The grapevine (Vitis vinifera L.) floral transcriptome in Pinot noir variety: identification of tissue-related gene networks and whorl-specific markers in pre- and post-anthesis phases

AbstractThe comprehension of molecular processes underlying the development and progression of flowering in plants is a hot topic, not only because that often the products of interest for human and animal nutrition are linked to the development of fruits or seeds, but also because the processes of gametes formation occurring in sexual organs are at the basis of recombination and genetic variability which constitutes the matter on which evolution acts, whether understood as natural or human driven. In the present study, we used an NGS approach to produce a grapevine flower transcriptome snapshot in different whorls and tissues including calyx, calyptra, filament, anther, stigma, ovary, and embryo in both pre- and post-anthesis phases. Our investigation aimed at identifying hub genes that unequivocally distinguish the different tissues providing insights into the molecular mechanisms that are at the basis of floral whorls and tissue development. To this end we have used different analytical approaches, some now consolidated in transcriptomic studies on plants, such as pairwise comparison and weighted-gene coexpression network analysis, others used mainly in studies on animals or human’s genomics, such as the tau (τ) analysis aimed at isolating highly and absolutely tissue-specific genes. The intersection of data obtained by these analyses allowed us to gradually narrow the field, providing evidence about the molecular mechanisms occurring in those whorls directly involved in reproductive processes, such as anther and stigma, and giving insights into the role of other whorls not directly related to reproduction, such as calyptra and calyx. We believe this work could represent an important genomic resource for functional analyses of grapevine floral organ growth and fruit development shading light on molecular networks underlying grapevine reproductive organ determination.

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Floral transcriptomes reveal gene networks in pineapple floral growth and fruit development

Communications Biology ◽

10.1038/s42003-020-01235-2 ◽

2020 ◽

Vol 3 (1) ◽

Cited By ~ 1

Author(s):

Lulu Wang ◽

Yi Li ◽

Xingyue Jin ◽

Liping Liu ◽

Xiaozhuan Dai ◽

...

Keyword(s):

Fruit Development ◽

Gene Networks ◽

Floral Organ ◽

Reproductive Organ ◽

Molecular Networks ◽

Organ Growth ◽

Petal Development ◽

Genomic Resource

AbstractProper flower development is essential for sexual reproductive success and the setting of fruits and seeds. The availability of a high quality genome sequence for pineapple makes it an excellent model for studying fruit and floral organ development. In this study, we sequenced 27 different pineapple floral samples and integrated nine published RNA-seq datasets to generate tissue- and stage-specific transcriptomic profiles. Pairwise comparisons and weighted gene co-expression network analysis successfully identified ovule-, stamen-, petal- and fruit-specific modules as well as hub genes involved in ovule, fruit and petal development. In situ hybridization confirmed the enriched expression of six genes in developing ovules and stamens. Mutant characterization and complementation analysis revealed the important role of the subtilase gene AcSBT1.8 in petal development. This work provides an important genomic resource for functional analysis of pineapple floral organ growth and fruit development and sheds light on molecular networks underlying pineapple reproductive organ growth.

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From leaf to flower: revisiting Goethe's concepts on the ¨metamorphosis¨ of plants

Brazilian Journal of Plant Physiology ◽

10.1590/s1677-04202005000400001 ◽

2005 ◽

Vol 17 (4) ◽

pp. 335-344 ◽

Cited By ~ 10

Author(s):

Marcelo Carnier Dornelas ◽

Odair Dornelas

Keyword(s):

Plant Development ◽

Molecular Mechanisms ◽

Molecular Model ◽

Scientific Work ◽

Floral Organ ◽

Molecular Networks ◽

Organ Identity ◽

Theoretical Frame ◽

Regulate Plant Development

Goethe’s seminal scientific work, Versuch die Metamorphose der Pflanzen zu erklaren (An Attempt to Interpret the Metamorphosis of Plants) dated from 1790, has created the foundations for many domains of modern plant biology. The archetypal leaf concept, which considers floral organs as modified leaves, besides being the best known has been proven true, following the description of the ABC molecular model of floral organ identity determination during the last decade. Here we analyze the whole theoretical frame of Goethe’s 1790 publication and present two previously misconsidered aspects of this work: The "refinement of the sap" concept as a directional principle and the "cycles of contractions and expansions" as cycles of differential determination of the shoot apical meristem. The reinterpretation of these concepts are in line with the modern view that molecular networks integrate both environmental and endogenous cues and regulate plant development. This reassessment also helps to elaborate a theoretical frame that considers the evolutionary conservation of the molecular mechanisms that regulate plant development.

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Determination of floral development stages in ‘Cabernet Sauvignon’ (Vitis vinifera L. cv.): highlighting the manifestation of stamens and pistil primordia with new intermediate stages linking the phenological stages

Ciência e Técnica Vitivinícola ◽

10.1051/ctv/20193402084 ◽

2019 ◽

Vol 34 (2) ◽

pp. 84-90

Author(s):

Z. Gökbayrak ◽

H. Engin

Keyword(s):

Fold Increase ◽

Floral Organ ◽

Reproductive Organ ◽

Vitis Vinifera L ◽

Initial Growth ◽

Phenological Stages ◽

Flower Primordia ◽

Pistil Length ◽

The Individual ◽

Intensive Work

Despite relatively intensive work on the development of inflorescence primordia during grapevine growth in season one, some informational gaps are present in the flower and floral organ development in the season two. In addition, concurrents events of phenology and formation of flowers and floral parts has not been dealt with. With the aid of digital imaging, this research had three objectives; a) describe the developmental events that take place during and after bud break in the buds and in the individual flowers in terms of differentiation, b) match these events with phenological stages, and c) determine size-related growth of the floral organs. After careful dissecting and examination of the samples under microscopy, taken ever 5-10 days between March 20 and May 10 in 2016, the results indicated that highly esteemed works regarding the reproductive anatomy of grapevines needed some additional stages to fully describe events in the stamen and pistil primordia after the appearance of petal primordia. Five intermediate stages were added to the stages of “formation of flowers”. Differentiation of inflorescence and individual flowers occurred in the second season as the buds swelled in the spring. Stamens and pistil could be seen about 3 weeks later and completed their initial growth in another 3 weeks. Flower primordia was visible on April 1 and showed a more than 9-fold increase over the course of 5 to 6 weeks. flowers increased their width and their length more than 9- and 15-fold, respectively, between stage 8.1 (April 1) and 10.3 (May 10). At first, they were wider than they were longer, but at later stages they grew longitudinally. Reproductive organ primordia were visualized around the time of 2-4 leaves separated on the shoots. Signs of generative parts become apparent in late April. Anthers were the smallest in the flower. Filaments, on the other hand, elongated almost 7-fold in a period of 20 days. Gynoecium growth was the most impressive and total pistil length increased from 52.8 to 162 μm, ovary width from 40.4 to 99.8 μm, and stigma diameter from 9.96 to 44.9 μm in twenty days. By the time the pistil took its final shape, 6-8 leaves grew on the shoot during which inflorescence could also be seen.

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Mutation of ACX1, a Jasmonic Acid Biosynthetic Enzyme, Leads to Petal Degeneration in Chinese Cabbage (Brassica campestris ssp. pekinensis)

International Journal of Molecular Sciences ◽

10.3390/ijms20092310 ◽

2019 ◽

Vol 20 (9) ◽

pp. 2310 ◽

Cited By ~ 1

Author(s):

Shenling Peng ◽

Shengnan Huang ◽

Zhiyong Liu ◽

Hui Feng

Keyword(s):

Jasmonic Acid ◽

Chinese Cabbage ◽

Gene Networks ◽

Molecular Mechanisms ◽

Doubled Haploid Line ◽

Floral Organ ◽

Organ Development ◽

Floral Organ Development ◽

Regulatory Pathways ◽

Petal Development

Petal color, size, and morphology play important roles in protecting other floral organs, attracting pollinators, and facilitating sexual reproduction in plants. In a previous study, we obtained a petal degeneration mutant (pdm) from the ‘FT’ doubled haploid line of Chinese cabbage and found that the candidate gene for pdm, Bra040093, encodes the enzyme acyl-CoA oxidase1. In this study, we sought to examine the gene networks regulating petal development in pdm plants. We show that the mRNA and protein expression of Bra040093, which is involved in the jasmonic acid (JA) biosynthetic pathway, were significantly lower in the petals of pdm plants than in those of ‘FT’ plants. Similarly, the JA and methyl jasmonate (MeJA) contents of petals were significantly lower in pdm plants than in ‘FT’ plants and we found that exogenous application of these hormones to the inflorescences of pdm plants restored the ‘FT’ phenotype. Comparative analyses of the transcriptomes of ‘FT’, pdm and pdm + JA (pJA) plants revealed 10,160 differentially expressed genes (DEGs) with consistent expression tendencies in ‘FT’ vs. pdm and pJA vs. pdm comparisons. Among these DEGs, we identified 69 DEGs related to floral organ development, 11 of which are involved in petal development regulated by JA. On the basis of qRT-PCR verification, we propose regulatory pathways whereby JA may mediate petal development in the pdm mutant. We demonstrate that mutation of Bra040093 in pdm plants leads to reduced JA levels and that this in turn promotes changes in the expression of genes that are expressed in response to JA, ultimately resulting in petal degeneration. These findings thus indicate that JA is associated with petal development in Chinese cabbage. These results enhance our knowledge on the molecular mechanisms underlying petal development and lay the foundations for further elucidation of the mechanisms associated with floral organ development in Chinese cabbage.

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High Altitude hypoxia

Current Proteomics ◽

10.2174/1570164617999201002144747 ◽

2020 ◽

Vol 17 ◽

Author(s):

Asma Babar ◽

Kifayatullah Mengal ◽

Abdul Hanan Babar ◽

Shixin Wu ◽

Mujahid Ali Shah ◽

...

Keyword(s):

Protein Synthesis ◽

High Altitude ◽

Molecular Mechanisms ◽

Strong Association ◽

Haemoglobin Concentration ◽

Metabolic Reprogramming ◽

Molecular Networks ◽

Whole Genome ◽

Gene Expressions ◽

Transcriptional Responses

: The world highest and largest altitude area is called the Qinghai-Tibetan plateau (QTB), which harbors unique animal and plant species. Mammals that inhabit the higher altitude regions have adapted well to the hypoxic conditions. One of the main stressors at high altitude is hypoxia. Metabolic responses to hypoxia play important roles in cell survival strategies and some diseases. However, the homeostatic alterations that equilibrate variations in the demand and supply of energy to maintain organismal function in a prolonged low O2 environment persist partly understood, making it problematic to differentiate adaptive from maladaptive responses in hypoxia. Tibetans and yaks are two perfect examples innate to the plateau for high altitude adaptation. By the scan of the whole-genome, EPAS1 and EGLN1 were identified as key genes associated with sustained haemoglobin concentration in high altitude mammals for adaptation. The yak is a much more ancient mammal which has existed on QTB longer than humans, it is, therefore, possible that natural selection represented a diverse group of genes/pathways in yaks. Physiological characteristics are extremely informative in revealing molecular networks associated with inherited adaptation, in addition to the whole-genome adaptive changes at the DNA sequence level. Gene-expression can be changed by a variety of signals originating from the environment, and hypoxia is the main factor amongst them. The hypoxia-inducible factors (HIF-1α and EPAS1/HIF-2α) are the main regulators of oxygen in homeostasis which play a role as maestro regulators of adaptation in hypoxic reaction of molecular mechanisms. (Vague) The basis of this review is to present recent information regarding the molecular mechanism involved in hypoxia that regulates candidate genes and proteins. Many transcriptional responses toward hypoxia are facilitated by HIFs that change the number of gene expressions and help in angiogenesis, erythropoiesis, metabolic reprogramming and metastasis. HIFs also activate several signals highlighting a strong association between hypoxia, the misfolded proteins’ accumulation in the endoplasmic reticulum in stress and activation of unfolded protein response (UPR). It was observed that at high-altitude, pregnancies yield a low birth weight ∼100 g per1000 m of the climb. (Vague) It may involve variation in the events of energy-demanding, like protein synthesis. Prolonged hypobaric hypoxia causes placental ER stress, which in turn, moderates protein synthesis and reduces proliferation. Further, Cardiac hypertrophy by cytosolic Ca2+ raises and Ca2+/calmodulin, calcineurin stimulation, NF-AT3 pathway might be caused by an imbalance in Sarcoplasmic reticulum ER Ca2, might be adaptive in beginning but severe later.

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Systems Biology Approaches Reveal a Multi-stress Responsive WRKY Transcription Factor and Stress Associated Gene Co-expression Networks in Chickpea

Current Bioinformatics ◽

10.2174/1574893614666190204152500 ◽

2019 ◽

Vol 14 (7) ◽

pp. 591-601 ◽

Cited By ~ 1

Author(s):

Aravind K. Konda ◽

Parasappa R. Sabale ◽

Khela R. Soren ◽

Shanmugavadivel P. Subramaniam ◽

Pallavi Singh ◽

...

Keyword(s):

Expression Pattern ◽

Gene Networks ◽

Molecular Mechanisms ◽

Enrichment Analysis ◽

Functional Enrichment Analysis ◽

Wrky Transcription Factor ◽

Functional Enrichment ◽

Differentially Expressed ◽

Callose Deposition ◽

Significant Probability

Background: Chickpea is a nutritional rich premier pulse crop but its production encounters setbacks due to various stresses and understanding of molecular mechanisms can be ascribed foremost importance. Objective: The investigation was carried out to identify the differentially expressed WRKY TFs in chickpea in response to herbicide stress and decipher their interacting partners. Methods: For this purpose, transcriptome wide identification of WRKY TFs in chickpea was done. Behavior of the differentially expressed TFs was compared between other stress conditions. Orthology based cofunctional gene networks were derived from Arabidopsis. Gene ontology and functional enrichment analysis was performed using Blast2GO and STRING software. Gene Coexpression Network (GCN) was constructed in chickpea using publicly available transcriptome data. Expression pattern of the identified gene network was studied in chickpea-Fusarium interactions. Results: A unique WRKY TF (Ca_08086) was found to be significantly (q value = 0.02) upregulated not only under herbicide stress but also in other stresses. Co-functional network of 14 genes, namely Ca_08086, Ca_19657, Ca_01317, Ca_20172, Ca_12226, Ca_15326, Ca_04218, Ca_07256, Ca_14620, Ca_12474, Ca_11595, Ca_15291, Ca_11762 and Ca_03543 were identified. GCN revealed 95 hub genes based on the significant probability scores. Functional annotation indicated role in callose deposition and response to chitin. Interestingly, contrasting expression pattern of the 14 network genes was observed in wilt resistant and susceptible chickpea genotypes, infected with Fusarium. Conclusion: This is the first report of identification of a multi-stress responsive WRKY TF and its associated GCN in chickpea.

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Feeding a Saccharomyces cerevisiae fermentation product improves udder health and immune response to a Streptococcus uberis mastitis challenge in mid-lactation dairy cows

Journal of Animal Science and Biotechnology ◽

10.1186/s40104-021-00560-8 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

M. Vailati-Riboni ◽

D. N. Coleman ◽

V. Lopreiato ◽

A. Alharthi ◽

R. E. Bucktrout ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Somatic Cell ◽

Pathway Analysis ◽

Molecular Mechanisms ◽

Somatic Cell Score ◽

Molecular Networks ◽

Epithelial Tissue ◽

Udder Health ◽

Streptococcus Uberis ◽

Fermentation Product

Abstract Background We aimed to characterize the protective effects and the molecular mechanisms of action of a Saccharomyces cerevisiae fermentation product (NTK) in response to a mastitis challenge. Eighteen mid-lactation multiparous Holstein cows (n = 9/group) were fed the control diet (CON) or CON supplemented with 19 g/d NTK for 45 d (phase 1, P1) and then infected in the right rear quarter with 2500 CFU of Streptococcus uberis (phase 2, P2). After 36-h, mammary gland and liver biopsies were collected and antibiotic treatment started until the end of P2 (9 d post challenge). Cows were then followed until day 75 (phase 3, P3). Milk yield (MY) and dry matter intake (DMI) were recorded daily. Milk samples for somatic cell score were collected, and rectal and udder temperature, heart and respiration rate were recorded during the challenge period (P2) together with blood samples for metabolite and immune function analyses. Data were analyzed by phase using the PROC MIXED procedure in SAS. Biopsies were used for transcriptomic analysis via RNA-sequencing, followed by pathway analysis. Results DMI and MY were not affected by diet in P1, but an interaction with time was recorded in P2 indicating a better recovery from the challenge in NTK compared with CON. NTK reduced rectal temperature, somatic cell score, and temperature of the infected quarter during the challenge. Transcriptome data supported these findings, as NTK supplementation upregulated mammary genes related to immune cell antibacterial function (e.g., CATHL4, NOS2), epithelial tissue protection (e.g. IL17C), and anti-inflammatory activity (e.g., ATF3, BAG3, IER3, G-CSF, GRO1, ZFAND2A). Pathway analysis indicated upregulation of tumor necrosis factor α, heat shock protein response, and p21 related pathways in the response to mastitis in NTK cows. Other pathways for detoxification and cytoprotection functions along with the tight junction pathway were also upregulated in NTK-fed cows. Conclusions Overall, results highlighted molecular networks involved in the protective effect of NTK prophylactic supplementation on udder health during a subclinical mastitic event.

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Oscillatory Ca2+ Signaling in the Isolated Caenorhabditis elegans Intestine

The Journal of General Physiology ◽

10.1085/jgp.200509355 ◽

2005 ◽

Vol 126 (4) ◽

pp. 379-392 ◽

Cited By ~ 110

Author(s):

Maria V. Espelt ◽

Ana Y. Estevez ◽

Xiaoyan Yin ◽

Kevin Strange

Keyword(s):

Caenorhabditis Elegans ◽

Intestinal Epithelium ◽

Oscillation Frequency ◽

Gene Networks ◽

Molecular Mechanisms ◽

Apical Cell ◽

Intestinal Cell ◽

C Elegans ◽

Contrast Gain ◽

Behavioral Rhythm

Defecation in the nematode Caenorhabditis elegans is a readily observable ultradian behavioral rhythm that occurs once every 45–50 s and is mediated in part by posterior body wall muscle contraction (pBoc). pBoc is not regulated by neural input but instead is likely controlled by rhythmic Ca2+ oscillations in the intestinal epithelium. We developed an isolated nematode intestine preparation that allows combined physiological, genetic, and molecular characterization of oscillatory Ca2+ signaling. Isolated intestines loaded with fluo-4 AM exhibit spontaneous rhythmic Ca2+ oscillations with a period of ∼50 s. Oscillations were only detected in the apical cell pole of the intestinal epithelium and occur as a posterior-to-anterior moving intercellular Ca2+ wave. Loss-of-function mutations in the inositol-1,4,5-trisphosphate (IP3) receptor ITR-1 reduce pBoc and Ca2+ oscillation frequency and intercellular Ca2+ wave velocity. In contrast, gain-of-function mutations in the IP3 binding and regulatory domains of ITR-1 have no effect on pBoc or Ca2+ oscillation frequency but dramatically increase the speed of the intercellular Ca2+ wave. Systemic RNA interference (RNAi) screening of the six C. elegans phospholipase C (PLC)–encoding genes demonstrated that pBoc and Ca2+ oscillations require the combined function of PLC-γ and PLC-β homologues. Disruption of PLC-γ and PLC-β activity by mutation or RNAi induced arrhythmia in pBoc and intestinal Ca2+ oscillations. The function of the two enzymes is additive. Epistasis analysis suggests that PLC-γ functions primarily to generate IP3 that controls ITR-1 activity. In contrast, IP3 generated by PLC-β appears to play little or no direct role in ITR-1 regulation. PLC-β may function instead to control PIP2 levels and/or G protein signaling events. Our findings provide new insights into intestinal cell Ca2+ signaling mechanisms and establish C. elegans as a powerful model system for defining the gene networks and molecular mechanisms that underlie the generation and regulation of Ca2+ oscillations and intercellular Ca2+ waves in nonexcitable cells.

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Sex differences in white adipose tissue expansion: emerging molecular mechanisms

Clinical Science ◽

10.1042/cs20210086 ◽

2021 ◽

Vol 135 (24) ◽

pp. 2691-2708

Author(s):

Simon T. Bond ◽

Anna C. Calkin ◽

Brian G. Drew

Keyword(s):

Sex Differences ◽

Sexual Dimorphism ◽

Gene Networks ◽

Large Scale ◽

Molecular Mechanisms ◽

Association Studies ◽

Tissue Expansion ◽

Economic Systems ◽

Genomic Association ◽

Males And Females

Abstract The escalating prevalence of individuals becoming overweight and obese is a rapidly rising global health problem, placing an enormous burden on health and economic systems worldwide. Whilst obesity has well described lifestyle drivers, there is also a significant and poorly understood component that is regulated by genetics. Furthermore, there is clear evidence for sexual dimorphism in obesity, where overall risk, degree, subtype and potential complications arising from obesity all differ between males and females. The molecular mechanisms that dictate these sex differences remain mostly uncharacterised. Many studies have demonstrated that this dimorphism is unable to be solely explained by changes in hormones and their nuclear receptors alone, and instead manifests from coordinated and highly regulated gene networks, both during development and throughout life. As we acquire more knowledge in this area from approaches such as large-scale genomic association studies, the more we appreciate the true complexity and heterogeneity of obesity. Nevertheless, over the past two decades, researchers have made enormous progress in this field, and some consistent and robust mechanisms continue to be established. In this review, we will discuss some of the proposed mechanisms underlying sexual dimorphism in obesity, and discuss some of the key regulators that influence this phenomenon.

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