Rapidly developing functional genomics in ecological model systems via 454 transcriptome sequencing

AbstractMosquitoes are emerging as model systems with which to study innate behaviours through neuroethology and functional genomics. Decades of work on these disease vectors have provided a solid behavioural framework describing the distinct repertoire of predominantly odour-mediated behaviours of female mosquitoes, and their dependence on life stage (intrinsic factors) and environmental cues (extrinsic factors). The purpose of this review is to provide an overview of how intrinsic factors, including adult maturation, age, nutritional status, and infection, affect the attraction to plants and feeding on plant fluids, host seeking, blood feeding, supplemental feeding behaviours, pre-oviposition behaviour, and oviposition in female mosquitoes. With the technological advancements in the recent two decades, we have gained a better understanding of which volatile organic compounds are used by mosquitoes to recognise and discriminate among various fitness-enhancing resources, and characterised their neural and molecular correlates. In this review, we present the state of the art of the peripheral olfactory system as described by the neural physiology, functional genomics, and genetics underlying the demonstrated changes in the behavioural repertoire in female mosquitoes. The review is meant as a summary introduction to the current conceptual thinking in the field.

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Delineating Calcium Signaling Machinery in Plants: Tapping the Potential through Functional Genomics

Current Genomics ◽

10.2174/1389202922666211130143328 ◽

2021 ◽

Vol 22 ◽

Author(s):

Soma Ghosh ◽

Malathi Bheri ◽

Girdhar K. Pandey

Keyword(s):

Functional Genomics ◽

Protein Kinases ◽

Regulatory Networks ◽

Crop Improvement ◽

Functional Characterization ◽

Genomic Analysis ◽

Major Elements ◽

Model Systems ◽

Plant Responses ◽

Dependent Protein

: Plant systems have developed calcium (Ca2+) signaling as an important mechanism of regulation of stress perception, developmental cues, and responsive gene expression. The post-genomic era has witnessed the successful unravelling of the functional characterization of genes and the creation of large datasets of molecular information. The major elements of Ca2+ signaling machinery involve Ca2+ sensors and responders such as Calmodulin (CaM), Calmodulin-like proteins (CMLs), Ca2+/CaM-dependent protein kinases (CCaMK), Ca2+-dependent protein kinases (CDPKs), Calcineurin B-like proteins (CBLs) as well as transporters, such as Cyclic nucleotide-gated channels (CNGCs), Glutamate-like receptors (GLRs), Ca2+-ATPases, Ca2+/H+ exchangers (CAXs) and mechanosensitive channels. These elements play an important role in the regulation of physiological processes and plant responses to various stresses. Detailed genomic analysis can help us in the identification of potential molecular targets that can be exploited towards the development of stress-tolerant crops. The information sourced from model systems through omics approaches helps in the prediction and simulation of regulatory networks involved in responses to different stimuli at the molecular and cellular levels. The molecular delineation of Ca2+ signaling pathways could be the stepping stone for engineering climate-resilient crop plants. Here, we review the recent developments in Ca2+ signaling in the context of transport, responses, and adaptations significant for crop improvement through functional genomics approaches.

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Organoid Models for Cancer Research

Annual Review of Cancer Biology ◽

10.1146/annurev-cancerbio-030518-055702 ◽

2019 ◽

Vol 3 (1) ◽

pp. 223-234 ◽

Cited By ~ 9

Author(s):

Hans Clevers ◽

David A. Tuveson

Keyword(s):

Cancer Research ◽

Tumor Microenvironment ◽

Personalized Medicine ◽

High Throughput ◽

Stromal Cells ◽

Transcriptome Sequencing ◽

Cancer Biology ◽

Three Dimensional ◽

Model Systems ◽

Liver Cancers

Organoid cultures have emerged as powerful model systems accelerating discoveries in cellular and cancer biology. These three-dimensional cultures are amenable to diverse techniques, including high-throughput genome and transcriptome sequencing, as well as genetic and biochemical perturbation, making these models well suited to answer a variety of questions. Recently, organoids have been generated from diverse human cancers, including breast, colon, pancreas, prostate, bladder, and liver cancers, and studies involving these models are expanding our knowledge of the etiology and characteristics of these malignancies. Co-cultures of cancer organoids with non-neoplastic stromal cells enable investigation of the tumor microenvironment. In addition, recent studies have established that organoids have a place in personalized medicine approaches. Here, we describe the application of organoid technology to cancer discovery and treatment.

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De novo transcriptome sequencing in a songbird, the dark-eyed junco (Junco hyemalis): genomic tools for an ecological model system

BMC Genomics ◽

10.1186/1471-2164-13-305 ◽

2012 ◽

Vol 13 (1) ◽

pp. 305 ◽

Cited By ~ 28

Author(s):

Mark P Peterson ◽

Danielle J Whittaker ◽

Shruthi Ambreth ◽

Suhas Sureshchandra ◽

Aaron Buechlein ◽

...

Keyword(s):

Transcriptome Sequencing ◽

Ecological Model ◽

De Novo ◽

Model System ◽

Junco Hyemalis ◽

De Novo Transcriptome ◽

Genomic Tools ◽

De Novo Transcriptome Sequencing ◽

Ecological Model System

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Gene discovery and annotation using LCM-454 transcriptome sequencing

Genome Research ◽

10.1101/gr.5145806 ◽

2006 ◽

Vol 17 (1) ◽

pp. 69-73 ◽

Cited By ~ 182

Author(s):

S. J. Emrich ◽

W. B. Barbazuk ◽

L. Li ◽

P. S. Schnable

Keyword(s):

Transcriptome Sequencing ◽

Gene Discovery ◽

454 Transcriptome Sequencing

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Functional genomics in the wild: a case study with paper wasps shows challenges and prospects for RNA interference in ecological systems

Genome ◽

10.1139/gen-2017-0066 ◽

2018 ◽

Vol 61 (4) ◽

pp. 266-272 ◽

Cited By ~ 2

Author(s):

S.A. Weiner ◽

A.G. Geffre ◽

A.L. Toth

Keyword(s):

Rna Interference ◽

Functional Genomics ◽

Gene Function ◽

Ecological Model ◽

Model Organisms ◽

Natural Environments ◽

Paper Wasps ◽

Fatty Acid Binding ◽

In The Wild

RNA interference (RNAi) is a useful tool to assess gene function by knocking down expression of a target gene and has been used successfully in domestic and laboratory organisms. However, the use of RNAi for functional genomics has not fully extended into ecological model organisms in natural environments. Assessment of gene function in the wild is important because gene function can be environmentally and context dependent. Here, we present a case study using RNAi to assess gene function in wild paper wasps Polistes metricus, to test roles for two candidate genes (NADH dehydrogenase (NADHdh) and retinoid and fatty acid binding protein (RfaBp)) in the development of reproductive castes. Previous studies have shown that these genes are upregulated in larvae that become queens compared to workers, but this pattern was reversed in the laboratory, making field-based studies necessary. We orally administered dsRNA to larvae in field colonies and found evidence of a short-term knockdown followed by a compensatory rebound in expression for RfaBp. We also observed the predicted worker-like decrease in lipid stores in NADHdh dsRNA treated wasps, suggesting a possible role for NADHdh in caste development. We discuss our results in the context of challenges for using RNAi for functional genomics in ecological model organisms in the field.

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Development of Molecular Resources for an Intertidal Clam, Sinonovacula constricta, Using 454 Transcriptome Sequencing

PLoS ONE ◽

10.1371/journal.pone.0067456 ◽

2013 ◽

Vol 8 (7) ◽

pp. e67456 ◽

Cited By ~ 31

Author(s):

Donghong Niu ◽

Lie Wang ◽

Fanyue Sun ◽

Zhanjiang Liu ◽

Jiale Li

Keyword(s):

Transcriptome Sequencing ◽

Sinonovacula Constricta ◽

454 Transcriptome Sequencing

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Peer Review #1 of "Brain transcriptome sequencing and assembly of three songbird model systems for the study of social behavior (v0.1)"

10.7287/peerj.396v0.1/reviews/1 ◽

2014 ◽

Keyword(s):

Social Behavior ◽

Peer Review ◽

Transcriptome Sequencing ◽

Model Systems ◽

Brain Transcriptome

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Environmentally-induced DNA methylation is inherited across generations in an aquatic keystone species (Daphnia magna)

10.1101/2021.12.05.471257 ◽

2021 ◽

Author(s):

Nathalie Feiner ◽

Reinder Radersma ◽

Louella Vasquez ◽

Markus Ringnér ◽

Björn Nystedt ◽

...

Keyword(s):

Dna Methylation ◽

Environmental Stress ◽

Daphnia Magna ◽

Evolutionary Dynamics ◽

Ecological Model ◽

Keystone Species ◽

Epigenetic Inheritance ◽

Model Systems ◽

Control Treatment ◽

Gene Frequencies

AbstractEnvironmental stress can result in epigenetic modifications that are passed down several generations. Such epigenetic inheritance can have significant impact on eco-evolutionary dynamics, but the phenomenon remains controversial in ecological model systems. Here, we used whole-genome bisulfite sequencing on individual water fleas (Daphnia magna) to assess whether environmentally-induced DNA methylation can persist for up to four generations. Genetically identical females were exposed to a control treatment, one of three natural stressors (high temperature, zinc, microcystin), or the methylation-inhibitor 5-azacytidine. After exposure, lines were propagated clonally for four generations under control conditions. We identified between 70 and 225 differentially methylated CpG positions (DMPs) between controls and F1 individuals whose mothers (and therefore they themselves as germ cells) were exposed to one of the three natural stressors. Between 46% and 58% of these environmentally-induced DMPs persisted until generation F4 without attenuation in their magnitude of differential methylation. DMPs were enriched in exons and largely stressor-specific, suggesting a possible role in environment-dependent gene regulation. In contrast, treatment with the compound 5-azacytidine demonstrated that pervasive hypo-methylation upon exposure is reset almost completely after a single generation. These results suggest that environmentally-induced DNA methylation is non-random and stably inherited across generations in Daphnia, making epigenetic inheritance a putative factor in the eco-evolutionary dynamics of fresh-water communities.Author summaryWater fleas are important keystone species mediating eco-evolutionary dynamics in lakes and ponds. It is currently an open question in how far epigenetic inheritance contributes to the ability of Daphnia populations to adapt to environmental stress. Using a range of naturally occurring stressors and a multi-generational design, we show that environmentally-induced DNA methylation variants are stably inherited for at least four generations in Daphnia magna. The induced variation in DNA methylation are stressor-specific and almost exclusively found in exons, bearing the signatures of functional adaptations. Our findings imply that ecological adaptations of Daphnia to seasonal fluctuations can be underpinned by epigenetic inheritance of DNA methylation without changes in gene frequencies.

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