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Yuan J, Zhang X, Zhang X, Sun Y, Liu C, Li S, Yu Y, Zhang C, Jin S, Wang M, Xiang J, Li F. An ancient whole-genome duplication in barnacles contributes to their diversification and intertidal sessile life adaptation. J Adv Res 2024; 62:91-103. [PMID: 37734567 PMCID: PMC11331182 DOI: 10.1016/j.jare.2023.09.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 09/01/2023] [Accepted: 09/18/2023] [Indexed: 09/23/2023] Open
Abstract
INTRODUCTION Whole-genome duplication (WGD) is one of the most sudden and dramatic events rarely reported in invertebrates, but its occurrence can lead to physiological, morphological, and behavioral diversification. WGD has also never been reported in barnacles, which is one of the most unique groups of crustaceans with extremely speciallized morphology (calcareous shells) and habits (intertidal sessile lifestyle). OBJECTIVES To investigate whether WGD has occurred in barnacles and examine its potential role in driving the adaptive evolution and diversification of barnacles. METHODS Based on a newly sequenced and assembled chromosome-level barnacle genome, a novel WGD event has been identified in barnacles through a comprehensive analysis of interchromosomal synteny, the Hox gene cluster, and synonymous substitution distribution. RESULTS We provide ample evidences for WGD in the barnacle genomes. Comparative genomic analysis indicates that this WGD event predates the divergence of Thoracicalcarea, occurring more than 247 million years ago. The retained ohnologs from the WGD are primarily enriched in various pathways related to environmental information processing, shedding light on the adaptive evolution and diversification of intertidal sessile lifestyle. In addition, transcriptomic analyses show that most of these ohnologs were differentially expressed following the ebb of tide. And the cytochrome P450 ohnologs with differential expression patterns are subject to subfunctionalization and/or neofunctionalization for intertidal adaptation. Besides WGD, parallel evolution underlying intertidal adaptation has also occurred in barnacles. CONCLUSION This study revealed an ancient WGD event in the barnacle genomes, which is potentially associated with the origin and diversification of thoracican barnacles, and may have contributed to the adaptive evolution of their intertidal sessile lifestyle.
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Affiliation(s)
- Jianbo Yuan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Xiaojun Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Xiaoxi Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yamin Sun
- Research Center for Functional Genomics and Biochip, Tianjin 300457, China
| | - Chengzhang Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Shihao Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Yang Yu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Chengsong Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Songjun Jin
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Min Wang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China; Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300071, China.
| | - Jianhai Xiang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
| | - Fuhua Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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Schultzhaus J, Hervey J, Fears K, Spillmann C. Proteomic comparison of the organic matrices from parietal and base plates of the acorn barnacle Amphibalanus amphitrite. Open Biol 2024; 14:230246. [PMID: 38806147 PMCID: PMC11293433 DOI: 10.1098/rsob.230246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 12/13/2023] [Accepted: 02/29/2024] [Indexed: 05/30/2024] Open
Abstract
Acorn barnacles are efficient colonizers on a wide variety of marine surfaces. As they proliferate on critical infrastructure, their settlement and growth have deleterious effects on performance. To address acorn barnacle biofouling, research has focused on the settlement and adhesion processes with the goal of informing the development of novel coatings. This effort has resulted in the discovery and characterization of several proteins found at the adhesive substrate interface, i.e. cement proteins, and a deepened understanding of the function and composition of the biomaterials within this region. While the adhesive properties at the interface are affected by the interaction between the proteins, substrate and mechanics of the calcified base plate, little attention has been given to the interaction between the proteins and the cuticular material present at the substrate interface. Here, the proteome of the organic matrix isolated from the base plate of the acorn barnacle Amphibalanus amphitrite is compared with the chitinous and proteinaceous matrix embedded within A. amphitrite parietal plates. The objective was to gain an understanding of how the basal organic matrix may be specialized for adhesion via an in-depth comparative proteome analysis. In general, the majority of proteins identified in the parietal matrix were also found in the basal organic matrix, including nearly all those grouped in classes of cement proteins, enzymes and pheromones. However, the parietal organic matrix was enriched with cuticle-associated proteins, of which ca 30% of those identified were unique to the parietal region. In contrast, ca 30-40% of the protease inhibitors, enzymes and pheromones identified in the basal organic matrix were unique to this region. Not unexpectedly, nearly 50% of the cement proteins identified in the basal region were significantly distinct from those found in the parietal region. The wider variety of identified proteins in the basal organic matrix indicates a greater diversity of biological function in the vicinity of the substrate interface where several processes related to adhesion, cuticle formation and expansion of the base synchronize to play a key role in organism survival.
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Affiliation(s)
- Janna Schultzhaus
- Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC, USA
| | - Judson Hervey
- Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC, USA
| | - Kenan Fears
- Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC, USA
| | - Christopher Spillmann
- Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC, USA
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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] [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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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] [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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Rutz C, Bonassin L, Kress A, Francesconi C, Boštjančić LL, Merlat D, Theissinger K, Lecompte O. Abundance and Diversification of Repetitive Elements in Decapoda Genomes. Genes (Basel) 2023; 14:1627. [PMID: 37628678 PMCID: PMC10454600 DOI: 10.3390/genes14081627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/05/2023] [Accepted: 08/12/2023] [Indexed: 08/27/2023] Open
Abstract
Repetitive elements are a major component of DNA sequences due to their ability to propagate through the genome. Characterization of Metazoan repetitive profiles is improving; however, current pipelines fail to identify a significant proportion of divergent repeats in non-model organisms. The Decapoda order, for which repeat content analyses are largely lacking, is characterized by extremely variable genome sizes that suggest an important presence of repetitive elements. Here, we developed a new standardized pipeline to annotate repetitive elements in non-model organisms, which we applied to twenty Decapoda and six other Crustacea genomes. Using this new tool, we identified 10% more repetitive elements than standard pipelines. Repetitive elements were more abundant in Decapoda species than in other Crustacea, with a very large number of highly repeated satellite DNA families. Moreover, we demonstrated a high correlation between assembly size and transposable elements and different repeat dynamics between Dendrobranchiata and Reptantia. The patterns of repetitive elements largely reflect the phylogenetic relationships of Decapoda and the distinct evolutionary trajectories within Crustacea. In summary, our results highlight the impact of repetitive elements on genome evolution in Decapoda and the value of our novel annotation pipeline, which will provide a baseline for future comparative analyses.
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Affiliation(s)
- Christelle Rutz
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000 Strasbourg, France; (C.R.); (L.B.); (A.K.); (L.L.B.); (D.M.)
| | - Lena Bonassin
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000 Strasbourg, France; (C.R.); (L.B.); (A.K.); (L.L.B.); (D.M.)
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany; (C.F.); (K.T.)
- Department of Molecular Ecology, Institute for Environmental Sciences, Rhineland-Palatinate Technical University Kaiserslautern Landau, Fortstr. 7, 76829 Landau, Germany
| | - Arnaud Kress
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000 Strasbourg, France; (C.R.); (L.B.); (A.K.); (L.L.B.); (D.M.)
| | - Caterina Francesconi
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany; (C.F.); (K.T.)
- Department of Molecular Ecology, Institute for Environmental Sciences, Rhineland-Palatinate Technical University Kaiserslautern Landau, Fortstr. 7, 76829 Landau, Germany
| | - Ljudevit Luka Boštjančić
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000 Strasbourg, France; (C.R.); (L.B.); (A.K.); (L.L.B.); (D.M.)
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany; (C.F.); (K.T.)
- Department of Molecular Ecology, Institute for Environmental Sciences, Rhineland-Palatinate Technical University Kaiserslautern Landau, Fortstr. 7, 76829 Landau, Germany
| | - Dorine Merlat
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000 Strasbourg, France; (C.R.); (L.B.); (A.K.); (L.L.B.); (D.M.)
| | - Kathrin Theissinger
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany; (C.F.); (K.T.)
| | - Odile Lecompte
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000 Strasbourg, France; (C.R.); (L.B.); (A.K.); (L.L.B.); (D.M.)
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Pei Y, Deng Z, Zhang X, Blair D, Hu W, Yin M. Chromosome-scale genome assembly of the freshwater cladoceran crustacean Chydorus sphaericus: A resource for discovery of genes responsive to ecological challenges. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2023; 260:106565. [PMID: 37186996 DOI: 10.1016/j.aquatox.2023.106565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 05/03/2023] [Accepted: 05/09/2023] [Indexed: 05/17/2023]
Abstract
The genus Chydorus Leach 1816 (family Chydoridae) is a diverse and ecologically important taxon within freshwater ecosystems. Despite having been widely used in ecological, evolutionary and eco-toxicological studies, no high-quality genomic resource is available for any member of the genus. Here, we present a high-quality chromosome-level assembly of the C. sphaericus genome by combining 7.40 Gb (∼ 50 × coverage) PacBio reads, 19.28 Gb (∼ 135 × coverage) Illumina paired-end reads, and 34.04 Gb Hi-C reads. Our genome assembly is approximately 151 Mb, with contig and scaffold N50 lengths of 1.09 Mb and 13.70 Mb, respectively. The assembly captured 94.9% of the complete eukaryotic BUSCO. Repetitive elements accounted for 17.6% of the genome, and 13,549 protein-coding genes were predicted (based on transcriptome sequencing data, ab-initio or homology-based prediction), of which 96.4% have been functionally annotated in the NCBI-NR database. We identified 303 gene families specific to C. sphaericus, mainly families enriched in functions related to immune response, visual senses and detoxification. Interestingly, we also found 53 significantly expanded gene families in C. sphaericus, mostly with functions related to detoxification. This high-quality assembly genome will act as a reference genome for C. sphaericus and benefit studies on functional and comparative genomics of Chydorus and other crustaceans.
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Affiliation(s)
- Yingbing Pei
- Department of Microbiology and Bioengineering, College of Life Sciences, Inner Mongolia University, Hohhot, China; MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China
| | - Zhixiong Deng
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China
| | - Xiuping Zhang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China
| | - David Blair
- College of Marine and Environmental Sciences, James Cook University, Townsville Qld 4811, Australia
| | - Wei Hu
- Department of Microbiology and Bioengineering, College of Life Sciences, Inner Mongolia University, Hohhot, China; MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China
| | - Mingbo Yin
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China.
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Martin S, Lesny P, Glenner H, Hecht J, Vilcinskas A, Bartolomaeus T, Podsiadlowski L. Genomic Adaptations to an Endoparasitic Lifestyle in the Morphologically Atypical Crustacean Sacculina carcini (Cirripedia: Rhizocephala). Genome Biol Evol 2022; 14:6758533. [PMID: 36221914 PMCID: PMC9582164 DOI: 10.1093/gbe/evac149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 09/16/2022] [Accepted: 09/26/2022] [Indexed: 01/24/2023] Open
Abstract
The endoparasitic crustacean Sacculina carcini (Cirripedia: Rhizocephala) has a much simpler morphology than conventional filter-feeding barnacles, reflecting its parasitic lifestyle. To investigate the molecular basis of its refined developmental program, we produced a draft genome sequence for comparison with the genomes of nonparasitic barnacles and characterized the transcriptomes of internal and external tissues. The comparison of clusters of orthologous genes revealed the depletion of multiple gene families but also several unanticipated expansions compared to non-parasitic crustaceans. Transcriptomic analyses comparing interna and externa tissues revealed an unexpected variation of gene expression between rootlets sampled around host midgut and thoracic ganglia. Genes associated with lipid uptake were strongly expressed by the internal tissues. We identified candidate genes probably involved in host manipulation (suppression of ecdysis and gonad development) including those encoding crustacean neurohormones and the juvenile hormone binding protein. The evolution of Rhizocephala therefore appears to have involved a rapid turnover of genes (losses and expansions) as well as the fine tuning of gene expression.
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Affiliation(s)
- Sebastian Martin
- Centre for Molecular Biodiversity Research (zmb), Zoological Research Museum Alexander Koenig (ZFMK), LIB, Bonn, Germany,Department of Comparative Ultrastructure and Evolution of Invertebrates, Institute for Evolutionary Biology & Animal Ecology, University Bonn, Bonn, Germany
| | - Peter Lesny
- Department of Comparative Ultrastructure and Evolution of Invertebrates, Institute for Evolutionary Biology & Animal Ecology, University Bonn, Bonn, Germany
| | - Henrik Glenner
- Department of Biol. Sciences, University Bergen, Bergen, Norway,Centre for Macroecology, Evolution and Climate, Copenhagen, Denmark
| | - Jochen Hecht
- Genomics Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Andreas Vilcinskas
- Department of Insect Biotechnology, Justus-Liebig-University of Giessen, Giessen, Germany,Department of Bioressources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
| | - Thomas Bartolomaeus
- Department of Comparative Ultrastructure and Evolution of Invertebrates, Institute for Evolutionary Biology & Animal Ecology, University Bonn, Bonn, Germany
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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] [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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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] [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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10
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Lin HC, Wong YH, Sung CH, Chan BKK. Histology and transcriptomic analyses of barnacles with different base materials and habitats shed lights on the duplication and chemical diversification of barnacle cement proteins. BMC Genomics 2021; 22:783. [PMID: 34724896 PMCID: PMC8561864 DOI: 10.1186/s12864-021-08049-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 09/14/2021] [Indexed: 11/26/2022] Open
Abstract
Background Barnacles are sessile crustaceans that attach to underwater surfaces using barnacle cement proteins. Barnacles have a calcareous or chitinous membranous base, and their substratum varies from biotic (e.g. corals/sponges) to abiotic surfaces. In this study, we tested the hypothesis that the cement protein (CP) composition and chemical properties of different species vary according to the attachment substrate and/or the basal structure. We examined the histological structure of cement glands and explored the variations in cement protein homologs of 12 barnacle species with different attachment habitats and base materials. Results Cement gland cells in the rocky shore barnacles Tetraclita japonica formosana and Amphibalanus amphitrite are eosinophilic, while others are basophilic. Transcriptome analyses recovered CP homologs from all species except the scleractinian coral barnacle Galkinia sp. A phylogenomic analysis based on sequences of CP homologs did not reflect a clear phylogenetic pattern in attachment substrates. In some species, certain CPs have a remarkable number of paralogous sequences, suggesting that major duplication events occurred in CP genes. The examined CPs across taxa show consistent bias toward particular sets of amino acid. However, the predicted isoelectric point (pI) and hydropathy are highly divergent. In some species, conserved regions are highly repetitive. Conclusions Instead of developing specific cement proteins for different attachment substrata, barnacles attached to different substrata rely on a highly duplicated cementation genetic toolkit to generate paralogous CP sequences with diverse chemical and biochemical properties. This general CP cocktail might be the key genetic feature enabling barnacles to adapt to a wide variety of substrata. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08049-4.
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Affiliation(s)
- Hsiu-Chin Lin
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, 80424, Kaohsiung, Taiwan
| | - Yue Him Wong
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Chia-Hsuan Sung
- Planning and Information Division, Fisheries Research Institute, Keelung, Taiwan
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11
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Kawato S, Nishitsuji K, Arimoto A, Hisata K, Kawamitsu M, Nozaki R, Kondo H, Shinzato C, Ohira T, Satoh N, Shoguchi E, Hirono I. Genome and transcriptome assemblies of the kuruma shrimp, Marsupenaeus japonicus. G3 (BETHESDA, MD.) 2021; 11:jkab268. [PMID: 34515781 PMCID: PMC8527471 DOI: 10.1093/g3journal/jkab268] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 07/18/2021] [Indexed: 11/25/2022]
Abstract
The kuruma shrimp Marsupenaeus japonicus (order Decapoda, family Penaeidae) is an economically important crustacean that occurs in shallow, warm seas across the Indo-Pacific. Here, using a combination of Illumina and Oxford Nanopore Technologies platforms, we produced a draft genome assembly of M. japonicus (1.70 Gbp; 18,210 scaffolds; scaffold N50 = 234.9 kbp; 34.38% GC, 93.4% BUSCO completeness) and a complete mitochondrial genome sequence (15,969 bp). As with other penaeid shrimp genomes, the M. japonicus genome is extremely rich in simple repeats, which occupies 27.4% of the assembly. A total of 26,381 protein-coding gene models (94.7% BUSCO completeness) were predicted, of which 18,005 genes (68.2%) were assigned functional description by at least one method. We also produced an Illumina-based transcriptome shotgun assembly (40,991 entries; 93.0% BUSCO completeness) and a PacBio Iso-Seq transcriptome assembly (25,415 entries; 67.5% BUSCO completeness). We envision that the M. japonicus genome and transcriptome assemblies will serve as useful resources for the basic research, fisheries management, and breeding programs of M. japonicus.
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Affiliation(s)
- Satoshi Kawato
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
| | - Koki Nishitsuji
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Asuka Arimoto
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Mayumi Kawamitsu
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Reiko Nozaki
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
| | - Hidehiro Kondo
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba 277-0882, Japan
| | - Tsuyoshi Ohira
- Faculty of Science, Department of Biological Sciences, Kanagawa University, Kanagawa 221-8686, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Ikuo Hirono
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
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12
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Schultzhaus JN, Hervey WJ, Taitt CR, So CR, Leary DH, Wahl KJ, Spillmann CM. Comparative analysis of stalked and acorn barnacle adhesive proteomes. Open Biol 2021; 11:210142. [PMID: 34404232 PMCID: PMC8371367 DOI: 10.1098/rsob.210142] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Barnacles interest the scientific community for multiple reasons: their unique evolutionary trajectory, vast diversity and economic impact—as a harvested food source and also as one of the most prolific macroscopic hard biofouling organisms. A common, yet novel, trait among barnacles is adhesion, which has enabled a sessile adult existence and global colonization of the oceans. Barnacle adhesive is primarily composed of proteins, but knowledge of how the adhesive proteome varies across the tree of life is unknown due to a lack of genomic information. Here, we supplement previous mass spectrometry analyses of barnacle adhesive with recently sequenced genomes to compare the adhesive proteomes of Pollicipes pollicipes (Pedunculata) and Amphibalanus amphitrite (Sessilia). Although both species contain the same broad protein categories, we detail differences that exist between these species. The barnacle-unique cement proteins show the greatest difference between species, although these differences are diminished when amino acid composition and glycosylation potential are considered. By performing an in-depth comparison of the adhesive proteomes of these distantly related barnacle species, we show their similarities and provide a roadmap for future studies examining sequence-specific differences to identify the proteins responsible for functional differences across the barnacle tree of life.
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Affiliation(s)
- Janna N Schultzhaus
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, USA
| | - William Judson Hervey
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, USA
| | - Chris R Taitt
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, USA
| | - Chris R So
- Chemistry Division, Naval Research Laboratory, Washington, DC, USA
| | - Dagmar H Leary
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, USA
| | - Kathryn J Wahl
- Chemistry Division, Naval Research Laboratory, Washington, DC, USA
| | - Christopher M Spillmann
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, USA
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13
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Ip JCH, Qiu JW, Chan BKK. Genomic insights into the sessile life and biofouling of barnacles (Crustacea: Cirripedia). Heliyon 2021; 7:e07291. [PMID: 34189321 PMCID: PMC8220330 DOI: 10.1016/j.heliyon.2021.e07291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 04/06/2021] [Accepted: 06/09/2021] [Indexed: 12/01/2022] Open
Abstract
Members of the infraclass Cirripedia, commonly called barnacles, are unique among the subphylum Crustacea in that they exhibit a biphasic life cycle with a planktonic larval stage and a sessile adult stage. Understanding their unique sessile life and mechanisms of attachment are hampered by the lack of genomic resources. Here, we present a 746 Mb genome assembly of Lepas anserifera – the first sequenced stalked barnacle genome. We estimate that Cirripedia first arose ~495 million years ago (MYA) and further diversified since Mesozoic. A demographic analysis revealed remarkable population changes of the barnacle in relation to sea-level fluctuations in the last 2 MYA. Comparative genomic analyses revealed the expansion of a number of developmental related genes families in barnacle genomes, such as Br–C, PCP20 and Lola, which are potentially important for the evolution of metamorphosis, cuticle development and central nervous system. Phylogenetic analysis and tissue expression profiling showed the possible roles of gene duplication, functional diversification and co-option in shaping the genomic evolution of barnacles. Overall, our study provides not only a valuable draft genome for comparative genomic analysis of crustacean evolution, but also facilitates studies of biofouling control.
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Affiliation(s)
- Jack Chi-Ho Ip
- Department of Biology and Hong Kong Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong Baptist University, Hong Kong.,Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,HKBU Institute of Research and Continuing Education, Virtual University Park, Shenzhen, China
| | - Jian-Wen Qiu
- Department of Biology and Hong Kong Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong Baptist University, Hong Kong.,Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,HKBU Institute of Research and Continuing Education, Virtual University Park, Shenzhen, China
| | - Benny K K Chan
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
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14
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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. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 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] [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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15
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Andrade Rodriguez N, Moya A, Jones R, Miller DJ, Cooke IR. The Significance of Genotypic Diversity in Coral Competitive Interaction: A Transcriptomic Perspective. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.659360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Competitive interactions shape coral assemblages and govern the dynamics of coral ecosystems. Although competition is an ecological concept, the outcomes of competitive interactions are ultimately determined by patterns of gene expression. These patterns are subject to genotypic variation on both sides of any interaction. Such variation is typically treated as “noise”, but it is sometimes possible to identify patterns within it that reveal important hidden factors in an experiment. To incorporate genotypic variation into the investigation of coral competitive interactions, we used RNA-sequencing to study changes in gene expression in a hard coral (Porites cylindrica) resulting from non-contact competition experiment with a soft coral (Lobophytum pauciflorum). Hard coral genotype explained the largest proportion of variation between samples; however, it was also possible to detect gene expression changes in 76 transcripts resulting from interaction with the soft coral. In addition, we found a group of 20 short secreted proteins that were expressed as a coordinated unit in three interacting Porites-Lobophytum pairs. The presence of this secretion response was idiosyncratic in that it could not be predicted based on polyp behaviour, or the genotype of hard or soft coral alone. This study illustrates the significance of individual variation as a determinant of competitive behaviour, and also provides some intriguing glimpses into the molecular mechanisms employed by hard corals competing at a distance.
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16
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Chitin Synthesis and Degradation in Crustaceans: A Genomic View and Application. Mar Drugs 2021; 19:md19030153. [PMID: 33804177 PMCID: PMC8002005 DOI: 10.3390/md19030153] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/10/2021] [Accepted: 03/10/2021] [Indexed: 12/29/2022] Open
Abstract
Chitin is among the most important components of the crustacean cuticular exoskeleton and intestinal peritrophic matrix. With the progress of genomics and sequencing technology, a large number of gene sequences related to chitin metabolism have been deposited in the GenBank database in recent years. Here, we summarized the genes and pathways associated with the biosynthesis and degradation of chitins in crustaceans based on genomic analyses. We found that chitin biosynthesis genes typically occur in single or two copies, whereas chitin degradation genes are all multiple copies. Moreover, the chitinase genes are significantly expanded in most crustacean genomes. The gene structure and expression pattern of these genes are similar to those of insects, albeit with some specific characteristics. Additionally, the potential applications of the chitin metabolism genes in molting regulation and immune defense, as well as industrial chitin degradation and production, are also summarized in this review.
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17
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Jeong JH, Kim H, Ryu S, Kim W. The First Pycnogonid Draft Genome of Nymphon striatum. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.554164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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