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Angst P, Dexter E, Stillman JH. Genome assemblies of two species of porcelain crab, Petrolisthes cinctipes and Petrolisthes manimaculis (Anomura: Porcellanidae). G3 (BETHESDA, MD.) 2024; 14:jkad281. [PMID: 38079165 PMCID: PMC10849366 DOI: 10.1093/g3journal/jkad281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 11/09/2023] [Indexed: 02/09/2024]
Abstract
Crabs are a large subtaxon of the Arthropoda, the most diverse and species-rich metazoan group. Several outstanding questions remain regarding crab diversification, including about the genomic capacitors of physiological and morphological adaptation, that cannot be answered with available genomic resources. Physiologically and ecologically diverse Anomuran porcelain crabs offer a valuable model for investigating these questions and hence genomic resources of these crabs would be particularly useful. Here, we present the first two genome assemblies of congeneric and sympatric Anomuran porcelain crabs, Petrolisthes cinctipes and Petrolisthes manimaculis from different microhabitats. Pacific Biosciences high-fidelity sequencing led to genome assemblies of 1.5 and 0.9 Gb, with N50s of 706.7 and 218.9 Kb, respectively. Their assembly length difference can largely be attributed to the different levels of interspersed repeats in their assemblies: The larger genome of P. cinctipes has more repeats (1.12 Gb) than the smaller genome of P. manimaculis (0.54 Gb). For obtaining high-quality annotations of 44,543 and 40,315 protein-coding genes in P. cinctipes and P. manimaculis, respectively, we used RNA-seq as part of a larger annotation pipeline. Contrarily to the large-scale differences in repeat content, divergence levels between the two species as estimated from orthologous protein-coding genes are moderate. These two high-quality genome assemblies allow future studies to examine the role of environmental regulation of gene expression in the two focal species to better understand physiological response to climate change, and provide the foundation for studies in fine-scale genome evolution and diversification of crabs.
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Affiliation(s)
- Pascal Angst
- Department of Environmental Sciences, Zoology, University of Basel, 4051 Basel, Switzerland
| | - Eric Dexter
- Department of Environmental Sciences, Zoology, University of Basel, 4051 Basel, Switzerland
| | - Jonathon H Stillman
- Department of Environmental Sciences, Zoology, University of Basel, 4051 Basel, Switzerland
- Department of Biology, San Francisco State University, San Francisco, CA 94132, USA
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
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Lam EK, Abegaz M, Gunderson AR, Tsukimura B, Stillman JH. Interactions Between Temperature Variability and Reproductive Physiology Across Traits in an Intertidal Crab. Front Physiol 2022; 13:796125. [PMID: 35350692 PMCID: PMC8957995 DOI: 10.3389/fphys.2022.796125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 02/07/2022] [Indexed: 11/13/2022] Open
Abstract
Thermal extremes alter population processes, which can result in part from temperature-induced movement at different spatial and temporal scales. Thermal thresholds for animal movement likely change based on underlying thermal physiology and life-history stage, a topic that requires greater study. The intertidal porcelain crab Petrolisthes cinctipes currently experiences temperatures that can reach near-lethal levels in the high-intertidal zone at low tide. However, the thermal thresholds that trigger migration to cooler microhabitats, and the extent to which crabs move in response to temperature, remain unknown. Moreover, the influence of reproductive status on these thresholds is rarely investigated. We integrated demographic, molecular, behavioral, and physiological measurements to determine if behavioral thermal limits varied due to reproductive state. Demographic data showed a trend for gravid, egg bearing, crabs to appear more often under rocks in the cooler intertidal zone where crab density is highest. In situ expression of 31 genes related to stress, metabolism, and growth in the field differed significantly based on intertidal elevation, with mid-intertidal crabs expressing the gene for the reproductive yolk protein vitellogenin (vg) earlier in the season. Furthermore, VG protein levels were shown to increase with density for female hemolymph. Testing for temperatures that elicit movement revealed that gravid females engage in heat avoidance behavior at lower temperatures (i.e., have a lower voluntary thermal maximum, VTmax) than non-gravid females. VTmax was positively correlated with the temperature of peak firing rate for distal afferent nerve fibers in the walking leg, a physiological relationship that could correspond to the mechanistic underpinning for temperature dependent movement. The vulnerability of marine organisms to global change is predicated by their ability to utilize and integrate physiological and behavioral strategies in response to temperature to maximize survival and reproduction. Interactions between fine-scale temperature variation and reproductive biology can have important consequences for the ecology of species, and is likely to influence how populations respond to ongoing climate change.
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Affiliation(s)
- Emily K. Lam
- Estuary and Ocean Science Center, San Francisco State University, Tiburon, CA, United States
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, United States
- Department of Biology, San Francisco State University, San Francisco, CA, United States
- *Correspondence: Emily K. Lam,
| | - Metadel Abegaz
- Estuary and Ocean Science Center, San Francisco State University, Tiburon, CA, United States
- Department of Biology, San Francisco State University, San Francisco, CA, United States
| | - Alex R. Gunderson
- Estuary and Ocean Science Center, San Francisco State University, Tiburon, CA, United States
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, United States
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, United States
| | - Brian Tsukimura
- Department of Biology, California State University, Fresno, CA, United States
| | - Jonathon H. Stillman
- Estuary and Ocean Science Center, San Francisco State University, Tiburon, CA, United States
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, United States
- Department of Biology, San Francisco State University, San Francisco, CA, United States
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Shyamal S, Das S, Guruacharya A, Mykles DL, Durica DS. Transcriptomic analysis of crustacean molting gland (Y-organ) regulation via the mTOR signaling pathway. Sci Rep 2018; 8:7307. [PMID: 29743490 PMCID: PMC5943448 DOI: 10.1038/s41598-018-25368-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 04/20/2018] [Indexed: 12/24/2022] Open
Abstract
The intermolt crustacean Y-organ (YO) maintains a basal state mediated by pulsatile release of molt inhibiting hormone (MIH), a neuropeptide produced in the eyestalk ganglia, inhibiting YO ecdysteroidogenesis. Reduction of MIH results in YO activation and the animal enters premolt. In the crab, Gecarcinus lateralis, molting was induced by eyestalk ablation (ESA). ESA animals were injected with either rapamycin, an mTOR inhibitor, or DMSO vehicle at Day 0. YOs were harvested at 1, 3, and 7 days post-ESA and processed for high throughput RNA sequencing. ESA-induced increases in mRNA levels of mTOR signaling genes (e.g., mTOR, Rheb, TSC1/2, Raptor, Akt, and S6 kinase) declined following rapamycin treatment. In concert with mTOR inhibition, mRNA levels of ecdysteroid biosynthesis genes (e.g., Nvd, Spo, Sad, Dib, and Phm) were decreased and accompanied by a decrease in hemolymph ecdysteroid titer. By contrast, rapamycin increased the mRNA level of FKBP12, the rapamycin-binding protein, as well as the mRNA levels of genes associated with Wnt and insulin-like growth factor signaling pathways. Many MIH and transforming growth factor-β signaling genes were down regulated in ESA animals. These results indicate that mTOR activity either directly or indirectly controls transcription of genes that drive activation of the YO.
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Affiliation(s)
- S Shyamal
- Department of Biology, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - S Das
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - A Guruacharya
- Department of Biology, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - D L Mykles
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - D S Durica
- Department of Biology, University of Oklahoma, Norman, Oklahoma, 73019, USA.
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Gunderson AR, King EE, Boyer K, Tsukimura B, Stillman JH. Species as Stressors: Heterospecific Interactions and the Cellular Stress Response under Global Change. Integr Comp Biol 2017; 57:90-102. [DOI: 10.1093/icb/icx019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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Mykles DL, Burnett KG, Durica DS, Joyce BL, McCarthy FM, Schmidt CJ, Stillman JH. Resources and Recommendations for Using Transcriptomics to Address Grand Challenges in Comparative Biology. Integr Comp Biol 2016; 56:1183-1191. [PMID: 27639274 PMCID: PMC5146710 DOI: 10.1093/icb/icw083] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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.
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Affiliation(s)
- Donald L Mykles
- *Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Karen G Burnett
- Grice Marine Laboratory, College of Charleston, Charleston, SC 29412, USA
- Hollings Marine Laboratory, Charleston, SC 29412, USA
| | - David S Durica
- Department of Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Blake L Joyce
- BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Fiona M McCarthy
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Carl J Schmidt
- Department of Animal and Food Sciences, University of Delaware, Newark, DE 19716
| | - Jonathon H Stillman
- Romberg Tiburon Center for Environmental Studies and Department of Biology, San Francisco State University, Tiburon, CA 94920, USA
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
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Mykles DL, Burnett KG, Durica DS, Stillman JH. Tapping the Power of Crustacean Transcriptomics to Address Grand Challenges in Comparative Biology: An Introduction to the Symposium. Integr Comp Biol 2016; 56:1047-1054. [PMID: 27591249 DOI: 10.1093/icb/icw116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
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.
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Affiliation(s)
- Donald L Mykles
- *Department of Biology, Colorado State University, 1878 Campus, Fort Collins, CO 80523, USA
| | - Karen G Burnett
- Grice Marine Laboratory, College of Charleston, 205 Fort Johnson Rd., Charleston, SC 29412, USA.,Hollings Marine Laboratory, Charleston, SC 29412, USA
| | - David S Durica
- Department of Biology, University of Oklahoma, 730 Van Vleet Oval, Norman, OK 73019, USA
| | - Jonathon H Stillman
- Romberg Tiburon Center for Environmental Studies, San Francisco State University, 3152 Paradise Drive, Tiburon, CA 94920, USA.,Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
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