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

Locomotor behavior of Neocaridina palmata: a study with leachates from UV-weathered microplastics

Weathering of plastics leads to the formation of increasingly smaller particles with the release of chemical compounds. The latter occurs with currently unknown environmental impacts. Leachate-induced effects of weathered microplastics (MPs) are therefore of increasing concern. To investigate the toxicity of the chemical mixtures from such plastics, we exposed the freshwater shrimp Neocaridina palmata to enriched leachates from unweathered and artificially weathered (UV-A/B light) MPs (≤1 mm) from recycled low-density polyethylene (LDPE-R) pellets and from a biodegradable, not fully bio-based starch blend (SB) foil. We analyzed the individual locomotor activity (moved distance and frozen events) on day 1, 3, 7 and 14 of exposure to five leachate concentrations equivalent to 0.40–15.6 g MPs L⁻¹, representing the upper scale of MPs that have been found in the environment. The median moved distance did not change as a function of concentration, except for the unweathered SB treatment on day 14 that indicated hyperactivity with increasing concentrations. Significant impacts were solely detected for few concentrations and exposure days. Generally, no consistent trend was observed across the experiments. We further assessed the baseline toxicity of the samples in the Microtox assay and detected high bioluminescence inhibitions of the bacterium Aliivibrio fischeri. This study demonstrates that neither the recycled nor the biodegradable material are without impacts on test parameters and therefore cannot be seen as safe alternative for conventional plastics regarding the toxicity. However, the observed in vitro toxicity did not result in substantial effects on the behavior of shrimps. Overall, we assume that the two endpoints examined in the atyid shrimp N. palmata were not sensitive to chemicals leaching from plastics or that effects on the in vivo level affect other toxic endpoints which were not considered in this study.

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

The ingestion of microplastics (MPs) is well documented for various animals and spherical MPs (beads) in many studies. However, the retention time and egestion of MPs have been examined less, especially for irregular MPs (fragments) which are predominantly found in the environment. Furthermore, the accumulation of such particles in the gastrointestinal tract is likely to determine whether adverse effects are induced. To address this, we investigated if the ingestion and egestion of beads are different to those of fragments in the freshwater shrimp Neocaridina palmata. Therefore, organisms were exposed to 20-20,000 particles L-1 of either polyethylene (PE) beads (41 μm and 87 μm) or polyvinyl chloride (PVC) fragments (<63 μm). Moreover, shrimps were exposed to 20,000 particles L-1 of either 41 μm PE and 11 μm polystyrene (PS) beads or the PVC fragments for 24 h, followed by a post-exposure period of 4 h to analyze the excretion of particles. To simulate natural conditions, an additional fragment ingestion study was performed in the presence of food. After each treatment, the shrimps were analyzed for retained or excreted particles. Our results demonstrate that the ingestion of beads and fragments were concentration-dependent. Shrimps egested 59% of beads and 18% of fragments within 4 h. Particle shape did not significantly affect MP ingestion or egestion, but size was a relevant factor. Medium- and small-sized beads were frequently ingested. Furthermore, fragment uptake decreased slightly when co-exposed to food, but was not significantly different to the treatments without food. Finally, the investigations highlight that the assessment of ingestion and egestion rates can help to clarify whether MPs remain in specific organisms and, thereby, become a potential health threat.

Signaling Pathways That Regulate the Crustacean Molting Gland

A pair of Y-organs (YOs) are the molting glands of decapod crustaceans. They synthesize and secrete steroid molting hormones (ecdysteroids) and their activity is controlled by external and internal signals. The YO transitions through four physiological states over the molt cycle, which are mediated by molt-inhibiting hormone (MIH; basal state), mechanistic Target of Rapamycin Complex 1 (mTORC1; activated state), Transforming Growth Factor-β (TGFβ)/Activin (committed state), and ecdysteroid (repressed state) signaling pathways. MIH, produced in the eyestalk X-organ/sinus gland complex, inhibits the synthesis of ecdysteroids. A model for MIH signaling is organized into a cAMP/Ca2+-dependent triggering phase and a nitric oxide/cGMP-dependent summation phase, which maintains the YO in the basal state during intermolt. A reduction in MIH release triggers YO activation, which requires mTORC1-dependent protein synthesis, followed by mTORC1-dependent gene expression. TGFβ/Activin signaling is required for YO commitment in mid-premolt. The YO transcriptome has 878 unique contigs assigned to 23 KEGG signaling pathways, 478 of which are differentially expressed over the molt cycle. Ninety-nine contigs encode G protein-coupled receptors (GPCRs), 65 of which bind a variety of neuropeptides and biogenic amines. Among these are putative receptors for MIH/crustacean hyperglycemic hormone neuropeptides, corazonin, relaxin, serotonin, octopamine, dopamine, allatostatins, Bursicon, ecdysis-triggering hormone (ETH), CCHamide, FMRFamide, and proctolin. Contigs encoding receptor tyrosine kinase insulin-like receptor, epidermal growth factor (EGF) receptor, and fibroblast growth factor (FGF) receptor and ligands EGF and FGF suggest that the YO is positively regulated by insulin-like peptides and growth factors. Future research should focus on the interactions of signaling pathways that integrate physiological status with environmental cues for molt control.

Recommendations for Advancing Genome to Phenome Research in Non-Model Organisms

The 2020 SICB Society-wide Symposium "Building Bridges from Genome to Phenome: Molecules, Methods and Models" brought together a diverse group of scientists to discuss recent progress in linking phenotype plasticity to changes at the level of the genome, epigenome, and proteome, while exploring the boundaries between variation and speciation. In a follow-up workshop, participants were asked to assess strengths and weaknesses of current approaches, to identify common barriers inhibiting their progress, and to outline the resources needed to overcome those barriers. Discussion groups generally recognized the absence of any overarching theoretical framework underlying current genome to phenome research and, therefore, called for a new emphasis on the development of conceptual models as well as the interdisciplinary collaborations needed to create and test those models. Participants also recognized a critical need for new and improved molecular and bioinformatic approaches to assist in describing function/phenotypes across phylogeny. Additionally, like all scientific endeavors, progress in genome to phenome research will be enhanced by improvements in science education and communication both within and among working groups.

Effects of dietary icariin supplementation on the ovary development-related transcriptome of Chinese mitten crab (Eriocheir sinensis)

The Chinese mitten crab (Eriocheir sinensis) is an economically important aquaculture species in China, with distinct differences in ovarian maturation status between crabs fed with natural diets and artificial diets during the listing period, thus, leading to selling price differentiation. Our previous study showed that dietary supplementation with 100 mg/kg icariin can effectively promote ovarian development of E. sinensis. However, the internal molecular mechanism has not yet been elucidated because of a lack of comprehensive genome sequence information. We compared the ovary transcriptomes of E. sinensis fed with two diets containing 0 and 100 mg/kg ICA using the BGISEQ-500 platform. This yielded 12.54 Gb clean bases and 54,794 unigenes, 13,832 of which were found to be differentially expressed after icariin exposure. Twenty pathways closely related to gonadal development were selected through KEGG analysis. Seven differentially expressed genes relevant to vitellogenesis and oocyte maturation (serine/threonine-protein kinase mos-like, Eg2, cytoplasmic polyadenylation element-binding protein, cyclin B, vitellogenin 1, cathepsin D, and juvenile hormone esterase-like carboxylesterase 1) were validated by qRT-PCR, and four proteins (MEK1/2, ERK1/2, Cyclin B and Cdc2) associated with the progesterone mediated oocyte maturation pathway (i.e., MAPK/MPF pathway) were analyzed by western-blot. The results showed that icariin could promote the synthesis, processing and deposition of vitellogenin in oocytes, and that it also has the potential to promote oocyte maturation (resumption of Meiosis I) by altering the expression of the relevant genes and proteins.

Hormonal control of the crustacean molting gland: Insights from transcriptomics and proteomics

Endocrine control of molting in decapod crustaceans involves the eyestalk neurosecretory center (X-organ/sinus gland complex), regenerating limbs, and a pair of Y-organs (YOs), as molting is induced by eyestalk ablation or multiple leg autotomy and suspended in early premolt by limb bud autotomy. Molt-inhibiting hormone (MIH) and crustacean hyperglycemic hormone (CHH), produced in the X-organ/sinus gland complex, inhibit the YO. The YO transitions through four physiological states over the molt cycle: basal in intermolt; activated in early premolt; committed in mid- and late premolt; and repressed in postmolt. We assembled the first comprehensive YO transcriptome over the molt cycle in the land crab, Gecarcinus lateralis, showing that as many as 23 signaling pathways may interact in controlling ecdysteroidogenesis. A proposed model of the MIH/cyclic nucleotide pathway, which maintains the basal YO, consists of cAMP/Ca²⁺ triggering and nitric oxide (NO)/cGMP summation phases. Mechanistic target of rapamycin (mTOR) signaling is required for YO activation in early premolt and affects the mRNA levels of thousands of genes. Transforming Growth Factor-β (TGFβ)/Activin signaling is required for YO commitment in mid-premolt and high ecdysteroid titers at the end of premolt may trigger YO repression. The G. lateralis YO expresses 99 G protein-coupled receptors, three of which are putative receptors for MIH/CHH. Proteomic analysis shows the importance of radical oxygen species scavenging, cytoskeleton, vesicular secretion, immune response, and protein homeostasis and turnover proteins associated with YO function over the molt cycle. In addition to eyestalk ganglia, MIH mRNA and protein are present in brain, optic nerve, ventral nerve cord, and thoracic ganglion, suggesting that they are secondary sources of MIH. Down-regulation of mTOR signaling genes, in particular Ras homolog enriched in brain or Rheb, compensates for the effects of elevated temperature in the YO, heart, and eyestalk ganglia in juvenile Metacarcinus magister. Rheb expression increases in the activated and committed YO. These data suggest that mTOR plays a central role in mediating molt regulation by physiological and environmental factors.

Building Bridges from Genome to Phenome: Molecules, Methods and Models—An Introduction to the Symposium

How stable genotypes interact with their environment to generate phenotypic variation that can be acted upon by evolutionary and ecological forces is a central focus of research across many scientific disciplines represented within SICB. The Building Bridges Symposium brought together scientists using a variety of organisms, methods, and levels of biological organization to study the emergent properties of genomes. Workshops associated with the Symposium aimed to identify the leading edges and major barriers to research in this field, and to recommend future directions that might accelerate the pace of progress. The papers included in this Symposium volume draw attention to the strength of using comparative approaches in non-model organisms to study the many aspects of genotype–environment interaction that drive phenotype variation. These contributions and the concluding white paper also illustrate the need for novel conceptual frameworks that can bridge and accommodate data and conclusions from the broad range of study systems employed by comparative and integrative biologists to address genome-to-phenome questions.

Trade-offs, Pleiotropy, and Shared Molecular Pathways: A Unified View of Constraints on Adaptation

The concept of trade-offs permeates our thinking about adaptive evolution because they are exhibited at every level of biological organization, from molecular and cellular processes to organismal and ecological functions. Trade-offs inevitably arise because different traits do not occur in isolation, but instead are imbedded within complex, integrated systems that make up whole organisms. The genetic and mechanistic underpinning of trade-offs can be found in the pleiotropic nodes that occur in the biological pathways shared between traits. Yet, often trade-offs are only understood as statistical correlations, limiting the ability to evaluate the interplay between how selection and constraint interact during adaptive evolution. Here, we first review the classic paradigms in which physiologists and evolutionary biologists have studied trade-offs and highlight the ways in which network and molecular pathway approaches unify these paradigms. We discuss how these approaches allow researchers to evaluate why trade-offs arise and how selection can act to overcome trait correlations and evolutionary constraints. We argue that understanding how the conserved molecular pathways are shared between different traits and functions provides a conceptual framework for evolutionary biologists, physiologists, and molecular biologists to meaningfully work together toward the goal of understanding why correlations and trade-offs occur between traits. We briefly highlight the melanocortin system and the hormonal control of osmoregulation as two case studies where an understanding of shared molecular pathways reveals why trade-offs occur between seemingly unrelated traits. While we recognize that applying such approaches poses challenges and limitations particularly in the context of natural populations, we advocate for the view that focusing on the biological pathways responsible for trade-offs provides a unified conceptual context accessible to a broad range of integrative biologists.

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

Abiotic stresses are among the principal limiting factors for productivity in agriculture. In the current era of continuous climate changes, the understanding of the molecular aspects involved in abiotic stress response in plants is a priority. The rise of -omics approaches provides key strategies to promote effective research in the field, facilitating the investigations from reference models to an increasing number of species, tolerant and sensitive genotypes. Integrated multilevel approaches, based on molecular investigations at genomics, transcriptomics, proteomics and metabolomics levels, are now feasible, expanding the opportunities to clarify key molecular aspects involved in responses to abiotic stresses. To this aim, bioinformatics has become fundamental for data production, mining and integration, and necessary for extracting valuable information and for comparative efforts, paving the way to the modeling of the involved processes. We provide here an overview of bioinformatics resources for research on plant abiotic stresses, describing collections from -omics efforts in the field, ranging from raw data to complete databases or platforms, highlighting opportunities and still open challenges in abiotic stress research based on -omics technologies.

Analysis of Annotation and Differential Expression Methods used in RNA-seq Studies in Crustacean Systems

In the field of crustacean biology, usage of RNA-seq to study gene expression is rapidly growing. Major advances in sequencing technology have contributed to the ability to examine complex patterns of genome activity in a wide range of organisms that are extensively used for comparative physiology, ecology and evolution, environmental monitoring, and commercial aquaculture. Relative to insect and vertebrate model organisms, however, information on the organization of crustacean genomes is virtually nonexistent, making de novo transcriptome assembly, annotation and quantification problematic and challenging. We present here a summary of the methodologies and software analyses employed in 23 recent publications, which describe de novo transcriptome assembly, annotation, and differential gene expression in a variety of crustacean experimental systems. We focus on establishing a series of best practices that will allow for investigators to produce datasets that are understandable, reproducible, and of general utility for related analyses and cross-study comparisons.

The utility of transcriptomics in fish conservation

There is growing recognition of the need to understand the mechanisms underlying organismal resilience (i.e. tolerance, acclimatization) to environmental change to support the conservation management of sensitive and economically important species. Here, we discuss how functional genomics can be used in conservation biology to provide a cellular-level understanding of organismal responses to environmental conditions. In particular, the integration of transcriptomics with physiological and ecological research is increasingly playing an important role in identifying functional physiological thresholds predictive of compensatory responses and detrimental outcomes, transforming the way we can study issues in conservation biology. Notably, with technological advances in RNA sequencing, transcriptome-wide approaches can now be applied to species where no prior genomic sequence information is available to develop species-specific tools and investigate sublethal impacts that can contribute to population declines over generations and undermine prospects for long-term conservation success. Here, we examine the use of transcriptomics as a means of determining organismal responses to environmental stressors and use key study examples of conservation concern in fishes to highlight the added value of transcriptome-wide data to the identification of functional response pathways. Finally, we discuss the gaps between the core science and policy frameworks and how thresholds identified through transcriptomic evaluations provide evidence that can be more readily used by resource managers.

Tapping the Power of Crustacean Transcriptomics to Address Grand Challenges in Comparative Biology: An Introduction to the Symposium

Crustaceans, and decapods in particular (i.e., crabs, shrimp, and lobsters), are a diverse and ecologically and commercially important group of organisms. Understanding responses to abiotic and biotic factors is critical for developing best practices in aquaculture and assessing the effects of changing environments on the biology of these important animals. A relatively small number of decapod crustacean species have been intensively studied at the molecular level; the availability, experimental tractability, and economic relevance factor into the selection of a particular species as a model. Transcriptomics, using high-throughput next generation sequencing (NGS, coupled with RNA sequencing or RNA-seq) is revolutionizing crustacean biology. The 11 symposium papers in this volume illustrate how RNA-seq is being used to study stress response, molting and limb regeneration, immunity and disease, reproduction and development, neurobiology, and ecology and evolution. This symposium occurred on the 10th anniversary of the symposium, "Genomic and Proteomic Approaches to Crustacean Biology", held at the Society for Integrative and Comparative Biology 2006 meeting. Two participants in the 2006 symposium, the late Paul Gross and David Towle, were recognized as leaders who pioneered the use of molecular techniques that would ultimately foster the transcriptomics research reviewed in this volume. RNA-seq is a powerful tool for hypothesis-driven research, as well as an engine for discovery. It has eclipsed the technologies available in 2006, such as microarrays, expressed sequence tags, and subtractive hybridization screening, as the millions of "reads" from NGS enable researchers to de novo assemble a comprehensive transcriptome without a complete genome sequence. The symposium series concludes with a policy paper that gives an overview of the resources available and makes recommendations for developing better tools for functional annotation and pathway and network analysis in organisms in which the genome is not available or is incomplete.