1
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Goodheart JA, Rio RA, Taraporevala NF, Fiorenza RA, Barnes SR, Morrill K, Jacob MAC, Whitesel C, Masterson P, Batzel GO, Johnston HT, Ramirez MD, Katz PS, Lyons DC. A chromosome-level genome for the nudibranch gastropod Berghia stephanieae helps parse clade-specific gene expression in novel and conserved phenotypes. BMC Biol 2024; 22:9. [PMID: 38233809 PMCID: PMC10795318 DOI: 10.1186/s12915-024-01814-3] [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: 08/07/2023] [Accepted: 01/03/2024] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND How novel phenotypes originate from conserved genes, processes, and tissues remains a major question in biology. Research that sets out to answer this question often focuses on the conserved genes and processes involved, an approach that explicitly excludes the impact of genetic elements that may be classified as clade-specific, even though many of these genes are known to be important for many novel, or clade-restricted, phenotypes. This is especially true for understudied phyla such as mollusks, where limited genomic and functional biology resources for members of this phylum have long hindered assessments of genetic homology and function. To address this gap, we constructed a chromosome-level genome for the gastropod Berghia stephanieae (Valdés, 2005) to investigate the expression of clade-specific genes across both novel and conserved tissue types in this species. RESULTS The final assembled and filtered Berghia genome is comparable to other high-quality mollusk genomes in terms of size (1.05 Gb) and number of predicted genes (24,960 genes) and is highly contiguous. The proportion of upregulated, clade-specific genes varied across tissues, but with no clear trend between the proportion of clade-specific genes and the novelty of the tissue. However, more complex tissue like the brain had the highest total number of upregulated, clade-specific genes, though the ratio of upregulated clade-specific genes to the total number of upregulated genes was low. CONCLUSIONS Our results, when combined with previous research on the impact of novel genes on phenotypic evolution, highlight the fact that the complexity of the novel tissue or behavior, the type of novelty, and the developmental timing of evolutionary modifications will all influence how novel and conserved genes interact to generate diversity.
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Affiliation(s)
- Jessica A Goodheart
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA.
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
| | - Robin A Rio
- Bioengineering Department, Stanford University, Stanford, CA, USA
| | - Neville F Taraporevala
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Department of Wildland Resources, Utah State University, Logan, UT, USA
| | - Rose A Fiorenza
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Seth R Barnes
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Kevin Morrill
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Mark Allan C Jacob
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Carl Whitesel
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Park Masterson
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Grant O Batzel
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Hereroa T Johnston
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - M Desmond Ramirez
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Paul S Katz
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Deirdre C Lyons
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
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2
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Goodheart JA, Rio RA, Taraporevala NF, Fiorenza RA, Barnes SR, Morrill K, Jacob MAC, Whitesel C, Masterson P, Batzel GO, Johnston HT, Ramirez MD, Katz PS, Lyons DC. A chromosome-level genome for the nudibranch gastropod Berghia stephanieae helps parse clade-specific gene expression in novel and conserved phenotypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.04.552006. [PMID: 38014205 PMCID: PMC10680569 DOI: 10.1101/2023.08.04.552006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
How novel phenotypes originate from conserved genes, processes, and tissues remains a major question in biology. Research that sets out to answer this question often focuses on the conserved genes and processes involved, an approach that explicitly excludes the impact of genetic elements that may be classified as clade-specific, even though many of these genes are known to be important for many novel, or clade-restricted, phenotypes. This is especially true for understudied phyla such as mollusks, where limited genomic and functional biology resources for members of this phylum has long hindered assessments of genetic homology and function. To address this gap, we constructed a chromosome-level genome for the gastropod Berghia stephanieae (Valdés, 2005) to investigate the expression of clade-specific genes across both novel and conserved tissue types in this species. The final assembled and filtered Berghia genome is comparable to other high quality mollusk genomes in terms of size (1.05 Gb) and number of predicted genes (24,960 genes), and is highly contiguous. The proportion of upregulated, clade-specific genes varied across tissues, but with no clear trend between the proportion of clade-specific genes and the novelty of the tissue. However, more complex tissue like the brain had the highest total number of upregulated, clade-specific genes, though the ratio of upregulated clade-specific genes to the total number of upregulated genes was low. Our results, when combined with previous research on the impact of novel genes on phenotypic evolution, highlight the fact that the complexity of the novel tissue or behavior, the type of novelty, and the developmental timing of evolutionary modifications will all influence how novel and conserved genes interact to generate diversity.
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Affiliation(s)
- Jessica A. Goodheart
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Robin A. Rio
- Bioengineering Department, Stanford University, Stanford, CA, USA
| | - Neville F. Taraporevala
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Department of Wildland Resources, Utah State University, Logan, UT, USA
| | - Rose A. Fiorenza
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Seth R. Barnes
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Kevin Morrill
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Mark Allan C. Jacob
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Carl Whitesel
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Park Masterson
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Grant O. Batzel
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Hereroa T. Johnston
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - M. Desmond Ramirez
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Paul S. Katz
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Deirdre C. Lyons
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
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Paz-Sedano S, Díaz-Agras G, Gosliner TM, Pola M. Revealing morphological characteristics of Goniodorididae genera (Mollusca: Nudibranchia). ORG DIVERS EVOL 2021. [DOI: 10.1007/s13127-021-00508-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
AbstractDetailed knowledge of the anatomy of the species is an essential element in taxonomic studies, since it allows the comparison and differentiation of separate groups of taxa. It becomes especially important when considering type species, as the subsequent identification of the species that compose the taxa is based on its characteristics, considered common in the group. However, despite its relevance, there are still numerous species without detailed descriptions, being especially significant among invertebrates. The family Goniodorididae is a little-known group of nudibranchs that includes eight recognized genera: Okenia, Goniodoris, Ancula, Lophodoris, Spahria, Trapania, Goniodoridella and Murphydoris. Several of their species are not completely described, including type species, and the systematics of the family is still unclear. Here we study in detail the external morphology and internal anatomy of the type species of five of the eight Goniodorididae genera using microcomputed tomography and scanning electron microscopy. We include the species Okenia elegans, Goniodoris nodosa, Ancula gibbosa, Goniodoridella savignyi and Murphydoris singaporensis as well as one species of Trapania, T. graeffei. We describe for the first time the detailed internal anatomy of the type species Goniodoridella savignyi. The diagnostic features of each genus are compared, and a preliminary framework is shown to clarify their systematics and identifications.
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Ip JCH, Xu T, Sun J, Li R, Chen C, Lan Y, Han Z, Zhang H, Wei J, Wang H, Tao J, Cai Z, Qian PY, Qiu JW. Host-Endosymbiont Genome Integration in a Deep-Sea Chemosymbiotic Clam. Mol Biol Evol 2021; 38:502-518. [PMID: 32956455 PMCID: PMC7826175 DOI: 10.1093/molbev/msaa241] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Endosymbiosis with chemosynthetic bacteria has enabled many deep-sea invertebrates to thrive at hydrothermal vents and cold seeps, but most previous studies on this mutualism have focused on the bacteria only. Vesicomyid clams dominate global deep-sea chemosynthesis-based ecosystems. They differ from most deep-sea symbiotic animals in passing their symbionts from parent to offspring, enabling intricate coevolution between the host and the symbiont. Here, we sequenced the genomes of the clam Archivesica marissinica (Bivalvia: Vesicomyidae) and its bacterial symbiont to understand the genomic/metabolic integration behind this symbiosis. At 1.52 Gb, the clam genome encodes 28 genes horizontally transferred from bacteria, a large number of pseudogenes and transposable elements whose massive expansion corresponded to the timing of the rise and subsequent divergence of symbiont-bearing vesicomyids. The genome exhibits gene family expansion in cellular processes that likely facilitate chemoautotrophy, including gas delivery to support energy and carbon production, metabolite exchange with the symbiont, and regulation of the bacteriocyte population. Contraction in cellulase genes is likely adaptive to the shift from phytoplankton-derived to bacteria-based food. It also shows contraction in bacterial recognition gene families, indicative of suppressed immune response to the endosymbiont. The gammaproteobacterium endosymbiont has a reduced genome of 1.03 Mb but retains complete pathways for sulfur oxidation, carbon fixation, and biosynthesis of 20 common amino acids, indicating the host’s high dependence on the symbiont for nutrition. Overall, the host–symbiont genomes show not only tight metabolic complementarity but also distinct signatures of coevolution allowing the vesicomyids to thrive in chemosynthesis-based ecosystems.
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Affiliation(s)
- Jack Chi-Ho Ip
- Department of Biology, Hong Kong Baptist University, Hong Kong, China.,HKBU Institute of Research and Continuing Education, Virtual University Park, Shenzhen, China.,Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
| | - Ting Xu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China.,HKBU Institute of Research and Continuing Education, Virtual University Park, Shenzhen, China.,Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
| | - Jin Sun
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China.,Division of Life Science, Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Runsheng Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Chong Chen
- X-STAR, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa Prefecture, Japan
| | - Yi Lan
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China.,Division of Life Science, Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Zhuang Han
- Sanya Institute of Deep-Sea Science and Engineering, Chinese Academy of Science, Sanya, Hainan, China
| | - Haibin Zhang
- Sanya Institute of Deep-Sea Science and Engineering, Chinese Academy of Science, Sanya, Hainan, China
| | - Jiangong Wei
- MLR Key Laboratory of Marine Mineral Resources, Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, China
| | - Hongbin Wang
- MLR Key Laboratory of Marine Mineral Resources, Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, China
| | - Jun Tao
- MLR Key Laboratory of Marine Mineral Resources, Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, China
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong, China
| | - Pei-Yuan Qian
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China.,Division of Life Science, Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China.,HKBU Institute of Research and Continuing Education, Virtual University Park, Shenzhen, China.,Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
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5
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Sigwart JD, Lindberg DR, Chen C, Sun J. Molluscan phylogenomics requires strategically selected genomes. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200161. [PMID: 33813889 DOI: 10.1098/rstb.2020.0161] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The extraordinary diversity in molluscan body plans, and the genomic mechanisms that enable it, remains one of the great questions of evolution. The eight distinct living taxonomic classes of molluscs are each unambiguously monophyletic; however, significant controversy remains about the phylogenetic relationships among those eight branches. Molluscs are the second-largest animal phylum, with over 100 000 living species with broad biological, economic and medical interest. To date, only around 53 genome assemblies have been accessioned to NCBI GenBank covering only four of the eight living molluscan classes. Furthermore, the molluscan taxa where partial or whole-genome assemblies are available are often aberrantly fast evolving or recently derived lineages. Characteristic adaptations provide interesting targets for whole-genome projects, in animals like the scaly-foot snail or octopus, but without basal-branching lineages for comparison, the context of recently derived features cannot be assessed. The currently available genomes also create a non-optimal set of taxa for resolving deeper phylogenetic branches: they are a small sample representing a large group, and those that are available come primarily from a rarefied pool. Thoughtful selection of taxa for future projects should focus on the blank areas of the molluscan tree, which are ripe with opportunities to delve into peculiarities of genome evolution, and reveal the biology and evolutionary history of molluscs. 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)
- Julia D Sigwart
- Senckenberg Research Institute, 60325 Frankfurt am Main, Germany.,Queen's University Belfast Marine Laboratory, Portaferry, Newtownards BT22 1PF, UK.,Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong
| | - David R Lindberg
- Department of Integrative Biology, University of California, Berkeley, USA
| | - Chong Chen
- X-STAR, Japan Agency for Marine Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Jin Sun
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, People's Republic of China
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6
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Choi EH, Choi NR, Hwang UW. The mitochondrial genome of an Endangered freshwater snail Koreoleptoxis nodifila (Caenogastropoda: Semisulcospiridae) from South Korea. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:1120-1123. [PMID: 33796761 PMCID: PMC7995809 DOI: 10.1080/23802359.2021.1901626] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
The mitochondrial genome of the Endangered freshwater snail Koreoleptoxis nodifila (Caenogastropoda: Semisulcospiridae) from South Korea is determined and characterized in detail. It is 15,737 bp in length being composed of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and one control region. It has a base composition of 31.23% for A, 16.29% for G, 17.84% for C, and 34.64% for T. The phylogenetic trees reconstructed based on the maximum-likelihood (ML) method and Bayesian inference (BI) confirmed that K. nodifila belongs to the Semisulcospiridae clade in the monophyletic caeonogastropod superfamily Cerithioidea.
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Affiliation(s)
- Eun Hwa Choi
- Department of Biology Education, Teachers College & Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, South Korea
| | - Na Rae Choi
- Department of Biology Education, Teachers College & Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, South Korea
| | - Ui Wook Hwang
- Department of Biology Education, Teachers College & Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, South Korea.,Institute for Korean Herb-Bio Convergence Promotion, Kyungpook National University, Daegu, South Korea.,Biomedical Convergence Science and Technology, Kyungpook National University, Daegu, South Korea
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7
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New data from Monoplacophora and a carefully-curated dataset resolve molluscan relationships. Sci Rep 2020; 10:101. [PMID: 31919367 PMCID: PMC6952402 DOI: 10.1038/s41598-019-56728-w] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 12/12/2019] [Indexed: 01/14/2023] Open
Abstract
Relationships among the major lineages of Mollusca have long been debated. Morphological studies have considered the rarely collected Monoplacophora (Tryblidia) to have several plesiomorphic molluscan traits. The phylogenetic position of this group is contentious as morphologists have generally placed this clade as the sister taxon of the rest of Conchifera whereas earlier molecular studies supported a clade of Monoplacophora + Polyplacophora (Serialia) and phylogenomic studies have generally recovered a clade of Monoplacophora + Cephalopoda. Phylogenomic studies have also strongly supported a clade including Gastropoda, Bivalvia, and Scaphopoda, but relationships among these taxa have been inconsistent. In order to resolve conchiferan relationships and improve understanding of early molluscan evolution, we carefully curated a high-quality data matrix and conducted phylogenomic analyses with broad taxon sampling including newly sequenced genomic data from the monoplacophoran Laevipilina antarctica. Whereas a partitioned maximum likelihood (ML) analysis using site-homogeneous models recovered Monoplacophora sister to Cephalopoda with moderate support, both ML and Bayesian inference (BI) analyses using mixture models recovered Monoplacophora sister to all other conchiferans with strong support. A supertree approach also recovered Monoplacophora as the sister taxon of a clade composed of the rest of Conchifera. Gastropoda was recovered as the sister taxon of Scaphopoda in most analyses, which was strongly supported when mixture models were used. A molecular clock based on our BI topology dates diversification of Mollusca to ~546 MYA (+/- 6 MYA) and Conchifera to ~540 MYA (+/- 9 MYA), generally consistent with previous work employing nuclear housekeeping genes. These results provide important resolution of conchiferan mollusc phylogeny and offer new insights into ancestral character states of major mollusc clades.
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8
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Jiang D, Zheng X, Zeng X, Kong L, Li Q. The complete mitochondrial genome of Harpago chiragra and Lambis lambis (Gastropoda: Stromboidea): implications on the Littorinimorpha phylogeny. Sci Rep 2019; 9:17683. [PMID: 31776396 PMCID: PMC6881320 DOI: 10.1038/s41598-019-54141-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 11/05/2019] [Indexed: 11/18/2022] Open
Abstract
The complete mitochondrial genomes of Harpago chiragra and Lambis lambis (Strombidae) were determined with the size of 15,460 bp and 15,481 bp, respectively, and both sequences contained 13 protein-coding genes, 22 tRNAs, and two rRNAs. H. chiragra and L. lambis have similar mitochondrial features, corresponding to typical gastropod mitochondrial genomes, such as the conserved gene order, a high A + T content (66.22% for H. chiragra and 66.10% for L. lambis), and preference for A + T-rich codons. The start or termination codon of same protein-coding gene in H. chiragra was consistent with that in L. lambis, except for the termination codon of cox1 gene (TAG for H. chiragra and TAA for L. lambis) and the start codon of nad4 (GTG for H. chiragra and ATG for L. lambis). Pairwise sequence alignments detected different degrees of variations in H. chiragra and L. lambis mitochondrial genomes; and the two species had lower levels of genetic distance (0.202 for nucleotide sequence) and closest relationships as compared to Strombus gigas and Oncomelania hupensis. The 13 partitioned nucleotide sequences of protein coding genes of H. chiragra and L. lambis were aligned with representatives of the main lineages of gastropods and their phylogenetic relationships were inferred. H. chiragra and L. lambis share the same gene order as Littorinimorpha species, except Vermetoidea, which demonstrate a gene rearrangement in species. The reconstructed phylogeny supports three major clades within Littorinimorpha: 1) Stromboidea, Tonnoidea, Littorinoidea, and Naticoidea, 2) Rissooidea and Truncatelloidea, and 3) Vermetoidea. In addition, a relaxed molecular clock calibrated with fossils dated the diversification of Strombidae near 112 (44–206) Mya and a possible radiation is detected to occur between 45–75 Mya, providing implications to understand the Cenozoic replacement event (65–135 Mya) of Aporrhaidae by Strombidae.
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Affiliation(s)
- Dianhang Jiang
- Institute of Evolution & Marine Biodiversity (IEMB), Ocean University of China, Qingdao, 266003, China.,Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Xiaodong Zheng
- Institute of Evolution & Marine Biodiversity (IEMB), Ocean University of China, Qingdao, 266003, China. .,Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
| | - Xiaoqi Zeng
- Institute of Evolution & Marine Biodiversity (IEMB), Ocean University of China, Qingdao, 266003, China.,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
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9
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Structure and function of the digestive system in molluscs. Cell Tissue Res 2019; 377:475-503. [DOI: 10.1007/s00441-019-03085-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 07/26/2019] [Indexed: 02/06/2023]
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10
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Evolutionary lineages of marine snails identified using molecular phylogenetics and geometric morphometric analysis of shells. Mol Phylogenet Evol 2018; 127:626-637. [PMID: 29913310 DOI: 10.1016/j.ympev.2018.06.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 06/05/2018] [Accepted: 06/05/2018] [Indexed: 01/12/2023]
Abstract
The relationship between morphology and inheritance is of perennial interest in evolutionary biology and palaeontology. Using three marine snail genera Penion, Antarctoneptunea and Kelletia, we investigate whether systematics based on shell morphology accurately reflect evolutionary lineages indicated by molecular phylogenetics. Members of these gastropod genera have been a taxonomic challenge due to substantial variation in shell morphology, conservative radular and soft tissue morphology, few known ecological differences, and geographical overlap between numerous species. Sampling all sixteen putative taxa identified across the three genera, we infer mitochondrial and nuclear ribosomal DNA phylogenetic relationships within the group, and compare this to variation in adult shell shape and size. Results of phylogenetic analysis indicate that each genus is monophyletic, although the status of some phylogenetically derived and likely more recently evolved taxa within Penion is uncertain. The recently described species P. lineatus is supported by genetic evidence. Morphology, captured using geometric morphometric analysis, distinguishes the genera and matches the molecular phylogeny, although using the same dataset, species and phylogenetic subclades are not identified with high accuracy. Overall, despite abundant variation, we find that shell morphology accurately reflects genus-level classification and the corresponding deep phylogenetic splits identified in this group of marine snails.
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11
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Sumner-Rooney L, Sigwart JD. Do chitons have a brain? New evidence for diversity and complexity in the polyplacophoran central nervous system. J Morphol 2018; 279:936-949. [PMID: 29683195 DOI: 10.1002/jmor.20823] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 03/19/2018] [Accepted: 03/22/2018] [Indexed: 01/26/2023]
Abstract
Molluscs demonstrate astonishing morphological diversity, and the relationships among clades have been debated for more than a century. Molluscan nervous systems range from simple 'ladder-like' cords to the complex brains of cephalopods. Chitons (Polyplacophora) are assumed to retain many molluscan plesiomorphies, lacking neural condensation and ganglionic structure, and therefore a brain. We reconstructed three-dimensional anatomical models of the nervous system in eight species of chitons in an attempt to clarify chiton neuroarchitecture and its variability. We combined new data with digitised historic slide material originally used by malacologist Johannes Thiele (1860-1935). Reconstructions of whole nervous systems in Acanthochitona fascicularis, Callochiton septemvalvis, Chiton olivaceus, Hemiarthrum setulosum, Lepidochitona cinerea, Lepidopleurus cajetanus and Leptochiton asellus, and the anterior nervous system of Schizoplax brandtii, demonstrated consistent and substantial anterior neural concentration in the circumoesophageal nerve ring. This is further organised into three concentric tracts, corresponding to the lateral, ventral and cerebral nerve cords. These represent homologues to the three main pairs of ganglia in other molluscs. Their relative size, shape and organisation are highly variable among the examined taxa, but consistent with previous studies of select species, and we formulated a set of neuroanatomical characters for chitons. These support anatomical transitions at the ordinal and subordinal levels; the identification of robust homologies in neural architecture will be central to future comparisons across Mollusca and, more broadly, Lophotrochozoa. Contrary to almost all previous descriptions, the size and structure of the chiton anterior nerve ring unambiguously qualify it as a true brain with cordal substructure.
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Affiliation(s)
- Lauren Sumner-Rooney
- Oxford University Museum of Natural History, Oxford, United Kingdom.,Museum für Naturkunde, Berlin, Germany
| | - Julia D Sigwart
- Queen's University Marine Laboratory, Portaferry, Northern Ireland.,Museum of Paleontology, University of California Berkeley, Berkeley, California
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12
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Avni E, Yona Z, Cohen R, Snir S. The Performance of Two Supertree Schemes Compared Using Synthetic and Real Data Quartet Input. J Mol Evol 2018; 86:150-165. [PMID: 29460038 DOI: 10.1007/s00239-018-9833-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 02/05/2018] [Indexed: 11/26/2022]
Abstract
Despite impressive advancements in technological and theoretical tools, construction of phylogenetic (evolutionary) trees is still a challenging task. The availability of enormous quantities of molecular data has made large-scale phylogenetic reconstruction involving thousands of species, a more viable goal. For this goal, separate trees over different, overlapping subsets of species, representing histories of various markers of these species, are collected. These trees, typically with conflicting signals, are subsequently combined into a single tree over the full set, an operation denoted as supertree construction. The amalgamation of such trees into a single tree lies at the heart of many tasks in phylogenetics, yet remains a daunting endeavor, especially in light of conflicting signals. In this work, we study the performance of matrix representation with parsimony (MRP), the most widely used supertree method to date, when confronted with quartet trees. Quartet trees are the most basic informational unit when amalgamation of unrooted trees is attempted, and they remain relevant in more general settings even though standard supertree methods are not necessarily confined to quartets. This study involves both real and simulated data, and the effects of several parameters on the results are evaluated, revealing a number of anomalies associated with MRP. We show that these anomalies are surmountable when using a recently introduced supertree method, weighted quartet MaxCut (wQMC).
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Affiliation(s)
- Eliran Avni
- Department of Evolutionary Biology, University of Haifa, 31905, Haifa, Israel
| | - Zahi Yona
- Department of Computer Scienece, University of Haifa, 31905, Haifa, Israel
| | - Reuven Cohen
- School of Engineering, Kinneret College, 15132, Tzemach, Israel
| | - Sagi Snir
- Department of Evolutionary Biology, University of Haifa, 31905, Haifa, Israel.
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Ponte G, Modica MV. Salivary Glands in Predatory Mollusks: Evolutionary Considerations. Front Physiol 2017; 8:580. [PMID: 28848453 PMCID: PMC5554399 DOI: 10.3389/fphys.2017.00580] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 07/27/2017] [Indexed: 12/20/2022] Open
Abstract
Many marine mollusks attain or increase their predatory efficiency using complex chemical secretions, which are often produced and delivered through specialized anatomical structures of the foregut. The secretions produced in venom glands of Conus snails and allies have been extensively studied, revealing an amazing chemical diversity of small, highly constrained neuropeptides, whose characterization led to significant pharmacological developments. Conversely, salivary glands, the other main secretory structures of molluscan foregut, have been neglected despite their shared occurrence in the two lineages including predatory members: Gastropoda and Cephalopoda. Over the last few years, the interest for the chemistry of salivary mixtures increased based on their potential biomedical applications. Recent investigation with -omics technologies are complementing the classical biochemical descriptions, that date back to the 1950s, highlighting the high level of diversification of salivary secretions in predatory mollusks, and suggesting they can be regarded as a pharmaceutical cornucopia. As with other animal venoms, some of the salivary toxins are reported to target, for example, sodium and/or potassium ion channels or receptors and transporters for neurotransmitters such as, glutamate, serotonin, neurotensin, and noradrenaline, thus manipulating the neuromuscular system of the preys. Other bioactive components possess anticoagulant, anesthetic and hypotensive activities. Here, we overview available knowledge on the salivary glands of key predatory molluscan taxa, gastropods, and cephalopods, summarizing their anatomical, physiological and biochemical complexity in order to facilitate future comparative studies on main evolutionary trends and functional convergence in the acquisition of successful predatory strategies.
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Affiliation(s)
- Giovanna Ponte
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton DohrnNapoli, Italy
- Association for Cephalopod Research - CephResNapoli, Italy
| | - Maria Vittoria Modica
- Department of Integrative Marine Ecology, Stazione Zoologica Anton DohrnNapoli, Italy
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Sigwart JD. Zoology: Molluscs All Beneath the Sun, One Shell, Two Shells, More, or None. Curr Biol 2017; 27:R708-R710. [DOI: 10.1016/j.cub.2017.05.075] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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15
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Sigwart JD, Sumner-Rooney LH, Dickey J, Carey N. The scaphopod foot is ventral: more evidence from the anatomy of Rhabdus rectius (Carpenter, 1864) (Dentaliida: Rhabdidae). MOLLUSCAN RESEARCH 2016. [DOI: 10.1080/13235818.2016.1257970] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Julia D. Sigwart
- Marine Laboratory, Queen’s University Belfast, Portaferry, Northern Ireland
- Museum of Paleontology, University of California, Berkeley, CA, USA
| | - Lauren H. Sumner-Rooney
- Marine Laboratory, Queen’s University Belfast, Portaferry, Northern Ireland
- Museum für Naturkunde, Invalidenstraße 43, Berlin, Germany
| | - James Dickey
- Marine Laboratory, Queen’s University Belfast, Portaferry, Northern Ireland
| | - Nicholas Carey
- Hopkins Marine Station, Stanford University, Pacific Grove, CA, USA
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16
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Affiliation(s)
- Gur Sevillya
- Department of Evolutionary and Environmental Biology University of Haifa Haifa 3498838 Israel
| | - Zeev Frenkel
- Department of Evolutionary and Environmental Biology University of Haifa Haifa 3498838 Israel
| | - Sagi Snir
- Department of Evolutionary and Environmental Biology University of Haifa Haifa 3498838 Israel
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Henry JQ, Lyons DC. Molluscan models: Crepidula fornicata. Curr Opin Genet Dev 2016; 39:138-148. [PMID: 27526387 DOI: 10.1016/j.gde.2016.05.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 05/16/2016] [Accepted: 05/30/2016] [Indexed: 12/11/2022]
Abstract
Gastropod snails in the genus Crepidula have emerged as model systems for studying a metazoan super clade, the Spiralia. Recent work on one species in particular, Crepidula fornicata, has produced high-resolution cell lineage fate maps, details of morphogenetic events during gastrulation, key insights into the molecular underpinnings of early development, and the first demonstration of CRISPR/Cas9 genome editing in the Spiralia. Furthermore, invasive species of Crepidula are a significant ecological threat, while one of these, C. fornicata, is also being harvested for food. This review highlights progress towards developing these animals as models for evolutionary, developmental, and ecological studies. Such studies have contributed greatly to our understanding of biology in a major clade of bilaterians. This information may also help us to control and cultivate these snails.
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Affiliation(s)
- Jonathan Q Henry
- University of Illinois, Department of Cell & Developmental Biology, 601 South Goodwin Avenue, Urbana, IL 61801, United States.
| | - Deirdre C Lyons
- University of California, San Diego, Scripps Institution of Oceanography, 9500 Gilman Drive, La Jolla, CA 92093, United States.
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19
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Sumner-Rooney LH, Schrödl M, Lodde-Bensch E, Lindberg DR, Heß M, Brennan GP, Sigwart JD. A neurophylogenetic approach provides new insight to the evolution of Scaphopoda. Evol Dev 2015; 17:337-46. [DOI: 10.1111/ede.12164] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Lauren H. Sumner-Rooney
- School of Biological Sciences; Queen's University Belfast; Northern Ireland
- Queen's University Marine Laboratory; Queen's University Belfast; Northern Ireland
| | - Michael Schrödl
- SNSB-Zoologische Staatssammlung M; ü; nchen; Germany
- Biozentrum; Ludwig-Maximilians-Universität München; Germany
| | | | - David R. Lindberg
- Department of Integrative Biology and Museum of Palaeontology; University of California; Berkeley CA USA
| | - Martin Heß
- Biozentrum; Ludwig-Maximilians-Universität München; Germany
| | - Gerard P. Brennan
- School of Biological Sciences; Queen's University Belfast; Northern Ireland
| | - Julia D. Sigwart
- School of Biological Sciences; Queen's University Belfast; Northern Ireland
- Queen's University Marine Laboratory; Queen's University Belfast; Northern Ireland
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Scherholz M, Redl E, Wollesen T, Todt C, Wanninger A. From complex to simple: myogenesis in an aplacophoran mollusk reveals key traits in aculiferan evolution. BMC Evol Biol 2015; 15:201. [PMID: 26385077 PMCID: PMC4575435 DOI: 10.1186/s12862-015-0467-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 08/26/2015] [Indexed: 11/23/2022] Open
Abstract
Background Recent studies suggest a bifurcation at the base of Mollusca, resulting in the primarily single-shelled Conchifera (Bivalvia, Gastropoda, Scaphopoda, Monoplacophora, Cephalopoda) and the spicule-bearing Aculifera (Polyplacophora, Neomeniomorpha, Chaetodermomorpha). A recent study revealed a complex larval musculature exclusively shared by Neomeniomorpha and Polyplacophora, supporting a close relationship of both taxa. However, the ontogenetic transition from the complex larval to the simple adult neomeniomorph musculature, which mainly consists of a three-layered body-wall musculature and serially iterated dorsoventral muscles, remains unknown. To close this gap in knowledge, we studied remodeling of the larval musculature during metamorphosis in the neomeniomorph Wirenia argentea. A comparative analysis with a novel data set of a polyplacophoran, Leptochiton asellus, allows us to infer the morphology of the last common ancestor of Aculifera and the evolution of its subclades therefrom. Results The complex larval musculature of Wirenia argentea persists through metamorphosis and becomes modified to form two of the three muscle layers of the adult body wall. The innermost longitudinal layer of the three-layered body wall musculature is generated by transformation and expansion of distinct larval longitudinal muscle bundles. The larval ventrolateral muscle strands are remodeled and eventually become the most ventral part of the adult longitudinal layer of the body wall musculature. The paired larval enrolling muscle forms the lateral parts and the former rectus muscle is destined to become the most dorsal part of the longitudinal layer of the body wall musculature. The transient ventromedian muscle is lost during postmetamorphic development. Conclusions Postmetamorphic remodeling in W. argentea supports the hypothesis of a complex myoanatomy rather than a three-layered body wall musculature at the base of Aculifera, and thus argues against homology of the body wall musculature of adult Neomeniomorpha and other potential molluscan sister groups. Our data show that the neomeniomorph body wall musculature is a derived condition and not an aculiferan or molluscan plesiomorphy.
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Affiliation(s)
- Maik Scherholz
- Department of Integrative Zoology, Faculty of Life Sciences, University of Vienna, Althanstraße 14, 1090, Vienna, Austria.
| | - Emanuel Redl
- Department of Integrative Zoology, Faculty of Life Sciences, University of Vienna, Althanstraße 14, 1090, Vienna, Austria.
| | - Tim Wollesen
- Department of Integrative Zoology, Faculty of Life Sciences, University of Vienna, Althanstraße 14, 1090, Vienna, Austria.
| | - Christiane Todt
- University Museum of Bergen, University of Bergen, Allégaten 41, 5007, Bergen, Norway.
| | - Andreas Wanninger
- Department of Integrative Zoology, Faculty of Life Sciences, University of Vienna, Althanstraße 14, 1090, Vienna, Austria.
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New animal phylogeny: future challenges for animal phylogeny in the age of phylogenomics. ORG DIVERS EVOL 2015. [DOI: 10.1007/s13127-015-0236-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Chen C, Copley JT, Linse K, Rogers AD, Sigwart J. How the mollusc got its scales: convergent evolution of the molluscan scleritome. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12462] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Chong Chen
- Department of Zoology; University of Oxford; The Tinbergen Building South Parks Road Oxford OX1 3PS UK
| | - Jonathan T. Copley
- Ocean and Earth Science; University of Southampton; European Way Southampton SO14 3ZH UK
| | - Katrin Linse
- British Antarctic Survey; High Cross Cambridge CB3 0ET UK
| | - Alex D. Rogers
- Department of Zoology; University of Oxford; The Tinbergen Building South Parks Road Oxford OX1 3PS UK
| | - Julia Sigwart
- Queen's University Belfast, Marine Laboratory; Portaferry BT22 1PF Northern Ireland UK
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