmental stages, including eggs of 24 h after oviposition (Ed) and eggs of 24 h after artificial egg-hatching (E); larvae from fist to fifth instar (L1–L5); early and late pupa (P4 and P8); and adult moth (M), were subjected to Illumina RNA-Seq and time-course analysis. Results: The summations of the gene expression of the silkworm ten developmental stages show: at Ed stage, eggs develop towards diapause status, the total gene expression level is relatively low; at E stage, after artificial egg-hatching, the expression level improves rapidly; during larval stages from L1–L5, the expression level rises gradually and reaches a peak at L5 stage; during pupae and moth stages, the total gene expression decline stage by stage. The results revealed a dynamical gene expression profile exhibiting significant differential expressions throughout the silkworm life cycle. Moreover, stage-specific key genes were identified at different developmental stages, suggesting their functions mainly characterized in maintaining insect development and immunity homeostasis or driving metamorphosis. GO annotation and KEGG enrichment analysis further revealed the most significantly enriched and fundamentally biological processes during silkworm growth. Conclusion: Collectively, our omics data depicted the first comprehensive landscape of dynamic transcriptome throughout complete developmental processes of B. mori. Our findings also provide valuable references and novel insights into understanding the molecular developmental remodeling events for other Lepidoptera species.

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Re-evaluation of the life cycle of Eimeria maxima Tyzzer, 1929 in chickens (Gallus domesticus)

Parasitology ◽

10.1017/s0031182017002153 ◽

2017 ◽

Vol 145 (8) ◽

pp. 1051-1058 ◽

Cited By ~ 4

Author(s):

J. P. Dubey ◽

M. C. Jenkins

Keyword(s):

Life Cycle ◽

Broiler Chickens ◽

Time Course ◽

Developmental Stages ◽

Parasitophorous Vacuole ◽

Fourth Generation ◽

Residual Body ◽

Tissue Sections ◽

Eimeria Maxima ◽

Time Course Study

AbstractA time-course study was conducted to resolve discrepancies in the literature and better define aspects of the Eimeria maxima life cycle such, as sites of development and both morphology and number of asexual stages. Broiler chickens were inoculated orally with five million E. maxima oocysts (APU1), and were necropsied at regular intervals from 12 to 120 h p.i. Small intestine tissue sections and smears were examined for developmental stages. The jejunum contained the highest numbers of developmental stages. At 12 h p.i., sporozoites were observed inside a parasitophorous vacuole (PV) in the epithelial villi and the lamina propria. By 24 h, sporozoites enclosed by a PV were observed in enterocytes of the glands of Lieberkühn. At 48 h p.i., sporozoites, elongated immature and mature schizonts, were all seen in the glands with merozoites budding off from a residual body. By 60 h, second-generation, sausage-shaped schizonts containing up to 12 merozoites were observed around a residual body in the villar tip of invaded enterocytes. At 72 and 96 h, profuse schizogony associated with third- and fourth-generation schizonts was observed throughout the villus. At 120 h, another generation (fifth) of schizonts were seen in villar tips as well as in subepithelium where gamonts and oocysts were also present; a few gamonts were in epithelium. Our finding of maximum parasitization of E. maxima in jejunum is important because this region is critical for nutrient absorption and weight gain.

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Gene expression after resumption of development of Artemia franciscana cryptobiotic embryos

Biochemistry and Cell Biology ◽

10.1139/o94-014 ◽

1994 ◽

Vol 72 (3-4) ◽

pp. 78-83 ◽

Cited By ~ 15

Author(s):

Ricardo Escalante ◽

Alberto García-Sáez ◽

Maria-Asunción Ortega ◽

Leandro Sastre

Keyword(s):

Gene Expression ◽

Time Course ◽

Developmental Stages ◽

Artemia Franciscana ◽

Mrna Levels ◽

Muscle Actin ◽

Mrna Accumulation ◽

Α Subunit ◽

Steady State Levels ◽

Cyst Development

The steady-state levels of six different mRNAs have been studied during Artemia franciscana development. Some of these mRNAs are present in the cryptobiotic cyst, like those coding for cytoplasmic actins, sarcoplasmic/endoplasmic reticulum Ca2+-ATPase, and the Na+,K+-ATPase α-subunit isoform coded by the clone pArATNa136. The expression of these mRNAs is markedly induced during cyst development. A small increase in mRNA levels can be observed for some genes at very early stages of development (2 h). The main increase is observed between 4 and 16 h of development for all these genes, although the time course of mRNA accumulation is different for each one of the genes studied. Some other genes, like those coding for muscle actin (actin 3) or the Na+,K+-ATPase α-subunit isoform coded by the cDNA clone α2850, are not expressed in the cyst before resumption of development and their expression is induced after 10 or 6 h of development, respectively. These data on the kinetic of mRNA accumulation provide the information required to determine transcriptionally active developmental stages, necessary to study in more detail the mechanisms of transcriptional regulation during activation of cryptobiotic cysts and resumption of embryonic development.Key words: Artemia, gene expression, actin, Na,K-ATPase, Ca2+-ATPase.

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Assessment of reference genes at six different developmental stages of Schistosoma mansoni for quantitative RT-PCR

Scientific Reports ◽

10.1038/s41598-021-96055-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Gilbert O. Silveira ◽

Murilo S. Amaral ◽

Helena S. Coelho ◽

Lucas F. Maciel ◽

Adriana S. A. Pereira ◽

...

Keyword(s):

Gene Expression ◽

Life Cycle ◽

Schistosoma Mansoni ◽

Reference Genes ◽

Large Scale ◽

Developmental Stages ◽

Adult Males ◽

Histone H4 ◽

Expression Levels ◽

Life Cycle Stages

AbstractReverse-transcription quantitative real-time polymerase chain reaction (RT-qPCR) is the most used, fast, and reproducible method to confirm large-scale gene expression data. The use of stable reference genes for the normalization of RT-qPCR assays is recognized worldwide. No systematic study for selecting appropriate reference genes for usage in RT-qPCR experiments comparing gene expression levels at different Schistosoma mansoni life-cycle stages has been performed. Most studies rely on genes commonly used in other organisms, such as actin, tubulin, and GAPDH. Therefore, the present study focused on identifying reference genes suitable for RT-qPCR assays across six S. mansoni developmental stages. The expression levels of 25 novel candidates that we selected based on the analysis of public RNA-Seq datasets, along with eight commonly used reference genes, were systematically tested by RT-qPCR across six developmental stages of S. mansoni (eggs, miracidia, cercariae, schistosomula, adult males and adult females). The stability of genes was evaluated with geNorm, NormFinder and RefFinder algorithms. The least stable candidate reference genes tested were actin, tubulin and GAPDH. The two most stable reference genes suitable for RT-qPCR normalization were Smp_101310 (Histone H4 transcription factor) and Smp_196510 (Ubiquitin recognition factor in ER-associated degradation protein 1). Performance of these two genes as normalizers was successfully evaluated with females maintained unpaired or paired to males in culture for 8 days, or with worm pairs exposed for 16 days to double-stranded RNAs to silence a protein-coding gene. This study provides reliable reference genes for RT-qPCR analysis using samples from six different S. mansoni life-cycle stages.

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BrassicaEDB: A Gene Expression Database for Brassica Crops

International Journal of Molecular Sciences ◽

10.3390/ijms21165831 ◽

2020 ◽

Vol 21 (16) ◽

pp. 5831 ◽

Cited By ~ 1

Author(s):

Haoyu Chao ◽

Tian Li ◽

Chaoyu Luo ◽

Hualei Huang ◽

Yingfei Ruan ◽

...

Keyword(s):

Gene Expression ◽

Target Genes ◽

Developmental Stages ◽

Expression Profiles ◽

Expression Patterns ◽

Gene Expression Profiles ◽

Expression Level ◽

Level Data ◽

Rapeseed Cultivar ◽

Transcriptome Level

The genus Brassica contains several economically important crops, including rapeseed (Brassica napus, 2n = 38, AACC), the second largest source of seed oil and protein meal worldwide. However, research in rapeseed is hampered because it is complicated and time-consuming for researchers to access different types of expression data. We therefore developed the Brassica Expression Database (BrassicaEDB) for the research community. In the current BrassicaEDB, we only focused on the transcriptome level in rapeseed. We conducted RNA sequencing (RNA-Seq) of 103 tissues from rapeseed cultivar ZhongShuang11 (ZS11) at seven developmental stages (seed germination, seedling, bolting, initial flowering, full-bloom, podding, and maturation). We determined the expression patterns of 101,040 genes via FPKM analysis and displayed the results using the eFP browser. We also analyzed transcriptome data for rapeseed from 70 BioProjects in the SRA database and obtained three types of expression level data (FPKM, TPM, and read counts). We used this information to develop the BrassicaEDB, including “eFP”, “Treatment”, “Coexpression”, and “SRA Project” modules based on gene expression profiles and “Gene Feature”, “qPCR Primer”, and “BLAST” modules based on gene sequences. The BrassicaEDB provides comprehensive gene expression profile information and a user-friendly visualization interface for rapeseed researchers. Using this database, researchers can quickly retrieve the expression level data for target genes in different tissues and in response to different treatments to elucidate gene functions and explore the biology of rapeseed at the transcriptome level.

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Transcriptome Profiling Reveals Differential Gene Expression of Secreted Proteases and Highly Specific Gene Repertoires Involved in Lactarius–Pinus Symbioses

Frontiers in Plant Science ◽

10.3389/fpls.2021.714393 ◽

2021 ◽

Vol 12 ◽

Author(s):

Nianwu Tang ◽

Annie Lebreton ◽

Wenjun Xu ◽

Yucheng Dai ◽

Fuqiang Yu ◽

...

Keyword(s):

Gene Expression ◽

Time Course ◽

Developmental Stages ◽

Transcriptome Profiling ◽

Specific Gene ◽

Gene Repertoire ◽

Symbiotic Gene ◽

Mutualistic Symbiosis ◽

Secreted Proteases ◽

Fungal Genes

Ectomycorrhizal fungi establish a mutualistic symbiosis in roots of most woody plants. The molecular underpinning of ectomycorrhizal development was only explored in a few lineages. Here, we characterized the symbiotic transcriptomes of several milkcap species (Lactarius, Russulales) in association with different pine hosts. A time-course study of changes in gene expression during the development of L. deliciosus–Pinus taeda symbiosis identified 6 to 594 differentially expressed fungal genes at various developmental stages. Up- or down-regulated genes are involved in signaling pathways, nutrient transport, cell wall modifications, and plant defenses. A high number of genes coding for secreted proteases, especially sedolisins, were induced during root colonization. In contrast, only a few genes encoding mycorrhiza-induced small secreted proteins were identified. This feature was confirmed in several other Lactarius species in association with various pines. Further comparison among all these species revealed that each Lactarius species encodes a highly specific symbiotic gene repertoire, a feature possibly related to their host-specificity. This study provides insights on the genetic basis of symbiosis in an ectomycorrhizal order, the Russulales, which was not investigated so far.

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Transcriptomic analysis of the early strobilar development of Echinococcus granulosus

10.1101/271767 ◽

2018 ◽

Author(s):

João Antonio Debarba ◽

Karina Mariante Monteiro ◽

Alexandra Lehmkuhl Gerber ◽

Ana Tereza Ribeiro de Vasconcelos ◽

Arnaldo Zaha

Keyword(s):

Gene Expression ◽

Life Cycle ◽

Echinococcus Granulosus ◽

Time Course ◽

Complex Life Cycle ◽

Rna Seq ◽

Transcription Profiles ◽

Gene Transcripts ◽

Key Genes

AbstractBackgroundEchinococcus granulosus has a complex life cycle involving two mammalian hosts. The transition from one host to another is accompanied by changes in gene expression, and the transcriptional events that underlie these processes have not yet been fully characterized.ResultsIn this study, RNA-seq is used to compare the transcription profiles of four time samples of E. granulosus protoscoleces in vitro induced to strobilar development. We identified 818 differentially expressed genes, which were divided into eight expression clusters formed over the entire 24 hours time course and indicated different transcriptional patterns. An enrichment of gene transcripts with molecular functions of signal transduction, enzymes and protein modifications was observed with progression of development.ConclusionThis transcriptomic study provides insight for understanding the complex life cycle of E. granulosus and contributes for searching for the key genes correlating with the strobilar development, providing interesting hints for further studies.

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Global Gene Expression Profiling through the Complete Life Cycle of Trypanosoma vivax

PLoS Neglected Tropical Diseases ◽

10.1371/journal.pntd.0003975 ◽

2015 ◽

Vol 9 (8) ◽

pp. e0003975 ◽

Cited By ~ 19

Author(s):

Andrew P. Jackson ◽

Sophie Goyard ◽

Dong Xia ◽

Bernardo J. Foth ◽

Mandy Sanders ◽

...

Keyword(s):

Gene Expression ◽

Life Cycle ◽

Gene Expression Profiling ◽

Expression Profiling ◽

Global Gene Expression ◽

Trypanosoma Vivax ◽

Complete Life Cycle ◽

Global Gene Expression Profiling

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Regulation of Photomorphogenic Development by Plant Phytochromes

International Journal of Molecular Sciences ◽

10.3390/ijms20246165 ◽

2019 ◽

Vol 20 (24) ◽

pp. 6165 ◽

Cited By ~ 4

Author(s):

Sharanya Tripathi ◽

Quyen T. N. Hoang ◽

Yun-Jeong Han ◽

Jeong-Il Kim

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

Life Cycle ◽

Growth And Development ◽

Developmental Stages ◽

Red Light ◽

Control Plant ◽

Plant Growth And Development ◽

Light Signals ◽

Key Events

Photomorphogenesis and skotomorphogenesis are two key events that control plant development, from seed germination to flowering and senescence. A group of wavelength-specific photoreceptors, E3 ubiquitin ligases, and various transcription factors work together to regulate these two critical processes. Phytochromes are the main photoreceptors in plants for perceiving red/far-red light and transducing the light signals to downstream factors that regulate the gene expression network for photomorphogenic development. In this review, we highlight key developmental stages in the life cycle of plants and how phytochromes and other components in the phytochrome signaling pathway play roles in plant growth and development.

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Expression analysis of sex-determining pathway genes during development in male and female Atlantic salmon (Salmo salar)

Physiological Genomics ◽

10.1152/physiolgenomics.00013.2015 ◽

2015 ◽

Vol 47 (12) ◽

pp. 581-587 ◽

Cited By ~ 8

Author(s):

Krzysztof P. Lubieniecki ◽

Natasha A. Botwright ◽

Richard S. Taylor ◽

Brad S. Evans ◽

Mathew T. Cook ◽

...

Keyword(s):

Gene Expression ◽

Atlantic Salmon ◽

Salmo Salar ◽

Time Course ◽

Developmental Stages ◽

Sex Differentiation ◽

Male And Female ◽

Expression Levels ◽

Atlantic Salmon Salmo Salar ◽

The Cross

We studied the expression of 28 genes that are involved in vertebrate sex-determination or sex-differentiation pathways, in male and female Atlantic salmon ( Salmo salar) in 11 stages of development from fertilization to after first feeding. Gene expression was measured in half-sibs that shared the same dam. The sire of family 1 was a sex-reversed female (i.e., genetically female but phenotypically male), and so the progeny of this family are all female. The sire of family 2 was a true male, and so the offspring were 50% male and 50% female. Gene expression levels were compared among three groups: 20 female offspring of the cross between a regular female and the sex-reversed female ( family 1, first group), ∼10 females from the cross between a regular female and a regular male ( family 2, second group) and ∼10 males from this same family ( family 2, third group). Statistically significant differences in expression levels between males and the two groups of females were observed for two genes, gsdf and amh/mis, in the last four developmental stages examined. SdY, the sex-determining gene in rainbow trout, appeared to be expressed in males from 58 days postfertilization (dpf). Starting at 83 dpf, ovarian aromatase, cyp19a, expression appeared to be greater in both groups of females compared with males, but this difference was not statistically significant. The time course of expression suggests that sdY may be involved in the upregulation of gsdf and amh/mis and the subsequent repression of cyp19a in males via the effect of amh/mis.

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