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Kim IH, Shin CR, Kim G, Park B, Kim KB, Choi EH, Hwang UW. Complete mitochondrial genome of Acanthochitona defilippii (Polyplacophora: Chitonida) from South Korea. Mitochondrial DNA B Resour 2024; 9:1029-1033. [PMID: 39135642 PMCID: PMC11318481 DOI: 10.1080/23802359.2024.2386403] [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: 05/10/2024] [Accepted: 07/25/2024] [Indexed: 08/15/2024] Open
Abstract
The chiton (Polyplacophora) occupies a significant position in molluscan evolutionary history as one of the most primitive groups within the phylum Mollusca. Acanthochitona defilippii (Tapparone-Canefri 1874) (Chitonida: Acanthochitonidae) is a commonly found intertidal chiton species in South Korea. In this study, we characterized the complete mitochondrial genome of A. defilippii (14,999 bp long), comprising 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and an A + T rich region (166 bp). The base composition is as follows: 31.82% for A, 11.63% for C, 16.69% for G, and 39.86% for T. We reconstructed a maximum likelihood (ML) tree to elucidate phylogenetic relationships among the eight chitonid families using the nucleotide sequences of all PCGs. The ML tree revealed that A. defilippii clustered with Acanthochitona avicula (BP 100) within the family Acanthochitonidae. Acanthochitonidae formed a sister group with Mopaliidae. The results could provide a valuable understanding the phylogenetic relationships of chitonid species.
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Affiliation(s)
- I Hyang Kim
- Department of Biomedical Convergence Science and Technology, School of Industrial Technology Advances, Kyungpook National University, Daegu, South Korea
| | - Cho Rong Shin
- Department of Biomedical Convergence Science and Technology, School of Industrial Technology Advances, Kyungpook National University, Daegu, South Korea
| | - Gyeongmin Kim
- School of Life Sciences, Graduate School, Kyungpook National University, Daegu, South Korea
| | - Bia Park
- Department of Biology Education, Teachers College & Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, South Korea
| | - Ki Beom Kim
- 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
| | - Eun Hwa Choi
- Department of Biology Education, Teachers College & Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, South Korea
- Phylomics Inc, Daegu, South Korea
| | - Ui Wook Hwang
- Department of Biomedical Convergence Science and Technology, School of Industrial Technology Advances, Kyungpook National University, Daegu, South Korea
- Department of Biology Education, Teachers College & Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, South Korea
- Phylomics Inc, Daegu, South Korea
- Institute for Korean Herb-Bio Convergence Promotion, Kyungpook National University, Daegu, South Korea
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Wang Y, Wang M, Li J, Zhang J, Zhang L. A chromosome-level genome assembly of a deep-sea symbiotic Aplacophora mollusc Chaetoderma sp. Sci Data 2024; 11:133. [PMID: 38272948 PMCID: PMC10810820 DOI: 10.1038/s41597-024-02940-x] [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: 09/25/2023] [Accepted: 01/10/2024] [Indexed: 01/27/2024] Open
Abstract
The worm-shaped, shell-less Caudofoveata is one of the least known groups of molluscs. As early-branching molluscs, the lack of high-quality genomes hinders our understanding of their evolution and ecology. Here, we report a high-quality chromosome-scale genome of Chaetoderma sp. combining PacBio, Illumina, and high-resolution chromosome conformation capture sequencing. The final assembly has a size of 2.45 Gb, with a scaffold N50 length of 141.46 Mb, and is anchored to 17 chromosomes. Gene annotations showed a high level of accuracy and completeness, with 23,675 predicted protein-coding genes and 94.44% of the metazoan conserved genes by BUSCO assessment. We further present 16S rRNA gene amplicon sequencing of the gut microbiota in Chaetoderma sp., which was dominated by the chemoautotrophic bacteria (phylum Gammaproteobacteria). This chromosome-level genome assembly presents the first genome for the Caudofoveata, which constitutes an important resource for studies ranging from molluscan evolution, symposium, to deep-sea adaptation.
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Affiliation(s)
- Yue Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, 430072, China
- College of Marine Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Minxiao Wang
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- College of Marine Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jie Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, 430072, China
- College of Marine Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Junlong Zhang
- College of Marine Science, University of Chinese Academy of Sciences, Beijing, 100049, China
- Department of Marine Organism Taxonomy & Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Linlin Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, 430072, China.
- College of Marine Science, University of Chinese Academy of Sciences, Beijing, 100049, China.
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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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Feng J, Guo Y, Yan C, Ye Y, Yan X, Li J, Xu K, Guo B, Lü Z. Novel gene rearrangement in the mitochondrial genome of Siliqua minima (Bivalvia, Adapedonta) and phylogenetic implications for Imparidentia. PLoS One 2021; 16:e0249446. [PMID: 33822813 PMCID: PMC8023497 DOI: 10.1371/journal.pone.0249446] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 03/18/2021] [Indexed: 11/19/2022] Open
Abstract
Siliqua minima (Gmelin, 1791) is an important economic shellfish species belonging to the family Pharidae. To date, the complete mitochondrial genome of only one species in this family (Sinonovacula constricta) has been sequenced. Research on the Pharidae family is very limited; to improve the evolution of this bivalve family, we sequenced the complete mitochondrial genome of S. minima by next-generation sequencing. The genome is 17,064 bp in length, consisting of 12 protein-coding genes (PCGs), 22 transfer RNA genes (tRNA), and two ribosomal RNA genes (rRNA). From the rearrangement analysis of bivalves, we found that the gene sequences of bivalves greatly variable among species, and with closer genetic relationship, the more consistent of the gene arrangement is higher among the species. Moreover, according to the gene arrangement of seven species from Adapedonta, we found that gene rearrangement among families is particularly obvious, while the gene order within families is relatively conservative. The phylogenetic analysis between species of the superorder Imparidentia using 12 conserved PCGs. The S. minima mitogenome was provided and will improve the phylogenetic resolution of Pharidae species.
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Affiliation(s)
- Jiantong Feng
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, China
| | - Yahong Guo
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, China
| | - Chengrui Yan
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, China
| | - Yingying Ye
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, China
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
| | - Xiaojun Yan
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, China
| | - Jiji Li
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, China
| | - Kaida Xu
- Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, MOA, Key Laboratory of Sustainable Utilization of Technology Research, Marine Fisheries Research Institute of Zhejiang, Zhoushan, China
| | - Baoying Guo
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, China
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
| | - Zhenming Lü
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, China
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
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Ghiselli F, Gomes-Dos-Santos A, Adema CM, Lopes-Lima M, Sharbrough J, Boore JL. Molluscan mitochondrial genomes break the rules. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200159. [PMID: 33813887 DOI: 10.1098/rstb.2020.0159] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The first animal mitochondrial genomes to be sequenced were of several vertebrates and model organisms, and the consistency of genomic features found has led to a 'textbook description'. However, a more broad phylogenetic sampling of complete animal mitochondrial genomes has found many cases where these features do not exist, and the phylum Mollusca is especially replete with these exceptions. The characterization of full mollusc mitogenomes required considerable effort involving challenging molecular biology, but has created an enormous catalogue of surprising deviations from that textbook description, including wide variation in size, radical genome rearrangements, gene duplications and losses, the introduction of novel genes, and a complex system of inheritance dubbed 'doubly uniparental inheritance'. Here, we review the extraordinary variation in architecture, molecular functioning and intergenerational transmission of molluscan mitochondrial genomes. Such features represent a great potential for the discovery of biological history, processes and functions that are novel for animal mitochondrial genomes. This provides a model system for studying the evolution and the manifold roles that mitochondria play in organismal physiology, and many ways that the study of mitochondrial genomes are useful for phylogeny and population biology. 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)
- Fabrizio Ghiselli
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Italy
| | - André Gomes-Dos-Santos
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, and Department of Biology, Faculty of Sciences, University of Porto, Portugal
| | - Coen M Adema
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, USA
| | - Manuel Lopes-Lima
- CIBIO/InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
| | - Joel Sharbrough
- Department of Biology, Colorado State University, Fort Collins, USA
| | - Jeffrey L Boore
- Providence St Joseph Health and the Institute for Systems Biology, Seattle, USA
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Tempestini A, Massamba-N'Siala G, Vermandele F, Beaudreau N, Mortz M, Dufresne F, Calosi P. Extensive gene rearrangements in the mitogenomes of congeneric annelid species and insights on the evolutionary history of the genus Ophryotrocha. BMC Genomics 2020; 21:815. [PMID: 33225885 PMCID: PMC7682095 DOI: 10.1186/s12864-020-07176-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 10/22/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Annelids are one the most speciose and ecologically diverse groups of metazoans. Although a significant effort has been recently invested in sequencing genomes of a wide array of metazoans, many orders and families within the phylum Annelida are still represented by a single specimen of a single species. The genus of interstitial annelids Ophryotrocha (Dorvilleidae, Errantia, Annelida) is among these neglected groups, despite its extensive use as model organism in numerous studies on the evolution of life history, physiological and ecological traits. To compensate for the paucity of genomic information in this genus, we here obtained novel complete mitochondrial genomes of six Ophryotrocha species using next generation sequencing. In addition, we investigated the evolution of the reproductive mode in the Ophryotrocha genus using a phylogeny based on two mitochondrial markers (COXI and 16S rDNA) and one nuclear fragment (Histone H3). RESULTS Surprisingly, gene order was not conserved among the six Ophryotrocha species investigated, and varied greatly as compared to those found in other annelid species within the class Errantia. The mitogenome phylogeny for the six Ophryotrocha species displayed a separation of gonochoric and hermaphroditic species. However, this separation was not observed in the phylogeny based on the COX1, 16S rDNA, and H3 genes. Parsimony and Bayesian ancestral trait reconstruction indicated that gonochorism was the most parsimonious ancestral reproductive mode in Ophryotrocha spp. CONCLUSIONS Our results highlight the remarkably high level of gene order variation among congeneric species, even in annelids. This encourages the need for additional mitogenome sequencing of annelid taxa in order to properly understand its mtDNA evolution, high biodiversity and phylogenetic relationships.
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Affiliation(s)
- Astrid Tempestini
- Département de Biologie, Chimie et Géographie, Université du Québec à Rimouski, 300 Allée des Ursulines, Rimouski, QC, G5L 3A1, Canada
| | - Gloria Massamba-N'Siala
- Département de Biologie, Chimie et Géographie, Université du Québec à Rimouski, 300 Allée des Ursulines, Rimouski, QC, G5L 3A1, Canada
| | - Fanny Vermandele
- Département de Biologie, Chimie et Géographie, Université du Québec à Rimouski, 300 Allée des Ursulines, Rimouski, QC, G5L 3A1, Canada
| | - Nicholas Beaudreau
- Département de Biologie, Chimie et Géographie, Université du Québec à Rimouski, 300 Allée des Ursulines, Rimouski, QC, G5L 3A1, Canada
| | - Mathieu Mortz
- Département de Biologie, Chimie et Géographie, Université du Québec à Rimouski, 300 Allée des Ursulines, Rimouski, QC, G5L 3A1, Canada
| | - France Dufresne
- Département de Biologie, Chimie et Géographie, Université du Québec à Rimouski, 300 Allée des Ursulines, Rimouski, QC, G5L 3A1, Canada
| | - Piero Calosi
- Département de Biologie, Chimie et Géographie, Université du Québec à Rimouski, 300 Allée des Ursulines, Rimouski, QC, G5L 3A1, Canada.
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Feng JT, Guo YH, Yan CR, Ye YY, Li JJ, Guo BY, Lü ZM. Comparative analysis of the complete mitochondrial genomes in two limpets from Lottiidae (Gastropoda: Patellogastropoda): rare irregular gene rearrangement within Gastropoda. Sci Rep 2020; 10:19277. [PMID: 33159159 PMCID: PMC7648102 DOI: 10.1038/s41598-020-76410-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 10/21/2020] [Indexed: 01/15/2023] Open
Abstract
To improve the systematics and taxonomy of Patellogastropoda within the evolution of gastropods, we determined the complete mitochondrial genome sequences of Lottia goshimai and Nipponacmea fuscoviridis in the family Lottiidae, which presented sizes of 18,192 bp and 18,720 bp, respectively. In addition to 37 common genes among metazoa, we observed duplication of the trnM gene in L. goshimai and the trnM and trnW genes in N. fuscoviridis. The highest A + T contents of the two species were found within protein-coding genes (59.95% and 54.55%), followed by rRNAs (56.50% and 52.44%) and tRNAs (56.42% and 52.41%). trnS1 and trnS2 could not form the canonical cloverleaf secondary structure due to the lack of a dihydrouracil arm in both species. The gene arrangements in all Patellogastropoda compared with those of ancestral gastropods showed different levels of gene rearrangement, including the shuffling, translocation and inversion of single genes or gene fragments. This kind of irregular rearrangement is particularly obvious in the Lottiidae family. The results of phylogenetic and gene rearrangement analyses showed that L. goshimai and Lottia digitalis clustered into one group, which in turn clustered with N. fuscoviridis in Patellogastropoda. This study demonstrates the significance of complete mitogenomes for phylogenetic analysis and enhances our understanding of the evolution of Patellogastropoda.
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Affiliation(s)
- Jian-Tong Feng
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Ya-Hong Guo
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Cheng-Rui Yan
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Ying-Ying Ye
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China.
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China.
| | - Ji-Ji Li
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Bao-Ying Guo
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Zhen-Ming Lü
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China
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Abstract
Ever since its discovery, the double-stranded DNA contained in the mitochondria of eukaryotes has fascinated researchers because of its bacterial endosymbiotic origin, crucial role in encoding subunits of the respiratory complexes, compact nature, and specific inheritance mechanisms. In the last few years, high-throughput sequencing techniques have accelerated the sequencing of mitochondrial genomes (mitogenomes) and uncovered the great diversity of organizations, gene contents, and modes of replication and transcription found in living eukaryotes. Some early divergent lineages of unicellular eukaryotes retain certain synteny and gene content resembling those observed in the genomes of alphaproteobacteria (the inferred closest living group of mitochondria), whereas others adapted to anaerobic environments have drastically reduced or even lost the mitogenome. In the three main multicellular lineages of eukaryotes, mitogenomes have pursued diverse evolutionary trajectories in which different types of molecules (circular versus linear and single versus multipartite), gene structures (with or without self-splicing introns), gene contents, gene orders, genetic codes, and transfer RNA editing mechanisms have been selected. Whereas animals have evolved a rather compact mitochondrial genome between 11 and 50 Kb in length with a highly conserved gene content in bilaterians, plants exhibit large mitochondrial genomes of 66 Kb to 11.3 Mb with large intergenic repetitions prone to recombination, and fungal mitogenomes have intermediate sizes of 12 to 236 Kb.
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Affiliation(s)
- Rafael Zardoya
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
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9
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Irisarri I, Uribe JE, Eernisse DJ, Zardoya R. A mitogenomic phylogeny of chitons (Mollusca: Polyplacophora). BMC Evol Biol 2020; 20:22. [PMID: 32024460 PMCID: PMC7003433 DOI: 10.1186/s12862-019-1573-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 12/30/2019] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Polyplacophora, or chitons, have long fascinated malacologists for their distinct and rather conserved morphology and lifestyle compared to other mollusk classes. However, key aspects of their phylogeny and evolution remain unclear due to the few morphological, molecular, or combined phylogenetic analyses, particularly those addressing the relationships among the major chiton lineages. RESULTS Here, we present a mitogenomic phylogeny of chitons based on 13 newly sequenced mitochondrial genomes along with eight available ones and RNAseq-derived mitochondrial sequences from four additional species. Reconstructed phylogenies largely agreed with the latest advances in chiton systematics and integrative taxonomy but we identified some conflicts that call for taxonomic revisions. Despite an overall conserved gene order in chiton mitogenomes, we described three new rearrangements that might have taxonomic utility and reconstructed the most likely scenario of gene order change in this group. Our phylogeny was time-calibrated using various fossils and relaxed molecular clocks, and the robustness of these analyses was assessed with several sensitivity analyses. The inferred ages largely agreed with previous molecular clock estimates and the fossil record, but we also noted that the ambiguities inherent to the chiton fossil record might confound molecular clock analyses. CONCLUSIONS In light of the reconstructed time-calibrated framework, we discuss the evolution of key morphological features and call for a continued effort towards clarifying the phylogeny and evolution of chitons.
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Affiliation(s)
- Iker Irisarri
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (MNCN-CSIC), c/ José Gutiérrez Abascal 2, 28006, Madrid, Spain.
- Department of Organismal Biology (Systematic Biology Program), Evolutionary Biology Centre, Uppsala University, Norbyv. 18C, 75236, Uppsala, Sweden.
| | - Juan E Uribe
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (MNCN-CSIC), c/ José Gutiérrez Abascal 2, 28006, Madrid, Spain
- Department of Invertebrate Zoology, Smithsonian Institution, National Museum of Natural History, 10th St. & Constitutional Ave. NW, Washington, DC, 20560, USA
| | - Douglas J Eernisse
- Department of Biological Science, California State University Fullerton, 800 N. State College Blvd, Fullerton, CA, 92831-3599, USA
| | - Rafael Zardoya
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (MNCN-CSIC), c/ José Gutiérrez Abascal 2, 28006, Madrid, Spain
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10
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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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Yang T, Xu G, Gu B, Shi Y, Mzuka HL, Shen H. The Complete Mitochondrial Genome Sequences of the Philomycus bilineatus (Stylommatophora: Philomycidae) and Phylogenetic Analysis. Genes (Basel) 2019; 10:E198. [PMID: 30841657 PMCID: PMC6471268 DOI: 10.3390/genes10030198] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 02/27/2019] [Accepted: 02/27/2019] [Indexed: 01/22/2023] Open
Abstract
The mitochondrial genome (mitogenome) can provide information for phylogenetic analyses and evolutionary biology. We first sequenced, annotated, and characterized the mitogenome of Philomycus bilineatus in this study. The complete mitogenome was 14,347 bp in length, containing 13 protein-coding genes (PCGs), 23 transfer RNA genes, two ribosomal RNA genes, and two non-coding regions (A + T-rich region). There were 15 overlap locations and 18 intergenic spacer regions found throughout the mitogenome of P. bilineatus. The A + T content in the mitogenome was 72.11%. All PCGs used a standard ATN as a start codon, with the exception of cytochrome c oxidase 1 (cox1) and ATP synthase F0 subunit 8 (atp8) with TTG and GTG. Additionally, TAA or TAG was identified as the typical stop codon. All transfer RNA (tRNA) genes had a typical clover-leaf structure, except for trnS1 (AGC), trnS2 (TCA), and trnK (TTT). A phylogenetic analysis with another 37 species of gastropods was performed using Bayesian inference, based on the amino acid sequences of 13 mitochondrial PCGs. The results indicated that P. bilineatus shares a close ancestry with Meghimatium bilineatum. It seems more appropriate to reclassify it as Arionoidea rather than Limacoidea, as previously thought. Our research may provide a new meaningful insight into the evolution of P. bilineatus.
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Affiliation(s)
- Tiezhu Yang
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai OceanUniversity, China.
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai OceanUniversity, Ministry of Education, China.
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution,Shanghai 201306, China.
| | - Guolyu Xu
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai OceanUniversity, China.
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai OceanUniversity, Ministry of Education, China.
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution,Shanghai 201306, China.
| | - Bingning Gu
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai OceanUniversity, China.
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai OceanUniversity, Ministry of Education, China.
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution,Shanghai 201306, China.
| | - Yanmei Shi
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai OceanUniversity, China.
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai OceanUniversity, Ministry of Education, China.
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution,Shanghai 201306, China.
| | - Hellen Lucas Mzuka
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai OceanUniversity, China.
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai OceanUniversity, Ministry of Education, China.
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution,Shanghai 201306, China.
| | - Heding Shen
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai OceanUniversity, China.
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai OceanUniversity, Ministry of Education, China.
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution,Shanghai 201306, China.
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Yang H, Zhang JE, Xia J, Yang J, Guo J, Deng Z, Luo M. Comparative Characterization of the Complete Mitochondrial Genomes of the Three Apple Snails (Gastropoda: Ampullariidae) and the Phylogenetic Analyses. Int J Mol Sci 2018; 19:E3646. [PMID: 30463257 PMCID: PMC6274680 DOI: 10.3390/ijms19113646] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 10/31/2018] [Accepted: 11/02/2018] [Indexed: 01/07/2023] Open
Abstract
The apple snails Pomacea canaliculata, Pomacea diffusa and Pomacea maculate (Gastropoda: Caenogastropoda: Ampullariidae) are invasive pests causing massive economic losses and ecological damage. We sequenced and characterized the complete mitochondrial genomes of these snails to conduct phylogenetic analyses based on comparisons with the mitochondrial protein coding sequences of 47 Caenogastropoda species. The gene arrangements, distribution and content were canonically identical and consistent with typical Mollusca except for the tRNA-Gln absent in P. diffusa. An identifiable control region (d-loop) was absent. Bayesian phylogenetic analysis indicated that all the Ampullariidae species clustered on the same branch. The genus Pomacea clustered together and then with the genus Marisa. The orders Architaenioglossa and Sorbeoconcha clustered together and then with the order Hypsogastropoda. Furthermore, the intergenic and interspecific taxonomic positions were defined. Unexpectedly, Ceraesignum maximum, Dendropoma gregarium, Eualetes tulipa and Thylacodes squamigerus, traditionally classified in order Hypsogastropoda, were isolated from the order Hypsogastropoda in the most external branch of the Bayesian inference tree. The divergence times of the Caenogastropoda indicated that their evolutionary process covered four geological epochs that included the Quaternary, Neogene, Paleogene and Cretaceous periods. This study will facilitate further investigation of species identification to aid in the implementation of effective management and control strategies of these invasive species.
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Affiliation(s)
- Huirong Yang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510640, China.
- Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, HI 96822, USA.
| | - Jia-En Zhang
- Institute of Tropical and Subtropical Ecology, South China Agricultural University, Guangzhou 510642, China.
| | - Jun Xia
- Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, HI 96822, USA.
- Xinjiang Acadamy of Animal Sciences, Institute of Veterinary Medicine (Research Center of Animal Clinical), Urumqi 830000, China.
| | - Jinzeng Yang
- Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, HI 96822, USA.
| | - Jing Guo
- Institute of Tropical and Subtropical Ecology, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Engineering Research Center for Modern Eco-Agriculture and Circular Agriculture, Guangzhou 510642, China.
| | - Zhixin Deng
- Institute of Tropical and Subtropical Ecology, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Engineering Research Center for Modern Eco-Agriculture and Circular Agriculture, Guangzhou 510642, China.
| | - Mingzhu Luo
- Institute of Tropical and Subtropical Ecology, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Engineering Research Center for Modern Eco-Agriculture and Circular Agriculture, Guangzhou 510642, China.
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Abalde S, Tenorio MJ, Afonso CML, Uribe JE, Echeverry AM, Zardoya R. Phylogenetic relationships of cone snails endemic to Cabo Verde based on mitochondrial genomes. BMC Evol Biol 2017; 17:231. [PMID: 29178825 PMCID: PMC5702168 DOI: 10.1186/s12862-017-1069-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 11/06/2017] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Due to their great species and ecological diversity as well as their capacity to produce hundreds of different toxins, cone snails are of interest to evolutionary biologists, pharmacologists and amateur naturalists alike. Taxonomic identification of cone snails still relies mostly on the shape, color, and banding patterns of the shell. However, these phenotypic traits are prone to homoplasy. Therefore, the consistent use of genetic data for species delimitation and phylogenetic inference in this apparently hyperdiverse group is largely wanting. Here, we reconstruct the phylogeny of the cones endemic to Cabo Verde archipelago, a well-known radiation of the group, using mitochondrial (mt) genomes. RESULTS The reconstructed phylogeny grouped the analyzed species into two main clades, one including Kalloconus from West Africa sister to Trovaoconus from Cabo Verde and the other with a paraphyletic Lautoconus due to the sister group relationship of Africonus from Cabo Verde and Lautoconus ventricosus from Mediterranean Sea and neighboring Atlantic Ocean to the exclusion of Lautoconus endemic to Senegal (plus Lautoconus guanche from Mauritania, Morocco, and Canary Islands). Within Trovaoconus, up to three main lineages could be distinguished. The clade of Africonus included four main lineages (named I to IV), each further subdivided into two monophyletic groups. The reconstructed phylogeny allowed inferring the evolution of the radula in the studied lineages as well as biogeographic patterns. The number of cone species endemic to Cabo Verde was revised under the light of sequence divergence data and the inferred phylogenetic relationships. CONCLUSIONS The sequence divergence between continental members of the genus Kalloconus and island endemics ascribed to the genus Trovaoconus is low, prompting for synonymization of the latter. The genus Lautoconus is paraphyletic. Lautoconus ventricosus is the closest living sister group of genus Africonus. Diversification of Africonus was in allopatry due to the direct development nature of their larvae and mainly triggered by eustatic sea level changes during the Miocene-Pliocene. Our study confirms the diversity of cone endemic to Cabo Verde but significantly reduces the number of valid species. Applying a sequence divergence threshold, the number of valid species within the sampled Africonus is reduced to half.
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Affiliation(s)
- Samuel Abalde
- Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Manuel J Tenorio
- Departamento CMIM y Q. Inorgánica-INBIO, Facultad de Ciencias, Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
| | - Carlos M L Afonso
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, 8005 - 139, Faro, Portugal
| | - Juan E Uribe
- Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Ana M Echeverry
- Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - Rafael Zardoya
- Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006, Madrid, Spain.
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14
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Stöger I, Kocot KM, Poustka AJ, Wilson NG, Ivanov D, Halanych KM, Schrödl M. Monoplacophoran mitochondrial genomes: convergent gene arrangements and little phylogenetic signal. BMC Evol Biol 2016; 16:274. [PMID: 27986078 PMCID: PMC5162086 DOI: 10.1186/s12862-016-0829-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 11/17/2016] [Indexed: 04/07/2023] Open
Abstract
BACKGROUND Although recent studies have greatly advanced understanding of deep molluscan phylogeny, placement of some taxa remains uncertain as different datasets support competing class-relationships. Traditionally, morphologists have placed Monoplacophora, a group of morphologically simple, limpet-like molluscs as sister group to all other conchiferans (shelled molluscs other than Polyplacophora), a grouping that is supported by the latest large-scale phylogenomic study that includes Laevipilina. However, molecular datasets dominated by nuclear ribosomal genes support Monoplacophora + Polyplacophora (Serialia). Here, we evaluate the potential of mitochondrial genome data for resolving placement of Monoplacophora. RESULTS Two complete (Laevipilina antarctica and Vema ewingi) and one partial (Laevipilina hyalina) mitochondrial genomes were sequenced, assembled, and compared. All three genomes show a highly similar architecture including an unusually high number of non-coding regions. Comparison of monoplacophoran gene order shows a gene arrangement pattern not previously reported; there is an inversion of one large gene cluster. Our reanalyses of recently published polyplacophoran mitogenomes show, however, that this feature is also present in some chiton species. Maximum Likelihood and Bayesian Inference analyses of 13 mitochondrial protein-coding genes failed to robustly place Monoplacophora and hypothesis testing could not reject any of the evaluated placements of Monoplacophora. CONCLUSIONS Under both serialian or aculiferan-conchiferan scenarios, the observed gene cluster inversion appears to be a convergent evolution of gene arrangements in molluscs. Our phylogenetic results are inconclusive and sensitive to taxon sampling. Aculifera (Polyplacophora + Aplacophora) and Conchifera were never recovered. However, some analyses recovered Serialia (Monoplacophora + Polyplacophora), Diasoma (Bivalvia + Scaphopoda) or Pleistomollusca (Bivalvia + Gastropoda). Although we could not shed light on deep evolutionary traits of Mollusca we found unique patterns of gene arrangements that are common to monoplacophoran and chitonine polyplacophoran species but not to acanthochitonine Polyplacophora. Complete mitochondrial genome of Laevipilina antarctica.
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Affiliation(s)
- I Stöger
- SNSB-Bavarian State Collection of Zoology, Muenchhausenstrasse 21, 81247, Munich, Germany.
| | - K M Kocot
- Department of Biological Sciences, University of Alabama, Box 870344, Tuscaloosa, AL, 35487, USA
| | - A J Poustka
- Max-Planck Institut fuer Molekulare Genetik, Evolution and Development Group, Ihnestrasse 73, 14195, Berlin, Germany.,Dahlem Center for Genome Research and Medical Systems Biology, Environmental and Phylogenomics Group, Fabeckstraße 60-62, 14195, Berlin, Germany.,Alacris Theranostics GmbH, Fabeckstr. 60-62, 14195, Berlin, Germany
| | - N G Wilson
- Western Australian Museum, Aquatic Zoology/Molecular Systematics Unit, 49 Kew Street, Welshpool, WA, 6106, Australia
| | - D Ivanov
- Zoological Museum, Moscow State University, Bolshaya Nikitskaya Str. 6, 225009, Moscow, Russia
| | - K M Halanych
- Biological Sciences Department, Auburn University, Life Sciences Bld. 101, Auburn, AL, 36849, USA
| | - M Schrödl
- SNSB-Bavarian State Collection of Zoology, Muenchhausenstrasse 21, 81247, Munich, Germany.,Faculty of Biology, Department II, Ludwig-Maximilians-Universitaet Muenchen, Großhaderner Strasse 2-4, 82152, Planegg-Martinsried, Germany.,GeoBio-Center at LMU, Richard-Wagner-Strasse 10, 80333, Munich, Germany
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15
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De Oliveira AL, Wollesen T, Kristof A, Scherholz M, Redl E, Todt C, Bleidorn C, Wanninger A. Comparative transcriptomics enlarges the toolkit of known developmental genes in mollusks. BMC Genomics 2016; 17:905. [PMID: 27832738 PMCID: PMC5103448 DOI: 10.1186/s12864-016-3080-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 09/08/2016] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Mollusks display a striking morphological disparity, including, among others, worm-like animals (the aplacophorans), snails and slugs, bivalves, and cephalopods. This phenotypic diversity renders them ideal for studies into animal evolution. Despite being one of the most species-rich phyla, molecular and in silico studies concerning specific key developmental gene families are still scarce, thus hampering deeper insights into the molecular machinery that governs the development and evolution of the various molluscan class-level taxa. RESULTS Next-generation sequencing was used to retrieve transcriptomes of representatives of seven out of the eight recent class-level taxa of mollusks. Similarity searches, phylogenetic inferences, and a detailed manual curation were used to identify and confirm the orthology of numerous molluscan Hox and ParaHox genes, which resulted in a comprehensive catalog that highlights the evolution of these genes in Mollusca and other metazoans. The identification of a specific molluscan motif in the Hox paralog group 5 and a lophotrochozoan ParaHox motif in the Gsx gene is described. Functional analyses using KEGG and GO tools enabled a detailed description of key developmental genes expressed in important pathways such as Hedgehog, Wnt, and Notch during development of the respective species. The KEGG analysis revealed Wnt8, Wnt11, and Wnt16 as Wnt genes hitherto not reported for mollusks, thereby enlarging the known Wnt complement of the phylum. In addition, novel Hedgehog (Hh)-related genes were identified in the gastropod Lottia cf. kogamogai, demonstrating a more complex gene content in this species than in other mollusks. CONCLUSIONS The use of de novo transcriptome assembly and well-designed in silico protocols proved to be a robust approach for surveying and mining large sequence data in a wide range of non-model mollusks. The data presented herein constitute only a small fraction of the information retrieved from the analysed molluscan transcriptomes, which can be promptly employed in the identification of novel genes and gene families, phylogenetic inferences, and other studies using molecular tools. As such, our study provides an important framework for understanding some of the underlying molecular mechanisms involved in molluscan body plan diversification and hints towards functions of key developmental genes in molluscan morphogenesis.
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Affiliation(s)
- A. L. De Oliveira
- Department of Integrative Zoology, Faculty of Life Sciences, University of Vienna, Althanstraße 14, Vienna, 1090 Austria
| | - T. Wollesen
- Department of Integrative Zoology, Faculty of Life Sciences, University of Vienna, Althanstraße 14, Vienna, 1090 Austria
| | - A. Kristof
- Department of Integrative Zoology, Faculty of Life Sciences, University of Vienna, Althanstraße 14, Vienna, 1090 Austria
| | - M. Scherholz
- Department of Integrative Zoology, Faculty of Life Sciences, University of Vienna, Althanstraße 14, Vienna, 1090 Austria
| | - E. Redl
- Department of Integrative Zoology, Faculty of Life Sciences, University of Vienna, Althanstraße 14, Vienna, 1090 Austria
| | - C. Todt
- University of Bergen, University Museum, The Natural History Collections, Allégaten 41, 5007 Bergen, Norway
| | - C. Bleidorn
- Museo Nacional de Ciencias Naturales, Spanish National Research Council (CSIC), José Gutiérrez Abascal 2, Madrid, 28006 Spain
- Institute of Biology, University of Leipzig, Leipzig, 04103 Germany
| | - A. Wanninger
- Department of Integrative Zoology, Faculty of Life Sciences, University of Vienna, Althanstraße 14, Vienna, 1090 Austria
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16
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Kristof A, de Oliveira AL, Kolbin KG, Wanninger A. Neuromuscular development in Patellogastropoda (Mollusca: Gastropoda) and its importance for reconstructing ancestral gastropod bodyplan features. J ZOOL SYST EVOL RES 2015; 54:22-39. [PMID: 26869747 PMCID: PMC4747121 DOI: 10.1111/jzs.12112] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Within Gastropoda, limpets (Patellogastropoda) are considered the most basal branching taxon and its representatives are thus crucial for research into evolutionary questions. Here, we describe the development of the neuromuscular system in Lottia cf. kogamogai. In trochophore larvae, first serotonin‐like immunoreactivity (lir) appears in the apical organ and in the prototroch nerve ring. The arrangement and number of serotonin‐lir cells in the apical organ (three flask‐shaped, two round cells) are strikingly similar to those in putatively derived gastropods. First, FMRFamide‐lir appears in veliger larvae in the Anlagen of the future adult nervous system including the cerebral and pedal ganglia. As in other gastropods, the larvae of this limpet show one main and one accessory retractor as well as a pedal retractor and a prototroch muscle ring. Of these, only the pedal retractor persists until after metamorphosis and is part of the adult shell musculature. We found a hitherto undescribed, paired muscle that inserts at the base of the foot and runs towards the base of the tentacles. An apical organ with flask‐shaped cells, one main and one accessory retractor muscle is commonly found among gastropod larvae and thus might have been part of the last common ancestor.
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Affiliation(s)
- Alen Kristof
- Department of Integrative Zoology, University of Vienna, Vienna Austria
| | | | - Konstantin G Kolbin
- Laboratory of Cell Differentiation, A.V. Zhirmunsky Institute for Marine Biology, Far East Branch of the Russian Academy of Sciences, Vladivostok Russian Federation
| | - Andreas Wanninger
- Department of Integrative Zoology, University of Vienna, Vienna Austria
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17
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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: 18] [Impact Index Per Article: 2.0] [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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18
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Fritsch M, Wollesen T, de Oliveira AL, Wanninger A. Unexpected co-linearity of Hox gene expression in an aculiferan mollusk. BMC Evol Biol 2015; 15:151. [PMID: 26243538 PMCID: PMC4524011 DOI: 10.1186/s12862-015-0414-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 06/08/2015] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Mollusca is an extremely diverse animal phylum that includes the aculiferans (worm-like aplacophorans and eight-shelled polyplacophorans) and their sister group, the conchiferans, comprising monoplacophorans, bivalves (clams, mussels), gastropods (snails, slugs), scaphopods (tusk shells) and cephalopods (squids, octopuses). Studies on mollusks have revealed an overall number of 11 Hox genes in seven out of eight molluscan "class"-level taxa, but expression data of key developmental regulators such as homeotic genes are only available for three gastropod and two cephalopod species. These show that Hox genes are involved in the formation of specific features including shell, foot, funnel or tentacles and not in antero-posterior body plan patterning as in most other bilaterian animals. The role of Hox genes in non-conchiferan (i.e., aculiferan) mollusks remains entirely unknown. RESULTS Here we present the first data on the expression of seven Hox genes in apolyplacophoran mollusk, Acanthochitona crinita. In A. crinita the Hox genes Acr-Hox1-5, Hox7 and Post2 are expressed in a co-linear pattern along the antero-posterior axis, but not in molluscan-specific features such as the shell or the foot. The expression pattern is restricted to the post-trochal region and the transcripts are present in ecto-, endo- and mesodermal cell layers. Contrary to the situation in gastropods and cephalopods, we did neither find Hox gene expression in distinct neural subsets of A. crinita, nor in its developing shell plates. CONCLUSIONS Our analysis and comparison with other lophotrochozoans indicate that the basal role of Hox genes is in antero-posterior axis patterning in mollusks, similar to the vast majority of bilaterian animals, and that this role has been conserved in polyplacophorans, while co-option into patterning of evolutionary novelties emerged either at the base of Conchifera or independently in gastropods and cephalopods. These morphological innovations most likely contributed to the evolutionary success of its representatives, as exemplified by, e.g., the wide ecological range and species richness of gastropods.
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Affiliation(s)
- M Fritsch
- Department of Integrative Zoology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
| | - T Wollesen
- Department of Integrative Zoology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
| | - A L de Oliveira
- Department of Integrative Zoology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
| | - A Wanninger
- Department of Integrative Zoology, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
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19
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Redl E, Scherholz M, Todt C, Wollesen T, Wanninger A. Development of the nervous system in Solenogastres (Mollusca) reveals putative ancestral spiralian features. EvoDevo 2014; 5:48. [PMID: 25904999 PMCID: PMC4406162 DOI: 10.1186/2041-9139-5-48] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 12/02/2014] [Indexed: 11/14/2022] Open
Abstract
Background The Solenogastres (or Neomeniomorpha) are a taxon of aplacophoran molluscs with contentious phylogenetic placement. Since available developmental data on non-conchiferan (that is, aculiferan) molluscs mainly stem from polyplacophorans, data on aplacophorans are needed to clarify evolutionary questions concerning the morphological features of the last common ancestor (LCA) of the Aculifera and the entire Mollusca. We therefore investigated the development of the nervous system in two solenogasters, Wirenia argentea and Gymnomenia pellucida, using immunocytochemistry and electron microscopy. Results Nervous system formation starts simultaneously from the apical and abapical pole of the larva with the development of a few cells of the apical organ and a posterior neurogenic domain. A pair of neurite bundles grows out from both the neuropil of the apical organ and the posterior neurogenic domain. After their fusion in the region of the prototroch, which is innervated by an underlying serotonin-like immunoreactive (−LIR) plexus, the larva exhibits two longitudinal neurite bundles - the future lateral nerve cords. The apical organ in its fully developed state exhibits approximately 8 to 10 flask-shaped cells but no peripheral cells. The entire ventral nervous system, which includes a pair of longitudinal neurite bundles (the future ventral nerve cords) and a serotonin-LIR ventromedian nerve plexus, appears simultaneously and is established after the lateral nervous system. During metamorphosis the apical organ and the prototrochal nerve plexus are lost. Conclusions The development of the nervous system in early solenogaster larvae shows striking similarities to other spiralians, especially polychaetes, in exhibiting an apical organ with flask-shaped cells, a single pair of longitudinal neurite bundles, a serotonin-LIR innervation of the prototroch, and formation of these structures from an anterior and a posterior neurogenic domain. This provides evidence for an ancestral spiralian pattern of early nervous system development and a LCA of the Spiralia with a single pair of nerve cords. In later nervous system development, however, the annelids deviate from all other spiralians including solenogasters in forming a posterior growth zone, which initiates teloblastic growth. Since this mode of organogenesis is confined to annelids, we conclude that the LCA of both molluscs and spiralians was unsegmented.
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Affiliation(s)
- Emanuel Redl
- Faculty of Life Sciences, Department of Integrative Zoology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Maik Scherholz
- Faculty of Life Sciences, Department of Integrative Zoology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Christiane Todt
- The Natural History Collections, University of Bergen, University Museum, Allégaten 41, 5007 Bergen, Norway
| | - Tim Wollesen
- Faculty of Life Sciences, Department of Integrative Zoology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Andreas Wanninger
- Faculty of Life Sciences, Department of Integrative Zoology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
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Irisarri I, Eernisse DJ, Zardoya R. Molecular phylogeny of Acanthochitonina (Mollusca: Polyplacophora: Chitonida): three new mitochondrial genomes, rearranged gene orders and systematics. J NAT HIST 2014. [DOI: 10.1080/00222933.2014.963721] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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