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Jackson DJ, Cerveau N, Posnien N. De novo assembly of transcriptomes and differential gene expression analysis using short-read data from emerging model organisms - a brief guide. Front Zool 2024; 21:17. [PMID: 38902827 DOI: 10.1186/s12983-024-00538-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 06/12/2024] [Indexed: 06/22/2024] Open
Abstract
Many questions in biology benefit greatly from the use of a variety of model systems. High-throughput sequencing methods have been a triumph in the democratization of diverse model systems. They allow for the economical sequencing of an entire genome or transcriptome of interest, and with technical variations can even provide insight into genome organization and the expression and regulation of genes. The analysis and biological interpretation of such large datasets can present significant challenges that depend on the 'scientific status' of the model system. While high-quality genome and transcriptome references are readily available for well-established model systems, the establishment of such references for an emerging model system often requires extensive resources such as finances, expertise and computation capabilities. The de novo assembly of a transcriptome represents an excellent entry point for genetic and molecular studies in emerging model systems as it can efficiently assess gene content while also serving as a reference for differential gene expression studies. However, the process of de novo transcriptome assembly is non-trivial, and as a rule must be empirically optimized for every dataset. For the researcher working with an emerging model system, and with little to no experience with assembling and quantifying short-read data from the Illumina platform, these processes can be daunting. In this guide we outline the major challenges faced when establishing a reference transcriptome de novo and we provide advice on how to approach such an endeavor. We describe the major experimental and bioinformatic steps, provide some broad recommendations and cautions for the newcomer to de novo transcriptome assembly and differential gene expression analyses. Moreover, we provide an initial selection of tools that can assist in the journey from raw short-read data to assembled transcriptome and lists of differentially expressed genes.
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Affiliation(s)
- Daniel J Jackson
- University of Göttingen, Department of Geobiology, Goldschmidtstr.3, Göttingen, 37077, Germany.
| | - Nicolas Cerveau
- University of Göttingen, Department of Geobiology, Goldschmidtstr.3, Göttingen, 37077, Germany
| | - Nico Posnien
- University of Göttingen, Department of Developmental Biology, GZMB, Justus-Von-Liebig-Weg 11, Göttingen, 37077, Germany.
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Stelbrink B, von Rintelen T, Marwoto RM, Salzburger W. Mitogenomes do not substantially improve phylogenetic resolution in a young non-model adaptive radiation of freshwater gastropods. BMC Ecol Evol 2024; 24:42. [PMID: 38589809 PMCID: PMC11000327 DOI: 10.1186/s12862-024-02235-0] [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: 12/15/2023] [Accepted: 04/01/2024] [Indexed: 04/10/2024] Open
Abstract
BACKGROUND Species flocks in ancient lakes, and particularly those arising from adaptive radiation, make up the bulk of overall taxonomic and morphological diversity in these insular ecosystems. For these mostly young species assemblages, classical mitochondrial barcoding markers have so far been key to disentangle interspecific relationships. However, with the rise and further development of next-generation sequencing (NGS) methods and mapping tools, genome-wide data have become an increasingly important source of information even for non-model groups. RESULTS Here, we provide, for the first time, a comprehensive mitogenome dataset of freshwater gastropods endemic to Sulawesi and thus of an ancient lake invertebrate species flock in general. We applied low-coverage whole-genome sequencing for a total of 78 individuals including 27 out of the 28 Tylomelania morphospecies from the Malili lake system as well as selected representatives from Lake Poso and adjacent catchments. Our aim was to assess whether mitogenomes considerably contribute to the phylogenetic resolution within this young species flock. Interestingly, we identified a high number of variable and parsimony-informative sites across the other 'non-traditional' mitochondrial loci. However, although the overall support was very high, the topology obtained was largely congruent with previously published single-locus phylogenies. Several clades remained unresolved and a large number of species was recovered polyphyletic, indicative of both rapid diversification and mitochondrial introgression. CONCLUSIONS This once again illustrates that, despite the higher number of characters available, mitogenomes behave like a single locus and thus can only make a limited contribution to resolving species boundaries, particularly when introgression events are involved.
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Affiliation(s)
- Björn Stelbrink
- Justus Liebig University Giessen, Giessen, Germany.
- University of Basel, Basel, Switzerland.
| | - Thomas von Rintelen
- Museum für Naturkunde - Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Ristiyanti M Marwoto
- Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, BRIN Gedung Widyasatwaloka, Cibinong, Indonesia
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McIlroy SE, Guibert I, Archana A, Chung WYH, Duffy JE, Gotama R, Hui J, Knowlton N, Leray M, Meyer C, Panagiotou G, Paulay G, Russell B, Thompson PD, Baker DM. Life goes on: Spatial heterogeneity promotes biodiversity in an urbanized coastal marine ecosystem. GLOBAL CHANGE BIOLOGY 2024; 30:e17248. [PMID: 38581126 DOI: 10.1111/gcb.17248] [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: 05/15/2023] [Revised: 02/09/2024] [Accepted: 02/18/2024] [Indexed: 04/08/2024]
Abstract
Both human populations and marine biodiversity are concentrated along coastlines, with growing conservation interest in how these ecosystems can survive intense anthropogenic impacts. Tropical urban centres provide valuable research opportunities because these megacities are often adjacent to mega-diverse coral reef systems. The Pearl River Delta is a prime exemplar, as it encompasses one of the most densely populated and impacted regions in the world and is located just northwest of the Coral Triangle. However, the spatial and taxonomic complexity of this biodiversity, most of which is small, cryptic in habitat and poorly known, make comparative analyses challenging. We deployed standardized settlement structures at seven sites differing in the intensity of human impacts and used COI metabarcoding to characterize benthic biodiversity, with a focus on metazoans. We found a total of 7184 OTUs, with an average of 665 OTUs per sampling unit; these numbers exceed those observed in many previous studies using comparable methods, despite the location of our study in an urbanized environment. Beta diversity was also high, with 52% of the OTUs found at just one site. As expected, we found that the sites close to point sources of pollution had substantially lower diversity (44% less) relative to sites bathed in less polluted oceanic waters. However, the polluted sites contributed substantially to the total animal diversity of the region, with 25% of all OTUs occurring only within polluted sites. Further analysis of Arthropoda, Annelida and Mollusca showed that phylogenetic clustering within a site was common, suggesting that environmental filtering reduced biodiversity to a subset of lineages present within the region, a pattern that was most pronounced in polluted sites and for the Arthropoda. The water quality gradients surrounding the PRD highlight the unique role of in situ studies for understanding the impacts of complex urbanization pressures on biodiversity.
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Affiliation(s)
- Shelby E McIlroy
- School of Biological Sciences, The Swire Institute of Marine Science, The University of Hong Kong, Hong Kong, P.R. China
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, P.R. China
| | - Isis Guibert
- School of Biological Sciences, The Swire Institute of Marine Science, The University of Hong Kong, Hong Kong, P.R. China
| | - Anand Archana
- School of Biological Sciences, The Swire Institute of Marine Science, The University of Hong Kong, Hong Kong, P.R. China
- San Francisco State University, San Francisco, California, USA
| | - Wing Yi Haze Chung
- School of Biological Sciences, The Swire Institute of Marine Science, The University of Hong Kong, Hong Kong, P.R. China
| | - J Emmett Duffy
- MarineGEO Program and Smithsonian Environmental Research Center, Edgewater, Maryland, USA
| | - Rinaldi Gotama
- School of Biological Sciences, The Swire Institute of Marine Science, The University of Hong Kong, Hong Kong, P.R. China
- Indo Ocean Project, Banjar Adegan Kawan, Desa Ped, Bali, Indonesia
| | - Jerome Hui
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, P.R. China
| | - Nancy Knowlton
- National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
| | - Matthieu Leray
- MarineGEO Program and Smithsonian Environmental Research Center, Edgewater, Maryland, USA
- Smithsonian Tropical Research Institute, Smithsonian Institution, Panama City, Balboa, Ancon, Republic of Panama
| | - Chris Meyer
- National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
| | - Gianni Panagiotou
- Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knoell-Institute, Jena, Germany
- Friedrich Schiller University, Faculty of Biological Sciences, Jena, Germany
- Department of Medicine and State Key Laboratory of Pharmaceutical Biotechnology, University of Hong Kong, Hong Kong, China
| | - Gustav Paulay
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
| | - Bayden Russell
- School of Biological Sciences, The Swire Institute of Marine Science, The University of Hong Kong, Hong Kong, P.R. China
| | - Philip D Thompson
- School of Biological Sciences, The Swire Institute of Marine Science, The University of Hong Kong, Hong Kong, P.R. China
| | - David M Baker
- School of Biological Sciences, The Swire Institute of Marine Science, The University of Hong Kong, Hong Kong, P.R. China
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Johannesson K, Faria R, Le Moan A, Rafajlović M, Westram AM, Butlin RK, Stankowski S. Diverse pathways to speciation revealed by marine snails. Trends Genet 2024; 40:337-351. [PMID: 38395682 DOI: 10.1016/j.tig.2024.01.002] [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: 09/30/2023] [Revised: 01/06/2024] [Accepted: 01/10/2024] [Indexed: 02/25/2024]
Abstract
Speciation is a key evolutionary process that is not yet fully understood. Combining population genomic and ecological data from multiple diverging pairs of marine snails (Littorina) supports the search for speciation mechanisms. Placing pairs on a one-dimensional speciation continuum, from undifferentiated populations to species, obscured the complexity of speciation. Adding multiple axes helped to describe either speciation routes or reproductive isolation in the snails. Divergent ecological selection repeatedly generated barriers between ecotypes, but appeared less important in completing speciation while genetic incompatibilities played a key role. Chromosomal inversions contributed to genomic barriers, but with variable impact. A multidimensional (hypercube) approach supported framing of questions and identification of knowledge gaps and can be useful to understand speciation in many other systems.
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Affiliation(s)
- Kerstin Johannesson
- Department of Marine Sciences, University of Gothenburg, Tjärnö Marine Laboratory, SE 45296 Strömstad, Sweden; The Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden.
| | - Rui Faria
- The Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden; CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Alan Le Moan
- The Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden; CNRS & Sorbonne Université, Station Biologique de Roscoff, Roscoff, France
| | - Marina Rafajlović
- The Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden; Department of Marine Sciences, University of Gothenburg, SE 41390 Gothenburg, Sweden; Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
| | - Anja Marie Westram
- Department of Marine Sciences, University of Gothenburg, Tjärnö Marine Laboratory, SE 45296 Strömstad, Sweden; The Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden; Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Roger K Butlin
- Department of Marine Sciences, University of Gothenburg, Tjärnö Marine Laboratory, SE 45296 Strömstad, Sweden; The Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden; Ecology and Evolutionary Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
| | - Sean Stankowski
- The Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden; Institute of Science and Technology Austria, Klosterneuburg, Austria; Department of Ecology and Evolution, University of Sussex, Brighton, UK
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Varney R. The Genomics in Emerging Marine Systems Checklist for Clear and Reproducible Genomics in Emerging, Marine Systems. Integr Comp Biol 2023; 63:1010-1016. [PMID: 37381586 DOI: 10.1093/icb/icad082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 05/24/2023] [Accepted: 06/11/2023] [Indexed: 06/30/2023] Open
Abstract
Genome sequencing becomes more accessible and powerful every year, but there is a lack of consensus on what information should be provided in publications that include genomic data. The result is a flood of sequencing data without a framework to evaluate its quality and completeness, hindering reproducibility. In non-model taxa in marine systems, a lack of detail in methods sections often hinders future researchers from adopting improved techniques, leaving them to repeat costly protocols and take up computational (wall) time with programs that are already known to fail. Here, I present a set of guidelines tailored for marine taxa (emerging model organisms) to promote consistency between publications, increase transparency of sequencing projects, and preserve the value of sequence data as sequencing technologies advance. Included is a checklist to (1) guide authors toward including more detailed information in their manuscripts, (2) expand data availability, and (3) assist reviewers to thoroughly vet methods and results of future 'omic publications. This set of guidelines will support the usefulness of 'omic data in future analyses by providing a framework to document and evaluate these data, leading to transparent and reproducible genomics research on emerging marine systems.
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Ortiz-Sepulveda CM, Genete M, Blassiau C, Godé C, Albrecht C, Vekemans X, Van Bocxlaer B. Target enrichment of long open reading frames and ultraconserved elements to link microevolution and macroevolution in non-model organisms. Mol Ecol Resour 2023; 23:659-679. [PMID: 36349833 DOI: 10.1111/1755-0998.13735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 10/09/2022] [Accepted: 10/19/2022] [Indexed: 11/10/2022]
Abstract
Despite the increasing accessibility of high-throughput sequencing, obtaining high-quality genomic data on non-model organisms without proximate well-assembled and annotated genomes remains challenging. Here, we describe a workflow that takes advantage of distant genomic resources and ingroup transcriptomes to select and jointly enrich long open reading frames (ORFs) and ultraconserved elements (UCEs) from genomic samples for integrative studies of microevolutionary and macroevolutionary dynamics. This workflow is applied to samples of the African unionid bivalve tribe Coelaturini (Parreysiinae) at basin and continent-wide scales. Our results indicate that ORFs are efficiently captured without prior identification of intron-exon boundaries. The enrichment of UCEs was less successful, but nevertheless produced substantial data sets. Exploratory continent-wide phylogenetic analyses with ORF supercontigs (>515,000 parsimony informative sites) resulted in a fully resolved phylogeny, the backbone of which was also retrieved with UCEs (>11,000 informative sites). Variant calling on ORFs and UCEs of Coelaturini from the Malawi Basin produced ~2000 SNPs per population pair. Estimates of nucleotide diversity and population differentiation were similar for ORFs and UCEs. They were low compared to previous estimates in molluscs, but comparable to those in recently diversifying Malawi cichlids and other taxa at an early stage of speciation. Skimming off-target sequence data from the same enriched libraries of Coelaturini from the Malawi Basin, we reconstructed the maternally-inherited mitogenome, which displays the gene order inferred for the most recent common ancestor of Unionidae. Overall, our workflow and results provide exciting perspectives for integrative genomic studies of microevolutionary and macroevolutionary dynamics in non-model organisms.
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Affiliation(s)
| | - Mathieu Genete
- CNRS, Univ. Lille, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
| | | | - Cécile Godé
- CNRS, Univ. Lille, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
| | - Christian Albrecht
- Department of Animal Ecology and Systematics, Justus Liebig University, D-35392 Giessen, Germany.,Department of Biology, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Xavier Vekemans
- CNRS, Univ. Lille, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
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Li X, Bai Y, Dong Z, Xu C, Liu S, Yu H, Kong L, Li Q. Chromosome-level genome assembly of the European flat oyster (Ostrea edulis) provides insights into its evolution and adaptation. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 45:101045. [PMID: 36470107 DOI: 10.1016/j.cbd.2022.101045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/17/2022] [Accepted: 11/25/2022] [Indexed: 11/30/2022]
Abstract
The European flat oyster (Ostrea edulis) is an endangered and economically important marine bivalve species that plays a critical role in the coastal ecosystem. Here, we report a high-quality chromosome-level genome assembly of O. edulis, generated using PacBio HiFi-CCS long reads and annotated with Nanopore full-length transcriptome. The O. edulis genome covers 946.06 Mb (scaffold N50 94.82 Mb) containing 34,495 protein-coding genes and a high proportion of repeat sequences (58.49 %). The reconstructed demographic histories show that O. edulis population might be shaped by breeding habit (embryo brooding) and historical climatic change. Comparative genomic analysis indicates that transposable elements may drive lineage-specific evolution in oysters. Notably, the O. edulis genome has a Hox gene cluster rearrangement that has never been reported in bivalves, making this species valuable for evolutionary studies of molluscan diversification. Moreover, genome expansion of O. edulis is probably central to its adaptation to filter-feeding and sessile lifestyles, as well as embryo brooding and pathogen resistance, in coastal ecosystems. This chromosome-level genome assembly provides new insights into the genome feature of oysters, and presents an important resource for genetic research, evolutionary studies, and biological conservation of O. edulis.
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Affiliation(s)
- Xinchun Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Yitian Bai
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Zhen Dong
- 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
| | - Shikai Liu
- 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
| | - 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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Ghaffari H, Ahmadzadeh F, Saberi-Pirooz R, Abtahi B. A molecular phylogeny of the Persian Gulf and the Gulf of Oman oyster species. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
The taxonomy of oysters along the northern coasts of the Persian Gulf and the Gulf of Oman is not well recognized. We present a phylogenetic analysis of oyster species in these regions. We combined morphological and molecular techniques to obtain the identity of oysters to the lowest taxonomic levels. Analysis of partial nucleotide sequences from mitochondrial cytochrome c oxidase subunit I (COI) was used for the phylogenetic evaluation. Based on our findings, Iranian samples nested within the genus Saccostrea and belonged to Saccostrea mordax and Saccostrea palmula clades. The shell morphology of the studied samples was variable, as in other rock oyster species. The examination of morphological features was in line with the molecular outcomes, but despite some similarities, Iranian S. palmula had well-developed and elongated chomata. The results also showed that S. mordax and S. palmula possessed significant relative abundance as dominant oysters in the Persian Gulf and the Gulf of Oman, respectively. Phylogenetic analysis revealed that Iranian samples of S. palmula formed a separate subclade from the Gulf of California and Panama samples, with large genetic distances (6–7%). Iranian specimens differed morphologically and genetically, suggesting that they could be a new species, although more research is needed.
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Affiliation(s)
- Hamze Ghaffari
- Iranian National Institute for Oceanography and Atmospheric Science (INIOAS) , No. 3, Etemadzadeh Street, Fatemi Avenue, Tehran 1411813389 , Islamic Republic of Iran
| | - Faraham Ahmadzadeh
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research Institute, Shahid Beheshti University , G.C., Tehran 1983963113 , Islamic Republic of Iran
| | - Reihaneh Saberi-Pirooz
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research Institute, Shahid Beheshti University , G.C., Tehran 1983963113 , Islamic Republic of Iran
| | - Behrooz Abtahi
- Faculty of Life Sciences and Biotechnology, Shahid Beheshti University , G.C. , Tehran 1983969411 , Islamic Republic of Iran
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Balakrishnan S, Singh ISB, Puthumana J. Status in molluscan cell line development in last one decade (2010–2020): impediments and way forward. Cytotechnology 2022; 74:433-457. [PMID: 36110153 PMCID: PMC9374870 DOI: 10.1007/s10616-022-00539-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 06/13/2022] [Indexed: 11/28/2022] Open
Abstract
Despite the attempts that have started since the 1960s, not even a single cell line of marine molluscs is available. Considering the vast contribution of marine bivalve aquaculture to the world economy, the prevailing viral threats, and the dismaying lack of advancements in molluscan virology, the requirement of a marine molluscan cell line is indispensable. This synthetic review discusses the obstacles in developing a marine molluscan cell line concerning the choice of species, the selection of tissue and decontamination, and cell culture media, with emphasis given on the current decade 2010-2020. Detailed accounts on the experiments on the virus cultivation in vitro and molluscan cell immortalization, with a brief note on the history and applications of the molluscan cell culture, are elucidated to give a holistic picture of the current status and future trends in molluscan cell line development. Supplementary Information The online version contains supplementary material available at 10.1007/s10616-022-00539-x.
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Corrochano-Fraile A, Davie A, Carboni S, Bekaert M. Evidence of multiple genome duplication events in Mytilus evolution. BMC Genomics 2022; 23:340. [PMID: 35501689 PMCID: PMC9063065 DOI: 10.1186/s12864-022-08575-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 04/20/2022] [Indexed: 12/12/2022] Open
Abstract
Background Molluscs remain one significantly under-represented taxa amongst available genomic resources, despite being the second-largest animal phylum and the recent advances in genomes sequencing technologies and genome assembly techniques. With the present work, we want to contribute to the growing efforts by filling this gap, presenting a new high-quality reference genome for Mytilus edulis and investigating the evolutionary history within the Mytilidae family, in relation to other species in the class Bivalvia. Results Here we present, for the first time, the discovery of multiple whole genome duplication events in the Mytilidae family and, more generally, in the class Bivalvia. In addition, the calculation of evolution rates for three species of the Mytilinae subfamily sheds new light onto the taxa evolution and highlights key orthologs of interest for the study of Mytilus species divergences. Conclusions The reference genome presented here will enable the correct identification of molecular markers for evolutionary, population genetics, and conservation studies. Mytilidae have the capability to become a model shellfish for climate change adaptation using genome-enabled systems biology and multi-disciplinary studies of interactions between abiotic stressors, pathogen attacks, and aquaculture practises. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08575-9.
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Affiliation(s)
- Ana Corrochano-Fraile
- Faculty of Natural Sciences, Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK
| | - Andrew Davie
- Faculty of Natural Sciences, Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK
| | - Stefano Carboni
- Faculty of Natural Sciences, Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK. .,International Marine Centre, Loc. Sa Mardini snc, 09170, Torre Grande, OR, Italy.
| | - Michaël Bekaert
- Faculty of Natural Sciences, Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK
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Chen Z, Schrödl M. How many single-copy orthologous genes from whole genomes reveal deep gastropod relationships? PeerJ 2022; 10:e13285. [PMID: 35497189 PMCID: PMC9048639 DOI: 10.7717/peerj.13285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/28/2022] [Indexed: 01/13/2023] Open
Abstract
The Gastropoda contains 80% of existing mollusks and is the most diverse animal class second only to the Insecta. However, the deep phylogeny of gastropods has been controversial for a long time. Especially the position of Patellogastropoda is a major uncertainty. Morphology and some mitochondria studies concluded that Patellogastropoda is likely to be sister to all other gastropods (Orthogastropoda hypothesis), while transcriptomic and other mitogenomic studies indicated that Patellogastropoda and Vetigastropoda are sister taxa (Psilogastropoda). With the release of high-quality genomes, orthologous genes can be better identified and serve as powerful candidates for phylogenetic analysis. The question is, given the current limitations on the taxon sampling side, how many markers are needed to provide robust results. Here, we identified single-copy orthologous genes (SOGs) from 14 gastropods species with whole genomes available which cover five main gastropod subclasses. We generated different datasets from 395 to 1610 SOGs by allowing species missing in different levels. We constructed gene trees of each SOG, and inferred species trees from different collections of gene trees. We found as the number of SOGs increased, the inferred topology changed from Patellogastropoda being sister to all other gastropods to Patellogastropoda being sister to Vetigastropoda + Neomphalina (Psilogastropoda s.l.), with considerable support. Our study thus rejects the Orthogastropoda concept showing that the selection of the representative species and use of sufficient informative sites greatly influence the analysis of deep gastropod phylogeny.
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Affiliation(s)
- Zeyuan Chen
- Mollusca, SNSB-Bavarian State Collection of Zoology, Munich, Bavaria, Germany,Department Biology II, Ludwig-Maximilians-Universität München, Munich, Bavaria, Germany
| | - Michael Schrödl
- Mollusca, SNSB-Bavarian State Collection of Zoology, Munich, Bavaria, Germany,Department Biology II, Ludwig-Maximilians-Universität München, Munich, Bavaria, Germany,GeoBio-Center LMU, Munich, Bavaria, Germany
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OUP accepted manuscript. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Davison A, Neiman M. Mobilizing molluscan models and genomes in biology. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200163. [PMID: 33813892 PMCID: PMC8059959 DOI: 10.1098/rstb.2020.0163] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2020] [Indexed: 12/11/2022] Open
Abstract
Molluscs are among the most ancient, diverse, and important of all animal taxa. Even so, no individual mollusc species has emerged as a broadly applied model system in biology. We here make the case that both perceptual and methodological barriers have played a role in the relative neglect of molluscs as research organisms. We then summarize the current application and potential of molluscs and their genomes to address important questions in animal biology, and the state of the field when it comes to the availability of resources such as genome assemblies, cell lines, and other key elements necessary to mobilising the development of molluscan model systems. We conclude by contending that a cohesive research community that works together to elevate multiple molluscan systems to 'model' status will create new opportunities in addressing basic and applied biological problems, including general features of animal evolution. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.
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Affiliation(s)
- Angus Davison
- School of Life Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, UK
| | - Maurine Neiman
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA
- Department of Gender, Women's, and Sexuality Studies, University of Iowa, Iowa City, IA 52242, USA
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Davison A, Neiman M. Pearls of wisdom-a Theo Murphy issue on molluscan genomics. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200151. [PMID: 33813890 DOI: 10.1098/rstb.2020.0151] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Angus Davison
- School of Life Sciences, University of Nottingham, Nottingham, Nottinghamshire NG7 2RD, UK
| | - Maurine Neiman
- Department of Biology, University of Iowa, Iowa City, IA 52245, USA
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