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Lee WK, Chan BKK, Kim JY, Ju SJ, Kim SJ. Comparative genomics reveals the dynamic evolutionary history of cement protein genes of barnacles from intertidal to deep-sea hydrothermal vents. Mol Ecol Resour 2024; 24:e13895. [PMID: 37955198 DOI: 10.1111/1755-0998.13895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 10/16/2023] [Accepted: 10/30/2023] [Indexed: 11/14/2023]
Abstract
Thoracican barnacles are a diverse group of marine organisms for which the availability of genome assemblies is currently limited. In this study, we sequenced the genomes of two neolepadoid species (Ashinkailepas kermadecensis, Imbricaverruca yamaguchii) from hydrothermal vents, in addition to two intertidal species. Genome sizes ranged from 481 to 1054 Mb, with repetitive sequence contents of 21.2% to 50.7%. Concordance rates of orthologs and heterozygosity rates were between 82.4% and 91.7% and between 1.0% and 2.1%, respectively, indicating high genetic diversity and heterozygosity. Based on phylogenomic analyses, we revised the nomenclature of cement genes encoding cement proteins that are not homologous to any known proteins. The major cement gene, CP100A, was found in all thoracican species, including vent-associated neolepadoids, and was hypothesised to be essential for thoracican settlement. Duplicated genes, CP100B and CP100C, were found only in balanids, suggesting potential functional redundancy or acquisition of new functions associated with the calcareous base. An ancestor of CP52 genes was duplicated dynamically among lepadids, pollicipedids with multiple copies on a single scaffold, and balanids with multiple sequential repeats of the conserved regions, but no CP52 genes were found in neolepadoids, providing insights into cement gene evolution among thoracican lineages. This study enhances our understanding of the adhesion mechanisms of thoracicans in underwater environments. The newly sequenced genomes provide opportunities for studying their evolution and ecology, shedding light on their adaptation to diverse marine environments, and contributing to our knowledge of barnacle biology with valuable genomic resources for further studies in this field.
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Affiliation(s)
- Won-Kyung Lee
- Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
- Division of EcoScience, Ewha Womans University, Seoul, Korea
| | - Benny K K Chan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Jae-Yoon Kim
- Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Se-Jong Ju
- Marine Resources & Environment Research Division, Korea Institute of Ocean Science and Technology, Busan, Korea
| | - Se-Joo Kim
- Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
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2
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Wong YH, Dreyer N, Liu H, Lan Y, Chen JJ, Sun J, Zhang WP, Qian PY, Chan BKK. Gene co-option, duplication and divergence of cement proteins underpin the evolution of bioadhesives across barnacle life histories. Mol Ecol 2023; 32:5071-5088. [PMID: 37584177 DOI: 10.1111/mec.17084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/30/2023] [Accepted: 07/12/2023] [Indexed: 08/17/2023]
Abstract
Acquisition of new genes often results in the emergence of novel functions and is a key step in lineage-specific adaptation. As a group of sessile crustaceans, barnacles establish permanent attachment through initial cement secretion at the larval phase followed by continuous cement secretion in juveniles and adults. However, the origins and evolution of barnacle larval and adult cement proteins remain poorly understood. By performing microdissection of larval cement glands, transcriptome and shotgun proteomics and immunohistochemistry validation, we identified 30 larval and 27 adult cement proteins of the epibiotic turtle barnacle Chelonibia testudinaria, of which the majority are stage- and barnacle-specific. While only two proteins, SIPC and CP100K, were expressed in both larvae and adults, detection of protease inhibitors and the cross-linking enzyme lysyl oxidase paralogs in larvae and adult cement. Other barnacle-specific cement proteins such as CP100k and CP52k likely share a common origin dating back at least to the divergence of Rhizocephala and Thoracica. Different CP52k paralogues could be detected in larval and adult cement, suggesting stage-specific cement proteins may arise from duplication followed by changes in expression timing of the duplicates. Interestingly, the biochemical properties of larval- and adult-specific CP52k paralogues exhibited remarkable differences. We conclude that barnacle larval and adult cement systems evolved independently, and both emerged from co-option of existing genes and de novo formation, duplication and functional divergence of lineage-specific cement protein genes. Our findings provide important insights into the evolutionary mechanisms of bioadhesives in sessile marine invertebrates.
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Affiliation(s)
- Yue Him Wong
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Niklas Dreyer
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Taiwan International Graduate Program, TIGP, Biodiversity, Academia Sinica, Taipei, Taiwan
- Department of Life Sciences, National Taiwan Normal University, Taipei, Taiwan
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - HaoCheng Liu
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Yi Lan
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Jamie J Chen
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Jin Sun
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Wei-Peng Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Pei-Yuan Qian
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Benny K K Chan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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Jia L, Yu Y, Zheng J, Zhou H, Liu Q, Wang W, Liu X, Zhang X, Ge D, Shi W, Sun Y. Self-assembling Bioadhesive Inspired by the Fourth Repetitive Sequence of Balanus albicostatus Cement Protein 20 kDa (Balcp-20 k). Mar Biotechnol (NY) 2022; 24:1148-1157. [PMID: 36319917 DOI: 10.1007/s10126-022-10177-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
Barnacle cement proteins are multi-protein complexes composed of a series of functionally related synergistic proteins that enable barnacles to adhere strongly and consistently to various underwater substrates. There is no post-translational modification of barnacle cement proteins, which provides a possibility for the synthesis of similar adhesive materials. Balcp-20 k has four repetitive sequences with multiple conserved cysteine groups. Whether these repeats are separate functional units and the role of cysteine in adhesion is not clear. In order to investigate the adhesion properties of Balcp-20 k, we amplified and expressed R4 (DHLACNAKHPCWHKHCDCFC)4, which is a quadruple repeat of Balcp-20 k's fourth repetitive sequence, and S0R4 (DHLASNAKHPSWHKHSDSFS)4, all cysteine of R4 replaced by serine. Analysis showed that R4 had a similar structure to Balcp-20 k, and the amyloid fibrils structure formed by self-assembly of R4 played an important role in improving the adhesion strength. The absence of disulfide bonds in S0R4 prevents self-assembly, and the failure of self-assembly after the reduction of disulfide bonds of R4 by DTT indicates that disulfide bonds play an important role in self-assembly. With adhesion and coating analysis, it was found that R4 has good adhesion on different materials surfaces, which is better than Balcp-20 k, while S0R4 has weak adhesion, which is only better than BSA.
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Affiliation(s)
- Li Jia
- The Higher Educational Key Laboratory for Biomedical Engineering of Fujian Province/Research Center of Biomedical Engineering of Xiamen, Xiamen Key Laboratory of Fire Retardant Materials/Fujian Provincial Key Laboratory of Fire Retardant Materials, Department of Biomaterials, College of Materials, Xiamen University, Xiamen, 361005, China
| | - Yabiao Yu
- The Higher Educational Key Laboratory for Biomedical Engineering of Fujian Province/Research Center of Biomedical Engineering of Xiamen, Xiamen Key Laboratory of Fire Retardant Materials/Fujian Provincial Key Laboratory of Fire Retardant Materials, Department of Biomaterials, College of Materials, Xiamen University, Xiamen, 361005, China
| | - Jinyang Zheng
- The Higher Educational Key Laboratory for Biomedical Engineering of Fujian Province/Research Center of Biomedical Engineering of Xiamen, Xiamen Key Laboratory of Fire Retardant Materials/Fujian Provincial Key Laboratory of Fire Retardant Materials, Department of Biomaterials, College of Materials, Xiamen University, Xiamen, 361005, China
| | - Hao Zhou
- The Higher Educational Key Laboratory for Biomedical Engineering of Fujian Province/Research Center of Biomedical Engineering of Xiamen, Xiamen Key Laboratory of Fire Retardant Materials/Fujian Provincial Key Laboratory of Fire Retardant Materials, Department of Biomaterials, College of Materials, Xiamen University, Xiamen, 361005, China
| | - Qiang Liu
- The Higher Educational Key Laboratory for Biomedical Engineering of Fujian Province/Research Center of Biomedical Engineering of Xiamen, Xiamen Key Laboratory of Fire Retardant Materials/Fujian Provincial Key Laboratory of Fire Retardant Materials, Department of Biomaterials, College of Materials, Xiamen University, Xiamen, 361005, China
| | - Wei Wang
- The Higher Educational Key Laboratory for Biomedical Engineering of Fujian Province/Research Center of Biomedical Engineering of Xiamen, Xiamen Key Laboratory of Fire Retardant Materials/Fujian Provincial Key Laboratory of Fire Retardant Materials, Department of Biomaterials, College of Materials, Xiamen University, Xiamen, 361005, China
| | - Xinxin Liu
- The Higher Educational Key Laboratory for Biomedical Engineering of Fujian Province/Research Center of Biomedical Engineering of Xiamen, Xiamen Key Laboratory of Fire Retardant Materials/Fujian Provincial Key Laboratory of Fire Retardant Materials, Department of Biomaterials, College of Materials, Xiamen University, Xiamen, 361005, China
| | - Xiuming Zhang
- The Higher Educational Key Laboratory for Biomedical Engineering of Fujian Province/Research Center of Biomedical Engineering of Xiamen, Xiamen Key Laboratory of Fire Retardant Materials/Fujian Provincial Key Laboratory of Fire Retardant Materials, Department of Biomaterials, College of Materials, Xiamen University, Xiamen, 361005, China
| | - Dongtao Ge
- The Higher Educational Key Laboratory for Biomedical Engineering of Fujian Province/Research Center of Biomedical Engineering of Xiamen, Xiamen Key Laboratory of Fire Retardant Materials/Fujian Provincial Key Laboratory of Fire Retardant Materials, Department of Biomaterials, College of Materials, Xiamen University, Xiamen, 361005, China
| | - Wei Shi
- The Higher Educational Key Laboratory for Biomedical Engineering of Fujian Province/Research Center of Biomedical Engineering of Xiamen, Xiamen Key Laboratory of Fire Retardant Materials/Fujian Provincial Key Laboratory of Fire Retardant Materials, Department of Biomaterials, College of Materials, Xiamen University, Xiamen, 361005, China
| | - Yanan Sun
- The Higher Educational Key Laboratory for Biomedical Engineering of Fujian Province/Research Center of Biomedical Engineering of Xiamen, Xiamen Key Laboratory of Fire Retardant Materials/Fujian Provincial Key Laboratory of Fire Retardant Materials, Department of Biomaterials, College of Materials, Xiamen University, Xiamen, 361005, China.
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Yuan J, Zhang X, Li S, Liu C, Yu Y, Zhang X, Xiang J, Li F. Convergent evolution of barnacles and molluscs sheds lights in origin and diversification of calcareous shell and sessile lifestyle. Proc Biol Sci 2022; 289:20221535. [PMID: 36100022 PMCID: PMC9470267 DOI: 10.1098/rspb.2022.1535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 08/22/2022] [Indexed: 11/12/2022] Open
Abstract
The calcareous shell and sessile lifestyle are the representative phenotypes of many molluscs, which happen to be present in barnacles, a group of unique crustaceans. The origin of these phenotypes is unclear, but it may be embodied in the convergent genetics of such distant groups (interphylum). Herein, we perform comprehensive comparative genomics analysis in barnacles and molluscs, and reveal a genome-wide strong convergent molecular evolution between them, including coexpansion of biomineralization and organic matrix genes for shell formation, and origination of lineage-specific orphan genes for settlement. Notably, the expanded biomineralization gene encoding alkaline phosphatase evolves a novel, highly conserved motif that may trigger the origin of barnacle shell formation. Unlike molluscs, barnacles adopt novel organic matrices and cement proteins for shell formation and settlement, respectively, and their calcareous shells have potentially originated from the cuticle system of crustaceans. Therefore, our study corroborates the idea that selection pressures driving convergent evolution may strongly act in organisms inhabiting similar environments regardless of phylogenetic distance. The convergence signatures shed light on the origin of the shell and sessile lifestyle of barnacles and molluscs. In addition, notable non-convergence signatures are also present and may contribute to morphological and functional specificities.
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Affiliation(s)
- Jianbo Yuan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, People's Republic of China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, People's Republic of China
| | - Xiaojun Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, People's Republic of China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, People's Republic of China
| | - Shihao Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, People's Republic of China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, People's Republic of China
| | - Chengzhang Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, People's Republic of China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, People's Republic of China
| | - Yang Yu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, People's Republic of China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, People's Republic of China
| | - Xiaoxi Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, People's Republic of China
| | - Jianhai Xiang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, People's Republic of China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, People's Republic of China
| | - Fuhua Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, People's Republic of China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, People's Republic of China
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Yang C, Shan B, Liu Y, Wang L, Liu M, Yao T, Sun D. Transcriptomic analysis of male three-spot swimming crab (Portunus sanguinolentus) infected with the parasitic barnacle Diplothylacus sinensis. Fish Shellfish Immunol 2022; 128:260-268. [PMID: 35934240 DOI: 10.1016/j.fsi.2022.07.074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 07/19/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
Diplothylacus sinensis is reported as an intriguing parasitic barnacle that can negatively affect the growth, molting, reproduction in several commercially important portunid crabs. To better understand the molecular mechanisms of host-parasite interactions, we characterized the gene expression profiles from the healthy and D. sinensis infected Portunus sanguinolentus by high-through sequence method. Totally, the transcriptomic analysis generated 52, 266, 600 and 51, 629, 604 high quality reads from the infected and control groups, respectively. The clean reads were assembled to 90,740 and 69,314 unigenes, with the average length of 760 bp and 709 bp, respectively. The expression analysis showed that 18,959 genes were significantly changed by the parasitism of D. sinensis, including 4769 activated genes and 14,190 suppressed genes. The differentially expressed genes were categorized into 258 KEGG pathways and 647 GO terms. The GO analysis mapped 13 DEGs related to immune system process and 32 DEGs related to immune response, respectively, suggesting a potential alteration of transcriptional expression patterns in complement cascades of P. sanguinolentus. Additionally, 4 representative molting-related genes were down-regulated in parasitized group, indicating D. sinensis infection appeared to suppress the producing of ecdysteroid hormones. In conclusion, the present study improves our understanding on parasite-host interaction mechanisms, which focuses the function of Ecdysone receptor, Toll-like receptor and cytokine receptor of crustacean crabs infestation with rhizocephalan parasites.
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Affiliation(s)
- Changping Yang
- Tropical Aquaculture Research and Development Center of South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Sanya, 572018, China; Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China; Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Binbin Shan
- Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Yan Liu
- Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Liangming Wang
- Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Manting Liu
- Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Tuo Yao
- Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China
| | - Dianrong Sun
- Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China.
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Nesterenko M, Miroliubov A. From head to rootlet: comparative transcriptomic analysis of a rhizocephalan barnacle Peltogaster reticulata (Crustacea: Rhizocephala). F1000Res 2022; 11:583. [PMID: 36447930 PMCID: PMC9664023 DOI: 10.12688/f1000research.110492.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/04/2023] [Indexed: 09/16/2023] Open
Abstract
Background: Rhizocephalan barnacles stand out in the diverse world of metazoan parasites. The body of a rhizocephalan female is modified beyond revealing any recognizable morphological features, consisting of the interna, a system of rootlets, and the externa, a sac-like reproductive body. Moreover, rhizocephalans have an outstanding ability to control their hosts, literally turning them into "zombies". Despite all these amazing traits, there are no genomic or transcriptomic data about any Rhizocephala. Methods: We collected transcriptomes from four body parts of an adult female rhizocephalan Peltogaster reticulata: the externa, and the main, growing, and thoracic parts of the interna. We used all prepared data for the de novo assembly of the reference transcriptome. Next, a set of encoded proteins was determined, the expression levels of protein-coding genes in different parts of the parasite's body were calculated and lists of enriched bioprocesses were identified. We also in silico identified and analyzed sets of potential excretory / secretory proteins. Finally, we applied phylostratigraphy and evolutionary transcriptomics approaches to our data. Results: The assembled reference transcriptome included transcripts of 12,620 protein-coding genes and was the first for any rhizocephalan. Based on the results obtained, the spatial heterogeneity of protein-coding gene expression in different regions of the adult female body of P. reticulata was established. The results of both transcriptomic analysis and histological studies indicated the presence of germ-like cells in the lumen of the interna. The potential molecular basis of the interaction between the nervous system of the host and the parasite's interna was also determined. Given the prolonged expression of development-associated genes, we suggest that rhizocephalans "got stuck in their metamorphosis", even at the reproductive stage. Conclusions: The results of the first comparative transcriptomic analysis for Rhizocephala not only clarified but also expanded the existing ideas about the biology of these extraordinary parasites.
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Affiliation(s)
- Maksim Nesterenko
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, 199034, Russian Federation
- Laboratory of parasitic worms and protists, Zoological Institute of Russian Academy of Sciences, St Petersburg, 199034, Russian Federation
| | - Aleksei Miroliubov
- Laboratory of parasitic worms and protists, Zoological Institute of Russian Academy of Sciences, St Petersburg, 199034, Russian Federation
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Bernot JP, Avdeyev P, Zamyatin A, Dreyer N, Alexeev N, Pérez-Losada M, Crandall KA. Chromosome-level genome assembly, annotation, and phylogenomics of the gooseneck barnacle Pollicipes pollicipes. Gigascience 2022; 11:giac021. [PMID: 35277961 PMCID: PMC8917513 DOI: 10.1093/gigascience/giac021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/09/2022] [Accepted: 02/11/2022] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The barnacles are a group of >2,000 species that have fascinated biologists, including Darwin, for centuries. Their lifestyles are extremely diverse, from free-swimming larvae to sessile adults, and even root-like endoparasites. Barnacles also cause hundreds of millions of dollars of losses annually due to biofouling. However, genomic resources for crustaceans, and barnacles in particular, are lacking. RESULTS Using 62× Pacific Biosciences coverage, 189× Illumina whole-genome sequencing coverage, 203× HiC coverage, and 69× CHi-C coverage, we produced a chromosome-level genome assembly of the gooseneck barnacle Pollicipes pollicipes. The P. pollicipes genome is 770 Mb long and its assembly is one of the most contiguous and complete crustacean genomes available, with a scaffold N50 of 47 Mb and 90.5% of the BUSCO Arthropoda gene set. Using the genome annotation produced here along with transcriptomes of 13 other barnacle species, we completed phylogenomic analyses on a nearly 2 million amino acid alignment. Contrary to previous studies, our phylogenies suggest that the Pollicipedomorpha is monophyletic and sister to the Balanomorpha, which alters our understanding of barnacle larval evolution and suggests homoplasy in a number of naupliar characters. We also compared transcriptomes of P. pollicipes nauplius larvae and adults and found that nearly one-half of the genes in the genome are differentially expressed, highlighting the vastly different transcriptomes of larvae and adult gooseneck barnacles. Annotation of the genes with KEGG and GO terms reveals that these stages exhibit many differences including cuticle binding, chitin binding, microtubule motor activity, and membrane adhesion. CONCLUSION This study provides high-quality genomic resources for a key group of crustaceans. This is especially valuable given the roles P. pollicipes plays in European fisheries, as a sentinel species for coastal ecosystems, and as a model for studying barnacle adhesion as well as its key position in the barnacle tree of life. A combination of genomic, phylogenetic, and transcriptomic analyses here provides valuable insights into the evolution and development of barnacles.
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Affiliation(s)
- James P Bernot
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20012, USA
| | - Pavel Avdeyev
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA
| | - Anton Zamyatin
- Computer Technologies Laboratory, ITMO University, Saint-Petersburg 197101, Russia
| | - Niklas Dreyer
- Department of Life Science, National Taiwan Normal University, Taipei 106, Taiwan
- Biodiversity Program, International Graduate Program, Academia Sinica, Taipei, Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
- Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark
| | - Nikita Alexeev
- Computer Technologies Laboratory, ITMO University, Saint-Petersburg 197101, Russia
| | - Marcos Pérez-Losada
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA
- Department of Biostatistics & Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal
| | - Keith A Crandall
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20012, USA
- Department of Biostatistics & Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC 20052, USA
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Alm Rosenblad M, Abramova A, Lind U, Ólason P, Giacomello S, Nystedt B, Blomberg A. Genomic Characterization of the Barnacle Balanus improvisus Reveals Extreme Nucleotide Diversity in Coding Regions. Mar Biotechnol (NY) 2021; 23:402-416. [PMID: 33931810 PMCID: PMC8270832 DOI: 10.1007/s10126-021-10033-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 04/05/2021] [Indexed: 05/11/2023]
Abstract
Barnacles are key marine crustaceans in several habitats, and they constitute a common practical problem by causing biofouling on man-made marine constructions and ships. Despite causing considerable ecological and economic impacts, there is a surprising void of basic genomic knowledge, and a barnacle reference genome is lacking. We here set out to characterize the genome of the bay barnacle Balanus improvisus (= Amphibalanus improvisus) based on short-read whole-genome sequencing and experimental genome size estimation. We show both experimentally (DNA staining and flow cytometry) and computationally (k-mer analysis) that B. improvisus has a haploid genome size of ~ 740 Mbp. A pilot genome assembly rendered a total assembly size of ~ 600 Mbp and was highly fragmented with an N50 of only 2.2 kbp. Further assembly-based and assembly-free analyses revealed that the very limited assembly contiguity is due to the B. improvisus genome having an extremely high nucleotide diversity (π) in coding regions (average π ≈ 5% and average π in fourfold degenerate sites ≈ 20%), and an overall high repeat content (at least 40%). We also report on high variation in the α-octopamine receptor OctA (average π = 3.6%), which might increase the risk that barnacle populations evolve resistance toward antifouling agents. The genomic features described here can help in planning for a future high-quality reference genome, which is urgently needed to properly explore and understand proteins of interest in barnacle biology and marine biotechnology and for developing better antifouling strategies.
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Affiliation(s)
- Magnus Alm Rosenblad
- Deparment of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg , Sweden
| | - Anna Abramova
- Deparment of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg , Sweden
| | - Ulrika Lind
- Deparment of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg , Sweden
| | - Páll Ólason
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Husargatan 3, 752 37, Uppsala, Sweden
| | - Stefania Giacomello
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Box 1031, 17121, Solna, Sweden
| | - Björn Nystedt
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Husargatan 3, 752 37, Uppsala, Sweden
| | - Anders Blomberg
- Deparment of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg , Sweden.
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Kobayashi M, Yusa Y, Sekino M. Microsatellite DNA markers applicable to paternity inference in the androdioecious gooseneck barnacle Octolasmis warwickii (Lepadiformes: Poecilasmatidae). Mol Biol Rep 2020; 47:4885-4890. [PMID: 32378167 DOI: 10.1007/s11033-020-05473-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 04/25/2020] [Indexed: 11/26/2022]
Abstract
The gooseneck barnacle Octolasmis warwickii has a rare sexual system called androdioecy, in which hermaphrodites and dwarf males co-occur. It has been hypothesized that dwarf males can coexist with conspecific hermaphrodites when dwarf males are capable of leaving more offspring than hermaphrodites via male reproduction. This hypothesis of reproductive superiority of dwarf males can be validated by comparing the reproductive success between dwarf males and hermaphrodites through DNA marker-based parentage testing. In the present study, we developed microsatellite DNA markers for O. warwickii, and evaluated the power of these markers to infer parentage based on simulation analysis. Using next generation sequencing, we obtained 344 microsatellite sequences suitable for designing primer sets for amplification in polymerase chain reaction (PCR). Of these, we examined the PCR amplification efficiency of 54 primer sets, of which 11 passed our primer screening in a population sample (n = 35). The developed markers exhibited moderate to high levels of polymorphisms, and met Hardy-Weinberg equilibrium with little evidence of significant allelic association to each other. Our simulated paternity inference suggested that the combinational use of the markers allows a high resolution of parentage (success rate of > 99.9%) if all candidate fathers are available.
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Affiliation(s)
- Mayumi Kobayashi
- National Research Institute of Fisheries Science, Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Yoichi Yusa
- Division of Natural Sciences, Nara Women's University, Nara, Japan
| | - Masashi Sekino
- National Research Institute of Fisheries Science, Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan.
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10
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Domínguez-Pérez D, Almeida D, Wissing J, Machado AM, Jänsch L, Castro LF, Antunes A, Vasconcelos V, Campos A, Cunha I. The Quantitative Proteome of the Cement and Adhesive Gland of the Pedunculate Barnacle, Pollicipes pollicipes. Int J Mol Sci 2020; 21:ijms21072524. [PMID: 32260514 PMCID: PMC7177777 DOI: 10.3390/ijms21072524] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/30/2020] [Accepted: 04/01/2020] [Indexed: 12/25/2022] Open
Abstract
Adhesive secretion has a fundamental role in barnacles’ survival, keeping them in an adequate position on the substrate under a variety of hydrologic regimes. It arouses special interest for industrial applications, such as antifouling strategies, underwater industrial and surgical glues, and dental composites. This study was focused on the goose barnacle Pollicipes pollicipes adhesion system, a species that lives in the Eastern Atlantic strongly exposed intertidal rocky shores and cliffs. The protein composition of P. pollicipes cement multicomplex and cement gland was quantitatively studied using a label-free LC-MS high-throughput proteomic analysis, searched against a custom transcriptome-derived database. Overall, 11,755 peptide sequences were identified in the gland while 2880 peptide sequences were detected in the cement, clustered in 1616 and 1568 protein groups, respectively. The gland proteome was dominated by proteins of the muscle, cytoskeleton, and some uncharacterized proteins, while the cement was, for the first time, reported to be composed by nearly 50% of proteins that are not canonical cement proteins, mainly unannotated proteins, chemical cues, and protease inhibitors, among others. Bulk adhesive proteins accounted for one-third of the cement proteome, with CP52k being the most abundant. Some unannotated proteins highly expressed in the proteomes, as well as at the transcriptomic level, showed similar physicochemical properties to the known surface-coupling barnacle adhesive proteins while the function of the others remains to be discovered. New quantitative and qualitative clues are provided to understand the diversity and function of proteins in the cement of stalked barnacles, contributing to the whole adhesion model in Cirripedia.
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Affiliation(s)
- Dany Domínguez-Pérez
- CIIMAR–Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua General Norton de Matos s/n, Terminal de Cruzeiros do Porto de Leixões, 4450-208 Matosinhos, Portugal; (D.D.-P.); (D.A.); (A.M.M.); (L.F.C.); (A.A.); (V.V.); (A.C.)
| | - Daniela Almeida
- CIIMAR–Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua General Norton de Matos s/n, Terminal de Cruzeiros do Porto de Leixões, 4450-208 Matosinhos, Portugal; (D.D.-P.); (D.A.); (A.M.M.); (L.F.C.); (A.A.); (V.V.); (A.C.)
| | - Josef Wissing
- Cellular Proteomics Research, Helmholtz Centre for Infection Research, Inhoffenstraße. 7, 38124 Braunschweig, Germany; (J.W.); (L.J.)
| | - André M. Machado
- CIIMAR–Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua General Norton de Matos s/n, Terminal de Cruzeiros do Porto de Leixões, 4450-208 Matosinhos, Portugal; (D.D.-P.); (D.A.); (A.M.M.); (L.F.C.); (A.A.); (V.V.); (A.C.)
| | - Lothar Jänsch
- Cellular Proteomics Research, Helmholtz Centre for Infection Research, Inhoffenstraße. 7, 38124 Braunschweig, Germany; (J.W.); (L.J.)
| | - Luís Filipe Castro
- CIIMAR–Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua General Norton de Matos s/n, Terminal de Cruzeiros do Porto de Leixões, 4450-208 Matosinhos, Portugal; (D.D.-P.); (D.A.); (A.M.M.); (L.F.C.); (A.A.); (V.V.); (A.C.)
- Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Agostinho Antunes
- CIIMAR–Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua General Norton de Matos s/n, Terminal de Cruzeiros do Porto de Leixões, 4450-208 Matosinhos, Portugal; (D.D.-P.); (D.A.); (A.M.M.); (L.F.C.); (A.A.); (V.V.); (A.C.)
- Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Vitor Vasconcelos
- CIIMAR–Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua General Norton de Matos s/n, Terminal de Cruzeiros do Porto de Leixões, 4450-208 Matosinhos, Portugal; (D.D.-P.); (D.A.); (A.M.M.); (L.F.C.); (A.A.); (V.V.); (A.C.)
- Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Alexandre Campos
- CIIMAR–Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua General Norton de Matos s/n, Terminal de Cruzeiros do Porto de Leixões, 4450-208 Matosinhos, Portugal; (D.D.-P.); (D.A.); (A.M.M.); (L.F.C.); (A.A.); (V.V.); (A.C.)
| | - Isabel Cunha
- CIIMAR–Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua General Norton de Matos s/n, Terminal de Cruzeiros do Porto de Leixões, 4450-208 Matosinhos, Portugal; (D.D.-P.); (D.A.); (A.M.M.); (L.F.C.); (A.A.); (V.V.); (A.C.)
- Correspondence: ; Tel.: +351-22-340-1800; Fax: +351-22-339-0608
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11
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Yan G, Sun J, Wang Z, Qian PY, He L. Insights into the Synthesis, Secretion and Curing of Barnacle Cyprid Adhesive via Transcriptomic and Proteomic Analyses of the Cement Gland. Mar Drugs 2020; 18:E186. [PMID: 32244485 PMCID: PMC7230167 DOI: 10.3390/md18040186] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 03/27/2020] [Accepted: 03/29/2020] [Indexed: 02/06/2023] Open
Abstract
Barnacles represent one of the model organisms used for antifouling research, however, knowledge regarding the molecular mechanisms underlying barnacle cyprid cementation is relatively scarce. Here, RNA-seq was used to obtain the transcriptomes of the cement glands where adhesive is generated and the remaining carcasses of Megabalanus volcano cyprids. Comparative transcriptomic analysis identified 9060 differentially expressed genes, with 4383 upregulated in the cement glands. Four cement proteins, named Mvcp113k, Mvcp130k, Mvcp52k and Mvlcp1-122k, were detected in the cement glands. The salivary secretion pathway was significantly enriched in the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of the differentially expressed genes, implying that the secretion of cyprid adhesive might be analogous to that of saliva. Lysyl oxidase had a higher expression level in the cement glands and was speculated to function in the curing of cyprid adhesive. Furthermore, the KEGG enrichment analysis of the 352 proteins identified in the cement gland proteome partially confirmed the comparative transcriptomic results. These results present insights into the molecular mechanisms underlying the synthesis, secretion and curing of barnacle cyprid adhesive and provide potential molecular targets for the development of environmentally friendly antifouling compounds.
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Affiliation(s)
- Guoyong Yan
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China;
- Center for Human Tissues and Organs Degeneration, Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jin Sun
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of The Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong 999077, China; (J.S.); (P.-Y.Q.)
| | - Zishuai Wang
- Department of Computer Science, City University of Hong Kong, Hong Kong 999077, China;
| | - Pei-Yuan Qian
- Department of Ocean Science, Division of Life Science and Hong Kong Branch of The Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong 999077, China; (J.S.); (P.-Y.Q.)
| | - Lisheng He
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China;
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12
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Gan Z, Yuan J, Liu X, Dong D, Li F, Li X. Comparative transcriptomic analysis of deep- and shallow-water barnacle species (Cirripedia, Poecilasmatidae) provides insights into deep-sea adaptation of sessile crustaceans. BMC Genomics 2020; 21:240. [PMID: 32183697 PMCID: PMC7077169 DOI: 10.1186/s12864-020-6642-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 03/03/2020] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Barnacles are specialized marine organisms that differ from other crustaceans in possession of a calcareous shell, which is attached to submerged surfaces. Barnacles have a wide distribution, mostly in the intertidal zone and shallow waters, but a few species inhabit the deep-sea floor. It is of interest to investigate how such sessile crustaceans became adapted to extreme deep-sea environments. We sequenced the transcriptomes of a deep-sea barnacle, Glyptelasma gigas collected at a depth of 731 m from the northern area of the Zhongjiannan Basin, and a shallow-water coordinal relative, Octolasmis warwicki. The purpose of this study was to provide genetic resources for investigating adaptation mechanisms of deep-sea barnacles. RESULTS Totals of 62,470 and 51,585 unigenes were assembled for G. gigas and O. warwicki, respectively, and functional annotation of these unigenes was made using public databases. Comparison of the protein-coding genes between the deep- and shallow-water barnacles, and with those of four other shallow-water crustaceans, revealed 26 gene families that had experienced significant expansion in G. gigas. Functional annotation showed that these expanded genes were predominately related to DNA repair, signal transduction and carbohydrate metabolism. Base substitution analysis on the 11,611 single-copy orthologs between G. gigas and O. warwicki indicated that 25 of them were distinctly positive selected in the deep-sea barnacle, including genes related to transcription, DNA repair, ligand binding, ion channels and energy metabolism, potentially indicating their importance for survival of G. gigas in the deep-sea environment. CONCLUSIONS The barnacle G. gigas has adopted strategies of expansion of specific gene families and of positive selection of key genes to counteract the negative effects of high hydrostatic pressure, hypoxia, low temperature and food limitation on the deep-sea floor. These expanded gene families and genes under positive selection would tend to enhance the capacities of G. gigas for signal transduction, genetic information processing and energy metabolism, and facilitate networks for perceiving and responding physiologically to the environmental conditions in deep-sea habitats. In short, our results provide genomic evidence relating to deep-sea adaptation of G. gigas, which provide a basis for further biological studies of sessile crustaceans in the deep sea.
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Affiliation(s)
- Zhibin Gan
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Jianbo Yuan
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Xinming Liu
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Dong Dong
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Fuhua Li
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China.
| | - Xinzheng Li
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China.
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13
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Abstract
The barnacle Balanus glandula is a broadly distributed species in the temperate northeastern Pacific that is notable for a robust genetic cline between about 36° and 40° N latitude. Prior work established the evolutionary origins of this pattern and proposed that it is maintained by environmental selection. In recent years, "climate velocity" studies in marine habitats have shown dramatic distributional shifts for many species as they track their preferred temperature range in a warming ocean. We re-sampled B. glandula across its entire geographic range to determine whether there has been any shift in this genetic distribution, a development signaling that temperature or other climate factors are maintaining this genetic cline. Additionally, we asked whether the spatially distributed mitochondrial lineages also vary in reproductive output with latitude, using location as a proxy for temperature and other coastal environmental factors. Here we show that although the distribution of the genetic cline has not appreciably changed, there is a notable association of decreased reproductive output at lower latitudes of the distribution in the "northern" lineage of B. glandula.
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14
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Rocha M, Antas P, Castro LFC, Campos A, Vasconcelos V, Pereira F, Cunha I. Comparative Analysis of the Adhesive Proteins of the Adult Stalked Goose Barnacle Pollicipes pollicipes (Cirripedia: Pedunculata). Mar Biotechnol (NY) 2019; 21:38-51. [PMID: 30413912 DOI: 10.1007/s10126-018-9856-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/14/2018] [Indexed: 06/08/2023]
Abstract
Adhesion in barnacles is still poorly understood. The cement gland secretes an insoluble multi-protein complex, which adheres very strongly to a variety of substrates in the presence of water. This adhesion mechanism is bioinspiring for the engineering of new adhesive materials, but to replicate this adhesive system, the genes coding for the cement constitutive proteins must be identified and elucidated, and their products characterised. Here, the complete sequences of three cement protein (CP) genes (CP-100K, CP-52K, and CP-19K) isolated from the cement gland of the stalked barnacle Pollicipes pollicipes (order Scalpelliformes) were obtained using RACE PCR. The three genes were compared to the 23 other acorn barnacle CP genes so far sequenced (order Sessilia) to determine common and differential patterns and molecular properties, since the adhesives of both orders have visibly different characteristics. A shotgun proteomic analysis was performed on the cement, excreted at the membranous base of specimens, where the products of the three genes sequenced in the gland were identified, validating their function as CPs. A principal component analysis (PCA) was performed, to cluster CPs into groups with similar amino acid composition. This analysis uncovered three CP groups, each characterised by similar residue composition, features in secondary structure, and some biochemical properties, including isoelectric point and residue accessibility to solvents. The similarity among proteins in each defined group was low despite comparable amino acid composition. PCA can identify putative adhesive proteins from NGS transcriptomic data regardless of their low homology. This analysis did not highlight significant differences in residue composition between homologous acorn and stalked barnacle CPs. The characteristics responsible for the structural differences between the cement of stalked and acorn barnacles are described, and the presence of nanostructures, such as repetitive homologous domains and low complexity regions, and repetitive β-sheets are discussed relatively to self-assembly and adhesion.
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Affiliation(s)
- Miguel Rocha
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal
- FCUP - Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - Paulo Antas
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal
| | - L Filipe C Castro
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal
- FCUP - Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - Alexandre Campos
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal
| | - Vítor Vasconcelos
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal
- FCUP - Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - Filipe Pereira
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal.
| | - Isabel Cunha
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal.
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Yorisue T, Yoshioka Y, Sakuma K, Iguchi A. Evaluating the occurrence of cryptic invasions of a rocky shore barnacle, Semibalanus cariosus, between the north-eastern Pacific and Japan. Biofouling 2018; 34:183-189. [PMID: 29378431 DOI: 10.1080/08927014.2017.1421636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 12/21/2017] [Indexed: 06/07/2023]
Abstract
Many coastal barnacles are introduced to non-native regions. However, data are lacking on cryptic invasion, which is defined as an invasion that remains unrecognised because the invader is mistaken for a native or previously introduced species or clade. In this work, cryptic invasions of an intertidal barnacle, Semibalanus cariosus, between Japan and the north-eastern Pacific were evaluated based on population genetic analyses. A significant genetic differentiation was found between the Japanese and north-eastern Pacific populations, suggesting a limited introduction of non-native genotypes between these regions. Haplotype frequencies did not differ significantly between the past (museum samples collected in 1971 from Hokkaido, Japan) and present Japanese populations, implying the rare occurrence of human-mediated migration from the north-eastern Pacific to Japan. Migrate-n analysis revealed a low level of directional gene flow in S. cariosus from the north-eastern Pacific to Japan, possibly by natural stepping-stone dispersal via directional water currents or human-mediated transport.
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Affiliation(s)
- Takefumi Yorisue
- a Akkeshi Marine Station, Field Science Center for Northern Biosphere , Hokkaido University , Akkeshi , Japan
| | - Yuki Yoshioka
- b Department of Bioresources Engineering , National Institute of Technology, Okinawa College , Nago , Japan
| | - Kay Sakuma
- c Japan Sea National Fisheries Research Institute , Fisheries Research and Education Agency , Niigata , Japan
| | - Akira Iguchi
- b Department of Bioresources Engineering , National Institute of Technology, Okinawa College , Nago , Japan
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Yan G, Zhang G, Huang J, Lan Y, Sun J, Zeng C, Wang Y, Qian PY, He L. Comparative Transcriptomic Analysis Reveals Candidate Genes and Pathways Involved in Larval Settlement of the Barnacle Megabalanus volcano. Int J Mol Sci 2017; 18:E2253. [PMID: 29077039 PMCID: PMC5713223 DOI: 10.3390/ijms18112253] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 10/14/2017] [Accepted: 10/23/2017] [Indexed: 12/16/2022] Open
Abstract
Megabalanus barnacle is one of the model organisms for marine biofouling research. However, further elucidation of molecular mechanisms underlying larval settlement has been hindered due to the lack of genomic information thus far. In the present study, cDNA libraries were constructed for cyprids, the key stage for larval settlement, and adults of Megabalanus volcano. After high-throughput sequencing and de novo assembly, 42,620 unigenes were obtained with a N50 value of 1532 bp. These unigenes were annotated by blasting against the NCBI non-redundant (nr), Swiss-Prot, Cluster of Orthologous Groups (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Finally, 19,522, 15,691, 14,459, and 10,914 unigenes were identified correspondingly. There were 22,158 differentially expressed genes (DEGs) identified between two stages. Compared with the cyprid stage, 8241 unigenes were down-regulated and 13,917 unigenes were up-regulated at the adult stage. The neuroactive ligand-receptor interaction pathway (ko04080) was significantly enriched by KEGG enrichment analysis of the DEGs, suggesting that it possibly involved in larval settlement. Potential functions of three conserved allatostatin neuropeptide-receptor pairs and two light-sensitive opsin proteins were further characterized, indicating that they might regulate attachment and metamorphosis at cyprid stage. These results provided a deeper insight into the molecular mechanisms underlying larval settlement of barnacles.
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Affiliation(s)
- Guoyong Yan
- Department of Life Sciences, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China.
- College of Earth Sciences, University of Chinese Academy of Sciences, Beijing 100864, China.
| | - Gen Zhang
- The Shenzhen Nobel Science and Technology Service Co., Ltd., Nanshan District, Shenzhen 440305, China.
| | - Jiaomei Huang
- Department of Life Sciences, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China.
| | - Yi Lan
- Division of Life Sciences, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.
| | - Jin Sun
- Division of Life Sciences, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.
| | - Cong Zeng
- Department of Life Sciences, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China.
| | - Yong Wang
- Department of Life Sciences, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China.
| | - Pei-Yuan Qian
- Division of Life Sciences, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.
| | - Lisheng He
- Department of Life Sciences, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China.
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17
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Lind U, Järvå M, Alm Rosenblad M, Pingitore P, Karlsson E, Wrange AL, Kamdal E, Sundell K, André C, Jonsson PR, Havenhand J, Eriksson LA, Hedfalk K, Blomberg A. Analysis of aquaporins from the euryhaline barnacle Balanus improvisus reveals differential expression in response to changes in salinity. PLoS One 2017; 12:e0181192. [PMID: 28715506 PMCID: PMC5513457 DOI: 10.1371/journal.pone.0181192] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 06/26/2017] [Indexed: 12/13/2022] Open
Abstract
Barnacles are sessile macro-invertebrates, found along rocky shores in coastal areas worldwide. The euryhaline bay barnacle Balanus improvisus (Darwin, 1854) (= Amphibalanus improvisus) can tolerate a wide range of salinities, but the molecular mechanisms underlying the osmoregulatory capacity of this truly brackish species are not well understood. Aquaporins are pore-forming integral membrane proteins that facilitate transport of water, small solutes and ions through cellular membranes, and that have been shown to be important for osmoregulation in many organisms. The knowledge of the function of aquaporins in crustaceans is, however, limited and nothing is known about them in barnacles. We here present the repertoire of aquaporins from a thecostracan crustacean, the barnacle B. improvisus, based on genome and transcriptome sequencing. Our analyses reveal that B. improvisus contains eight genes for aquaporins. Phylogenetic analysis showed that they represented members of the classical water aquaporins (Aqp1, Aqp2), the aquaglyceroporins (Glp1, Glp2), the unorthodox aquaporin (Aqp12) and the arthropod-specific big brain aquaporin (Bib). Interestingly, we also found two big brain-like proteins (BibL1 and BibL2) constituting a new group of aquaporins not yet described in arthropods. In addition, we found that the two water-specific aquaporins were expressed as C-terminal splice variants. Heterologous expression of some of the aquaporins followed by functional characterization showed that Aqp1 transported water and Glp2 water and glycerol, agreeing with the predictions of substrate specificity based on 3D modeling and phylogeny. To investigate a possible role for the B. improvisus aquaporins in osmoregulation, mRNA expression changes in adult barnacles were analysed after long-term acclimation to different salinities. The most pronounced expression difference was seen for AQP1 with a substantial (>100-fold) decrease in the mantle tissue in low salinity (3 PSU) compared to high salinity (33 PSU). Our study provides a base for future mechanistic studies on the role of aquaporins in osmoregulation.
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Affiliation(s)
- Ulrika Lind
- Department of Marine Sciences, Lundberg laboratory, University of Gothenburg, Gothenburg, Sweden
| | - Michael Järvå
- Department of Chemistry and Molecular Biology, Lundberg laboratory, University of Gothenburg, Gothenburg, Sweden
| | - Magnus Alm Rosenblad
- Department of Marine Sciences, National Infrastructure of Bioinformatics (NBIS), Lundberg laboratory, University of Gothenburg, Gothenburg, Sweden
| | - Piero Pingitore
- Department of Molecular and Clinical Medicine, Wallenberg Laboratory, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Emil Karlsson
- Department of Marine Sciences, Lundberg laboratory, University of Gothenburg, Gothenburg, Sweden
| | - Anna-Lisa Wrange
- RISE Research Institute of Sweden, Section for Chemistry and Materials, Borås, Sweden
| | - Emelie Kamdal
- Department of Chemistry and Molecular Biology, Lundberg laboratory, University of Gothenburg, Gothenburg, Sweden
| | - Kristina Sundell
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Carl André
- Department of Marine Sciences-Tjärnö, University of Gothenburg, Strömstad, Sweden
| | - Per R. Jonsson
- Department of Marine Sciences-Tjärnö, University of Gothenburg, Strömstad, Sweden
| | - Jon Havenhand
- Department of Marine Sciences-Tjärnö, University of Gothenburg, Strömstad, Sweden
| | - Leif A. Eriksson
- Department of Chemistry and Molecular Biology, Lundberg laboratory, University of Gothenburg, Gothenburg, Sweden
| | - Kristina Hedfalk
- Department of Chemistry and Molecular Biology, Lundberg laboratory, University of Gothenburg, Gothenburg, Sweden
| | - Anders Blomberg
- Department of Marine Sciences, Lundberg laboratory, University of Gothenburg, Gothenburg, Sweden
- * E-mail:
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18
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Ewers-Saucedo C, Chan BKK, Zardus JD, Wares JP. Parallel Patterns of Host-Specific Morphology and Genetic Admixture in Sister Lineages of a Commensal Barnacle. Biol Bull 2017; 232:171-185. [PMID: 28898602 DOI: 10.1086/693356] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Symbiotic relationships are often species specific, allowing symbionts to adapt to their host environments. Host generalists, on the other hand, have to cope with diverse environments. One coping strategy is phenotypic plasticity, defined by the presence of host-specific phenotypes in the absence of genetic differentiation. Recent work indicates that such host-specific phenotypic plasticity is present in the West Pacific lineage of the commensal barnacle Chelonibia testudinaria (Linnaeus, 1758). We investigated genetic and morphological host-specific structure in the genetically distinct Atlantic sister lineage of C. testudinaria. We collected adult C. testudinaria from loggerhead sea turtles, horseshoe crabs, and blue crabs along the eastern U.S. coast between Delaware and Florida and in the Gulf of Mexico off Mississippi. We find that shell morphology, especially shell thickness, is host specific and comparable in similar host species between the Atlantic and West Pacific lineages. We did not detect significant genetic differentiation related to host species when analyzing data from 11 nuclear microsatellite loci and mitochondrial sequence data, which is comparable to findings for the Pacific lineage. The most parsimonious explanation for these parallel patterns between distinct lineages of C. testudinaria is that C. testudinaria maintained phenotypic plasticity since the lineages diverged 4-5 mya.
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Panova M, Aronsson H, Cameron RA, Dahl P, Godhe A, Lind U, Ortega-Martinez O, Pereyra R, Tesson SVM, Wrange AL, Blomberg A, Johannesson K. DNA Extraction Protocols for Whole-Genome Sequencing in Marine Organisms. Methods Mol Biol 2016; 1452:13-44. [PMID: 27460368 DOI: 10.1007/978-1-4939-3774-5_2] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The marine environment harbors a large proportion of the total biodiversity on this planet, including the majority of the earths' different phyla and classes. Studying the genomes of marine organisms can bring interesting insights into genome evolution. Today, almost all marine organismal groups are understudied with respect to their genomes. One potential reason is that extraction of high-quality DNA in sufficient amounts is challenging for many marine species. This is due to high polysaccharide content, polyphenols and other secondary metabolites that will inhibit downstream DNA library preparations. Consequently, protocols developed for vertebrates and plants do not always perform well for invertebrates and algae. In addition, many marine species have large population sizes and, as a consequence, highly variable genomes. Thus, to facilitate the sequence read assembly process during genome sequencing, it is desirable to obtain enough DNA from a single individual, which is a challenge in many species of invertebrates and algae. Here, we present DNA extraction protocols for seven marine species (four invertebrates, two algae, and a marine yeast), optimized to provide sufficient DNA quality and yield for de novo genome sequencing projects.
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Affiliation(s)
- Marina Panova
- Department of Marine Sciences, University of Gothenburg, Strömstad, Sweden.
| | - Henrik Aronsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - R Andrew Cameron
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Peter Dahl
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Anna Godhe
- Department of Marine Sciences, University of Gothenburg, Strömstad, Sweden
| | - Ulrika Lind
- Department of Marine Sciences, University of Gothenburg, Strömstad, Sweden
| | | | - Ricardo Pereyra
- Department of Marine Sciences, University of Gothenburg, Strömstad, Sweden
| | - Sylvie V M Tesson
- Department of Marine Sciences, University of Gothenburg, Strömstad, Sweden
| | - Anna-Lisa Wrange
- Department of Marine Sciences, University of Gothenburg, Strömstad, Sweden
| | - Anders Blomberg
- Department of Marine Sciences, University of Gothenburg, Strömstad, Sweden
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Liang C, Li Y, Liu Z, Wu W, Hu B. Protein Aggregation Formed by Recombinant cp19k Homologue of Balanus albicostatus Combined with an 18 kDa N-Terminus Encoded by pET-32a(+) Plasmid Having Adhesion Strength Comparable to Several Commercial Glues. PLoS One 2015; 10:e0136493. [PMID: 26317205 PMCID: PMC4552757 DOI: 10.1371/journal.pone.0136493] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 08/04/2015] [Indexed: 01/17/2023] Open
Abstract
The barnacle is well known for its tenacious and permanent attachment to a wide variety of underwater substrates, which is accomplished by synthesizing, secreting and curing a mixture of adhesive proteins termed “barnacle cement”. In order to evaluate interfacial adhesion abilities of barnacle cement proteins, the cp19k homologous gene in Balanus albicostatus (Balcp19k) was cloned and expressed in Escherichia coli. Here, we report an intriguing discovery of a gel-like super adhesive aggregation produced by Trx-Balcp19k, a recombinant Balcp19k fusion protein. The Trx-Balcp19k consists of an 18 kDa fragment at the N-terminus, which is encoded by pET-32a(+) plasmid and mainly comprised of a thioredoxin (Trx) tag, and Balcp19k at the C-terminus. The sticky aggregation was designated as “Trx-Balcp19k gel”, and the bulk adhesion strength, biochemical composition, as well as formation conditions were all carefully investigated. The Trx-Balcp19k gel exhibited strong adhesion strength of 2.10 ± 0.67 MPa, which was approximately fifty folds higher than that of the disaggregated Trx-Balcp19k (40 ± 8 kPa) and rivaled those of commercial polyvinyl acetate (PVA) craft glue (Mont Marte, Australia) and UHU glue (UHU GmbH & Co. KG, Germany). Lipids were absent from the Trx-Balcp19k gel and only a trace amount of carbohydrates was detected. We postulate that the electrostatic interactions play a key role in the formation of Trx-Balcp19k gel, by mediating self-aggregation of Trx-Balcp19k based on its asymmetric distribution pattern of charged amino acids. Taken together, we believe that our discovery not only presents a promising biological adhesive with potential applications in both biomedical and technical fields, but also provides valuable paradigms for molecular design of bio-inspired peptide- or protein-based materials.
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Affiliation(s)
- Chao Liang
- Department of Chemistry and Biology, College of Science, National University of Defense Technology, Changsha, Hunan, China
| | - Yunqiu Li
- Department of Chemistry and Biology, College of Science, National University of Defense Technology, Changsha, Hunan, China
| | - Zhiming Liu
- Department of Chemistry and Biology, College of Science, National University of Defense Technology, Changsha, Hunan, China
| | - Wenjian Wu
- Department of Chemistry and Biology, College of Science, National University of Defense Technology, Changsha, Hunan, China
- State Key Laboratory of NBC Protection for Civilian, Beijing, China
| | - Biru Hu
- Department of Chemistry and Biology, College of Science, National University of Defense Technology, Changsha, Hunan, China
- * E-mail:
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21
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Quinteiro J, Manent P, Pérez-Diéguez L, González JA, Almeida C, Lopes E, Araújo R, Carreira GP, Rey-Méndez M, González-Henríquez N. Phylogeography of a Marine Insular Endemic in the Atlantic Macaronesia: The Azorean Barnacle, Megabalanus azoricus (Pilsbry, 1916). PLoS One 2015; 10:e0124707. [PMID: 25919141 PMCID: PMC4412576 DOI: 10.1371/journal.pone.0124707] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 03/03/2015] [Indexed: 12/14/2022] Open
Abstract
The Azorean barnacle, Megabalanus azoricus (Pilsbry, 1916), is a Macaronesian endemic whose obscure taxonomy and the unknown relationships among forms inhabiting isolated Northern Atlantic oceanic islands is investigated by means of molecular analysis herein. Mitochondrial data from the 16S rRNA and COX1 genes support its current species status, tropical ancestry, and the taxonomic homogeneity throughout its distribution range. In contrast, at the intraspecific level and based on control region sequences, we detected an overall low level of genetic diversity and three divergent lineages. The haplogroups α and γ were sampled in the Azores, Madeira, Canary, and Cabo Verde archipelagos; whereas haplogroup β was absent from Cabo Verde. Consequently, population analysis suggested a differentiation of the Cabo Verde population with respect to the genetically homogenous northern archipelagos generated by current oceanographic barriers. Furthermore, haplogroup α, β, and γ demographic expansions occurred during the interglacial periods MIS5 (130 Kya - thousands years ago -), MIS3 (60 Kya), and MIS7 (240 Kya), respectively. The evolutionary origin of these lineages is related to its survival in the stable southern refugia and its demographic expansion dynamics are associated with the glacial-interglacial cycles. This phylogeographic pattern suggests the occurrence of genetic discontinuity informative to the delimitation of an informally defined biogeographic entity, Macaronesia, and its generation by processes that delineate genetic diversity of marine taxa in this area.
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Affiliation(s)
- Javier Quinteiro
- Molecular Systematics Laboratory, Department of Biochemistry and Molecular Biology, University Santiago de Compostela, A Coruña, Galicia, Spain
- * E-mail:
| | - Pablo Manent
- Departament of Biology, University of Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Lois Pérez-Diéguez
- Molecular Systematics Laboratory, Department of Biochemistry and Molecular Biology, University Santiago de Compostela, A Coruña, Galicia, Spain
| | - José A. González
- Departament of Biology, University of Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Corrine Almeida
- Departament of Enginery and Sea Sciences. University of Cabo Verde, Mindelo, São Vicente, Cabo Verde
| | - Evandro Lopes
- Departament of Enginery and Sea Sciences. University of Cabo Verde, Mindelo, São Vicente, Cabo Verde
| | - Ricardo Araújo
- Natural History Museum of Funchal, Funchal, Madeira, Portugal
| | - Gilberto P. Carreira
- Regional Directorate of Sea Affaires, Regional Secretary of Natural Resources, Horta, Açores, Portugal
| | - Manuel Rey-Méndez
- Molecular Systematics Laboratory, Department of Biochemistry and Molecular Biology, University Santiago de Compostela, A Coruña, Galicia, Spain
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Herrera S, Watanabe H, Shank TM. Evolutionary and biogeographical patterns of barnacles from deep-sea hydrothermal vents. Mol Ecol 2015; 24:673-89. [PMID: 25602032 PMCID: PMC5006861 DOI: 10.1111/mec.13054] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 12/14/2014] [Accepted: 12/20/2014] [Indexed: 01/16/2023]
Abstract
The characterization of evolutionary and biogeographical patterns is of fundamental importance to identify factors driving biodiversity. Due to their widespread but discontinuous distribution, deep-sea hydrothermal vent barnacles represent an excellent model for testing biogeographical hypotheses regarding the origin, dispersal and diversity of modern vent fauna. Here, we characterize the global genetic diversity of vent barnacles to infer their time of radiation, place of origin, mode of dispersal and diversification. Our approach was to target a suite of multiple loci in samples representing seven of the eight described genera. We also performed restriction-site associated DNA sequencing on individuals from each species. Phylogenetic inferences and topology hypothesis tests indicate that vent barnacles have colonized deep-sea hydrothermal vents at least twice in history. Consistent with preliminary estimates, we find a likely radiation of barnacles in vent ecosystems during the Cenozoic. Our analyses suggest that the western Pacific was the place of origin of the major vent barnacle lineage, followed by circumglobal colonization eastwards through the Southern Hemisphere during the Neogene. The inferred time of radiation rejects the classic hypotheses of antiquity of vent taxa. The timing and the mode of origin, radiation and dispersal are consistent with recent inferences made for other deep-sea taxa, including nonvent species, and are correlated with the occurrence of major geological events and mass extinctions. Thus, we suggest that the geological processes and dispersal mechanisms discussed here can explain the current distribution patterns of many other marine taxa and have played an important role shaping deep-sea faunal diversity. These results also constitute the critical baseline data with which to assess potential effects of anthropogenic disturbances on deep-sea ecosystems.
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Affiliation(s)
- Santiago Herrera
- Massachusetts Institute of Technology77 Massachusetts AvenueCambridgeMA02139USA
- Biology DepartmentWoods Hole Oceanographic Institution266 Woods Hole RoadWoods HoleMA02543USA
| | - Hiromi Watanabe
- Institute of BiogeosciencesJapan Agency for Marine‐Earth Science and TechnologyYokosukaKanagawaJapan
| | - Timothy M. Shank
- Biology DepartmentWoods Hole Oceanographic Institution266 Woods Hole RoadWoods HoleMA02543USA
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Abstract
Amphibalanus amphitrite is a common fouling barnacle distributed globally in tropical and subtropical waters. In the present study, the genetic (mitochondrial cytochrome oxidase subunit I) and morphological differentiation in A. amphitrite from 25 localities around the world were investigated. The results revealed three clades within A. amphitrite with a genetic divergence of ~ 4% among clades, whereas there were no diagnostic morphological differences among clades. Clade 1 is widely distributed in both temperate and tropical waters, whereas Clade 3 is currently restricted to the tropical region. The deep divergence among clades suggests historical isolation within A. amphitrite; thus, the present geographical overlaps are possibly a result of the combined effects of rising sea level and human-mediated dispersals. This study highlights the genetic differentiation that exists in a common, widely distributed fouling organism with great dispersal potential; future antifouling research should take into account the choice of lineages.
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Affiliation(s)
- Hsi-Nien Chen
- a Institute of Ecology and Evolutionary Biology , National Taiwan University , Taipei , Taiwan , ROC
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24
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Nakajima Y, Shinzato C, Khalturina M, Watanabe H, Inagaki F, Satoh N, Mitarai S. Cross-species, amplifiable microsatellite markers for neoverrucid barnacles from deep-sea hydrothermal vents developed using next-generation sequencing. Int J Mol Sci 2014; 15:14364-71. [PMID: 25196437 PMCID: PMC4159855 DOI: 10.3390/ijms150814364] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 07/16/2014] [Accepted: 08/12/2014] [Indexed: 11/19/2022] Open
Abstract
Barnacles of the genus Neoverruca are abundant near deep-sea hydrothermal vents of the northwestern Pacific Ocean, and are useful for understanding processes of population formation and maintenance of deep-sea vent faunas. Using next-generation sequencing, we isolated 12 polymorphic microsatellite loci from Neoverruca sp., collected in the Okinawa Trough. These microsatellite loci revealed 2–19 alleles per locus. The expected and observed heterozygosities ranged from 0.286 to 1.000 and 0.349 to 0.935, respectively. Cross-species amplification showed that 9 of the 12 loci were successfully amplified for Neoverruca brachylepadoformis in the Mariana Trough. A pairwise FST value calculated using nine loci showed significant genetic differentiation between the two species. Consequently, the microsatellite markers we developed will be useful for further population genetic studies to elucidate genetic diversity, differentiation, classification, and evolutionary processes in the genus Neoverruca.
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Affiliation(s)
- Yuichi Nakajima
- Marine Biophysics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa 904-0495, Japan.
| | - Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa 904-0495, Japan.
| | - Mariia Khalturina
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa 904-0495, Japan.
| | - Hiromi Watanabe
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan.
| | - Fumio Inagaki
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology, B-200 Monobe, Nankoku, Kochi 783-8502, Japan.
| | - Nori Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa 904-0495, Japan.
| | - Satoshi Mitarai
- Marine Biophysics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa 904-0495, Japan.
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Reynolds TV, Matthee CA, von der Heyden S. The influence of Pleistocene climatic changes and ocean currents on the phylogeography of the southern African barnacle, Tetraclita serrata (Thoracica; Cirripedia). PLoS One 2014; 9:e102115. [PMID: 25054971 PMCID: PMC4108325 DOI: 10.1371/journal.pone.0102115] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 06/15/2014] [Indexed: 11/19/2022] Open
Abstract
The evolutionary effects of glacial periods are poorly understood for Southern Hemisphere marine intertidal species, particularly obligatory sessile organisms. We examined this by assessing the phylogeographic patterns of the southern African volcano barnacle, Tetraclita serrata, a dominant species on rocky intertidal shores. Restricted gene flow in some geographical areas was hypothesized based on oceanic circulation patterns and known biogeographic regions. Barnacle population genetic structure was investigated using the mitochondrial cytochrome oxidase subunit 1 (COI) region for 410 individuals sampled from 20 localities spanning the South African coast. The mtDNA data were augmented by generating nuclear internal transcribed spacer 1 (ITS1) sequences from a subset of samples. Phylogenetic and population genetic analyses of mitochondrial DNA data reveal two distinct clades with mostly sympatric distributions, whereas nuclear analyses reveal only a single lineage. Shallow, but significant structure (0.0041-0.0065, P<0.01) was detected for the mtDNA data set, with the south-west African region identified as harbouring the highest levels of genetic diversity. Gene flow analyses on the mtDNA data show that individuals sampled in south-western localities experience gene flow primarily in the direction of the Benguela Current, while south and eastern localities experience bi-directional gene flow, suggesting an influence of both the inshore currents and the offshore Agulhas Current in the larval distribution of T. serrata. The mtDNA haplotype network, Bayesian Skyline Plots, mismatch distributions and time since expansion indicate that T. serrata population numbers were not severely affected by the Last Glacial Maximum (LGM), unlike other southern African marine species. The processes resulting in the two morphologically cryptic mtDNA lineages may be the result of a recent historical allopatric event followed by secondary contact or could reflect selective pressures due to differing environmental conditions.
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Affiliation(s)
- Terry V. Reynolds
- Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Matieland, South Africa
| | - Conrad A. Matthee
- Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Matieland, South Africa
| | - Sophie von der Heyden
- Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Matieland, South Africa
- * E-mail:
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Chen ZF, Zhang H, Wang H, Matsumura K, Wong YH, Ravasi T, Qian PY. Quantitative proteomics study of larval settlement in the Barnacle Balanus amphitrite. PLoS One 2014; 9:e88744. [PMID: 24551147 PMCID: PMC3923807 DOI: 10.1371/journal.pone.0088744] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 01/08/2014] [Indexed: 01/06/2023] Open
Abstract
Barnacles are major sessile components of the intertidal areas worldwide, and also one of the most dominant fouling organisms in fouling communities. Larval settlement has a crucial ecological effect not only on the distribution of the barnacle population but also intertidal community structures. However, the molecular mechanisms involved in the transition process from the larval to the juvenile stage remain largely unclear. In this study, we carried out comparative proteomic profiles of stage II nauplii, stage VI nauplii, cyprids, and juveniles of the barnacle Balanus amphitrite using label-free quantitative proteomics, followed by the measurement of the gene expression levels of candidate proteins. More than 700 proteins were identified at each stage; 80 were significantly up-regulated in cyprids and 95 in juveniles vs other stages. Specifically, proteins involved in energy and metabolism, the nervous system and signal transduction were significantly up-regulated in cyprids, whereas proteins involved in cytoskeletal remodeling, transcription and translation, cell proliferation and differentiation, and biomineralization were up-regulated in juveniles, consistent with changes associated with larval metamorphosis and tissue remodeling in juveniles. These findings provided molecular evidence for the morphological, physiological and biological changes that occur during the transition process from the larval to the juvenile stages in B. amphitrite.
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Affiliation(s)
- Zhang-Fan Chen
- KAUST Global Collaborative Research Program, Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Huoming Zhang
- Bioscience Core Laboratory, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Hao Wang
- KAUST Global Collaborative Research Program, Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Kiyotaka Matsumura
- KAUST Global Collaborative Research Program, Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Yue Him Wong
- KAUST Global Collaborative Research Program, Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Timothy Ravasi
- Integrative Systems Biology Lab, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Pei-Yuan Qian
- KAUST Global Collaborative Research Program, Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
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Lin HC, Wong YH, Tsang LM, Chu KH, Qian PY, Chan BKK. First study on gene expression of cement proteins and potential adhesion-related genes of a membranous-based barnacle as revealed from Next-Generation Sequencing technology. Biofouling 2014; 30:169-181. [PMID: 24329402 DOI: 10.1080/08927014.2013.853051] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
This is the first study applying Next-Generation Sequencing (NGS) technology to survey the kinds, expression location, and pattern of adhesion-related genes in a membranous-based barnacle. A total of 77,528,326 and 59,244,468 raw sequence reads of total RNA were generated from the prosoma and the basis of Tetraclita japonica formosana, respectively. In addition, 55,441 and 67,774 genes were further assembled and analyzed. The combined sequence data from both body parts generates a total of 79,833 genes of which 47.7% were shared. Homologues of barnacle cement proteins - CP-19K, -52K, and -100K - were found and all were dominantly expressed at the basis where the cement gland complex is located. This is the main area where transcripts of cement proteins and other potential adhesion-related genes were detected. The absence of another common barnacle cement protein, CP-20K, in the adult transcriptome suggested a possible life-stage restricted gene function and/or a different mechanism in adhesion between membranous-based and calcareous-based barnacles.
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Affiliation(s)
- Hsiu-Chin Lin
- a Biodiversity Research Center, Academia Sinica , Taipei 115 , Taiwan
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28
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Rivera A, Weidberg N, Pardiñas AF, González-Gil R, García-Flórez L, Acuña JL. Role of upwelling on larval dispersal and productivity of gooseneck barnacle populations in the Cantabrian Sea: management implications. PLoS One 2013; 8:e78482. [PMID: 24236020 PMCID: PMC3827236 DOI: 10.1371/journal.pone.0078482] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 09/12/2013] [Indexed: 11/19/2022] Open
Abstract
The effect of coastal upwelling on the recruitment and connectivity of coastal marine populations has rarely been characterized to a level of detail to be included into sound fishery management strategies. The gooseneck barnacle (Pollicipes pollicipes) fishery at the Cantabrian Coast (Northern Spain) is located at the fringes of the NW Spanish Upwelling system. This fishery is being co-managed through a fine-scale, interspersed set of protected rocks where each rock receives a distinct level of protection. Such interspersion is potentially beneficial, but the extent to which such spacing is consistent with mean larval dispersal distances is as yet unknown. We have simulated the spread of gooseneck barnacle larvae in the Central Cantabrian Coast using a high-resolution time-series of current profiles measured at a nearshore location. During a year of high upwelling activity (2009), theoretical recruitment success was 94% with peak recruitment predicted 56 km west of the emission point. However, for a year of low upwelling activity (2011) theoretical recruitment success dropped to 15.4% and peak recruitment was expected 13 km east of the emission point. This is consistent with a positive correlation between catch rates and the Integrated Upwelling Index, using a 4-year lag to allow recruits to reach commercial size. Furthermore, a net long-term westward larval transport was estimated by means of mitochondrial cytochrome c oxidase subunit I (COI) sequences for five populations in the Cantabrian Sea. Our results call into question the role of long distance dispersal, driven by the mesoscale processes in the area, in gooseneck barnacle populations and point to the prevalent role of small-scale, asymmetric connectivity more consistent with the typical scale of the co-management process in this fishery.
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Affiliation(s)
- Antonella Rivera
- Departamento de Biología de Organismos y Sistemas, Universidad de Oviedo, Oviedo, Spain
- * E-mail:
| | - Nicolás Weidberg
- Departamento de Biología de Organismos y Sistemas, Universidad de Oviedo, Oviedo, Spain
| | - Antonio F. Pardiñas
- Departamento de Biología de Organismos y Sistemas, Universidad de Oviedo, Oviedo, Spain
| | - Ricardo González-Gil
- Departamento de Biología de Organismos y Sistemas, Universidad de Oviedo, Oviedo, Spain
| | - Lucía García-Flórez
- Centro de Experimentación Pesquera. Consejería de Agroganadería y Recursos Autóctonos, Gijón, Spain
| | - J. L. Acuña
- Departamento de Biología de Organismos y Sistemas, Universidad de Oviedo, Oviedo, Spain
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Chen HN, Høeg JT, Chan BKK. Morphometric and molecular identification of individual barnacle cyprids from wild plankton: an approach to detecting fouling and invasive barnacle species. Biofouling 2013; 29:133-145. [PMID: 23327366 DOI: 10.1080/08927014.2012.753061] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The present study used DNA barcodes to identify individual cyprids to species. This enables accurate quantification of larvae of potential fouling species in the plankton. In addition, it explains the settlement patterns of barnacles and serves as an early warning system of unwanted immigrant species. Sequences from a total of 540 individual cypris larvae from Taiwanese waters formed 36 monophyletic clades (species) in a phylogenetic tree. Of these clades, 26 were identified to species, but 10 unknown monophyletic clades represented non-native species. Cyprids of the invasive barnacle, Megabalanus cocopoma, were identified. Multivariate analysis of antennular morphometric characters revealed three significant clusters in a nMDS plot, viz. a bell-shaped attachment organ (most species), a shoe-shaped attachment organ (some species), and a spear-shaped attachment organ (coral barnacles only). These differences in attachment organ structure indicate that antennular structures interact directly with the diverse substrata involved in cirripede settlement.
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Affiliation(s)
- Hsi-Nien Chen
- Institute of Ecology and Evolutionary Biology, National Taiwan University, No 1, Sec 4, Roosevelt Road, Taipei 106, Taipei, Taiwan
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Abstract
Various antifouling (AF) coatings have been developed to protect submerged surfaces by deterring the settlement of the colonizing stages of fouling organisms. A review of the literature shows that effective AF compounds with specific targets are ones often considered non-toxic. Such compounds act variously on ion channels, quorum sensing systems, neurotransmitters, production/release of adhesive, and specific enzymes that regulate energy production or primary metabolism. In contrast, AF compounds with general targets may or may not act through toxic mechanisms. These compounds affect a variety of biological activities including algal photosynthesis, energy production, stress responses, genotoxic damage, immunosuppressed protein expression, oxidation, neurotransmission, surface chemistry, the formation of biofilms, and adhesive production/release. Among all the targets, adhesive production/release is the most common, possibly due to a more extensive research effort in this area. Overall, the specific molecular targets and the molecular mechanisms of most AF compounds have not been identified. Thus, the information available is insufficient to draw firm conclusions about the types of molecular targets to be used as sensitive biomarkers for future design and screening of compounds with AF potential. In this review, the relevant advantages and disadvantages of the molecular tools available for studying the molecular targets of AF compounds are highlighted briefly and the molecular mechanisms of the AF compounds, which are largely a source of speculation in the literature, are discussed.
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Affiliation(s)
- Pei-Yuan Qian
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, HKSAR, China.
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Tsang LM, Achituv Y, Chu KH, Chan BKK. Zoogeography of intertidal communities in the West Indian Ocean as determined by ocean circulation systems: patterns from the Tetraclita barnacles. PLoS One 2012; 7:e45120. [PMID: 23024801 PMCID: PMC3443201 DOI: 10.1371/journal.pone.0045120] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2012] [Accepted: 08/14/2012] [Indexed: 11/24/2022] Open
Abstract
The Indian Ocean is the least known ocean in the world with the biogeography of marine species in the West Indian Ocean (WIO) understudied. The hydrography of WIO is characterized by four distinct oceanographic systems and there were few glacial refugia formations in the WIO during the Pleistocene. We used the widely distributed intertidal barnacle Tetraclita to test the hypothesis that the distribution and connectivity of intertidal animals in the WIO are determined by the major oceanographic regime but less influenced by historical events such as Pleistocene glaciations. Tetraclita were studied from 32 locations in the WIO. The diversity and distribution of Tetraclita species in the Indian Ocean were examined based on morphological examination and sequence divergence of two mitochondrial genes (12S rDNA and COI) and one nuclear gene (histone 3, H3). Divergence in DNA sequences revealed the presence of seven evolutionarily significant units (ESUs) of Tetraclita in WIO, with most of them recognized as valid species. The distribution of these ESUs is closely tied to the major oceanographic circulation systems. T. rufotincta is distributed in the Monsoonal Gyre. T. ehsani is present in the Gulf of Oman and NW India. Tetraclita sp. nov. is associated with the Hydrochemical Front at 10°S latitude. T. reni is confined to southern Madagascan and Mauritian waters, influenced by the West Wind Drift. The endemic T. achituvi is restricted to the Red Sea. Tetraclita serrata consists of two ESUs (based on mtDNA analysis) along the east to west coast of South Africa. The two ESUs could not be distinguished from morphological analysis and nuclear H3 sequences. Our results support that intertidal species in the West Indian Ocean are associated with each of the major oceanographic circulation systems which determine gene flow. Geographical distribution is, however, less influenced by the geological history of the region.
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Affiliation(s)
- Ling Ming Tsang
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Yair Achituv
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Ka Hou Chu
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
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Tsang LM, Wu TH, Shih HT, Williams GA, Chu KH, Chan BK. Genetic and morphological differentiation of the Indo-West Pacific intertidal barnacle Chthamalus malayensis. Integr Comp Biol 2012; 52:388-409. [PMID: 22523127 PMCID: PMC3417159 DOI: 10.1093/icb/ics044] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Chthamalus malayensis is a common intertidal acorn barnacle widely distributed in the Indo-West Pacific. Analysis of sequences of mitochondrial cytochrome c oxidase subunit I reveals four genetically differentiated clades with almost allopatric distribution in this region. The four clades exhibit morphological differences in arthropodal characters, including the number of conical spines and number of setules of the basal guard setae on the cirri. These characters are, however, highly variable within each clade; such that the absolute range of the number of conical spines and setules overlaps between clades, and therefore, these are not diagnostic characters for taxonomic identification. The geographic distribution of the four clades displays a strong relationship between surface temperatures of the sea and ocean-current realms. The Indo-Malay (IM) clade is widespread in the tropical, equatorial region, including the Indian Ocean, Malay Peninsula, and North Borneo. The South China (SC) and Taiwan (TW) clades are found in tropical to subtropical regions, with the former distributed along the coasts of southern China, Vietnam, Thailand, and the western Philippines under the influence of the South China Warm Current. The TW clade is endemic to Taiwan, while the Christmas Island (CI) clade is confined to CI. There was weak or no population subdivision observed within these clades, suggesting high gene flow within the range of the clades. The clades demonstrate clear signatures of recent demographic expansion that predated the Last Glacial Maximum (LGM), but they have maintained a relatively stable effective population in the past 100,000 years. The persistence of intertidal fauna through the LGM may, therefore, be a common biogeographic pattern. The lack of genetic subdivision in the IM clade across the Indian and Pacific Oceans may be attributed to recent expansion of ranges and the fact that a mutation-drift equilibrium has not been reached, or the relaxed habitat requirements of C. malayensis that facilitates high concurrent gene flow. Further studies are needed to determine between these alternative hypotheses.
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Affiliation(s)
- Ling Ming Tsang
- *Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong; Department of Life Science, National Chung Hsing University, Taichung 402, Taiwan; The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong; Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Tsz Huen Wu
- *Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong; Department of Life Science, National Chung Hsing University, Taichung 402, Taiwan; The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong; Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Hsi-Te Shih
- *Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong; Department of Life Science, National Chung Hsing University, Taichung 402, Taiwan; The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong; Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Gray A. Williams
- *Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong; Department of Life Science, National Chung Hsing University, Taichung 402, Taiwan; The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong; Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Ka Hou Chu
- *Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong; Department of Life Science, National Chung Hsing University, Taichung 402, Taiwan; The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong; Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Benny K.K. Chan
- *Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong; Department of Life Science, National Chung Hsing University, Taichung 402, Taiwan; The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong; Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
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Chen ZF, Wang H, Matsumura K, Qian PY. Expression of calmodulin and myosin light chain kinase during larval settlement of the Barnacle Balanus amphitrite. PLoS One 2012; 7:e31337. [PMID: 22348072 PMCID: PMC3278446 DOI: 10.1371/journal.pone.0031337] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Accepted: 01/06/2012] [Indexed: 11/18/2022] Open
Abstract
Barnacles are one of the most common organisms in intertidal areas. Their life cycle includes seven free-swimming larval stages and sessile juvenile and adult stages. The transition from the swimming to the sessile stages, referred to as larval settlement, is crucial for their survivor success and subsequent population distribution. In this study, we focused on the involvement of calmodulin (CaM) and its binding proteins in the larval settlement of the barnacle, Balanus ( = Amphibalanus) amphitrite. The full length of CaM gene was cloned from stage II nauplii of B. amphitrite (referred to as Ba-CaM), encoding 149 amino acid residues that share a high similarity with published CaMs in other organisms. Quantitative real-time PCR showed that Ba-CaM was highly expressed in cyprids, the stage at which swimming larvae are competent to attach and undergo metamorphosis. In situ hybridization revealed that the expressed Ba-CaM gene was localized in compound eyes, posterior ganglion and cement glands, all of which may have essential functions during larval settlement. Larval settlement assays showed that both the CaM inhibitor compound 48/80 and the CaM-dependent myosin light chain kinase (MLCK) inhibitor ML-7 effectively blocked barnacle larval settlement, whereas Ca(2+)/CaM-dependent kinase II (CaMKII) inhibitors did not show any clear effects. The subsequent real-time PCR assay showed a higher expression level of Ba-MLCK gene in larval stages than in adults, suggesting an important role of Ba-MLCK gene in larval development and competency. Overall, the results suggest that CaM and CaM-dependent MLCK function during larval settlement of B. amphitrite.
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Affiliation(s)
- Zhang-Fan Chen
- KAUST Global Collaborative Research Program, Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Hao Wang
- KAUST Global Collaborative Research Program, Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Kiyotaka Matsumura
- KAUST Global Collaborative Research Program, Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Pei-Yuan Qian
- KAUST Global Collaborative Research Program, Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
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Yorisue T, Matsumura K, Hirota H, Dohmae N, Kojima S. Possible molecular mechanisms of species recognition by barnacle larvae inferred from multi-specific sequencing analysis of proteinaceous settlement-inducing pheromone. Biofouling 2012; 28:605-611. [PMID: 22709314 DOI: 10.1080/08927014.2012.695776] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Gregarious settlement is essential for reproduction and survival of many barnacles. A glycoprotein, settlement-inducing protein complex (SIPC) has been recognized as a signal for settlement and it is expressed in both conspecific adults and larvae. Although the settlement-inducing activities of SIPC are species-specific, the molecular-based mechanism by which larvae distinguish conspecific SIPC from the SIPC of other species is still unknown. Here, the complete primary structure of the SIPC of Megabalanus coccopoma, as well as the partial structure of the SIPCs of Balanus improvisus, Megabalanus rosa, and Elminius modestus are reported. These SIPCs contain highly variable regions that possibly modulate the affinity for the receptor, resulting in the species specificity of SIPC. In addition, the distribution patterns of potential N-glycosylation sites were seen to be different among the various species. Differences in such post-translational modifications may contribute to the species specificity of SIPC.
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Affiliation(s)
- Takefumi Yorisue
- Graduate School of Frontier Sciences, the University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan.
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Chen ZF, Matsumura K, Wang H, Arellano SM, Yan X, Alam I, Archer JAC, Bajic VB, Qian PY. Toward an understanding of the molecular mechanisms of barnacle larval settlement: a comparative transcriptomic approach. PLoS One 2011; 6:e22913. [PMID: 21829555 PMCID: PMC3146488 DOI: 10.1371/journal.pone.0022913] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Accepted: 07/01/2011] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND The barnacle Balanus amphitrite is a globally distributed biofouler and a model species in intertidal ecology and larval settlement studies. However, a lack of genomic information has hindered the comprehensive elucidation of the molecular mechanisms coordinating its larval settlement. The pyrosequencing-based transcriptomic approach is thought to be useful to identify key molecular changes during larval settlement. METHODOLOGY AND PRINCIPAL FINDINGS Using 454 pyrosequencing, we collected totally 630,845 reads including 215,308 from the larval stages and 415,537 from the adults; 23,451 contigs were generated while 77,785 remained as singletons. We annotated 31,720 of the 92,322 predicted open reading frames, which matched hits in the NCBI NR database, and identified 7,954 putative genes that were differentially expressed between the larval and adult stages. Of these, several genes were further characterized with quantitative real-time PCR and in situ hybridization, revealing some key findings: 1) vitellogenin was uniquely expressed in late nauplius stage, suggesting it may be an energy source for the subsequent non-feeding cyprid stage; 2) the locations of mannose receptors suggested they may be involved in the sensory system of cyprids; 3) 20 kDa-cement protein homologues were expressed in the cyprid cement gland and probably function during attachment; and 4) receptor tyrosine kinases were expressed higher in cyprid stage and may be involved in signal perception during larval settlement. CONCLUSIONS Our results provide not only the basis of several new hypotheses about gene functions during larval settlement, but also the availability of this large transcriptome dataset in B. amphitrite for further exploration of larval settlement and developmental pathways in this important marine species.
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Affiliation(s)
- Zhang-Fan Chen
- KAUST Global Collaborative Research Program, Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Kiyotaka Matsumura
- KAUST Global Collaborative Research Program, Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Hao Wang
- KAUST Global Collaborative Research Program, Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Shawn M. Arellano
- KAUST Global Collaborative Research Program, Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, United States of America
| | - Xingcheng Yan
- KAUST Global Collaborative Research Program, Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Intikhab Alam
- Red Sea Laboratory for Integrative Systems Biology, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - John A. C. Archer
- Red Sea Laboratory for Integrative Systems Biology, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Vladimir B. Bajic
- Red Sea Laboratory for Integrative Systems Biology, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Pei-Yuan Qian
- KAUST Global Collaborative Research Program, Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
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De Gregoris TB, Rupp O, Klages S, Knaust F, Bekel T, Kube M, Burgess JG, Arnone MI, Goesmann A, Reinhardt R, Clare AS. Deep sequencing of naupliar-, cyprid- and adult-specific normalised Expressed Sequence Tag (EST) libraries of the acorn barnacle Balanus amphitrite. Biofouling 2011; 27:367-374. [PMID: 21526438 DOI: 10.1080/08927014.2011.577211] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
In order to improve the genetic characterisation of the barnacle Balanus amphitrite, normalised EST libraries for the developmental stages, viz. nauplius (a mix of instars I and II), cyprid and adult, were generated. The libraries were sequenced independently using 454 technologies and 575,666 reads were generated. For adults, 4843 unique isotigs were estimated and 6754 and 7506 in the cyprid and naupliar stage, respectively. It was found that some of the previously proposed cyprid-specific bcs genes were also expressed during the naupliar and adult stage. Furthermore, as lectins have been hypothesised to influence settlement cue recognition in barnacles, the database was searched for lectin-like isotigs. Two proteins, uniquely expressed in either the cyprid or the adult stage, matched a mannose receptor, and their nucleotide sequences were 33% and 31% identical to a lectin (BRA-3) isolated from Megabalanus rosa. Further characterisation of these genes may suggest their involvement in settlement.
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Mannouris C. Darwin's "beloved barnacles": tough lessons in variation. Hist Philos Life Sci 2011; 33:51-70. [PMID: 21789955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
In 1846, burdened by insecurity and self-doubt, and having been convinced that he needed to study some group of organisms closely, Darwin embarked on an eight-year odyssey in the protean and perplexing world of barnacles. At the time, he was searching for evidence in support of his theory of evolution by natural selection. In the course of his long study of barnacles, however, he was not just validating his preexisting theoretical system, but was also modifying his views on such fundamental aspects as the universality of individual variation, which is the focus of this paper. According to this notion, the members of any population of living things are expected to exhibit sufficient differences from one another for natural selection to operate. By emphasizing the theoretical value of the barnacle project, my analysis contributes to the historiographic tradition which highlights the significance of the period between the first comprehensive formulation of the theory of evolution by natural selection in 1844 and its urgent publication in the late 1850s. In the course of these years, Darwin's theory was not just accumulating empirical laurels, but was also expected to adapt to a changing conceptual landscape.
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Affiliation(s)
- Costas Mannouris
- Department of Philosophy and History of Science, University of Athens, University Campus 157 71, Athens, Greece
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Endo N, Sato K, Matsumura K, Yoshimura E, Odaka Y, Nogata Y. Species-specific detection and quantification of common barnacle larvae from the Japanese coast using quantitative real-time PCR. Biofouling 2010; 26:901-911. [PMID: 21038150 DOI: 10.1080/08927014.2010.531389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Species-specific detection and quantification methods for barnacle larvae using quantitative real-time polymerase chain reaction (qPCR) were developed. Species-specific primers for qPCR were designed for 13 barnacle species in the mitochondrial 12S ribosomal RNA gene region. Primer specificity was examined by PCR using template DNA extracted from each of the 13 barnacle species, other unidentified barnacle species, and field collected zooplankton samples. The resulting PCR products comprised single bands following agarose gel electrophoresis when the templates corresponded to primers. The amplifications were highly species-specific even for the field plankton samples. The field plankton samples were subjected to qPCR assay. The calculated DNA contents for each barnacle species were closely correlated with the number of larvae measured by microscopic examination. The method could be applied to quantify barnacle larvae in natural plankton samples.
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Affiliation(s)
- Noriyuki Endo
- Environmental Science Research Laboratory, Central Research Institute of Electric Power Industry, Abiko-shi, Chiba-ken, Japan.
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Abstract
BACKGROUND We present a multi-locus phylogenetic analysis of the shallow water (high intertidal) barnacle genus Chthamalus, focusing on member species in the western hemisphere. Understanding the phylogeny of this group improves interpretation of classical ecological work on competition, distributional changes associated with climate change, and the morphological evolution of complex cirripede phenotypes. METHODOLOGY AND FINDINGS We use traditional and Bayesian phylogenetic and 'deep coalescent' approaches to identify a phylogeny that supports the monophyly of the mostly American 'fissus group' of Chthamalus, but that also supports a need for taxonomic revision of Chthamalus and Microeuraphia. Two deep phylogeographic breaks were also found within the range of two tropical American taxa (C. angustitergum and C. southwardorum) as well. CONCLUSIONS Our data, which include two novel gene regions for phylogenetic analysis of cirripedes, suggest that much more evaluation of the morphological evolutionary history and taxonomy of Chthamalid barnacles is necessary. These data and associated analyses also indicate that the radiation of species in the late Pliocene and Pleistocene was very rapid, and may provide new insights toward speciation via transient allopatry or ecological barriers.
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Affiliation(s)
- John P Wares
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America.
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Yamaguchi T, Prabowo RE, Ohshiro Y, Shimono T, Jones D, Kawai H, Otani M, Oshino A, Inagawa S, Akaya T, Tamura I. The introduction to Japan of the Titan barnacle, Megabalanus coccopoma (Darwin, 1854) (Cirripedia: Balanomorpha) and the role of shipping in its translocation. Biofouling 2009; 25:325-333. [PMID: 19219673 DOI: 10.1080/08927010902738048] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The Titan Acorn barnacle, Megabalanus coccopoma, a native of the tropical eastern Pacific, has become established in the western Atlantic (Brazil and the northern Gulf of Mexico to the Carolinas), northwestern Europe and the western Indian Ocean (Mauritius), and therefore its dispersal capabilities are well known. This study reports its introduction to Japan and confirms its occurrence in Australia. In an attempt to determine the source of this introduction, phylogeographic techniques, involving cytochrome c oxidase I sequences of various widely separate populations of M. rosa and M. volcano, were utilized. No significant genetic differentiation or haplotype patterns between widely separated populations of each of the three species were found. Lack of such differentiation indicates recent geographical isolation and thus negates a null hypothesis predicting that the occurrence of one of more of these species in Australia was natural.
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Affiliation(s)
- Toshiyuki Yamaguchi
- Department of Earth Sciences, Graduate School of Science, Chiba University, Chiba, Japan.
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Tsang LM, Chan BKK, Ma KY, Chu KH. Genetic differentiation, hybridization and adaptive divergence in two subspecies of the acorn barnacleTetraclita japonicain the northwestern Pacific. Mol Ecol 2008; 17:4151-63. [PMID: 19238711 DOI: 10.1111/j.1365-294x.2008.03907.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ling Ming Tsang
- Department of Biology, Chinese University of Hong Kong, Shatin, Hong Kong
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Lieb J. Variations: Darwin's finches, sea barnacles and the side effects of antidepressants. Med Hypotheses 2007; 70:221-3. [PMID: 17681431 DOI: 10.1016/j.mehy.2007.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2007] [Revised: 06/12/2007] [Accepted: 06/13/2007] [Indexed: 11/20/2022]
Abstract
"It may metaphorically be said," Darwin wrote, "that natural selection is daily and hourly scrutinizing, throughout the world, the slightest variations; rejecting those that are bad, preserving and adding up all that are good; silently and insensibly working, whenever and wherever opportunity offers..." Variation is a principle of nature, without which natural selection could not operate, and life exist. Darwin believed that natural selection would make nature "more and more diversified." Variation occurs in the clutch sizes of birds, the color of hair and skin, the annual temperature, in language and speech, the direction of local Magnetic North and True North, and the variation of pathogens (antigenic variation). Antidepressants act as probes, burrowing into the deepest recesses of cells, and signaling physiological and pathological information to observers. They have at least forty side effects that are not only variations, but often paradoxes that would have fascinated Charles Darwin, who had the keenest interest in the variation of the beaks of finches and in sea barnacles.
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Urushida Y, Nakano M, Matsuda S, Inoue N, Kanai S, Kitamura N, Nishino T, Kamino K. Identification and functional characterization of a novel barnacle cement protein. FEBS J 2007; 274:4336-46. [PMID: 17683335 DOI: 10.1111/j.1742-4658.2007.05965.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Barnacle attachment to various foreign materials in water is guided by an extracellular multiprotein complex. A 19 kDa cement protein was purified from the Megabalanus rosa cement, and its cDNA was cloned and sequenced. The gene was expressed only in the basal portion of the animal, where the histologically identified cement gland is located. The sequence of the protein showed no homology to other known proteins in the databases, indicating that it is a novel protein. Agreement between the molecular mass determined by MS and the molecular weight estimated from the cDNA indicated that the protein bears no post-translational modifications. The bacterial recombinant was prepared in soluble form under physiologic conditions, and was demonstrated to have underwater irreversible adsorption activity to a variety of surface materials, including positively charged, negatively charged and hydrophobic ones. Thus, the function of the protein was suggested to be coupling to foreign material surfaces during underwater attachment. Homologous genes were isolated from Balanus albicostatus and B. improvisus, and their amino acid compositions showed strong resemblance to that of M. rosa, with six amino acids, Ser, Thr, Ala, Gly, Val and Lys, comprising 66-70% of the total, suggesting that such a biased amino acid composition may be important for the function of this protein.
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Kruse I, Hare MP. GENETIC DIVERSITY AND EXPANDING NONINDIGENOUS RANGE OF THE RHIZOCEPHALAN LOXOTHYLACUS PANOPAEI PARASITIZING MUD CRABS IN THE WESTERN NORTH ATLANTIC. J Parasitol 2007; 93:575-82. [PMID: 17626349 DOI: 10.1645/ge-888r.1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Nonindigenous parasite introductions and range expansions have become a major concern because of their potential to restructure communities and impact fisheries. Molecular markers provide an important tool for reconstructing the pattern of introduction. The parasitic castrator Loxothylacus panopaei, a rhizocephalan barnacle, infects estuarine mud crabs in the Gulf of Mexico and southeastern Florida. A similar parasite introduced into Chesapeake Bay before 1964, presumably via infected crabs associated with oysters from the Gulf of Mexico, was identified as L. panopaei. Our samples of this species during 2004 and 2005 show that the introduced range has expanded as far south as Edgewater, Florida, just north of the northern endemic range limit. The nonindigenous range expanded southward at a rate of up to 165 km/yr with relatively high prevalence, ranging from 30 to 93%. Mitochondrial DNA sequences from the cytochrome oxidase I gene showed that these nonindigenous L. panopaei are genetically distinct from the endemic parasites in southeastern Florida and the eastern Gulf of Mexico. The genetic difference was also associated with distinct host spectra. These results are incompatible with an eastern Gulf source population, but suggest that unrecognized genetic and phenotypic population structure may occur among Gulf of Mexico populations of Loxothvlacus.
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Affiliation(s)
- Inken Kruse
- Department of Biology, University of Maryland, College Park, Maryland 20742, USA.
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Suma Y, Ishizaki S, Nagashima Y, Lu Y, Ushio H, Shiomi K. Comparative analysis of barnacle tropomyosin: Divergence from decapod tropomyosins and role as a potential allergen. Comp Biochem Physiol B Biochem Mol Biol 2007; 147:230-6. [PMID: 17321773 DOI: 10.1016/j.cbpb.2007.01.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2006] [Revised: 01/16/2007] [Accepted: 01/16/2007] [Indexed: 11/22/2022]
Abstract
Tropomyosin, a myofibrillar protein of 35-38 kDa, represents a major and cross-reactive allergen in decapod crustaceans. This study was initiated to clarify whether decapod-allergic patients also recognize tropomyosins of barnacles, crustaceans phylogenetically remote from decapods, which are locally consumed as a delicacy. On SDS-PAGE, a 37 kDa protein was observed in all the heated extracts prepared from two species of decapods (American lobster Homarus americanus and black tiger prawn Penaeus monodon) and two species of barnacles (acorn barnacle Balanus rostratus and goose barnacle Capitulum mitella). In immunoblotting, the 37 kDa protein was found to react with monoclonal antibodies against American lobster tropomyosin and hence identified as tropomyosin. The patient sera reacted to tropomyosins from both decapods and barnacles and the reactivity was abolished by preincubation with American lobster tropomyosin, demonstrating that barnacle tropomyosins are allergens cross-reactive with decapod tropomyosins. However, the amino acid sequence of acorn barnacle tropomyosin, deduced by cDNA cloning experiments, shares higher sequence identity with abalone tropomyosins than with decapod tropomyosins. In accordance with this, the phylogenetic tree made for tropomyosins from various animals showed that the acorn barnacle tropomyosin is evolutionally classified not into the decapod tropomyosin family but into the molluscan tropomyosin family.
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Affiliation(s)
- Yota Suma
- Department of Food Science and Technology, Tokyo University of Marine Science and Technology, Konan-4, Tokyo 108-8477, Japan
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Simon-Blecher N, Huchon D, Achituv Y. Phylogeny of coral-inhabiting barnacles (Cirripedia; Thoracica; Pyrgomatidae) based on 12S, 16S and 18S rDNA analysis. Mol Phylogenet Evol 2007; 44:1333-41. [PMID: 17560131 DOI: 10.1016/j.ympev.2007.03.026] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2006] [Revised: 03/08/2007] [Accepted: 03/29/2007] [Indexed: 11/24/2022]
Abstract
The traditional phylogeny of the coral-inhabiting barnacles, the Pyrgomatidae, is based on morphological characteristics, mainly of the hard parts. It has been difficult to establish the phylogenetic relationships among Pyrgomatidae because of the apparent convergence of morphological characteristics, and due to the use of non-cladistic systematics, which emphasize ancestor-descendant relationships rather than sister-clade relationships. We used partial sequences of two mithochondrial genes, 12S rDNA and 16S rDNA, and a nuclear gene, 18S rDNA, to infer the molecular phylogeny of the pyrgomatids. Our phylogenetic results allowed us to reject previous classifications of Pyrgomatidae based on morphological characteristics. Our results also suggested the possibility of paraphyly of the Pyrgomatidae. The hydrocoral barnacle Wanella is not found on the same clade as the other pyrgomatids, but rather, with the free-living balanids. The basal position of Megatrema and Ceratoconcha is supported. The archeaobalanid Armatobalanus is grouped with Cantellius at the base of the Indo-Pacific pyrgomatines. Fusion of the shell plate and modification of the opercular valves are homoplasious features that occurred more than three times on different clades. The monophyly of the "Savignium" group, comprising four nominal genera, is also not supported, and the different taxa are placed on different clades.
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MESH Headings
- Animals
- Anthozoa
- Base Sequence
- DNA Primers/genetics
- DNA, Mitochondrial/genetics
- DNA, Ribosomal/genetics
- Evolution, Molecular
- Genes, Mitochondrial
- Likelihood Functions
- Models, Genetic
- Molecular Sequence Data
- Phylogeny
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 18S/genetics
- Symbiosis
- Thoracica/classification
- Thoracica/genetics
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Affiliation(s)
- N Simon-Blecher
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
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Shukalyuk AI, Golovnina KA, Baiborodin SI, Gunbin KV, Blinov AG, Isaeva VV. vasa-related genes and their expression in stem cells of colonial parasitic rhizocephalan barnacle Polyascus polygenea (Arthropoda: Crustacea: Cirripedia: Rhizocephala). Cell Biol Int 2007; 31:97-108. [PMID: 17085060 DOI: 10.1016/j.cellbi.2006.09.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2005] [Revised: 08/03/2006] [Accepted: 09/14/2006] [Indexed: 11/18/2022]
Abstract
vasa (vas)-related genes are members of the DEAD-box protein family and are expressed in the germ cells of many Metazoa. We cloned vasa-related genes (PpVLG, CpVLG) and other DEAD-box family related genes (PpDRH1, PpDRH2, CpDRH, AtDRHr) from the colonial parasitic rhizocephalan barnacle Polyascus polygenea, the non-colonial Clistosaccus paguri (Crustacea: Cirripedia: Rhizocephala), and the parasitic isopodan Athelgis takanoshimensis (Crustacea: Isopoda). The colonial Polyascus polygenea, a parasite of the coastal crabs Hemigrapsus sanguineus and Hemigrapsus longitarsis was used as a model object for further detailed investigations. Phylogenetic analysis suggested that PpVLG and CpVLG are closely related to vasa-like genes of other Arthropoda. The rest of the studied genes form their own separate branch on the phylogenetic tree and have a common ancestry with the p68 and PL10 subfamilies. We suppose this group may be a new subfamily of the DEAD-box RNA helicases that is specific for parasitic Crustacea. We found PpVLG and PpDRH1 expression products in stem cells from stolons and buds of internae, during asexual reproduction of colonial P. polygenea, and in germ cells from sexually reproducing externae, including male spermatogenic cells and female oogenic cells.
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Affiliation(s)
- Andrey I Shukalyuk
- Institute of Marine Biology, Far Eastern Branch of Russian Academy of Sciences, Laboratory of Embryology, 17, Pal'chevskogo Street, Vladivostok 690041, Russia.
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Waples RS, Yokota M. Temporal estimates of effective population size in species with overlapping generations. Genetics 2007; 175:219-33. [PMID: 17110487 PMCID: PMC1775005 DOI: 10.1534/genetics.106.065300] [Citation(s) in RCA: 151] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2006] [Accepted: 10/18/2006] [Indexed: 11/18/2022] Open
Abstract
The standard temporal method for estimating effective population size (N(e)) assumes that generations are discrete, but it is routinely applied to species with overlapping generations. We evaluated bias in the estimates N(e) caused by violation of this assumption, using simulated data for three model species: humans (type I survival), sparrow (type II), and barnacle (type III). We verify a previous proposal by Felsenstein that weighting individuals by reproductive value is the correct way to calculate parametric population allele frequencies, in which case the rate of change in age-structured populations conforms to that predicted by discrete-generation models. When the standard temporal method is applied to age-structured species, typical sampling regimes (sampling only newborns or adults; randomly sampling the entire population) do not yield properly weighted allele frequencies and result in biased N(e). The direction and magnitude of the bias are shown to depend on the sampling method and the species' life history. Results for populations that grow (or decline) at a constant rate paralleled those for populations of constant size. If sufficient demographic data are available and certain sampling restrictions are met, the Jorde-Ryman modification of the temporal method can be applied to any species with overlapping generations. Alternatively, spacing the temporal samples many generations apart maximizes the drift signal compared to sampling biases associated with age structure.
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Affiliation(s)
- Robin S Waples
- Northwest Fisheries Science Center, Seattle, Washington 98112, USA.
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Abstract
It is generally assumed that larvae of benthic species are thoroughly mixed in the plankton and distributed randomly at settlement. Yet, it has also been hypothesized that a combination of larval gregarious behaviour coupled with particular oceanographic conditions may prevent larvae from mixing completely, and result in nonrandom spatial distributions following settlement. Using microsatellite markers, the main objective of this study was to investigate the occurrence of statistical connections between relatedness and settlement in the intertidal acorn barnacle from the Gulf of St Lawrence, Canada. A second objective was to test the hypothesis that patches of kin-related individuals came from a common parental site. Our results indicated that a significant number of barnacles within a given sample were more closely related than expected by chance despite the enormous potential for admixture during the planktonic phase. Thus, eight out of 37 samples analysed had relatedness values significantly higher than expected from random settlement. Moreover, analyses of sibship network construction and network complexity tests provided evidence for the occurrence of networks within several samples that were characterized by strong connections among individuals. Thus, nonrandom planktonic dispersal associated with relatively stable oceanic currents, as well as additional ecological factors to be rigorously investigated (e.g. behavioural mechanisms), may be more important in determining patterns of genetic structure in marine benthic invertebrates than generally assumed. Therefore, documenting genetic patterns associated with kin aggregation should be a fruitful and an important avenue for future studies in marine invertebrates.
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Affiliation(s)
- David Veliz
- Québec Océan, Université Laval, Département de Biologie, Québec City, Québec, Canada G1K 7P4
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Glenner H, Hebsgaard MB. Phylogeny and evolution of life history strategies of the Parasitic Barnacles (Crustacea, Cirripedia, Rhizocephala). Mol Phylogenet Evol 2006; 41:528-38. [PMID: 16876443 DOI: 10.1016/j.ympev.2006.06.004] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2006] [Revised: 06/06/2006] [Accepted: 06/07/2006] [Indexed: 11/25/2022]
Abstract
The barnacles (Crustacea, Cirripedia) consist of three well-defined orders: the conventional filter-feeding barnacles (Thoracica), the burrowing barnacles (Acrothoracica), and the parasitic barnacles (Rhizocephala). Thoracica and Acrothoracica feed by catching food particles from the surrounding seawater using their thoracic appendages while members of Rhizocephala are exclusively parasitic. The parasite consists of a sac-shaped, external reproductive organ situated on the abdomen of its crustacean host and a nutrient-absorbing root system embedded into the heamolymph of the host. In order to resolve the phylogenetic relationship of the order Rhizocephala and elucidate the evolution of the different life history strategies found within the Rhizocephala, we have performed the first comprehensive phylogenetic analysis of the group. Our results indicate that Rhizocephala is monophyletic with a filter-feeding barnacle-like ancestor. The host-infective stage, the kentrogon larva, inserted in the lifecycle of the rhizocephalan suborder, Kentrogonida, is shown to be ancestral and most likely a homologue of the juvenile stage of a conventional thoracican barnacle. The mode of host inoculation found in the suborder Akentrogonida, where the last pelagic larval stage directly injects the parasitic material into the heamolymph of the host is derived, and has evolved only once within the Rhizocephala. Lastly, our results show that the ancestral host for extant rhizocephalans appears to be the anomuran crustaceans (Anomura), which includes hermit crabs and squat lobsters.
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Affiliation(s)
- Henrik Glenner
- Ancient DNA and Evolution, Niels Bohr Institute and Institute of Biology, University of Copenhagen, Juliane Maries Vej 30, DK-2100 Copenhagen, Denmark.
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