Resources and Recommendations for Using Transcriptomics to Address Grand Challenges in Comparative Biology

Abstract

High-throughput RNA sequencing (RNA-seq) technology has become an important tool for studying physiological responses of organisms to changes in their environment. De novo assembly of RNA-seq data has allowed researchers to create a comprehensive catalog of genes expressed in a tissue and to quantify their expression without a complete genome sequence. The contributions from the “Tapping the Power of Crustacean Transcriptomics to Address Grand Challenges in Comparative Biology” symposium in this issue show the successes and limitations of using RNA-seq in the study of crustaceans. In conjunction with the symposium, the Animal Genome to Phenome Research Coordination Network collated comments from participants at the meeting regarding the challenges encountered when using transcriptomics in their research. Input came from novices and experts ranging from graduate students to principal investigators. Many were unaware of the bioinformatics analysis resources currently available on the CyVerse platform. Our analysis of community responses led to three recommendations for advancing the field: (1) integration of genomic and RNA-seq sequence assemblies for crustacean gene annotation and comparative expression; (2) development of methodologies for the functional analysis of genes; and (3) information and training exchange among laboratories for transmission of best practices. The field lacks the methods for manipulating tissue-specific gene expression. The decapod crustacean research community should consider the cherry shrimp, Neocaridina denticulata, as a decapod model for the application of transgenic tools for functional genomics. This would require a multi-investigator effort.

Signaling Pathways That Regulate the Crustacean Molting Gland

“…Transcriptomics and proteomics have revolutionized crustacean physiology ( 22 , 23 ). These approaches have shown that the YO undergoes molt stage-specific changes in phenotype that differ quantitatively and qualitatively in mRNA and protein levels ( 2 , 16 , 21 , 24 ).…”

Particle shape does not affect ingestion and egestion of microplastics by the freshwater shrimp Neocaridina palmata

“…The genus is native to Asia (Karge and Klotz 2013) and typically used there as a model organism in ecotoxicology (EPA/ ROC 2013) due to its wide distribution in lakes, streams and ponds (de Grave et al 2008;Karge and Klotz 2013;Kohal et al 2018), adaptation to diverse water parameters, relatively short reproduction period and sensitivity to endocrine disrupting chemicals (Huang et al 2006;Mykles et al 2016;Huang et al 2020). Besides, the freshwater organism is increasingly used to address questions relating to decapod physiology (Sonakowska et al 2015(Sonakowska et al , 2016Włodarczyk et al 2017) and genomics (Mykles and Hui 2015;Mykles et al 2016). Today, it has been found in European rivers (Klotz et al 2013;Jabłońska et al 2018), most likely as a result of global trade as an exotic species for hobby aquarists and the unintentional release into the aquatic environment (Schoolmann and Arndt 2018;Jaskuła et al 2019).…”

Bioinformatics Resources for Plant Abiotic Stress Responses: State of the Art and Opportunities in the Fast Evolving -Omics Era

“…Comparison of transcriptome data is highly exploited to understand gene functionality and expression mechanisms in different tissues in various conditions [136][137][138]. Due to the general importance of transcriptomic data to depict gene expression patterns and to infer on gene control and regulatory mechanisms of cell functionality, the processes involved in plant responses to abiotic stress are being largely investigated at the transcriptome level through microarray and RNA sequencing analyses, such as expressed sequence tags (ESTs) and RNA-seq [32,44,[139][140][141].…”