Micro-Variations from RNA-seq Experiments for Non-model Organisms

Whole genome sequencing (WGS) is a very valuable resource to understand the evolutionary history of poorly known species. However, in organisms with large genomes, as most amphibians, WGS is still excessively challenging and transcriptome sequencing (RNA-seq) represents a cost-effective tool to explore genome-wide variability. Non-model organisms do not usually have a reference genome and the transcriptome must be assembledde-novo. We used RNA-seq to obtain the transcriptomic profile forOreobates cruralis, a poorly known South American direct-developing frog. In total, 550,871 transcripts were assembled, corresponding to 422,999 putative genes. Of those, we identified 23,500, 37,349, 38,120 and 45,885 genes present in the Pfam, EggNOG, KEGG and GO databases, respectively. Interestingly, our results suggested that genes related to immune system and defense mechanisms are abundant in the transcriptome ofO. cruralis. We also present a pipeline to assist with pre-processing, assembling, evaluating and functionally annotating ade-novotranscriptome from RNA-seq data of non-model organisms. Our pipeline guides the inexperienced user in an intuitive way through all the necessary steps to buildde-novotranscriptome assemblies using readily available software and is freely available at:https://github.com/biomendi/TRANSCRIPTOME-ASSEMBLY-PIPELINE/wiki.

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Transcriptomic responses to environmental change in fishes: Insights from RNA sequencing

FACETS ◽

10.1139/facets-2017-0015 ◽

2017 ◽

Vol 2 (2) ◽

pp. 610-641 ◽

Cited By ~ 23

Author(s):

Rebekah A. Oomen ◽

Jeffrey A. Hutchings

Keyword(s):

Climate Change ◽

Rna Sequencing ◽

Molecular Mechanisms ◽

Environmental Variability ◽

Global Climate ◽

Genetic Research ◽

Model Organisms ◽

Rna Seq ◽

Transcriptomic Responses ◽

Ecological Importance

The need to better understand how plasticity and evolution affect organismal responses to environmental variability is paramount in the face of global climate change. The potential for using RNA sequencing (RNA-seq) to study complex responses by non-model organisms to the environment is evident in a rapidly growing body of literature. This is particularly true of fishes for which research has been motivated by their ecological importance, socioeconomic value, and increased use as model species for medical and genetic research. Here, we review studies that have used RNA-seq to study transcriptomic responses to continuous abiotic variables to which fishes have likely evolved a response and that are predicted to be affected by climate change (e.g., salinity, temperature, dissolved oxygen concentration, and pH). Field and laboratory experiments demonstrate the potential for individuals to respond plastically to short- and long-term environmental stress and reveal molecular mechanisms underlying developmental and transgenerational plasticity, as well as adaptation to different environmental regimes. We discuss experimental, analytical, and conceptual issues that have arisen from this work and suggest avenues for future study.

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Quantitative trait locus mapping identifies Col4a6 as a novel regulator of striatal dopamine level and axonal branching in mice

10.1101/2020.06.28.176206 ◽

2020 ◽

Author(s):

Mélanie H. Thomas ◽

Yujuan Gui ◽

Pierre Garcia ◽

Mona Karout ◽

Christian Jaeger ◽

...

Keyword(s):

Neural Development ◽

Quantitative Trait ◽

Radial Glia ◽

Dorsal Striatum ◽

Striatal Dopamine ◽

Model Organisms ◽

Mouse Strains ◽

Dopamine Level ◽

Rna Seq ◽

Axonal Branching

AbstractThe features of dopaminergic neurons (DAns) of nigrostriatal circuitry are orchestrated by a multitude of yet unknown factors, many of them genetic. Genetic variation between individuals at baseline can lead to differential susceptibility to and severity of diseases. As decline of DAns, a characteristic of Parkinson’s disease, heralds a significant decrease in dopamine level, measuring dopamine can reflect the integrity of DAns. To identify novel genetic regulators of the integrity of DAns, we used the Collaborative Cross (CC) mouse strains as model system to search for quantitative trait loci (QTLs) related to dopamine levels in the dorsal striatum. The dopamine levels in dorsal striatum varied greatly in the eight CC founder strains, and the differences were inheritable in 32 derived CC strains. QTL mapping in these CC strains identified a QTL associated with dopamine level on chromosome X containing 393 genes. RNA-seq analysis of the ventral midbrain of two of the founder strains with large striatal dopamine difference (C57BL/6J and A/J) revealed 24 differentially expressed genes within the QTL. The protein-coding gene with the highest expression difference was Col4a6, which exhibited a 9-fold reduction in A/J compared to C57BL/6J, consistent with decreased dopamine levels in A/J. Publicly available single cell RNA-seq data from developing human midbrain suggests that Col4a6 is highly expressed in radial glia-like cells and neuronal progenitors, indicating possible involvement in neurogenesis. Interestingly, the lowered dopamine levels were accompanied by reduced striatal axonal branching of striatal DAns in A/J compared to C57BL/6J. Because Col4a6 is known to control axogenesis in non-mammal model organisms, we hypothesize that different dopamine levels in mouse dorsal striatum are due to differences in axogenesis induced by varying COL4A6 levels during neural development.

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De novo transcriptomes of 14 gammarid individuals for proteogenomic analysis of seven taxonomic groups

Scientific Data ◽

10.1038/s41597-019-0192-5 ◽

2019 ◽

Vol 6 (1) ◽

Cited By ~ 5

Author(s):

Yannick Cogne ◽

Davide Degli-Esposti ◽

Olivier Pible ◽

Duarte Gouveia ◽

Adeline François ◽

...

Keyword(s):

Aquatic Ecosystems ◽

Molecular Diversity ◽

De Novo ◽

Model Organisms ◽

Rna Seq ◽

Specific Expression ◽

Gammarus Fossarum ◽

Male Individual ◽

Taxonomic Groups ◽

Whole Transcriptome

Abstract Gammarids are amphipods found worldwide distributed in fresh and marine waters. They play an important role in aquatic ecosystems and are well established sentinel species in ecotoxicology. In this study, we sequenced the transcriptomes of a male individual and a female individual for seven different taxonomic groups belonging to the two genera Gammarus and Echinogammarus: Gammarus fossarum A, G. fossarum B, G. fossarum C, Gammarus wautieri, Gammarus pulex, Echinogammarus berilloni, and Echinogammarus marinus. These taxa were chosen to explore the molecular diversity of transcribed genes of genotyped individuals from these groups. Transcriptomes were de novo assembled and annotated. High-quality assembly was confirmed by BUSCO comparison against the Arthropod dataset. The 14 RNA-Seq-derived protein sequence databases proposed here will be a significant resource for proteogenomics studies of these ecotoxicologically relevant non-model organisms. These transcriptomes represent reliable reference sequences for whole-transcriptome and proteome studies on other gammarids, for primer design to clone specific genes or monitor their specific expression, and for analyses of molecular differences between gammarid species.

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Mapping and differential expression analysis from short-read RNA-Seq data in model organisms

Quantitative Biology ◽

10.1007/s40484-016-0060-7 ◽

2016 ◽

Vol 4 (1) ◽

pp. 22-35 ◽

Cited By ~ 2

Author(s):

Qiong-Yi Zhao ◽

Jacob Gratten ◽

Restuadi Restuadi ◽

Xuan Li

Keyword(s):

Differential Expression ◽

Expression Analysis ◽

Differential Expression Analysis ◽

Model Organisms ◽

Rna Seq ◽

Short Read

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Inferring bona fide transfrags in RNA-Seq derived-transcriptome assemblies of non-model organisms

BMC Bioinformatics ◽

10.1186/s12859-015-0492-5 ◽

2015 ◽

Vol 16 (1) ◽

Cited By ~ 7

Author(s):

Stanley Kimbung Mbandi ◽

Uljana Hesse ◽

Peter van Heusden ◽

Alan Christoffels

Keyword(s):

Model Organisms ◽

Rna Seq ◽

Bona Fide

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Transcriptome Analysis in Domesticated Species: Challenges and Strategies

Bioinformatics and Biology Insights ◽

10.4137/bbi.s29334 ◽

2015 ◽

Vol 9S4 ◽

pp. BBI.S29334 ◽

Cited By ~ 4

Author(s):

Jessica P. Hekman ◽

Jennifer L Johnson ◽

Anna V. Kukekova

Keyword(s):

Complex Traits ◽

Gene Networks ◽

Association Studies ◽

Cultural Value ◽

Genomic Research ◽

Model Organisms ◽

Genome Wide Association Studies ◽

Rna Seq ◽

Genome Wide ◽

Genome Assemblies

Domesticated species occupy a special place in the human world due to their economic and cultural value. In the era of genomic research, domesticated species provide unique advantages for investigation of diseases and complex phenotypes. RNA sequencing, or RNA-seq, has recently emerged as a new approach for studying transcriptional activity of the whole genome, changing the focus from individual genes to gene networks. RNA-seq analysis in domesticated species may complement genome-wide association studies of complex traits with economic importance or direct relevance to biomedical research. However, RNA-seq studies are more challenging in domesticated species than in model organisms. These challenges are at least in part associated with the lack of quality genome assemblies for some domesticated species and the absence of genome assemblies for others. In this review, we discuss strategies for analyzing RNA-seq data, focusing particularly on questions and examples relevant to domesticated species.

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RASflow: An RNA-Seq Analysis Workflow with Snakemake

10.1101/839191 ◽

2019 ◽

Author(s):

Xiaokang Zhang ◽

Inge Jonassen

Keyword(s):

Gene Expression ◽

Management System ◽

Workflow Management ◽

Model Organisms ◽

Gene Transcript ◽

Rna Seq ◽

Public Data ◽

Wide Range ◽

Analysis Workflow ◽

Programming Skills

AbstractBackgroundWith the cost of DNA sequencing decreasing, increasing amounts of RNA-Seq data are being generated giving novel insight into gene expression and regulation. Prior to analysis of gene expression, the RNA-Seq data has to be processed through a number of steps resulting in a quantification of expression of each gene / transcript in each of the analyzed samples. A number of workflows are available to help researchers perform these steps on their own data, or on public data to take advantage of novel software or reference data in data re-analysis. However, many of the existing workflows are limited to specific types of studies. We therefore aimed to develop a maximally general workflow, applicable to a wide range of data and analysis approaches and at the same time support research on both model and non-model organisms. Furthermore, we aimed to make the workflow usable also for users with limited programming skills.ResultsUtilizing the workflow management system Snakemake and the package management system Conda, we have developed a modular, flexible and user-friendly RNA-Seq analysis pipeline: RNA-Seq Analysis Snakemake Workflow (RASflow). Utilizing Snakemake and Conda alleviates challenges with library dependencies and version conflicts and also supports reproducibility. To be applicable for a wide variety of applications, RASflow supports mapping of reads to both genomic and transcriptomic assemblies. RASflow has a broad range of potential users: it can be applied by researchers interested in any organism and since it requires no programming skills, it can be used by researchers with different backgrounds. RASflow is an open source tool and source code as well as documentation, tutorials and example data sets can be found on GitHub: https://github.com/zhxiaokang/RASflowConclusionsRASflow is a simple and reliable RNA-Seq analysis workflow which is a full pack of RNA-Seq analysis.

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rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data

10.1101/420208 ◽

2018 ◽

Cited By ~ 13

Author(s):

Elena Bushmanova ◽

Dmitry Antipov ◽

Alla Lapidus ◽

Andrey D. Prjibelski

Keyword(s):

De Novo ◽

Transcriptome Assembly ◽

Model Organisms ◽

Challenging Problem ◽

Rna Seq ◽

De Novo Transcriptome ◽

Weak Points ◽

Transcriptome Reconstruction ◽

Evaluation Approaches ◽

Genome Assembler

AbstractSummaryPossibility to generate large RNA-seq datasets has led to development of various reference-based and de novo transcriptome assemblers with their own strengths and limitations. While reference-based tools are widely used in various transcriptomic studies, their application is limited to the model organisms with finished and annotated genomes. De novo transcriptome reconstruction from short reads remains an open challenging problem, which is complicated by the varying expression levels across different genes, alternative splicing and paralogous genes. In this paper we describe a novel transcriptome assembler called rnaSPAdes, which is developed on top of SPAdes genome assembler and explores surprising computational parallels between assembly of transcriptomes and single-cell genomes. We also present quality assessment reports for rnaSPAdes assemblies, compare it with modern transcriptome assembly tools using several evaluation approaches on various RNA-Seq datasets, and briefly highlight strong and weak points of different assemblers.Availability and implementationrnaSPAdes is implemented in C++ and Python and is freely available at cab.spbu.ru/software/rnaspades/.

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Deep sequencing analysis of the circadian transcriptome of the jewel wasp Nasonia vitripennis

10.1101/048736 ◽

2016 ◽

Cited By ~ 3

Author(s):

Nathaniel J. Davies ◽

Eran Tauber

Keyword(s):

Circadian Clock ◽

Deep Sequencing ◽

Clock Genes ◽

Model System ◽

Model Organisms ◽

Constant Darkness ◽

Sequencing Analysis ◽

Rna Seq ◽

Nasonia Vitripennis ◽

Deep Sequencing Analysis

AbstractThe study of the circadian clock has benefited greatly from using Drosophila as a model system. Yet, accumulating evidence suggests that the fly might not be the canonical insect model. Here, we have analysed the circadian transcriptome of the Jewl wasp Nasonia vitripennis by using RNA-seq in both constant darkness (DD) and constant light (LL, the wasps are rhythmic in LL with period shortening). At a relatively stringent FDR (q < 0.1), we identified 1,057 cycling transcripts in DD and 929 in LL (fraction of 6.7% and 5.9% of all transcripts analysed in DD and LL respectively). Although there was little similarity between cycling genes in Drosophila and Nasonia, the functions fulfilled by cycling transcripts were similar in both species. Of the known Drosophila core clock genes, only pdp1e, shaggy and Clok showed a significant cycling in Nasonia, underscoring the importance of studying the clock in non-model organisms.

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