scholarly journals Gene expression analysis of Cyanophora paradoxa reveals conserved abiotic stress responses between basal algae and flowering plants

2019 ◽  
Author(s):  
Camilla Ferrari ◽  
Marek Mutwil
Keyword(s):  
Gene Expression ◽  
Stress Responses ◽  
Land Plants ◽  
List Type ◽  
Cyanophora Paradoxa ◽  
Plant Kingdom ◽  
Gene Expression Atlas ◽  
Expression Atlas ◽  
Gene Modules ◽  
The Impact

SummaryThe glaucophyte Cyanophora paradoxa represents the most basal member of the Archaeplastida kingdom, however the function and expression of most of its genes are unknown. This information is needed to uncover how functional gene modules, i.e. groups of genes performing a given function, evolved in the plant kingdom.We have generated a gene expression atlas capturing responses of Cyanophora to various abiotic stresses. This data was included in the CoNekT-Plants database, enabling comparative transcriptomic analyses across two algae and six land plants.We demonstrate how the database can be used to study gene expression, co-expression networks and gene function in Cyanophora, and how conserved transcriptional programs can be identified. We identified gene modules involved in phycobilisome biosynthesis, response to high light and cell division. While we observed no correlation between the number of differentially expressed genes and the impact on growth of Cyanophora, we found that the response to stress involves a conserved, kingdom-wide transcriptional reprogramming, which is activated upon most stresses in algae and land plants.The Cyanophora stress gene expression atlas and the tools found in https://conekt.plant.tools/ database provide a useful resource to reveal functionally related genes and stress responses in the plant kingdom.

scholarly journals Expression atlas of Selaginella moellendorffii provides insights into the evolution of vasculature, secondary metabolism and roots

2019 ◽  
Author(s):  
Camilla Ferrari ◽  
Devendra Shivhare ◽  
Bjoern Oest Hansen ◽  
Nikola Winter ◽  
Asher Pasha ◽  
...  
Keyword(s):  
Gene Expression ◽  
Secondary Metabolism ◽  
Vascular Plants ◽  
Expression Profiles ◽  
Genetic Material ◽  
Gene Families ◽  
List Type ◽  
Expression Atlas ◽  
Gene Modules ◽  
Selaginella Moellendorffii

SummaryThe lycophyte Selaginella moellendorffii represents early vascular plants and is studied to understand the evolution of higher plant traits such as the vasculature, leaves, stems, roots, and secondary metabolism. However, little is known about the gene expression and transcriptional coordination of Selaginella genes, which precludes us from understanding the evolution of transcriptional programs behind these traits.We here present a gene expression atlas comprising all major organs, tissue types, and the diurnal gene expression profiles for S. moellendorffii. The atlas is part of the CoNekT-Plants database (conekt.plant.tools), which enables comparative transcriptomic analyses across two algae and seven land plants.We show that the transcriptional gene module responsible for the biosynthesis of lignocellulose evolved in the ancestor of vascular plants, and pinpoint the duplication and subfunctionalization events that generated multiple gene modules involved in the biosynthesis of various cell wall types. We further demonstrate how secondary metabolism is transcriptionally coordinated and integrated with other cellular pathways. Finally, we identify root-specific genes in vascular plants and show that the evolution of roots did not coincide with an increased appearance of gene families, suggesting that the existing genetic material was sufficient to generate new organs.Our updated database at conekt.plant.tools provides a unique resource to study the evolution of genes, gene families, transcriptomes, and functional gene modules in the Archaeplastida kingdom.

scholarly journals Marchantia polymorpha gene expression atlas reveals the hierarchy of abiotic stress responses and conservation of diurnal gene expression

2021 ◽  
Author(s):  
Qiao Wen Tan ◽  
Peng Ken Lim ◽  
Zhong Chen ◽  
Asher Pasha ◽  
Nicholas J. Provart ◽  
...  
Keyword(s):  
Gene Expression ◽  
Abiotic Stress ◽  
Stress Responses ◽  
Model Organisms ◽  
Signalling Pathways ◽  
Marchantia Polymorpha ◽  
Expression Data ◽  
Gene Expression Atlas ◽  
Online Databases ◽  
Expression Atlas

Abiotic stress has a dramatic impact on ecosystems and the yield of crops, and global warming will likely result in more frequent and intense stresses. However, due to the complexity of the underlying signalling pathways and the fact that stresses often occur in combinations in nature, our knowledge of how plants acclimatize to abiotic stress is still lacking. Here, we used a plant with minimal regulatory network redundancy, Marchantia polymorpha, to study how seven abiotic stresses alone and in combination affect the phenotype, gene expression, and activity of biological pathways. Worryingly, we see no evidence of conservation of gene expression to abiotic stress between model organisms, suggesting that each species develops unique strategies to cope with abiotic stress. Interestingly, we observed that certain stresses are able to suppress others, while specific combinations can elucidate novel transcriptomic responses. Finally, we provide two online databases to study abiotic stress responses and diurnal gene expression data in Marchantia.

An Organ-Wide Gene Expression Atlas of the Developing Human Heart

2018 ◽  
Author(s):  
Michaela Asp ◽  
Stefania Giacomello ◽  
Daniel Fürth ◽  
Johan Reimegård ◽  
Eva Wärdell ◽  
...  
Keyword(s):  
Gene Expression ◽  
Human Heart ◽  
Gene Expression Atlas ◽  
Expression Atlas

scholarly journals A gene expression atlas for different kinds of stress in the mouse brain

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Tiziano Flati ◽  
Silvia Gioiosa ◽  
Giovanni Chillemi ◽  
Andrea Mele ◽  
Alberto Oliverio ◽  
...  
Keyword(s):  
Gene Expression ◽  
Coping With Stress ◽  
Gene Expression Atlas ◽  
Sequence Read Archive ◽  
Brain Transcriptome ◽  
Expression Atlas ◽  
Differential Gene ◽  
Stress Related Genes ◽  
Public Repositories ◽  
The Brain

AbstractStressful experiences are part of everyday life and animals have evolved physiological and behavioral responses aimed at coping with stress and maintaining homeostasis. However, repeated or intense stress can induce maladaptive reactions leading to behavioral disorders. Adaptations in the brain, mediated by changes in gene expression, have a crucial role in the stress response. Recent years have seen a tremendous increase in studies on the transcriptional effects of stress. The input raw data are freely available from public repositories and represent a wealth of information for further global and integrative retrospective analyses. We downloaded from the Sequence Read Archive 751 samples (SRA-experiments), from 18 independent BioProjects studying the effects of different stressors on the brain transcriptome in mice. We performed a massive bioinformatics re-analysis applying a single, standardized pipeline for computing differential gene expression. This data mining allowed the identification of novel candidate stress-related genes and specific signatures associated with different stress conditions. The large amount of computational results produced was systematized in the interactive “Stress Mice Portal”.

scholarly journals A comprehensive RNA-Seq-based gene expression atlas of the summer squash (Cucurbita pepo) provides insights into fruit morphology and ripening mechanisms

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Aliki Xanthopoulou ◽  
Javier Montero-Pau ◽  
Belén Picó ◽  
Panagiotis Boumpas ◽  
Eleni Tsaliki ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cucurbita Pepo ◽  
Developmental Stages ◽  
Lateral Roots ◽  
Expression Patterns ◽  
Male Flower ◽  
Differentially Expressed ◽  
Gene Expression Atlas ◽  
Summer Squash ◽  
Expression Atlas

Abstract Background Summer squash (Cucurbita pepo: Cucurbitaceae) are a popular horticultural crop for which there is insufficient genomic and transcriptomic information. Gene expression atlases are crucial for the identification of genes expressed in different tissues at various plant developmental stages. Here, we present the first comprehensive gene expression atlas for a summer squash cultivar, including transcripts obtained from seeds, shoots, leaf stem, young and developed leaves, male and female flowers, fruits of seven developmental stages, as well as primary and lateral roots. Results In total, 27,868 genes and 2352 novel transcripts were annotated from these 16 tissues, with over 18,000 genes common to all tissue groups. Of these, 3812 were identified as housekeeping genes, half of which assigned to known gene ontologies. Flowers, seeds, and young fruits had the largest number of specific genes, whilst intermediate-age fruits the fewest. There also were genes that were differentially expressed in the various tissues, the male flower being the tissue with the most differentially expressed genes in pair-wise comparisons with the remaining tissues, and the leaf stem the least. The largest expression change during fruit development was early on, from female flower to fruit two days after pollination. A weighted correlation network analysis performed on the global gene expression dataset assigned 25,413 genes to 24 coexpression groups, and some of these groups exhibited strong tissue specificity. Conclusions These findings enrich our understanding about the transcriptomic events associated with summer squash development and ripening. This comprehensive gene expression atlas is expected not only to provide a global view of gene expression patterns in all major tissues in C. pepo but to also serve as a valuable resource for functional genomics and gene discovery in Cucurbitaceae.

scholarly journals PEATmoss ( Physcomitrella Expression Atlas Tool): a unified gene expression atlas for the model plant Physcomitrella patens

2020 ◽  
Vol 102 (1) ◽  
pp. 165-177 ◽  
Author(s):  
Noe Fernandez‐Pozo ◽  
Fabian B. Haas ◽  
Rabea Meyberg ◽  
Kristian K. Ullrich ◽  
Manuel Hiss ◽  
...  
Keyword(s):  
Gene Expression ◽  
Physcomitrella Patens ◽  
Model Plant ◽  
Gene Expression Atlas ◽  
Expression Atlas

Gene expression atlas of fruit ripening of octoploid strawberry (Fragaria×ananassa) and transcriptome assembly from RNA-seq data

2016 ◽  
Vol 33 ◽  
pp. S156
Author(s):  
José Federico Sánchez Sevilla ◽  
José G. Vallarino ◽  
Sonia Osorio ◽  
Aureliano Bombarely ◽  
Katharina Merchante ◽  
...  
Keyword(s):  
Gene Expression ◽  
Fruit Ripening ◽  
Transcriptome Assembly ◽  
Fragaria Ananassa ◽  
Rna Seq ◽  
Gene Expression Atlas ◽  
Expression Atlas

scholarly journals A comprehensive gene expression atlas of sex- and tissue-specificity in the malaria vector, Anopheles gambiae

BMC Genomics ◽  
2011 ◽  
Vol 12 (1) ◽  
Author(s):  
Dean A Baker ◽  
Tony Nolan ◽  
Bettina Fischer ◽  
Alex Pinder ◽  
Andrea Crisanti ◽  
...  
Keyword(s):  
Gene Expression ◽  
Anopheles Gambiae ◽  
Malaria Vector ◽  
Tissue Specificity ◽  
Gene Expression Atlas ◽  
Expression Atlas
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