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Peng M, Cardoso JCR, Pearson G, Vm Canário A, Power DM. Core genes of biomineralization and cis-regulatory long non-coding RNA regulate shell growth in bivalves. J Adv Res 2024; 64:117-129. [PMID: 37995944 DOI: 10.1016/j.jare.2023.11.024] [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: 06/09/2023] [Revised: 10/02/2023] [Accepted: 11/20/2023] [Indexed: 11/25/2023] Open
Abstract
INTRODUCTION Bivalve molluscs are abundant in marine and freshwater systems and contribute essential ecosystem services. They are characterized by an exuberant diversity of biomineralized shells and typically have two symmetric valves (a.k.a shells), but oysters (Ostreidae), some clams (Anomiidae and Chamidae) and scallops (Pectinida) have two asymmetrical valves. Predicting and modelling the likely consequences of ocean acidification on bivalve survival, biodiversity and aquaculture makes understanding shell biomineralization and its regulation a priority. OBJECTIVES This study aimed to a) exploit the atypical asymmetric shell growth of some bivalves and through comparative analysis of the genome and transcriptome pinpoint candidate biomineralization-related genes and regulatory long non-coding RNAs (LncRNAs) and b) demonstrate their roles in regulating shell biomineralization/growth. METHODS Meta-analysis of genomes, de novo generated mantle transcriptomes or transcriptomes and proteomes from public databases for six asymmetric to symmetric bivalve species was used to identify biomineralization-related genes. Bioinformatics filtering uncovered genes and regulatory modules characteristic of bivalves with asymmetric shells and identified candidate biomineralization-related genes and lncRNAs with a biased expression in asymmetric valves. A shell regrowth model in oyster and gene silencing experiments, were used to characterize candidate gene function. RESULTS Shell matrix genes with asymmetric expression in the mantle of the two valves were identified and unique cis-regulatory lncRNA modules characterized in Ostreidae. LncRNAs that regulate the expression of the tissue inhibitor of metalloproteinases gene family (TIMPDR) and of the shell matrix protein domain family (SMPDR) were identified. In vitro and in vivo silencing experiments revealed the candidate genes and lncRNA were associated with divergent shell growth rates and modified the microstructure of calcium carbonate (CaCO3) crystals. CONCLUSION LncRNAs are putative regulatory factors of the bivalve biomineralization toolbox. In the Ostreidae family of bivalves biomineralization-related genes are cis-regulated by lncRNA and modify the planar growth rate and spatial orientation of crystals in the shell.
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Affiliation(s)
- Maoxiao Peng
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - João C R Cardoso
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal.
| | - Gareth Pearson
- Biogeographical Ecology and Evolution, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Adelino Vm Canário
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Deborah M Power
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China.
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McElroy KE, Masonbrink R, Chudalayandi S, Severin AJ, Serb JM. A chromosome-level genome assembly of the disco clam, Ctenoides ales. G3 (BETHESDA, MD.) 2024; 14:jkae115. [PMID: 38805695 PMCID: PMC11373642 DOI: 10.1093/g3journal/jkae115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 12/22/2023] [Accepted: 05/22/2024] [Indexed: 05/30/2024]
Abstract
The bivalve subclass Pteriomorphia, which includes the economically important scallops, oysters, mussels, and ark clams, exhibits extreme ecological, morphological, and behavioral diversity. Among this diversity are five morphologically distinct eye types, making Pteriomorphia an excellent setting to explore the molecular basis for the evolution of novel traits. Of pteriomorphian bivalves, Limida is the only order lacking genomic resources, greatly limiting the potential phylogenomic analyses related to eyes and phototransduction. Here, we present a limid genome assembly, the disco clam, Ctenoides ales (C. ales), which is characterized by invaginated eyes, exceptionally long tentacles, and a flashing light display. This genome assembly was constructed with PacBio long reads and Dovetail Omni-CTM proximity-ligation sequencing. The final assembly is ∼2.3Gb and over 99% of the total length is contained in 18 pseudomolecule scaffolds. We annotated 41,064 protein coding genes and reported a BUSCO completeness of 91.9% for metazoa_obd10. Additionally, we report a complete and annotated mitochondrial genome, which also had been lacking from Limida. The ∼20Kb mitogenome has 12 protein coding genes, 22 tRNAs, 2 rRNA genes, and a 1,589 bp duplicated sequence containing the origin of replication. The C. ales nuclear genome size is substantially larger than other pteriomorphian genomes, mainly accounted for by transposable element sequences. We inventoried the genome for opsins, the signaling proteins that initiate phototransduction, and found that, unlike its closest eyed-relatives, the scallops, C. ales lacks duplication of the rhabdomeric Gq-protein-coupled opsin that is typically used for invertebrate vision. In fact, C. ales has uncharacteristically few opsins relative to the other pteriomorphian families, all of which have unique expansions of xenopsins, a recently discovered opsin subfamily. This chromosome-level assembly, along with the mitogenome, is a valuable resource for comparative genomics and phylogenetics in bivalves and particularly for the understudied but charismatic limids.
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Affiliation(s)
- Kyle E McElroy
- Department of Ecology, Evolutionary, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Rick Masonbrink
- Genome Informatics Facility, Iowa State University, Ames, IA 50011, USA
| | | | - Andrew J Severin
- Genome Informatics Facility, Iowa State University, Ames, IA 50011, USA
| | - Jeanne M Serb
- Department of Ecology, Evolutionary, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
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Sukumaran S, Vysakh VG, Sebastian W, Gopalakrishnan A, Dharani LH, Pandey A, Kumar A, Jena JK. The chromosome level genome assembly of the Asian green mussel, Perna viridis. Sci Data 2024; 11:930. [PMID: 39198463 PMCID: PMC11358141 DOI: 10.1038/s41597-024-03802-2] [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: 03/20/2024] [Accepted: 08/20/2024] [Indexed: 09/01/2024] Open
Abstract
The Asian green mussel, Perna viridis is an important aquaculture species in the family Mytilidae contributing substantially to molluscan aquaculture. We generated a high-quality chromosome level assembly of this species by combining PacBio single molecule sequencing technique (SMRT), Illumina paired-end sequencing, high-throughput chromosome conformation capture technique (Hi-C) and Bionano mapping. The final assembly resulted in a genome of 723.49 Mb in size with a scaffold N50 of 49.74 Mb with 99% anchored into 15 chromosomes. A total of 49654 protein-coding genes were predicted from the genome. The presence of 634 genes associated with the cancer pathway and 408 genes associated with viral carcinogenesis indicates the potential of this species to be used as a model for cancer studies. The chromosome-level assembly of this species is also a valuable resource for further genomic selection and selective breeding for improving economically important aquaculture traits and augmenting aquaculture productivity.
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Affiliation(s)
- Sandhya Sukumaran
- ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India.
| | - V G Vysakh
- ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India
| | - Wilson Sebastian
- ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India
| | - A Gopalakrishnan
- ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India
| | - Lalitha Hari Dharani
- Nucleome Informatics Pvt. Ltd., NKC Centre for Genomics Research, 2nd Floor, 3 Cube Towers, White Field Rd, HITEC City, Hyderabad, Telangana, 500081, India
| | - Akhilesh Pandey
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
| | - Abhishek Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
| | - J K Jena
- ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India
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Matsuyama T, Miwa S, Mekata T, Kiryu I, Kuriyama I, Atsumi T, Itano T, Kawakami H. A novel birnavirus identified as the causative agent of summer atrophy of pearl oyster ( Pinctada fucata (Gould)). PeerJ 2024; 12:e17321. [PMID: 38708355 PMCID: PMC11067908 DOI: 10.7717/peerj.17321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 04/09/2024] [Indexed: 05/07/2024] Open
Abstract
The Akoya pearl oyster (Pinctada fucata (Gould)) is the most important species for pearl cultivation in Japan. Mass mortality of 0-year-old juvenile oysters and anomalies in adults, known as summer atrophy, have been observed in major pearl farming areas during the season when seawater temperatures exceed about 20 °C since 2019. In this study, we identified a novel birnavirus as the pathogen of summer atrophy and named it Pinctada birnavirus (PiBV). PiBV was first presumed to be the causative agent when it was detected specifically and frequently in the infected oysters in a comparative metatranscriptomics of experimentally infected and healthy pearl oysters. Subsequently, the symptoms of summer atrophy were reproduced by infection tests using purified PiBV. Infection of juvenile oysters with PiBV resulted in an increase in the PiBV genome followed by the atrophy of soft body and subsequent mortality. Immunostaining with a mouse antiserum against a recombinant PiBV protein showed that the virus antigen was localized mainly in the epithelial cells on the outer surface of the mantle. Although the phylogenetic analysis using maximum likelihood method placed PiBV at the root of the genus Entomobirnavirus, the identity of the bi-segmented, genomic RNA to that of known birnaviruses at the full-length amino acid level was low, suggesting that PiBV forms a new genus. The discovery of PiBV will be the basis for research to control this emerging disease.
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Affiliation(s)
- Tomomasa Matsuyama
- Japan Fisheries Research and Education Agency, Pathology Division, Aquaculture Research Department, Fisheries Technology Institute, Minami-Ise, Mie, Japan
| | - Satoshi Miwa
- Japan Fisheries Research and Education Agency, Pathology Division, Aquaculture Research Department, Fisheries Technology Institute, Minami-Ise, Mie, Japan
| | - Tohru Mekata
- Japan Fisheries Research and Education Agency, Pathology Division, Aquaculture Research Department, Fisheries Technology Institute, Minami-Ise, Mie, Japan
- Okayama University of Science, Department of Veterinary Medicine, Faculty of Veterinary Medicine, Imabari, Ehime, Japan
| | - Ikunari Kiryu
- Japan Fisheries Research and Education Agency, Pathology Division, Aquaculture Research Department, Fisheries Technology Institute, Minami-Ise, Mie, Japan
| | - Isao Kuriyama
- Mie Prefecture Fisheries Research Institute, Shima, Mie, Japan
- Mie Prefectural Government Department of Agriculture, Forestry and Fisheries, Tsu, Mie, Japan
| | - Takashi Atsumi
- Mie Prefecture Fisheries Research Institute, Shima, Mie, Japan
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Liao IJY, Lu TM, Chen ME, Luo YJ. Spiralian genomics and the evolution of animal genome architecture. Brief Funct Genomics 2023; 22:498-508. [PMID: 37507111 DOI: 10.1093/bfgp/elad029] [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: 05/05/2023] [Revised: 06/27/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
Recent developments in sequencing technologies have greatly improved our knowledge of phylogenetic relationships and genomic architectures throughout the tree of life. Spiralia, a diverse clade within Protostomia, is essential for understanding the evolutionary history of parasitism, gene conversion, nervous systems and animal body plans. In this review, we focus on the current hypotheses of spiralian phylogeny and investigate the impact of long-read sequencing on the quality of genome assemblies. We examine chromosome-level assemblies to highlight key genomic features that have driven spiralian evolution, including karyotype, synteny and the Hox gene organization. In addition, we show how chromosome rearrangement has influenced spiralian genomic structures. Although spiralian genomes have undergone substantial changes, they exhibit both conserved and lineage-specific features. We recommend increasing sequencing efforts and expanding functional genomics research to deepen insights into spiralian biology.
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Saco A, Rey-Campos M, Gallardo-Escárate C, Gerdol M, Novoa B, Figueras A. Gene presence/absence variation in Mytilus galloprovincialis and its implications in gene expression and adaptation. iScience 2023; 26:107827. [PMID: 37744033 PMCID: PMC10514466 DOI: 10.1016/j.isci.2023.107827] [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: 05/16/2023] [Revised: 07/12/2023] [Accepted: 09/01/2023] [Indexed: 09/26/2023] Open
Abstract
Presence/absence variation (PAV) is a well-known phenomenon in prokaryotes that was described for the first time in bivalves in 2020 in Mytilus galloprovincialis. The objective of the present study was to further our understanding of the PAV phenomenon in mussel biology. The distribution of PAV was studied in a mussel chromosome-level genome assembly, revealing a widespread distribution but with hotspots of dispensability. Special attention was given to the effect of PAV in gene expression, since dispensable genes were found to be inherently subject to distortions due to their sparse distribution among individuals. Furthermore, the high expression and strong tissue specificity of some dispensable genes, such as myticins, strongly supported their biological relevance. The significant differences in the repertoire of dispensable genes associated with two geographically distinct populations suggest that PAV is involved in local adaptation. Overall, the PAV phenomenon would provide a key selective advantage at the population level.
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Affiliation(s)
- Amaro Saco
- Institute of Marine Research, Spanish National Research Council, Vigo, Spain
| | - Magalí Rey-Campos
- Institute of Marine Research, Spanish National Research Council, Vigo, Spain
| | | | - Marco Gerdol
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Beatriz Novoa
- Institute of Marine Research, Spanish National Research Council, Vigo, Spain
| | - Antonio Figueras
- Institute of Marine Research, Spanish National Research Council, Vigo, Spain
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Bai Y, Liu S, Hu Y, Yu H, Kong L, Xu C, Li Q. Multi-omic insights into the formation and evolution of a novel shell microstructure in oysters. BMC Biol 2023; 21:204. [PMID: 37775818 PMCID: PMC10543319 DOI: 10.1186/s12915-023-01706-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 09/18/2023] [Indexed: 10/01/2023] Open
Abstract
BACKGROUND Molluscan shell, composed of a diverse range of architectures and microstructures, is a classic model system to study the relationships between molecular evolution and biomineralized structure formation. The shells of oysters differ from those of other molluscs by possessing a novel microstructure, chalky calcite, which facilitates adaptation to the sessile lifestyle. However, the genetic basis and evolutionary origin of this adaptive innovation remain largely unexplored. RESULTS We report the first whole-genome assembly and shell proteomes of the Iwagaki oyster Crassostrea nippona. Multi-omic integrative analyses revealed that independently expanded and co-opted tyrosinase, peroxidase, TIMP genes may contribute to the chalky layer formation in oysters. Comparisons with other molluscan shell proteomes imply that von Willebrand factor type A and chitin-binding domains are basic members of molluscan biomineralization toolkit. Genome-wide identification and analyses of these two domains in 19 metazoans enabled us to propose that the well-known Pif may share a common origin in the last common ancestor of Bilateria. Furthermore, Pif and LamG3 genes acquire new genetic function for shell mineralization in bivalves and the chalky calcite formation in oysters likely through a combination of gene duplication and domain reorganization. CONCLUSIONS The spatial expression of SMP genes in the mantle and molecular evolution of Pif are potentially involved in regulation of the chalky calcite deposition, thereby shaping the high plasticity of the oyster shell to adapt to a sessile lifestyle. This study further highlights neo-functionalization as a crucial mechanism for the diversification of shell mineralization and microstructures in molluscs, which may be applied more widely for studies on the evolution of metazoan biomineralization.
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Affiliation(s)
- Yitian Bai
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Shikai Liu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Yiming Hu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Chengxun Xu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
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Francis WR, Eitel M, Vargas S, Garcia-Escudero CA, Conci N, Deister F, Mah JL, Guiglielmoni N, Krebs S, Blum H, Leys SP, Wörheide G. The genome of the reef-building glass sponge Aphrocallistes vastus provides insights into silica biomineralization. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230423. [PMID: 37351491 PMCID: PMC10282587 DOI: 10.1098/rsos.230423] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/26/2023] [Indexed: 06/24/2023]
Abstract
Well-annotated and contiguous genomes are an indispensable resource for understanding the evolution, development, and metabolic capacities of organisms. Sponges, an ecologically important non-bilaterian group of primarily filter-feeding sessile aquatic organisms, are underrepresented with respect to available genomic resources. Here we provide a high-quality and well-annotated genome of Aphrocallistes vastus, a glass sponge (Porifera: Hexactinellida) that forms large reef structures off the coast of British Columbia (Canada). We show that its genome is approximately 80 Mb, small compared to most other metazoans, and contains nearly 2500 nested genes, more than other genomes. Hexactinellida is characterized by a unique skeletal architecture made of amorphous silicon dioxide (SiO2), and we identified 419 differentially expressed genes between the osculum, i.e. the vertical growth zone of the sponge, and the main body. Among the upregulated ones, mineralization-related genes such as glassin, as well as collagens and actins, dominate the expression profile during growth. Silicateins, suggested being involved in silica mineralization, especially in demosponges, were not found at all in the A. vastus genome and suggests that the underlying mechanisms of SiO2 deposition in the Silicea sensu stricto (Hexactinellida + Demospongiae) may not be homologous.
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Affiliation(s)
- Warren R. Francis
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Michael Eitel
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sergio Vargas
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Catalina A. Garcia-Escudero
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Nicola Conci
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Fabian Deister
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jasmine L. Mah
- Department of Biological Sciences, University of Alberta, Edmonton, Canada T6G 2E9
| | - Nadège Guiglielmoni
- Service Evolution Biologique et Ecologie, Université libre de Bruxelles (ULB), 1050 Brussels, Belgium
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sally P. Leys
- Department of Biological Sciences, University of Alberta, Edmonton, Canada T6G 2E9
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
- Staatliche Naturwissenschaftliche Sammlungen Bayerns (SNSB)–Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany
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