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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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Jiang Q, Bao C, Yang Y, Liu A, Liu F, Huang H, Ye H. Transcriptome profiling of claw muscle of the mud crab (Scylla paramamosain) at different fattening stages. PLoS One 2017; 12:e0188067. [PMID: 29141033 PMCID: PMC5687733 DOI: 10.1371/journal.pone.0188067] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Accepted: 10/31/2017] [Indexed: 01/29/2023] Open
Abstract
In crustaceans, muscle growth and development is complicated, and to date substantial knowledge gaps exist. In this study, the claw muscle, hepatopancreas and nervous tissue of the mud crab (Scylla paramamosain) were collected at three fattening stages for sequence by the Illumina sequencing. A total of 127.87 Gb clean data with no less than 3.94 Gb generated for each sample and the cycleQ30 percentages were more than 86.13% for all samples. De Bruijn assembly of these clean data produced 94,853 unigenes, thereinto, 50,059 unigenes were found in claw muscle. A total of 121 differentially expressed genes (DEGs) were revealed in claw muscle from the three fattening stages with a Padj value < 0.01, including 63 genes with annotation. Functional annotation and enrichment analysis showed that the DEGs clusters represented the predominant gene catalog with roles in biochemical processes (glycolysis, phosphorylation and regulation of transcription), molecular function (ATP binding, 6-phosphofructokinase activity, and sequence-specific DNA binding) and cellular component (6-phosphofructokinase complex, plasma membrane, and integral component of membrane). qRT-PCR was employed to further validate certain DEGs. Single nucleotide polymorphism (SNP) analysis obtained 159,322, 125,963 and 166,279 potential SNPs from the muscle transcriptome at stage B, stage C and stage D, respectively. In addition, there were sixteen neuropeptide transcripts being predicted in the claw muscle. The present study provides a comprehensive transcriptome of claw muscle of S. paramamosain during fattening, providing a basis for screening the functional genes that may affect muscle growth of S. paramamosain.
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Affiliation(s)
- Qingling Jiang
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Chenchang Bao
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Ya’nan Yang
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - An Liu
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Fang Liu
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Huiyang Huang
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Haihui Ye
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Collaborative Innovation Center for Development and Utilization of Marine Biological Resources, Xiamen, China
- * E-mail:
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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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Waiho K, Fazhan H, Shahreza MS, Moh JHZ, Noorbaiduri S, Wong LL, Sinnasamy S, Ikhwanuddin M. Transcriptome Analysis and Differential Gene Expression on the Testis of Orange Mud Crab, Scylla olivacea, during Sexual Maturation. PLoS One 2017; 12:e0171095. [PMID: 28135340 PMCID: PMC5279790 DOI: 10.1371/journal.pone.0171095] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 01/15/2017] [Indexed: 01/04/2023] Open
Abstract
Adequate genetic information is essential for sustainable crustacean fisheries and aquaculture management. The commercially important orange mud crab, Scylla olivacea, is prevalent in Southeast Asia region and is highly sought after. Although it is a suitable aquaculture candidate, full domestication of this species is hampered by the lack of knowledge about the sexual maturation process and the molecular mechanisms behind it, especially in males. To date, data on its whole genome is yet to be reported for S. olivacea. The available transcriptome data published previously on this species focus primarily on females and the role of central nervous system in reproductive development. De novo transcriptome sequencing for the testes of S. olivacea from immature, maturing and mature stages were performed. A total of approximately 144 million high-quality reads were generated and de novo assembled into 160,569 transcripts with a total length of 142.2 Mb. Approximately 15–23% of the total assembled transcripts were annotated when compared to public protein sequence databases (i.e. UniProt database, Interpro database, Pfam database and Drosophila melanogaster protein database), and GO-categorised with GO Ontology terms. A total of 156,181 high-quality Single-Nucleotide Polymorphisms (SNPs) were mined from the transcriptome data of present study. Transcriptome comparison among the testes of different maturation stages revealed one gene (beta crystallin like gene) with the most significant differential expression—up-regulated in immature stage and down-regulated in maturing and mature stages. This was further validated by qRT-PCR. In conclusion, a comprehensive transcriptome of the testis of orange mud crabs from different maturation stages were obtained. This report provides an invaluable resource for enhancing our understanding of this species’ genome structure and biology, as expressed and controlled by their gonads.
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Affiliation(s)
- Khor Waiho
- Institute of Tropical Aquaculture, Universiti Malaysia Terengganu, Kuala Terengganu, Terengganu, Malaysia
- * E-mail: (KW); (MI)
| | - Hanafiah Fazhan
- Institute of Tropical Aquaculture, Universiti Malaysia Terengganu, Kuala Terengganu, Terengganu, Malaysia
| | - Md Sheriff Shahreza
- Institute of Tropical Aquaculture, Universiti Malaysia Terengganu, Kuala Terengganu, Terengganu, Malaysia
- School of Fisheries and Aquaculture Sciences, Universiti Malaysia Terengganu, Kuala Terengganu, Terengganu, Malaysia
| | - Julia Hwei Zhong Moh
- Institute of Tropical Aquaculture, Universiti Malaysia Terengganu, Kuala Terengganu, Terengganu, Malaysia
| | - Shaibani Noorbaiduri
- Institute of Tropical Aquaculture, Universiti Malaysia Terengganu, Kuala Terengganu, Terengganu, Malaysia
| | - Li Lian Wong
- Institute of Tropical Aquaculture, Universiti Malaysia Terengganu, Kuala Terengganu, Terengganu, Malaysia
| | - Saranya Sinnasamy
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu, Terengganu, Malaysia
| | - Mhd Ikhwanuddin
- Institute of Tropical Aquaculture, Universiti Malaysia Terengganu, Kuala Terengganu, Terengganu, Malaysia
- * E-mail: (KW); (MI)
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Armstrong EJ, Stillman JH. Construction and Characterization of Two Novel Transcriptome Assemblies in the Congeneric Porcelain Crabs Petrolisthes cinctipes and P. manimaculis. Integr Comp Biol 2016; 56:1092-1102. [PMID: 27375271 DOI: 10.1093/icb/icw043] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Crustaceans have commonly been used as non-model systems in basic biological research, especially physiological regulation. With the recent and rapid adoption of functional genomic tools, crustaceans are increasingly becoming model systems for ecological investigations of development and evolution and for mechanistic examinations of genotype-phenotype interactions and molecular pathways of response to environmental stressors. Comparative transcriptomic approaches, however, remain constrained by a lack of sequence data in closely related crustacean taxa. We identify challenges in the use of functional genomics tools in comparative analysis among decapod crustacean in light of recent advances. We present RNA-seq data from two congeneric species of porcelain crabs (Petrolisthes cinctipes and P. manimaculis) used to construct two de novo transcriptome assemblies with ∼194K and ∼278K contigs, respectively. We characterize and contrast these assemblies and compare them to a previously generated EST sequence library for P. cinctipes We also discuss the potential use of these data as a case-study system in the broader context of crustacean comparative transcriptomics.
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Affiliation(s)
- Eric J Armstrong
- *Department of Integrative Biology, University of California, 3040 Valley Life Sciences Bldg, Berkeley, CA 94720, USA .,Romberg Tiburon Center for Environmental Studies, San Francisco State University, 3152 Paradise Drive, Tiburon, CA 94920, USA
| | - Jonathon H Stillman
- *Department of Integrative Biology, University of California, 3040 Valley Life Sciences Bldg, Berkeley, CA 94720, USA.,Romberg Tiburon Center for Environmental Studies, San Francisco State University, 3152 Paradise Drive, Tiburon, CA 94920, USA
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Garland MA, Stillman JH, Tomanek L. The proteomic response of cheliped myofibril tissue in the eurythermal porcelain crab Petrolisthes cinctipes to heat shock following acclimation to daily temperature fluctuations. J Exp Biol 2015; 218:388-403. [DOI: 10.1242/jeb.112250] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The porcelain crab Petrolisthes cinctipes lives under rocks and in mussel beds in the mid-intertidal zone where it experiences immersion during high tide and saturating humid conditions in air during low tide, which can increase habitat temperature by up to 20°C. To identify the biochemical changes affected by increasing temperature fluctuations and subsequent heat shock, we acclimated P. cinctipes for 30 days to one of three temperature regimes: (1) constant 10°C, (2) daily temperature fluctuations between 10 and 20°C (5 h up-ramp to 20°C, 1 h down-ramp to 10°C) and (3) 10–30°C (up-ramp to 30°C). After acclimation, animals were exposed to either 10°C or a 30°C heat shock to analyze the proteomic changes in claw muscle tissue. Following acclimation to 10–30°C (measured at 10°C), enolase and ATP synthase increased in abundance. Following heat shock, isoforms of arginine kinase and glycolytic enzymes such as aldolase, triose phosphate isomerase and glyceraldehyde 3-phosphate dehydrogenase increased across all acclimation regimes. Full-length isoforms of hemocyanin increased abundance following acclimation to 10–30°C, but hemocyanin fragments increased after heat shock following constant 10°C and fluctuating 10–20°C, possibly playing a role as antimicrobial peptides. Following constant 10°C and fluctuating 10–20°C, paramyosin and myosin heavy chain type-B increased in abundance, respectively, whereas myosin light and heavy chain decreased with heat shock. Actin-binding proteins, which stabilize actin filaments (filamin and tropomyosin), increased during heat shock following 10–30°C; however, actin severing and depolymerization proteins (gelsolin and cofilin) increased during heat shock following 10–20°C, possibly promoting muscle fiber restructuring. RAF kinase inhibitor protein and prostaglandin reductase increased during heat shock following constant 10°C and fluctuating 10–20°C, possibly inhibiting an immune response during heat shock. The results suggest that ATP supply, muscle fiber restructuring and immune responses are all affected by temperature fluctuations and subsequent acute heat shock in muscle tissue. Furthermore, although heat shock after acclimation to constant 10°C and fluctuating 10–30°C showed the greatest effects on the proteome, moderately fluctuating temperatures (10–20°C) broadened the temperature range over which claw muscle was able to respond to an acute heat shock with limited changes in the muscle proteome.
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Affiliation(s)
- Michael A. Garland
- California Polytechnic State University, Department of Biological Sciences, Center for Coastal Marine Studies, Environmental Proteomics Laboratory, 1 Grand Avenue, San Luis Obispo, CA 93407-0401, USA
| | - Jonathon H. Stillman
- Romberg Tiburon Center for Environmental Studies, San Francisco State University, 3152 Paradise Drive, Tiburon, CA 94920-1205, USA
| | - Lars Tomanek
- California Polytechnic State University, Department of Biological Sciences, Center for Coastal Marine Studies, Environmental Proteomics Laboratory, 1 Grand Avenue, San Luis Obispo, CA 93407-0401, USA
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Tan MH, Gan HM, Lee YP, Austin CM. The complete mitogenome of the porcelain crab Petrolisthes haswelli Miers, 1884 (Crustacea: Decapoda: Anomura). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:3983-3984. [DOI: 10.3109/19401736.2014.989515] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Mun Hua Tan
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Petaling Jaya, Selangor, Malaysia and
- Monash University Malaysia Genomics Facility, Jalan Lagoon Selatan, Bandar Sunway, Petaling Jaya, Selangor, Malaysia
| | - Han Ming Gan
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Petaling Jaya, Selangor, Malaysia and
- Monash University Malaysia Genomics Facility, Jalan Lagoon Selatan, Bandar Sunway, Petaling Jaya, Selangor, Malaysia
| | - Yin Peng Lee
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Petaling Jaya, Selangor, Malaysia and
- Monash University Malaysia Genomics Facility, Jalan Lagoon Selatan, Bandar Sunway, Petaling Jaya, Selangor, Malaysia
| | - Christopher M. Austin
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Petaling Jaya, Selangor, Malaysia and
- Monash University Malaysia Genomics Facility, Jalan Lagoon Selatan, Bandar Sunway, Petaling Jaya, Selangor, Malaysia
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Short S, Yang G, Guler Y, Green Etxabe A, Kille P, Ford AT. Crustacean intersexuality is feminization without demasculinization: implications for environmental toxicology. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:13520-13529. [PMID: 25343324 DOI: 10.1021/es5050503] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The dysfunction associated with intersexuality in vertebrates and molluscs is often a serious threat to ecosystems. Although poorly understood, crustacean intersexuality is associated with contamination and includes forms linked to increased sex-ratio distorting parasites at polluted sites. Despite the importance of crustaceans for monitoring vulnerable aquatic habitats, little is known about the molecular basis of this abnormal sexual differentiation and any associated sexual dysfunction. To increase the relevance of crustaceans to environmental toxicologists, we comprehensively analyzed gene expression in amphipods presenting parasite- and nonparasite-associated intersexuality. Our findings reveal existing vertebrate biomarkers of feminization should not be applied to crustaceans, as orthologous genes are not induced in feminized amphipods. Furthermore, in contrast to vertebrates, where feminization and intersexuality is often associated with deleterious demasculinization, we find males maintain masculinity even when unambiguously feminized. This reveals a considerable regulatory separation of the gene pathways responsible for male and female characteristics and demonstrates that evidence of feminization (even if detected with appropriate biomarkers) is not a proxy for demasculinization in crustaceans. This study has also produced a comprehensive spectrum of potential molecular biomarkers that, when combined with our new molecular understanding, will greatly facilitate the use of crustaceans to monitor aquatic habitats.
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Affiliation(s)
- Stephen Short
- Institute of Marine Sciences, School of Biological Sciences, University of Portsmouth , Ferry Road, Portsmouth, Hampshire PO4 9LY, United Kingdom
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Perina A, von Reumont BM, Martínez-Lage A, González-Tizón AM. Accessing transcriptomic data for ecologically important genes in the goose barnacle (Pollicipes pollicipes), with particular focus on cement proteins. Mar Genomics 2014; 15:9-11. [PMID: 24606915 DOI: 10.1016/j.margen.2014.02.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 02/19/2014] [Accepted: 02/19/2014] [Indexed: 11/24/2022]
Abstract
In this study 4310 expressed sequence tags (ESTs) were used to identify potentially useful transcripts for future studies in the gooseneck barnacle Pollicipes pollicipes (Gmelin, 1789). 119 ESTs were obtained in this work and 4191 were taken from Meusemann et al. (2010). The gooseneck barnacle is a sessile pedunculate cirripede of great economic importance that occurs in dense aggregations, and is harvested for human consumption. The assembly of these ESTs yielded 1805 unigenes (461 contigs and 1344 singlets). The identification of cement proteins in our data is particularly interesting for cirripedes. Only a small part of the assembled unigenes could be functionally annotated. However, our results greatly improve our understanding of the biological features of P. pollicipes. In addition to this, a large number of potentially interesting genes were identified in order to serve as the base for future evolutionary studies in P. pollicipes.
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Affiliation(s)
- A Perina
- Department of Cell and Molecular Biology, Evolutionary Biology Group (GIBE), Universidade da Coruña, A Fraga 10, E-15008 A Coruña, Spain
| | - B M von Reumont
- Department of Life Sciences, The Natural History Museum, London, United Kingdom
| | - A Martínez-Lage
- Department of Cell and Molecular Biology, Evolutionary Biology Group (GIBE), Universidade da Coruña, A Fraga 10, E-15008 A Coruña, Spain
| | - A M González-Tizón
- Department of Cell and Molecular Biology, Evolutionary Biology Group (GIBE), Universidade da Coruña, A Fraga 10, E-15008 A Coruña, Spain.
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Harms L, Frickenhaus S, Schiffer M, Mark FC, Storch D, Pörtner HO, Held C, Lucassen M. Characterization and analysis of a transcriptome from the boreal spider crab Hyas araneus. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2013; 8:344-51. [PMID: 24212285 DOI: 10.1016/j.cbd.2013.09.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 09/05/2013] [Accepted: 09/30/2013] [Indexed: 10/26/2022]
Abstract
Research investigating the genetic basis of physiological responses has significantly broadened our understanding of the mechanisms underlying organismic response to environmental change. However, genomic data are currently available for few taxa only, thus excluding physiological model species from this approach. In this study we report the transcriptome of the model organism Hyas araneus from Spitsbergen (Arctic). We generated 20,479 transcripts, using the 454 GS FLX sequencing technology in combination with an Illumina HiSeq sequencing approach. Annotation by Blastx revealed 7159 blast hits in the NCBI non-redundant protein database. The comparison between the spider crab H. araneus transcriptome and EST libraries of the European lobster Homarus americanus and the porcelain crab Petrolisthes cinctipes yielded 3229/2581 sequences with a significant hit, respectively. The clustering by the Markov Clustering Algorithm (MCL) revealed a common core of 1710 clusters present in all three species and 5903 unique clusters for H. araneus. The combined sequencing approaches generated transcripts that will greatly expand the limited genomic data available for crustaceans. We introduce the MCL clustering for transcriptome comparisons as a simple approach to estimate similarities between transcriptomic libraries of different size and quality and to analyze homologies within the selected group of species. In particular, we identified a large variety of reverse transcriptase (RT) sequences not only in the H. araneus transcriptome and other decapod crustaceans, but also sea urchin, supporting the hypothesis of a heritable, anti-viral immunity and the proposed viral fragment integration by host-derived RTs in marine invertebrates.
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Affiliation(s)
- Lars Harms
- Integrative Ecophysiology, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.
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Singh R, Yang H, Dalziel B, Asarnow D, Murad W, Foote D, Gormley M, Stillman J, Fisher S. Towards human-computer synergetic analysis of large-scale biological data. BMC Bioinformatics 2013; 14 Suppl 14:S10. [PMID: 24267485 PMCID: PMC3851181 DOI: 10.1186/1471-2105-14-s14-s10] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Advances in technology have led to the generation of massive amounts of complex and multifarious biological data in areas ranging from genomics to structural biology. The volume and complexity of such data leads to significant challenges in terms of its analysis, especially when one seeks to generate hypotheses or explore the underlying biological processes. At the state-of-the-art, the application of automated algorithms followed by perusal and analysis of the results by an expert continues to be the predominant paradigm for analyzing biological data. This paradigm works well in many problem domains. However, it also is limiting, since domain experts are forced to apply their instincts and expertise such as contextual reasoning, hypothesis formulation, and exploratory analysis after the algorithm has produced its results. In many areas where the organization and interaction of the biological processes is poorly understood and exploratory analysis is crucial, what is needed is to integrate domain expertise during the data analysis process and use it to drive the analysis itself. RESULTS In context of the aforementioned background, the results presented in this paper describe advancements along two methodological directions. First, given the context of biological data, we utilize and extend a design approach called experiential computing from multimedia information system design. This paradigm combines information visualization and human-computer interaction with algorithms for exploratory analysis of large-scale and complex data. In the proposed approach, emphasis is laid on: (1) allowing users to directly visualize, interact, experience, and explore the data through interoperable visualization-based and algorithmic components, (2) supporting unified query and presentation spaces to facilitate experimentation and exploration, (3) providing external contextual information by assimilating relevant supplementary data, and (4) encouraging user-directed information visualization, data exploration, and hypotheses formulation. Second, to illustrate the proposed design paradigm and measure its efficacy, we describe two prototype web applications. The first, called XMAS (Experiential Microarray Analysis System) is designed for analysis of time-series transcriptional data. The second system, called PSPACE (Protein Space Explorer) is designed for holistic analysis of structural and structure-function relationships using interactive low-dimensional maps of the protein structure space. Both these systems promote and facilitate human-computer synergy, where cognitive elements such as domain knowledge, contextual reasoning, and purpose-driven exploration, are integrated with a host of powerful algorithmic operations that support large-scale data analysis, multifaceted data visualization, and multi-source information integration. CONCLUSIONS The proposed design philosophy, combines visualization, algorithmic components and cognitive expertise into a seamless processing-analysis-exploration framework that facilitates sense-making, exploration, and discovery. Using XMAS, we present case studies that analyze transcriptional data from two highly complex domains: gene expression in the placenta during human pregnancy and reaction of marine organisms to heat stress. With PSPACE, we demonstrate how complex structure-function relationships can be explored. These results demonstrate the novelty, advantages, and distinctions of the proposed paradigm. Furthermore, the results also highlight how domain insights can be combined with algorithms to discover meaningful knowledge and formulate evidence-based hypotheses during the data analysis process. Finally, user studies against comparable systems indicate that both XMAS and PSPACE deliver results with better interpretability while placing lower cognitive loads on the users. XMAS is available at: http://tintin.sfsu.edu:8080/xmas. PSPACE is available at: http://pspace.info/.
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Mohd-Shamsudin MI, Kang Y, Lili Z, Tan TT, Kwong QB, Liu H, Zhang G, Othman RY, Bhassu S. In-depth tanscriptomic analysis on giant freshwater prawns. PLoS One 2013; 8:e60839. [PMID: 23734171 PMCID: PMC3667022 DOI: 10.1371/journal.pone.0060839] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Accepted: 03/05/2013] [Indexed: 11/30/2022] Open
Abstract
Gene discovery in the Malaysian giant freshwater prawn (Macrobrachium rosenbergii) has been limited to small scale data collection, despite great interest in various research fields related to the commercial significance of this species. Next generation sequencing technologies that have been developed recently and enabled whole transcriptome sequencing (RNA-seq), have allowed generation of large scale functional genomics data sets in a shorter time than was previously possible. Using this technology, transcriptome sequencing of three tissue types: hepatopancreas, gill and muscle, has been undertaken to generate functional genomics data for M. rosenbergii at a massive scale. De novo assembly of 75-bp paired end Ilumina reads has generated 102,230 unigenes. Sequence homology search and in silico prediction have identified known and novel protein coding candidate genes (∼24%), non-coding RNA, and repetitive elements in the transcriptome. Potential markers consisting of simple sequence repeats associated with known protein coding genes have been successfully identified. Using KEGG pathway enrichment, differentially expressed genes in different tissues were systematically represented. The functions of gill and hepatopancreas in the context of neuroactive regulation, metabolism, reproduction, environmental stress and disease responses are described and support relevant experimental studies conducted previously in M. rosenbergii and other crustaceans. This large scale gene discovery represents the most extensive transcriptome data for freshwater prawn. Comparison with model organisms has paved the path to address the possible conserved biological entities shared between vertebrates and crustaceans. The functional genomics resources generated from this study provide the basis for constructing hypotheses for future molecular research in the freshwater shrimp.
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Affiliation(s)
- Maizatul Izzah Mohd-Shamsudin
- Genomics and Evolutionary Biology Lab, Centre for Research in Biotechnology for Agriculture (CEBAR) and Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
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Piednoël M, Donnart T, Esnault C, Graça P, Higuet D, Bonnivard E. LTR-retrotransposons in R. exoculata and other crustaceans: the outstanding success of GalEa-like copia elements. PLoS One 2013; 8:e57675. [PMID: 23469217 PMCID: PMC3587641 DOI: 10.1371/journal.pone.0057675] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 01/24/2013] [Indexed: 12/29/2022] Open
Abstract
Transposable elements are major constituents of eukaryote genomes and have a great impact on genome structure and stability. They can contribute to the genetic diversity and evolution of organisms. Knowledge of their distribution among several genomes is an essential condition to study their dynamics and to better understand their role in species evolution. LTR-retrotransposons have been reported in many diverse eukaryote species, describing a ubiquitous distribution. Given their abundance, diversity and their extended ranges in C-values, environment and life styles, crustaceans are a great taxon to investigate the genomic component of adaptation and its possible relationships with TEs. However, crustaceans have been greatly underrepresented in transposable element studies. Using both degenerate PCR and in silico approaches, we have identified 35 Copia and 46 Gypsy families in 15 and 18 crustacean species, respectively. In particular, we characterized several full-length elements from the shrimp Rimicaris exoculata that is listed as a model organism from hydrothermal vents. Phylogenic analyses show that Copia and Gypsy retrotransposons likely present two opposite dynamics within crustaceans. The Gypsy elements appear relatively frequent and diverse whereas Copia are much more homogeneous, as 29 of them belong to the single GalEa clade, and species- or lineage-dependent. Our results also support the hypothesis of the Copia retrotransposon scarcity in metazoans compared to Gypsy elements. In such a context, the GalEa-like elements present an outstanding wide distribution among eukaryotes, from fishes to red algae, and can be even highly predominant within a large taxon, such as Malacostraca. Their distribution among crustaceans suggests a dynamics that follows a "domino days spreading" branching process in which successive amplifications may interact positively.
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Affiliation(s)
- Mathieu Piednoël
- UMR 7138 Systématique Adaptation Evolution, Equipe Génétique et Evolution, Université Pierre et Marie Curie, Paris, France
- Systematic Botany and Mycology, University of Munich (LMU), Munich, Germany
| | - Tifenn Donnart
- UMR 7138 Systématique Adaptation Evolution, Equipe Génétique et Evolution, Université Pierre et Marie Curie, Paris, France
| | - Caroline Esnault
- UMR 7138 Systématique Adaptation Evolution, Equipe Génétique et Evolution, Université Pierre et Marie Curie, Paris, France
| | - Paula Graça
- UMR 7138 Systématique Adaptation Evolution, Equipe Génétique et Evolution, Université Pierre et Marie Curie, Paris, France
| | - Dominique Higuet
- UMR 7138 Systématique Adaptation Evolution, Equipe Génétique et Evolution, Université Pierre et Marie Curie, Paris, France
| | - Eric Bonnivard
- UMR 7138 Systématique Adaptation Evolution, Equipe Génétique et Evolution, Université Pierre et Marie Curie, Paris, France
- * E-mail:
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Li C, Weng S, Chen Y, Yu X, Lü L, Zhang H, He J, Xu X. Analysis of Litopenaeus vannamei transcriptome using the next-generation DNA sequencing technique. PLoS One 2012; 7:e47442. [PMID: 23071809 PMCID: PMC3469548 DOI: 10.1371/journal.pone.0047442] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 09/14/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Pacific white shrimp (Litopenaeus vannamei), the major species of farmed shrimps in the world, has been attracting extensive studies, which require more and more genome background knowledge. The now available transcriptome data of L. vannamei are insufficient for research requirements, and have not been adequately assembled and annotated. METHODOLOGY/PRINCIPAL FINDINGS This is the first study that used a next-generation high-throughput DNA sequencing technique, the Solexa/Illumina GA II method, to analyze the transcriptome from whole bodies of L. vannamei larvae. More than 2.4 Gb of raw data were generated, and 109,169 unigenes with a mean length of 396 bp were assembled using the SOAP denovo software. 73,505 unigenes (>200 bp) with good quality sequences were selected and subjected to annotation analysis, among which 37.80% can be matched in NCBI Nr database, 37.3% matched in Swissprot, and 44.1% matched in TrEMBL. Using BLAST and BLAST2Go softwares, 11,153 unigenes were classified into 25 Clusters of Orthologous Groups of proteins (COG) categories, 8171 unigenes were assigned into 51 Gene ontology (GO) functional groups, and 18,154 unigenes were divided into 220 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. To primarily verify part of the results of assembly and annotations, 12 assembled unigenes that are homologous to many embryo development-related genes were chosen and subjected to RT-PCR for electrophoresis and Sanger sequencing analyses, and to real-time PCR for expression profile analyses during embryo development. CONCLUSIONS/SIGNIFICANCE The L. vannamei transcriptome analyzed using the next-generation sequencing technique enriches the information of L. vannamei genes, which will facilitate our understanding of the genome background of crustaceans, and promote the studies on L. vannamei.
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Affiliation(s)
- Chaozheng Li
- MOE Key Laboratory of Aquatic Product Safety/State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Shaoping Weng
- MOE Key Laboratory of Aquatic Product Safety/State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Yonggui Chen
- MOE Key Laboratory of Aquatic Product Safety/State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Xiaoqiang Yu
- Division of Cell Biology and Biophysics, School of Biological Science, University of Missouri-Kansas City, Kansas City, United States of America
| | - Ling Lü
- MOE Key Laboratory of Aquatic Product Safety/State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Haiqing Zhang
- MOE Key Laboratory of Aquatic Product Safety/State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Jianguo He
- MOE Key Laboratory of Aquatic Product Safety/State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People’s Republic of China
- School of Marine Sciences, Sun Yat-sen University, Guangzhou, People’s Republic of China
- * E-mail: (XX); (JH)
| | - Xiaopeng Xu
- MOE Key Laboratory of Aquatic Product Safety/State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, People’s Republic of China
- * E-mail: (XX); (JH)
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Ronges D, Walsh JP, Sinclair BJ, Stillman JH. Changes in extreme cold tolerance, membrane composition and cardiac transcriptome during the first day of thermal acclimation in the porcelain crab Petrolisthes cinctipes. ACTA ACUST UNITED AC 2012; 215:1824-36. [PMID: 22573761 DOI: 10.1242/jeb.069658] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Intertidal zone organisms can experience transient freezing temperatures during winter low tides, but their extreme cold tolerance mechanisms are not known. Petrolisthes cinctipes is a temperate mid-high intertidal zone crab species that can experience wintertime habitat temperatures below the freezing point of seawater. We examined how cold tolerance changed during the initial phase of thermal acclimation to cold and warm temperatures, as well as the persistence of cold tolerance during long-term thermal acclimation. Thermal acclimation for as little as 6 h at 8°C enhanced cold tolerance during a 1 h exposure to -2°C relative to crabs acclimated to 18°C. Potential mechanisms for this enhanced tolerance were elucidated using cDNA microarrays to probe for differences in gene expression in cardiac tissue of warm- and cold-acclimated crabs during the first day of thermal acclimation. No changes in gene expression were detected until 12 h of thermal acclimation. Genes strongly upregulated in warm-acclimated crabs represented immune response and extracellular/intercellular processes, suggesting that warm-acclimated crabs had a generalized stress response and may have been remodelling tissues or altering intercellular processes. Genes strongly upregulated in cold-acclimated crabs included many that are involved in glucose production, suggesting that cold acclimation involves increasing intracellular glucose as a cryoprotectant. Structural cytoskeletal proteins were also strongly represented among the genes upregulated in only cold-acclimated crabs. There were no consistent changes in composition or the level of unsaturation of membrane phospholipid fatty acids with cold acclimation, which suggests that neither short- nor long-term changes in cold tolerance are mediated by changes in membrane fatty acid composition. Overall, our study demonstrates that initial changes in cold tolerance are likely not regulated by transcriptomic responses, but that gene-expression-related changes in homeostasis begin within 12 h, the length of a tidal cycle.
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Affiliation(s)
- Daria Ronges
- Romberg Tiburon Center and Department of Biology, San Francisco State University, Tiburon, CA 94920, USA
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Chevalier F, Herbinière-Gaboreau J, Charif D, Mitta G, Gavory F, Wincker P, Grève P, Braquart-Varnier C, Bouchon D. Feminizing Wolbachia: a transcriptomics approach with insights on the immune response genes in Armadillidium vulgare. BMC Microbiol 2012; 12 Suppl 1:S1. [PMID: 22375708 PMCID: PMC3287506 DOI: 10.1186/1471-2180-12-s1-s1] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Wolbachia are vertically transmitted bacteria known to be the most widespread endosymbiont in arthropods. They induce various alterations of the reproduction of their host, including feminization of genetic males in isopod crustaceans. In the pill bug Armadillidium vulgare, the presence of Wolbachia is also associated with detrimental effects on host fertility and lifespan. Deleterious effects have been demonstrated on hemocyte density, phenoloxidase activity, and natural hemolymph septicemia, suggesting that infected individuals could have defective immune capacities. Since nothing is known about the molecular mechanisms involved in Wolbachia-A. vulgare interactions and its secondary immunocompetence modulation, we developed a transcriptomics strategy and compared A. vulgare gene expression between Wolbachia-infected animals (i.e., "symbiotic" animals) and uninfected ones (i.e., "asymbiotic" animals) as well as between animals challenged or not challenged by a pathogenic bacteria. RESULTS Since very little genetic data is available on A. vulgare, we produced several EST libraries and generated a total of 28 606 ESTs. Analyses of these ESTs revealed that immune processes were over-represented in most experimental conditions (responses to a symbiont and to a pathogen). Considering canonical crustacean immune pathways, these genes encode antimicrobial peptides or are involved in pathogen recognition, detoxification, and autophagy. By RT-qPCR, we demonstrated a general trend towards gene under-expression in symbiotic whole animals and ovaries whereas the same gene set tends to be over-expressed in symbiotic immune tissues. CONCLUSION This study allowed us to generate the first reference transcriptome ever obtained in the Isopoda group and to identify genes involved in the major known crustacean immune pathways encompassing cellular and humoral responses. Expression of immune-related genes revealed a modulation of host immunity when females are infected by Wolbachia, including in ovaries, the crucial tissue for the Wolbachia route of transmission.
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Zeng V, Villanueva KE, Ewen-Campen BS, Alwes F, Browne WE, Extavour CG. De novo assembly and characterization of a maternal and developmental transcriptome for the emerging model crustacean Parhyale hawaiensis. BMC Genomics 2011; 12:581. [PMID: 22118449 PMCID: PMC3282834 DOI: 10.1186/1471-2164-12-581] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Accepted: 11/25/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Arthropods are the most diverse animal phylum, but their genomic resources are relatively few. While the genome of the branchiopod Daphnia pulex is now available, no other large-scale crustacean genomic resources are available for comparison. In particular, genomic resources are lacking for the most tractable laboratory model of crustacean development, the amphipod Parhyale hawaiensis. Insight into shared and divergent characters of crustacean genomes will facilitate interpretation of future developmental, biomedical, and ecological research using crustacean models. RESULTS To generate a transcriptome enriched for maternally provided and zygotically transcribed developmental genes, we created cDNA from ovaries and embryos of P. hawaiensis. Using 454 pyrosequencing, we sequenced over 1.1 billion bases of this cDNA, and assembled them de novo to create, to our knowledge, the second largest crustacean genomic resource to date. We found an unusually high proportion of C2H2 zinc finger-containing transcripts, as has also been reported for the genome of the pea aphid Acyrthosiphon pisum. Consistent with previous reports, we detected trans-spliced transcripts, but found that they did not noticeably impact transcriptome assembly. Our assembly products yielded 19,067 unique BLAST hits against nr (E-value cutoff e-10). These included over 400 predicted transcripts with significant similarity to D. pulex sequences but not to sequences of any other animal. Annotation of several hundred genes revealed P. hawaiensis homologues of genes involved in development, gametogenesis, and a majority of the members of six major conserved metazoan signaling pathways. CONCLUSIONS The amphipod P. hawaiensis has higher transcript complexity than known insect transcriptomes, and trans-splicing does not appear to be a major contributor to this complexity. We discuss the importance of a reliable comparative genomic framework within which to consider findings from new crustacean models such as D. pulex and P. hawaiensis, as well as the need for development of further substantial crustacean genomic resources.
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Affiliation(s)
- Victor Zeng
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Karina E Villanueva
- Department of Biology, University of Miami, 234 Cox Science Center, 1301 Memorial Drive, Coral Gables, FL 33146, USA
| | - Ben S Ewen-Campen
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Frederike Alwes
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - William E Browne
- Department of Biology, University of Miami, 234 Cox Science Center, 1301 Memorial Drive, Coral Gables, FL 33146, USA
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
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Cayenne AP, Gabert B, Stillman JH. Identification of proteins interacting with lactate dehydrogenase in claw muscle of the porcelain crab Petrolisthes cinctipes. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2011; 6:393-8. [PMID: 21968246 DOI: 10.1016/j.cbd.2011.09.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Revised: 09/08/2011] [Accepted: 09/08/2011] [Indexed: 01/11/2023]
Abstract
Biochemical adaptation of enzymes involves conservation of activity, stability and affinity across a wide range of intracellular and environmental conditions. Enzyme adaptation by alteration of primary structure is well known, but the roles of protein-protein interactions in enzyme adaptation are less well understood. Interspecific differences in thermal stability of lactate dehydrogenase (LDH) in porcelain crabs (genus Petrolisthes) are related to intrinsic differences among LDH molecules and by interactions with other stabilizing proteins. Here, we identified proteins that interact with LDH in porcelain crab claw muscle tissue using co-immunoprecipitation, and showed LDH exists in high molecular weight complexes using size exclusion chromatography and Western blot analyses. Co-immunoprecipitated proteins were separated using 2D SDS PAGE and analyzed by LC/ESI using peptide MS/MS. Peptide MS/MS ions were compared to an EST database for Petrolisthes cinctipes to identify proteins. Identified proteins included cytoskeletal elements, glycolytic enzymes, a phosphagen kinase, and the respiratory protein hemocyanin. Our results support the hypothesis that LDH interacts with glycolytic enzymes in a metabolon structured by cytoskeletal elements that may also include the enzyme for transfer of the adenylate charge in glycolytically produced ATP. Those interactions may play specific roles in biochemical adaptation of glycolytic enzymes.
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Affiliation(s)
- Andrea P Cayenne
- Romberg Tiburon Center and Department of Biology, San Francisco State University, 3152 Paradise Drive, Tiburon California 94920, USA
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