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González-Delgado S, Rodríguez-Flores PC, Giribet G. Testing ultraconserved elements (UCEs) for phylogenetic inference across bivalves (Mollusca: Bivalvia). Mol Phylogenet Evol 2024; 198:108129. [PMID: 38878989 DOI: 10.1016/j.ympev.2024.108129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 05/15/2024] [Accepted: 06/07/2024] [Indexed: 06/20/2024]
Abstract
Bivalves constitute an important resource for fisheries and as cultural objects. Bivalve phylogenetics has had a long tradition using both morphological and molecular characters, and genomic resources are available for a good number of commercially important species. However, relationships among bivalve families have been unstable and major conflicting results exist between mitogenomics and results based on Sanger-based amplicon sequencing or phylotranscriptomics. Here we design and test an ultraconserved elements probe set for the class Bivalvia with the aim to use hundreds of loci without the need to sequence full genomes or transcriptomes, which are expensive and complex to analyze, and to open bivalve phylogenetics to museum specimens. Our probe set successfully captured 1,513 UCEs for a total of 263,800 bp with an average length of 174.59 ± 3.44 per UCE (ranging from 28 to 842 bp). Phylogenetic testing of this UCE probe set across Bivalvia and within the family Donacidae using different data matrices and methods for phylogenetic inference shows promising results at multiple taxonomic levels. In addition, our probe set was able to capture large numbers of UCEs for museum specimens collected before 1900 and from DNAs properly stored, of which many museums and laboratories are well stocked. Overall, this constitutes a novel and useful resource for bivalve phylogenetics.
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Affiliation(s)
- Sara González-Delgado
- Departamento de Biología Animal, Edafología y Geología, Universidad de La Laguna, Santa Cruz de Tenerife, Canary Islands, Spain; Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Paula C Rodríguez-Flores
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Gonzalo Giribet
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
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2
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Nikishchenko VE, Dyachuk VA. Comparison of neurogenesis in bivalves with different types of development. Sci Rep 2024; 14:19495. [PMID: 39174570 PMCID: PMC11341568 DOI: 10.1038/s41598-024-67622-5] [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: 01/22/2024] [Accepted: 07/14/2024] [Indexed: 08/24/2024] Open
Abstract
The presence of different types of larvae within the same class suggests a broad ecological diversification. A clear comparison of bivalve larval nervous systems would give a broader view on evolutionary and ecological picture of the clade in question. The present study focused on the neurodevelopment in two bivalve species with different larval types: pericalymma of Acila insignis (Bivalvia: Protobranchia) and veliger of Spisula sybillae (Bivalvia: Autobranchia). It was shown that the pioneer dorsal and ventral neurons in S. sybillae appear at the trochophore stage. Subsequently, future three paired ganglia are developed on the nerve cords in pediveliger. In the pericalymma of A. insignis, serotonin- and FMRFamide-positive cells are found in the apical organ (AO), as well as two pairs of FMRFamide positive neurons are detected on dorsal and posterior part of pericalymma. A comparative analysis showed significant differences in the larval neuromorphology between veliger and pericalymma. In contrast to the S. sybillae veliger, the nervous system of the A. insignis pericalymma is simple, likely due to its different lifestyle. The larval nervous system in the species under study has features characteristic of Lophotrochozoa and Spiralia.
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Affiliation(s)
- Viktoria E Nikishchenko
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia
| | - Vyacheclav A Dyachuk
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia.
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3
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Jackson DJ, Cerveau N, Posnien N. De novo assembly of transcriptomes and differential gene expression analysis using short-read data from emerging model organisms - a brief guide. Front Zool 2024; 21:17. [PMID: 38902827 PMCID: PMC11188175 DOI: 10.1186/s12983-024-00538-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 06/12/2024] [Indexed: 06/22/2024] Open
Abstract
Many questions in biology benefit greatly from the use of a variety of model systems. High-throughput sequencing methods have been a triumph in the democratization of diverse model systems. They allow for the economical sequencing of an entire genome or transcriptome of interest, and with technical variations can even provide insight into genome organization and the expression and regulation of genes. The analysis and biological interpretation of such large datasets can present significant challenges that depend on the 'scientific status' of the model system. While high-quality genome and transcriptome references are readily available for well-established model systems, the establishment of such references for an emerging model system often requires extensive resources such as finances, expertise and computation capabilities. The de novo assembly of a transcriptome represents an excellent entry point for genetic and molecular studies in emerging model systems as it can efficiently assess gene content while also serving as a reference for differential gene expression studies. However, the process of de novo transcriptome assembly is non-trivial, and as a rule must be empirically optimized for every dataset. For the researcher working with an emerging model system, and with little to no experience with assembling and quantifying short-read data from the Illumina platform, these processes can be daunting. In this guide we outline the major challenges faced when establishing a reference transcriptome de novo and we provide advice on how to approach such an endeavor. We describe the major experimental and bioinformatic steps, provide some broad recommendations and cautions for the newcomer to de novo transcriptome assembly and differential gene expression analyses. Moreover, we provide an initial selection of tools that can assist in the journey from raw short-read data to assembled transcriptome and lists of differentially expressed genes.
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Affiliation(s)
- Daniel J Jackson
- University of Göttingen, Department of Geobiology, Goldschmidtstr.3, Göttingen, 37077, Germany.
| | - Nicolas Cerveau
- University of Göttingen, Department of Geobiology, Goldschmidtstr.3, Göttingen, 37077, Germany
| | - Nico Posnien
- University of Göttingen, Department of Developmental Biology, GZMB, Justus-Von-Liebig-Weg 11, Göttingen, 37077, Germany.
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4
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Gao Q, Tang Y, Zhang J. A new species of the genus Yoldiella (Bivalvia, Protobranchia, Yoldiidae) from Haima Cold Seep, South China Sea, China. Zookeys 2024; 1204:223-240. [PMID: 38882561 PMCID: PMC11176815 DOI: 10.3897/zookeys.1204.121088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 05/08/2024] [Indexed: 06/18/2024] Open
Abstract
In present study, a previously unidentified but frequently encountered species of deep-sea protobranch, Yoldiellahaimaensis sp. nov., is described new to science from the Haima Cold Seep on the northwestern slope of the South China Sea. A morphological analysis confirmed that this species belongs to a previously undescribed species of the genus Yoldiella A.E. Verrill & K.J. Bush, 1897. It differs morphologically from other known species within the genus in its shell shape, degree of inflation, beaks, and number of hinge teeth. Furthermore, we sequenced three gene segments of Y.haimaensis sp. nov., comprising a nuclear ribosomal gene (18S rRNA), a nuclear protein-coding gene (histone H3), and a mitochondrial gene (cytochrome c oxidase subunit I, COI). Our phylogenetic analysis performed on the superfamily Nuculanoidea and family Yoldiidae indicates that the genus Yoldiella is non-monophyletic, and the widely recognized families within the superfamily Nuculanoidea are also not monophyletic. Our results provide molecular insights into the Protobranchia and highlight the necessity for further samples and data to revise the classification of families and genera within the superfamily using an integrative approach that combines morphological analysis and molecular data.
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Affiliation(s)
- Qi Gao
- School of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China Institute of Oceanology, Chinese Academy of Sciences Qingdao China
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China Qingdao Agricultural University Qingdao China
| | - Yan Tang
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China Qingdao Agricultural University Qingdao China
| | - Junlong Zhang
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China Qingdao Agricultural University Qingdao China
- Marine Biological Museum, Chinese Academy of Sciences, Qingdao 266071, China Marine Biological Museum, Chinese Academy of Sciences Qingdao China
- University of Chinese Academy of Sciences, Beijing 100049, China University of Chinese Academy of Sciences Beijing China
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Iannello M, Forni G, Piccinini G, Xu R, Martelossi J, Ghiselli F, Milani L. Signatures of Extreme Longevity: A Perspective from Bivalve Molecular Evolution. Genome Biol Evol 2023; 15:evad159. [PMID: 37647860 PMCID: PMC10646442 DOI: 10.1093/gbe/evad159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 08/04/2023] [Accepted: 08/25/2023] [Indexed: 09/01/2023] Open
Abstract
Among Metazoa, bivalves have the highest lifespan disparity, ranging from 1 to 500+ years, making them an exceptional testing ground to understand mechanisms underlying aging and the evolution of extended longevity. Nevertheless, comparative molecular evolution has been an overlooked approach in this instance. Here, we leveraged transcriptomic resources spanning 30 bivalve species to unravel the signatures of convergent molecular evolution in four long-lived species: Margaritifera margaritifera, Elliptio complanata, Lampsilis siliquoidea, and Arctica islandica (the latter represents the longest-lived noncolonial metazoan known so far). We applied a comprehensive approach-which included inference of convergent dN/dS, convergent positive selection, and convergent amino acid substitution-with a strong focus on the reduction of false positives. Genes with convergent evolution in long-lived bivalves show more physical and functional interactions to each other than expected, suggesting that they are biologically connected; this interaction network is enriched in genes for which a role in longevity has been experimentally supported in other species. This suggests that genes in the network are involved in extended longevity in bivalves and, consequently, that the mechanisms underlying extended longevity are-at least partially-shared across Metazoa. Although we believe that an integration of different genes and pathways is required for the extended longevity phenotype, we highlight the potential central roles of genes involved in cell proliferation control, translational machinery, and response to hypoxia, in lifespan extension.
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Affiliation(s)
- Mariangela Iannello
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Giobbe Forni
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Giovanni Piccinini
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Ran Xu
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Jacopo Martelossi
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Fabrizio Ghiselli
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Liliana Milani
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
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Nikishchenko V, Kolotukhina N, Dyachuk V. Comparative Neuroanatomy of Pediveliger Larvae of Various Bivalves from the Sea of Japan. BIOLOGY 2023; 12:1341. [PMID: 37887051 PMCID: PMC10604817 DOI: 10.3390/biology12101341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 08/30/2023] [Accepted: 08/31/2023] [Indexed: 10/28/2023]
Abstract
Here, we describe the nervous system structures from pediveligers of eight bivalve species (Callista brevisiphonata, Mactromeris polynyma, Crenomytilus grayanus, Kellia japonica, Mizuhopecten yessoensis, and Azumapecten farreri) with different modes of life in their adult stages, corresponding to the ecological niches that they occupy (burrowing, cemented, byssally attached, and mobile forms). We have identified neuromorphological features of the central and peripheral nervous systems in larval bivalves. We show that the unpaired sensory apical organ is still present in pediveligers along with the developing paired cerebral ganglia characteristic of an adult mollusk. Pediveligers have the pleural ganglia connected to the pedal ganglia via the pedal nerve cords and to the visceral ganglia via the lateral nerve cords. We have found a number of structures of the peripheral nervous system whose presence varies between pediveligers of different species. Mactromeris, Callista, and Pododesmus have 5-HT-immunopositive stomatogastric neurons, whereas the Yesso and Farrer's scallops have an FMRFamide-immunopositive enteric nervous system. The innervation of the anterior part of the velum is connected to a system of the apical organ and cerebral ganglia, and the innervation of the posterior part is connected to the visceral ganglia. Most differences in the structure of the peripheral elements of the nervous system are species-specific and weakly depend on the ecological niche that pediveligers occupy.
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Affiliation(s)
| | | | - Vyacheslav Dyachuk
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, 690041 Vladivostok, Russia; (V.N.); (N.K.)
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Gonzalez BC, González VL, Martínez A, Worsaae K, Osborn KJ. A transcriptome-based phylogeny for Polynoidae (Annelida: Aphroditiformia). Mol Phylogenet Evol 2023:107811. [PMID: 37169231 DOI: 10.1016/j.ympev.2023.107811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 03/31/2023] [Accepted: 05/05/2023] [Indexed: 05/13/2023]
Abstract
Polynoidae is the most diverse radiation of Aphroditiformia and one of the most successful groups of all Annelida in terms of diversity and habitats colonized. With such an unmatched diversity, phylogenetic investigations have struggled to understand their evolutionary relationships. Previous phylogenetic analyses have slowly increased taxon sampling and employed methodologies, but despite their diversity and biological importance, large genomic sampling is limited. To investigate the internal relationships within Polynoidae, we conducted the first phylogenomic analyses of the group based on 12 transcriptomes collected from species inhabiting a broad array of habitats, including shallow and deep waters, as well as hydrothermal vents, anchialine caves and the midwater. Our phylogenomic analyses of Polynoidae recovered congruent tree topologies representing the clades Polynoinae, Macellicephalinae and Lepidonotopodinae. Members of Polynoinae and Macellicephalinae clustered in well supported and independent clades. In contrast, Lepidonotopodinae taxa were always recovered nested within Macellicephalinae. Though our sampling only covers a small proportion of the species known for Polynoidae, our results provide a robust phylogenomic framework to build from, emphasizing previously hypothesized relationships between Macellicephalinae and Lepidonotopodinae taxa, while providing new insights on the origin of enigmatic cave and pelagic lineages.
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Affiliation(s)
- Brett C Gonzalez
- Smithsonian Institution, National Museum of Natural History, Department of Invertebrate Zoology, P.O. Box 37012, Washington D.C., USA.
| | - Vanessa L González
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, Washington, D.C., USA
| | - Alejandro Martínez
- Molecular Ecology Group (MEG), Water Research Institute (IRSA), National Research Council of Italy (CNR), Largo Tonolli, 50, 28922. Pallanza, Italy
| | - Katrine Worsaae
- Marine Biological Section, Department of Biology, University of Copenhagen, Universitetsparken 4, Copenhagen Ø, Denmark
| | - Karen J Osborn
- Smithsonian Institution, National Museum of Natural History, Department of Invertebrate Zoology, P.O. Box 37012, Washington D.C., USA; Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, CA 95039, USA
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8
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Gomes-dos-Santos A, Lopes-Lima M, Machado AM, Forest T, Achaz G, Teixeira A, Prié V, C. Castro LF, Froufe E. The Crown Pearl V2: an improved genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758). GIGABYTE 2023; 2023:gigabyte81. [PMID: 37207176 PMCID: PMC10189783 DOI: 10.46471/gigabyte.81] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/10/2023] [Indexed: 05/21/2023] Open
Abstract
Contiguous assemblies are fundamental to deciphering the composition of extant genomes. In molluscs, this is considerably challenging owing to the large size of their genomes, heterozygosity, and widespread repetitive content. Consequently, long-read sequencing technologies are fundamental for high contiguity and quality. The first genome assembly of Margaritifera margaritifera (Linnaeus, 1758) (Mollusca: Bivalvia: Unionida), a culturally relevant, widespread, and highly threatened species of freshwater mussels, was recently generated. However, the resulting genome is highly fragmented since the assembly relied on short-read approaches. Here, an improved reference genome assembly was generated using a combination of PacBio CLR long reads and Illumina paired-end short reads. This genome assembly is 2.4 Gb long, organized into 1,700 scaffolds with a contig N50 length of 3.4 Mbp. The ab initio gene prediction resulted in 48,314 protein-coding genes. Our new assembly is a substantial improvement and an essential resource for studying this species' unique biological and evolutionary features, helping promote its conservation.
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Affiliation(s)
- André Gomes-dos-Santos
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
- Faculty of Sciences, University of Porto, , Porto, Portugal
- Corresponding authors. E-mail: ;
| | - Manuel Lopes-Lima
- CIBIO/InBIO - Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
- IUCN SSC Mollusc Specialist Group, c/o IUCN, David Attenborough Building, Pembroke St., Cambridge, England
| | - André M. Machado
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - Thomas Forest
- Éco-anthropologie, Muséum National d’Histoire Naturelle, CNRS UMR 7206, Paris, France
- SMILE Group, Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241, INSERM U 1050, Paris, France
- Institut de Systématique Evolution Biodiversité, CNRS MNHN SU EPHE, CP 51, 55 rue Buffon, 75005, Paris, France
| | - Guillaume Achaz
- Éco-anthropologie, Muséum National d’Histoire Naturelle, CNRS UMR 7206, Paris, France
- SMILE Group, Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241, INSERM U 1050, Paris, France
| | - Amílcar Teixeira
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Bragança, Portugal
| | - Vincent Prié
- CIBIO/InBIO - Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
- IUCN SSC Mollusc Specialist Group, c/o IUCN, David Attenborough Building, Pembroke St., Cambridge, England
| | - L. Filipe C. Castro
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
- Faculty of Sciences, University of Porto, , Porto, Portugal
| | - Elsa Froufe
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
- Corresponding authors. E-mail: ;
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Khurshid B, Jackson DJ, Engilberge S, Motreuil S, Broussard C, Thomas J, Immel F, Harrington MJ, Crowley PB, Vielzeuf D, Perrin J, Marin F. Molecular characterization of accripin11, a soluble shell protein with an acidic C-terminus, identified in the prismatic layer of the Mediterranean fan mussel Pinna nobilis (Bivalvia, Pteriomorphia). FEBS Open Bio 2022; 13:10-25. [PMID: 36219517 PMCID: PMC9808598 DOI: 10.1002/2211-5463.13497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 08/23/2022] [Accepted: 10/10/2022] [Indexed: 01/07/2023] Open
Abstract
We have identified a novel shell protein, accripin11, as a major soluble component of the calcitic prisms of the fan mussel Pinna nobilis. Initially retrieved from a cDNA library, its full sequence is confirmed here by transcriptomic and proteomic approaches. The sequence of the mature protein is 103 residues with a theoretical molecular weight of 11 kDa and is moderately acidic (pI 6.74) except for its C-terminus which is highly enriched in aspartic acid. The protein exhibits a peculiar cysteine pattern in its central domain. The full sequence shares similarity with six other uncharacterized molluscan shell proteins from the orders Ostreida, Pteriida and Mytilida, all of which are pteriomorphids and produce a phylogenetically restricted pattern of nacro-prismatic shell microstructures. This suggests that accripin11 is a member of a family of clade-specific shell proteins. A 3D model of accripin11 was predicted with AlphaFold2, indicating that it possesses three short alpha helices and a disordered C-terminus. Recombinant accripin11 was tested in vitro for its ability to influence the crystallization of CaCO3 , while a polyclonal antibody was able to locate accripin11 to prismatic extracts, particularly in the acetic acid-soluble matrix. The putative functions of accripin11 are further discussed in relation to shell biomineralization.
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Affiliation(s)
- Benazir Khurshid
- Laboratoire Biogéosciences, UMR CNRS‐EPHE 6282Université de Bourgogne – Franche‐ComtéDijonFrance,Synchrotron SOLEILBeamline ANATOMIXGif‐sur‐YvetteFrance
| | | | - Sylvain Engilberge
- Structural Biology GroupEuropean Synchrotron Radiation FacilityGrenobleFrance
| | - Sébastien Motreuil
- Laboratoire Biogéosciences, UMR CNRS‐EPHE 6282Université de Bourgogne – Franche‐ComtéDijonFrance
| | | | - Jérôme Thomas
- Laboratoire Biogéosciences, UMR CNRS‐EPHE 6282Université de Bourgogne – Franche‐ComtéDijonFrance
| | - Françoise Immel
- Chrono‐Environnement, UMR 6249 CNRSUniversité de Bourgogne Franche‐ComtéBesançonFrance
| | | | - Peter B. Crowley
- School of Biological and Chemical SciencesNational University of IrelandGalwayIreland
| | | | | | - Frédéric Marin
- Laboratoire Biogéosciences, UMR CNRS‐EPHE 6282Université de Bourgogne – Franche‐ComtéDijonFrance
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10
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Mito-nuclear coevolution and phylogenetic artifacts: the case of bivalve mollusks. Sci Rep 2022; 12:11040. [PMID: 35773462 PMCID: PMC9247169 DOI: 10.1038/s41598-022-15076-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/17/2022] [Indexed: 11/08/2022] Open
Abstract
Mito-nuclear phylogenetic discordance in Bivalvia is well known. In particular, the monophyly of Amarsipobranchia (Heterodonta + Pteriomorphia), retrieved from mitochondrial markers, contrasts with the monophyly of Heteroconchia (Heterodonta + Palaeoheterodonta), retrieved from nuclear markers. However, since oxidative phosphorylation nuclear markers support the Amarsipobranchia hypothesis instead of the Heteroconchia one, interacting subunits of the mitochondrial complexes ought to share the same phylogenetic signal notwithstanding the genomic source, which is different from the signal obtained from other nuclear markers. This may be a clue of coevolution between nuclear and mitochondrial genes. In this work we inferred the phylogenetic signal from mitochondrial and nuclear oxidative phosphorylation markers exploiting different phylogenetic approaches and added two more datasets for comparison: genes of the glycolytic pathway and genes related to the biogenesis of regulative small noncoding RNAs. All trees inferred from mitochondrial and nuclear subunits of the mitochondrial complexes support the monophyly of Amarsipobranchia, regardless of the phylogenetic pipeline. However, not every single marker agrees with this topology: this is clearly visible in nuclear subunits that do not directly interact with the mitochondrial counterparts. Overall, our data support the hypothesis of a coevolution between nuclear and mitochondrial genes for the oxidative phosphorylation. Moreover, we suggest a relationship between mitochondrial topology and different nucleotide composition between clades, which could be associated to the highly variable gene arrangement in Bivalvia.
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11
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Yurchenko OV, Dyachuk VA. Characterization of Neurodevelopment in Larvae of the Protobranch Acila insignis (Gould, 1861) in Order to Reconstruct the Last Common Ancestor of Bivalves. MALACOLOGIA 2022. [DOI: 10.4002/040.064.0207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Olga V. Yurchenko
- A. V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, russian Academy of Sciences, Vladivostok 690041, russia
| | - Vyacheslav A. Dyachuk
- A. V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, russian Academy of Sciences, Vladivostok 690041, russia
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12
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Morino Y. Dynamic evolutionary history of spiralian-specific TALE homeobox genes in mollusks. Dev Growth Differ 2022; 64:198-209. [PMID: 35441397 DOI: 10.1111/dgd.12779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/17/2022] [Accepted: 03/22/2022] [Indexed: 12/18/2022]
Abstract
Homeobox genes play essential roles in the early development of many animals. Although the repertoire of most homeobox genes, including three amino acid loop extension (TALE)-type homeobox genes, is conserved in animals, spiralian-TALE (SPILE) genes are a notable exception. In this study, SPILE genes were extracted from the genomic data of 22 mollusk species and classified into four clades (-A/C, -B, -D, and -E) to determine which SPILE genes exhibit dynamic repertoire changes. While SPILE-D and -E duplications were rarely observed, SPILE-B duplication was observed in the bivalve lineage and SPILE-A/C duplication was observed in multiple clades. Conversely, most or all SPILE genes were lost in cephalopods and in some gastropod lineages. SPILE gene expression patterns were also analyzed in multiple mollusk species using publicly available RNA-seq data. The majority of SPILE genes examined, particularly those in the A/C- and B-clades, were specifically expressed during early development, suggesting that most SPILE genes exert specific roles in early development. This comprehensive cataloging and characterization revealed a dynamic evolutionary history, including SPILE-A/C and -B gene duplications and the loss of SPILE genes in several lineages. Furthermore, this study provides a useful resource for studying the molecular mechanism of spiralian early development and the evolution of young and lineage-specific transcription factors.
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Affiliation(s)
- Yoshiaki Morino
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
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13
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Wang J, Bai Y, Zhao H, Mu R, Dong Y. Reinvestigating the phylogeny of Myriapoda with more extensive taxon sampling and novel genetic perspective. PeerJ 2022; 9:e12691. [PMID: 35036164 PMCID: PMC8710254 DOI: 10.7717/peerj.12691] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 12/05/2021] [Indexed: 11/20/2022] Open
Abstract
Background There have been extensive debates on the interrelationships among the four major classes of Myriapoda-Chilopoda, Symphyla, Diplopoda, and Pauropoda. The core controversy is the position of Pauropoda; that is, whether it should be grouped with Symphyla or Diplopoda as a sister group. Two recent phylogenomic studies separately investigated transcriptomic data from 14 and 29 Myriapoda species covering all four groups along with outgroups, and proposed two different topologies of phylogenetic relationships. Methods Building on these studies, we extended the taxon sampling by investigating 39 myriapods and integrating the previously available data with three new transcriptomic datasets generated in this study. Our analyses present the phylogenetic relationships among the four major classes of Myriapoda with a more abundant taxon sampling and provide a new perspective to investigate the above-mentioned question, where visual genes' identification were conducted. We compared the appearance pattern of genes, grouping them according to their classes and the visual pathways involved. Positive selection was detected for all identified visual genes between every pair of 39 myriapods, and 14 genes showed positive selection among 27 pairs. Results From the results of phylogenomic analyses, we propose that Symphyla is a sister group of Pauropoda. This stance has also received strong support from tree inference and topology tests.
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Affiliation(s)
- Jiajia Wang
- College of Biology and Food Engineering, Chuzhou University, Chuzhou, Anhui, China
| | - Yu Bai
- College of Biology and Food Engineering, Chuzhou University, Chuzhou, Anhui, China
| | - Haifeng Zhao
- Key Laboratory of Space Utilization, Technology and Engineering Center for Space Utilization, Chinese Academy of Sciences, Beijing, China
| | - Ruinan Mu
- University of Chinese Academy of Sciences, Beijing, China
| | - Yan Dong
- College of Biology and Food Engineering, Chuzhou University, Chuzhou, Anhui, China
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14
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What Is an “Arachnid”? Consensus, Consilience, and Confirmation Bias in the Phylogenetics of Chelicerata. DIVERSITY 2021. [DOI: 10.3390/d13110568] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The basal phylogeny of Chelicerata is one of the opaquest parts of the animal Tree of Life, defying resolution despite application of thousands of loci and millions of sites. At the forefront of the debate over chelicerate relationships is the monophyly of Arachnida, which has been refuted by most analyses of molecular sequence data. A number of phylogenomic datasets have suggested that Xiphosura (horseshoe crabs) are derived arachnids, refuting the traditional understanding of arachnid monophyly. This result is regarded as controversial, not least by paleontologists and morphologists, due to the widespread perception that arachnid monophyly is unambiguously supported by morphological data. Moreover, some molecular datasets have been able to recover arachnid monophyly, galvanizing the belief that any result that challenges arachnid monophyly is artefactual. Here, we explore the problems of distinguishing phylogenetic signal from noise through a series of in silico experiments, focusing on datasets that have recently supported arachnid monophyly. We assess the claim that filtering by saturation rate is a valid criterion for recovering Arachnida. We demonstrate that neither saturation rate, nor the ability to assemble a molecular phylogenetic dataset supporting a given outcome with maximal nodal support, is a guarantor of phylogenetic accuracy. Separately, we review empirical morphological phylogenetic datasets to examine characters supporting Arachnida and the downstream implication of a single colonization of terrestrial habitats. We show that morphological support of arachnid monophyly is contingent upon a small number of ambiguous or incorrectly coded characters, most of these tautologically linked to adaptation to terrestrial habitats.
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15
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Phuangphong S, Tsunoda J, Wada H, Morino Y. Duplication of spiralian-specific TALE genes and evolution of the blastomere specification mechanism in the bivalve lineage. EvoDevo 2021; 12:11. [PMID: 34663437 PMCID: PMC8524836 DOI: 10.1186/s13227-021-00181-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/04/2021] [Indexed: 12/24/2022] Open
Abstract
Background Despite the conserved pattern of the cell-fate map among spiralians, bivalves display several modified characteristics during their early development, including early specification of the D blastomere by the cytoplasmic content, as well as the distinctive fate of the 2d blastomere. However, it is unclear what changes in gene regulatory mechanisms led to such changes in cell specification patterns. Spiralian-TALE (SPILE) genes are a group of spiralian-specific transcription factors that play a role in specifying blastomere cell fates during early development in limpets. We hypothesised that the expansion of SPILE gene repertoires influenced the evolution of the specification pattern of blastomere cell fates. Results We performed a transcriptome analysis of early development in the purplish bifurcate mussel and identified 13 SPILE genes. Phylogenetic analysis of the SPILE gene in molluscs suggested that duplications of SPILE genes occurred in the bivalve lineage. We examined the expression patterns of the SPILE gene in mussels and found that some SPILE genes were expressed in quartet-specific patterns, as observed in limpets. Furthermore, we found that several SPILE genes that had undergone gene duplication were specifically expressed in the D quadrant, C and D quadrants or the 2d blastomere. These expression patterns were distinct from the expression patterns of SPILE in their limpet counterparts. Conclusions These results suggest that, in addition to their ancestral role in quartet specification, certain SPILE genes in mussels contribute to the specification of the C and D quadrants. We suggest that the expansion of SPILE genes in the bivalve lineage contributed to the evolution of a unique cell fate specification pattern in bivalves. Supplementary Information The online version contains supplementary material available at 10.1186/s13227-021-00181-2.
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Affiliation(s)
- Supanat Phuangphong
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan.
| | - Jumpei Tsunoda
- College of Biological Sciences, School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Hiroshi Wada
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Yoshiaki Morino
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan.
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16
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Piccinini G, Iannello M, Puccio G, Plazzi F, Havird JC, Ghiselli F. Mitonuclear Coevolution, but not Nuclear Compensation, Drives Evolution of OXPHOS Complexes in Bivalves. Mol Biol Evol 2021; 38:2597-2614. [PMID: 33616640 PMCID: PMC8136519 DOI: 10.1093/molbev/msab054] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In Metazoa, four out of five complexes involved in oxidative phosphorylation (OXPHOS) are formed by subunits encoded by both the mitochondrial (mtDNA) and nuclear (nuDNA) genomes, leading to the expectation of mitonuclear coevolution. Previous studies have supported coadaptation of mitochondria-encoded (mtOXPHOS) and nuclear-encoded OXPHOS (nuOXPHOS) subunits, often specifically interpreted with regard to the “nuclear compensation hypothesis,” a specific form of mitonuclear coevolution where nuclear genes compensate for deleterious mitochondrial mutations due to less efficient mitochondrial selection. In this study, we analyzed patterns of sequence evolution of 79 OXPHOS subunits in 31 bivalve species, a taxon showing extraordinary mtDNA variability and including species with “doubly uniparental” mtDNA inheritance. Our data showed strong and clear signals of mitonuclear coevolution. NuOXPHOS subunits had concordant topologies with mtOXPHOS subunits, contrary to previous phylogenies based on nuclear genes lacking mt interactions. Evolutionary rates between mt and nuOXPHOS subunits were also highly correlated compared with non-OXPHO-interacting nuclear genes. Nuclear subunits of chimeric OXPHOS complexes (I, III, IV, and V) also had higher dN/dS ratios than Complex II, which is formed exclusively by nuDNA-encoded subunits. However, we did not find evidence of nuclear compensation: mitochondria-encoded subunits showed similar dN/dS ratios compared with nuclear-encoded subunits, contrary to most previously studied bilaterian animals. Moreover, no site-specific signals of compensatory positive selection were detected in nuOXPHOS genes. Our analyses extend the evidence for mitonuclear coevolution to a new taxonomic group, but we propose a reconsideration of the nuclear compensation hypothesis.
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Affiliation(s)
- Giovanni Piccinini
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Mariangela Iannello
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Guglielmo Puccio
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Federico Plazzi
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Justin C Havird
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Fabrizio Ghiselli
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
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17
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Stewart DT, Robicheau BM, Youssef N, Garrido-Ramos MA, Chase EE, Breton S. Expanding the Search for Sperm Transmission Elements in the Mitochondrial Genomes of Bivalve Mollusks. Genes (Basel) 2021; 12:1211. [PMID: 34440385 PMCID: PMC8394068 DOI: 10.3390/genes12081211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 11/16/2022] Open
Abstract
Doubly uniparental inheritance (DUI) of mitochondrial DNA (mtDNA) in bivalve mollusks is one of the most notable departures from the paradigm of strict maternal inheritance of mtDNA among metazoans. Recently, work on the Mediterranean mussel Mytilus galloprovincialis suggested that a nucleotide motif in the control region of this species, known as the sperm transmission element (STE), helps protect male-transmitted mitochondria from destruction during spermatogenesis. Subsequent studies found similar, yet divergent, STE motifs in other marine mussels. Here, we extend the in silico search for mtDNA signatures resembling known STEs. This search is carried out for the large unassigned regions of 157 complete mitochondrial genomes from within the Mytiloida, Veneroida, Unionoida, and Ostreoida bivalve orders. Based on a sliding window approach, we present evidence that there are additional putative STE signatures in the large unassigned regions of several marine clams and freshwater mussels with DUI. We discuss the implications of this finding for interpreting the origin of doubly uniparental inheritance in ancestral bivalve mollusks, as well as potential future in vitro and in silico studies that could further refine our understanding of the early evolution of this unusual system of mtDNA inheritance.
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Affiliation(s)
- Donald T. Stewart
- Department of Biology, Acadia University, Wolfville, NS B4P 2R6, Canada
| | - Brent M. Robicheau
- Department of Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada; (B.M.R.); (N.Y.)
| | - Noor Youssef
- Department of Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada; (B.M.R.); (N.Y.)
| | - Manuel A. Garrido-Ramos
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain;
| | - Emily E. Chase
- Institut Méditerranéen d’Océanologie, Aix-Marseille University, 13288 Marseille, France;
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Sophie Breton
- Département de Sciences Biologiques, Université de Montréal, Montréal, QC H3C 3J7, Canada;
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18
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Gomes-Dos-Santos A, Lopes-Lima M, Machado AM, Marcos Ramos A, Usié A, Bolotov IN, Vikhrev IV, Breton S, Castro LFC, da Fonseca RR, Geist J, Österling ME, Prié V, Teixeira A, Gan HM, Simakov O, Froufe E. The Crown Pearl: a draft genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758). DNA Res 2021; 28:6182681. [PMID: 33755103 PMCID: PMC8088596 DOI: 10.1093/dnares/dsab002] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 03/22/2021] [Indexed: 11/17/2022] Open
Abstract
Since historical times, the inherent human fascination with pearls turned the freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758) into a highly valuable cultural and economic resource. Although pearl harvesting in M. margaritifera is nowadays residual, other human threats have aggravated the species conservation status, especially in Europe. This mussel presents a myriad of rare biological features, e.g. high longevity coupled with low senescence and Doubly Uniparental Inheritance of mitochondrial DNA, for which the underlying molecular mechanisms are poorly known. Here, the first draft genome assembly of M. margaritifera was produced using a combination of Illumina Paired-end and Mate-pair approaches. The genome assembly was 2.4 Gb long, possessing 105,185 scaffolds and a scaffold N50 length of 288,726 bp. The ab initio gene prediction allowed the identification of 35,119 protein-coding genes. This genome represents an essential resource for studying this species’ unique biological and evolutionary features and ultimately will help to develop new tools to promote its conservation.
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Affiliation(s)
- André Gomes-Dos-Santos
- CIIMAR/CIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, P 4450-208 Matosinhos, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Manuel Lopes-Lima
- CIIMAR/CIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, P 4450-208 Matosinhos, Portugal.,CIBIO/InBIO-Research Center in Biodiversity and Genetic Resources, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal.,IUCN SSC Mollusc Specialist Group, c/o IUCN, Cambridge, England
| | - André M Machado
- CIIMAR/CIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, P 4450-208 Matosinhos, Portugal
| | - António Marcos Ramos
- Centro de Biotecnologia Agrícola e Agro-alimentar do Alentejo (CEBAL), Instituto Politécnico de Beja (IPBeja), 7801-908 Beja, Portugal.,MED-Mediterranean Institute for Agriculture, Environment and Development, CEBAL-Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo, 7801-908 Beja, Portugal
| | - Ana Usié
- Centro de Biotecnologia Agrícola e Agro-alimentar do Alentejo (CEBAL), Instituto Politécnico de Beja (IPBeja), 7801-908 Beja, Portugal.,MED-Mediterranean Institute for Agriculture, Environment and Development, CEBAL-Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo, 7801-908 Beja, Portugal
| | - Ivan N Bolotov
- Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Arkhangelsk 163000, Russia
| | - Ilya V Vikhrev
- Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Arkhangelsk 163000, Russia
| | - Sophie Breton
- Department of Biological Sciences, University of Montreal, Montreal, Canada
| | - L Filipe C Castro
- CIIMAR/CIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, P 4450-208 Matosinhos, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Rute R da Fonseca
- Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Juergen Geist
- Aquatic Systems Biology Unit, Technical University of Munich, TUM School of Life Sciences, D-85354 Freising, Germany
| | - Martin E Österling
- Department of Environmental and Life Sciences-Biology, Karlstad University, 651 88 Karlstad, Sweden
| | - Vincent Prié
- Research Associate, Institute of Systematics, Evolution, Biodiversity (ISYEB), National Museum of Natural History (MNHN), CNRS, SU, EPHE, 75005 Paris, France
| | - Amílcar Teixeira
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Bragança, Portugal
| | - Han Ming Gan
- GeneSEQ Sdn Bhd, Bandar Bukit Beruntung, Rawang 48300, Selangor, Malaysia
| | - Oleg Simakov
- Department of Neurosciences and Developmental Biology, University of Vienna, 1010 Vienna, Austria
| | - Elsa Froufe
- CIIMAR/CIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, P 4450-208 Matosinhos, Portugal
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19
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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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20
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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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21
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Caurcel C, Laetsch DR, Challis R, Kumar S, Gharbi K, Blaxter M. MolluscDB: a genome and transcriptome database for molluscs. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200157. [PMID: 33813885 PMCID: PMC8059625 DOI: 10.1098/rstb.2020.0157] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
As sequencing becomes more accessible and affordable, the analysis of genomic and transcriptomic data has become a cornerstone of many research initiatives. Communities with a focus on particular taxa or ecosystems need solutions capable of aggregating genomic resources and serving them in a standardized and analysis-friendly manner. Taxon-focussed resources can be more flexible in addressing the needs of a research community than can universal or general databases. Here, we present MolluscDB, a genome and transcriptome database for molluscs. MolluscDB offers a rich ecosystem of tools, including an Ensembl browser, a BLAST server for homology searches and an HTTP server from which any dataset present in the database can be downloaded. To demonstrate the utility of the database and verify the quality of its data, we imported data from assembled genomes and transcriptomes of 22 species, estimated the phylogeny of Mollusca using single-copy orthologues, explored patterns of gene family size change and interrogated the data for biomineralization-associated enzymes and shell matrix proteins. MolluscDB provides an easy-to-use and openly accessible data resource for the research community. 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)
- Carlos Caurcel
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Dominik R Laetsch
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Richard Challis
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK.,Tree of Life Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Sujai Kumar
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK.,Tree of Life Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Karim Gharbi
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK.,Edinburgh Genomics, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Mark Blaxter
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK.,Tree of Life Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
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22
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Mortz M, Levivier A, Lartillot N, Dufresne F, Blier PU. Long-Lived Species of Bivalves Exhibit Low MT-DNA Substitution Rates. Front Mol Biosci 2021; 8:626042. [PMID: 33791336 PMCID: PMC8005583 DOI: 10.3389/fmolb.2021.626042] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/28/2021] [Indexed: 01/21/2023] Open
Abstract
Bivalves represent valuable taxonomic group for aging studies given their wide variation in longevity (from 1–2 to >500 years). It is well known that aging is associated to the maintenance of Reactive Oxygen Species homeostasis and that mitochondria phenotype and genotype dysfunctions accumulation is a hallmark of these processes. Previous studies have shown that mitochondrial DNA mutation rates are linked to lifespan in vertebrate species, but no study has explored this in invertebrates. To this end, we performed a Bayesian Phylogenetic Covariance model of evolution analysis using 12 mitochondrial protein-coding genes of 76 bivalve species. Three life history traits (maximum longevity, generation time and mean temperature tolerance) were tested against 1) synonymous substitution rates (dS), 2) conservative amino acid replacement rates (Kc) and 3) ratios of radical over conservative amino acid replacement rates (Kr/Kc). Our results confirm the already known correlation between longevity and generation time and show, for the first time in an invertebrate class, a significant negative correlation between dS and longevity. This correlation was not as strong when generation time and mean temperature tolerance variations were also considered in our model (marginal correlation), suggesting a confounding effect of these traits on the relationship between longevity and mtDNA substitution rate. By confirming the negative correlation between dS and longevity previously documented in birds and mammals, our results provide support for a general pattern in substitution rates.
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Affiliation(s)
- Mathieu Mortz
- Institut Des Sciences De La Mer De Rimouski, Université Du Québec à Rimouski, Rimouski, QC, Canada
| | - Aurore Levivier
- Institut Des Sciences De La Mer De Rimouski, Université Du Québec à Rimouski, Rimouski, QC, Canada
| | - Nicolas Lartillot
- Laboratoire De Biométrie et Biologie Evolutive, UMR CNRS, Université Lyon 1, Villeurbanne, France
| | - France Dufresne
- Laboratoire D'écologie Moléculaire, Département De Biologie, Université Du Québec à Rimouski, Rimouski, QC, Canada.,Laboratoire De Physiologie Intégrative Et Evolutive, Département De Biologie, Université Du Québec à Rimouski, Rimouski, QC, Canada
| | - Pierre U Blier
- Laboratoire De Physiologie Intégrative Et Evolutive, Département De Biologie, Université Du Québec à Rimouski, Rimouski, QC, Canada
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23
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Rogers RL, Grizzard SL, Titus-McQuillan JE, Bockrath K, Patel S, Wares JP, Garner JT, Moore CC. Gene family amplification facilitates adaptation in freshwater unionid bivalve Megalonaias nervosa. Mol Ecol 2021; 30:1155-1173. [PMID: 33382161 DOI: 10.1111/mec.15786] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 12/01/2020] [Accepted: 12/14/2020] [Indexed: 01/05/2023]
Abstract
Freshwater unionid bivalves currently face severe anthropogenic challenges. Over 70% of species in the United States are threatened, endangered or extinct due to pollution, damming of waterways and overfishing. These species are notable for their unusual life history strategy, parasite-host co-evolution and biparental mitochondrial inheritance. Among this clade, the washboard mussel Megalonaias nervosa is one species that remains prevalent across the Southeastern United States, with robust population sizes. We have created a reference genome for M. nervosa to determine how genome content has evolved in the face of these widespread environmental challenges. We observe dynamic changes in genome content, with a burst of recent transposable element proliferation causing a 382 Mb expansion in genome content. Birth-death models suggest rapid expansions among gene families, with a mutation rate of 1.16 × 10-8 duplications per gene per generation. Cytochrome P450 gene families have experienced exceptional recent amplification beyond expectations based on genome-wide birth-death processes. These genes are associated with increased rates of amino acid changes, a signature of selection driving evolution of detox genes. Fitting evolutionary models of adaptation from standing genetic variation, we can compare adaptive potential across species and mutation types. The large population size in M. nervosa suggests a 4.7-fold advantage in the ability to adapt from standing genetic variation compared with a low diversity endemic E. hopetonensis. Estimates suggest that gene family evolution may offer an exceptional substrate of genetic variation in M. nervosa, with Psgv = 0.185 compared with Psgv = 0.067 for single nucleotide changes. Hence, we suggest that gene family evolution is a source of 'hopeful monsters' within the genome that may facilitate adaptation when selective pressures shift. These results suggest that gene family expansion is a key driver of adaptive evolution in this key species of freshwater Unionidae that is currently facing widespread environmental challenges. This work has clear implications for conservation genomics on freshwater bivalves as well as evolutionary theory. This genome represents a first step to facilitate reverse ecological genomics in Unionidae and identify the genetic underpinnings of phenotypic diversity.
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Affiliation(s)
- Rebekah L Rogers
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, NC, USA
| | - Stephanie L Grizzard
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, NC, USA.,Department of Biological Sciences, Old Dominion University, Norfolk, VA, USA
| | | | - Katherine Bockrath
- Department of Genetics, University of Georgia, Athens, GA, USA.,U.S. Fish and Wildlife Service, Midwest Fisheries Center Whitney Genetics Lab, Onalaska, WI, USA
| | - Sagar Patel
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, NC, USA.,Department of Biology, Saint Louis University, St. Louis, MO, USA.,Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - John P Wares
- Department of Genetics, University of Georgia, Athens, GA, USA.,Odum School of Ecology, University of Georgia, Athens, GA, USA
| | - Jeffrey T Garner
- Division of Wildlife and Freshwater Fisheries, Alabama Department of Conservation and Natural Resources, Florence, AL, USA
| | - Cathy C Moore
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, NC, USA
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Knutson VL, Brenzinger B, Schrödl M, Wilson NG, Giribet G. Most Cephalaspidea have a shell, but transcriptomes can provide them with a backbone (Gastropoda: Heterobranchia). Mol Phylogenet Evol 2020; 153:106943. [DOI: 10.1016/j.ympev.2020.106943] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 08/21/2020] [Indexed: 01/14/2023]
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Moles J, Giribet G. A polyvalent and universal tool for genomic studies in gastropod molluscs (Heterobranchia). Mol Phylogenet Evol 2020; 155:106996. [PMID: 33148425 DOI: 10.1016/j.ympev.2020.106996] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 10/20/2020] [Accepted: 10/20/2020] [Indexed: 10/23/2022]
Abstract
Molluscs are the second most diverse animal phylum and heterobranch gastropods present ~ 44,000 species. These comprise fascinating creatures with huge morphological and ecological disparity. Such great diversity comes with even larger phylogenetic uncertainty and many taxa have been largely neglected in molecular assessments. Genomic tools have provided resolution to deep cladogenic events but generating large numbers of transcriptomes/genomes is expensive and usually requires fresh material. Here we leverage a target enrichment approach to design and synthesize a probe set based on available genomes and transcriptomes across Heterobranchia. Our probe set contains 57,606 70mer baits and targets a total of 2,259 ultra-conserved elements (UCEs). Post-sequencing capture efficiency was tested against 31 marine heterobranchs from major groups, including Acochlidia, Acteonoidea, Aplysiida, Cephalaspidea, Pleurobranchida, Pteropoda, Runcinida, Sacoglossa, and Umbraculida. The combined Trinity and Velvet assemblies recovered up to 2,211 UCEs in Tectipleura, up to 1,978 in Nudipleura, and up to 1,927 in Acteonoidea, the latter two being the most distantly related taxa to our core study group. Total alignment length was 525,599 bp and contained 52% informative sites and 21% missing data. Maximum-likelihood and Bayesian inference approaches recovered the monophyly of all orders tested as well as the larger clades Nudipleura, Panpulmonata, and Euopisthobranchia. The successful enrichment of diversely preserved material and DNA concentrations demonstrate the polyvalent nature of UCEs, and the universality of the probe set designed. We believe this probe set will enable multiple, interesting lines of research, that will benefit from an inexpensive and largely informative tool that will, additionally, benefit from the access to museum collections to gather genomic data.
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Affiliation(s)
- Juan Moles
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA.
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA.
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Mitogenomic architecture of the multivalent endemic black clam (Villorita cyprinoides) and its phylogenetic implications. Sci Rep 2020; 10:15438. [PMID: 32963308 PMCID: PMC7508841 DOI: 10.1038/s41598-020-72194-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 08/03/2020] [Indexed: 11/24/2022] Open
Abstract
The Indian black clam Villorita cyprinoides (Family: Cyrenidae), an extractive commercially exploited species with aquaculture importance contributing more than 70% of clam fishery in India, is endemic to the Indian peninsula. Currently, there is very sparse information, especially on the molecular data of Villorita. The present study aims to provide a comprehensive knowledge of mitogenome architecture and assess the phylogenetic status of Cyrenidae. This has resulted in reporting the first complete mitogenome of V. cyprinoides using next-generation sequencing technology. The A+T circular mitogenome was 15,880 bp long, exhibiting 13 protein-coding genes (PCGs) including ATP8 (absent in several bivalves), 22 transfer RNA, and two ribosomal RNA genes residing in the heavy strand in a clockwise orientation and a gene order akin to Corbicula fluminea. The molecular phylogeny inferred from a concatenated multi-gene sequence [14 mitochondrial (12 PCGs, rrnS and rrnL) and two nuclear genes (Histone H3, 18S rRNA)] from 47 representative species of superorder Imparidentia, clustered V. cyprinoides and Cyrenid clams to a single clade supporting the monophyly of Cyrenidae. The subsequent mitochondrial gene order analysis substantiates the close relationship of V. cyprinoides and C. fluminea, analogous to phylogenetic output. The multilocus tree topology calibrated with verified fossil data deciphered the origin and diversification of Cyrenid clams during late Triassic-early Jurassic. The data derived from this study shall contribute remarkably for further insights on cryptic species identification, molecular characterization of bivalve mitogenomes and mitochondrial evolutionary history of genus Villorita. Moreover, complete mitogenome can aid in potential marker development for assessing the genetic health of black clam populations.
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Mitogenomics reveals phylogenetic relationships of Arcoida (Mollusca, Bivalvia) and multiple independent expansions and contractions in mitochondrial genome size. Mol Phylogenet Evol 2020; 150:106857. [PMID: 32473333 DOI: 10.1016/j.ympev.2020.106857] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 04/09/2020] [Accepted: 05/21/2020] [Indexed: 11/24/2022]
Abstract
Arcoida, comprising about 570 species of blood cockles, is an ecologically and economically important lineage of bivalve molluscs. Current classification of arcoids is largely based on morphology, which shows widespread homoplasy. Despite two recent studies employing multi-locus analyses with broad sampling of Arcoida, evolutionary relationships among major lineages remain controversial. Interestingly, mitochondrial genomes of several ark shell species are 2-3 times larger than those found in most bilaterians, and are among the largest bilaterian mitochondrial genomes reported to date. These results highlight the need of detailed phylogenetic study to explore evolutionary relationships within Arcoida so that the evolution of mitochondrial genome size can be understood. To this end, we sequenced 17 mitochondrial genomes and compared them with publicly available data, including those from other lineages of Arcoida with emphasis on the subclade Arcoidea species. Our phylogenetic analyses indicate that Noetiidae, Cucullaeidae and Glycymerididae are nested within a polyphyletic Arcidae. Moreover, we find multiple independent expansions and potential contractions of mitochondrial genome size, suggesting that the large mitochondrial genome is not a shared ancestral feature in Arcoida. We also examined tandem repeats and inverted repeats in non-coding regions and investigated the presence of such repeats with relation to genome size variation. Our results suggest that tandem repeats might facilitate intraspecific mitochondrial genome size variation, and that inverted repeats, which could be derived from transposons, might be responsible for mitochondrial genome expansions and contractions. We show that mitochondrial genome size in Arcoida is more dynamic than previously understood and provide insights into evolution of mitochondrial genome size variation in metazoans.
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Shedding light: a phylotranscriptomic perspective illuminates the origin of photosymbiosis in marine bivalves. BMC Evol Biol 2020; 20:50. [PMID: 32357841 PMCID: PMC7195748 DOI: 10.1186/s12862-020-01614-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 04/15/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Photosymbiotic associations between metazoan hosts and photosynthetic dinoflagellates are crucial to the trophic and structural integrity of many marine ecosystems, including coral reefs. Although extensive efforts have been devoted to study the short-term ecological interactions between coral hosts and their symbionts, long-term evolutionary dynamics of photosymbiosis in many marine animals are not well understood. Within Bivalvia, the second largest class of mollusks, obligate photosymbiosis is found in two marine lineages: the giant clams (subfamily Tridacninae) and the heart cockles (subfamily Fraginae), both in the family Cardiidae. Morphologically, giant clams show relatively conservative shell forms whereas photosymbiotic fragines exhibit a diverse suite of anatomical adaptations including flattened shells, leafy mantle extensions, and lens-like microstructural structures. To date, the phylogenetic relationships between these two subfamilies remain poorly resolved, and it is unclear whether photosymbiosis in cardiids originated once or twice. RESULTS In this study, we establish a backbone phylogeny for Cardiidae utilizing RNASeq-based transcriptomic data from Tridacninae, Fraginae and other cardiids. A variety of phylogenomic approaches were used to infer the relationship between the two groups. Our analyses found conflicting gene signals and potential rapid divergence among the lineages. Overall, results support a sister group relationship between Tridacninae and Fraginae, which diverged during the Cretaceous. Although a sister group relationship is recovered, ancestral state reconstruction using maximum likelihood-based methods reveals two independent origins of photosymbiosis, one at the base of Tridacninae and the other within a symbiotic Fraginae clade. CONCLUSIONS The newly revealed common ancestry between Tridacninae and Fraginae brings a possibility that certain genetic, metabolic, and/or anatomical exaptations existed in their last common ancestor, which promoted both lineages to independently establish photosymbiosis, possibly in response to the modern expansion of reef habitats.
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Kenny NJ, McCarthy SA, Dudchenko O, James K, Betteridge E, Corton C, Dolucan J, Mead D, Oliver K, Omer AD, Pelan S, Ryan Y, Sims Y, Skelton J, Smith M, Torrance J, Weisz D, Wipat A, Aiden EL, Howe K, Williams ST. The gene-rich genome of the scallop Pecten maximus. Gigascience 2020; 9:giaa037. [PMID: 32352532 PMCID: PMC7191990 DOI: 10.1093/gigascience/giaa037] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 02/26/2020] [Accepted: 03/24/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The king scallop, Pecten maximus, is distributed in shallow waters along the Atlantic coast of Europe. It forms the basis of a valuable commercial fishery and plays a key role in coastal ecosystems and food webs. Like other filter feeding bivalves it can accumulate potent phytotoxins, to which it has evolved some immunity. The molecular origins of this immunity are of interest to evolutionary biologists, pharmaceutical companies, and fisheries management. FINDINGS Here we report the genome assembly of this species, conducted as part of the Wellcome Sanger 25 Genomes Project. This genome was assembled from PacBio reads and scaffolded with 10X Chromium and Hi-C data. Its 3,983 scaffolds have an N50 of 44.8 Mb (longest scaffold 60.1 Mb), with 92% of the assembly sequence contained in 19 scaffolds, corresponding to the 19 chromosomes found in this species. The total assembly spans 918.3 Mb and is the best-scaffolded marine bivalve genome published to date, exhibiting 95.5% recovery of the metazoan BUSCO set. Gene annotation resulted in 67,741 gene models. Analysis of gene content revealed large numbers of gene duplicates, as previously seen in bivalves, with little gene loss, in comparison with the sequenced genomes of other marine bivalve species. CONCLUSIONS The genome assembly of P. maximus and its annotated gene set provide a high-quality platform for studies on such disparate topics as shell biomineralization, pigmentation, vision, and resistance to algal toxins. As a result of our findings we highlight the sodium channel gene Nav1, known to confer resistance to saxitoxin and tetrodotoxin, as a candidate for further studies investigating immunity to domoic acid.
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Affiliation(s)
- Nathan J Kenny
- Natural History Museum, Department of Life Sciences,Cromwell Road, London SW7 5BD, UK
| | - Shane A McCarthy
- University of Cambridge, Department of Genetics,Cambridge CB2 3EH, UK
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- The Center for Theoretical Biological Physics, Rice University, 6100 Main St, Houston, TX 77005-1827, USA
| | - Katherine James
- Natural History Museum, Department of Life Sciences,Cromwell Road, London SW7 5BD, UK
| | | | - Craig Corton
- Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Jale Dolucan
- Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Dan Mead
- Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Karen Oliver
- Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Arina D Omer
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sarah Pelan
- Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Yan Ryan
- School of Computing, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
- Institute of Infection and Global Health, Liverpool University, iC2, 146 Brownlow Hill, Liverpool L3 5RF, UK
| | - Ying Sims
- Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | | | | | | | - David Weisz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anil Wipat
- School of Computing, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Erez L Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- The Center for Theoretical Biological Physics, Rice University, 6100 Main St, Houston, TX 77005-1827, USA
- Shanghai Institute for Advanced Immunochemical Studies, Shanghai Tech University, Shanghai, China
- School of Agriculture and Environment, University of Western Australia, Perth, Australia
| | - Kerstin Howe
- Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Suzanne T Williams
- Natural History Museum, Department of Life Sciences,Cromwell Road, London SW7 5BD, UK
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30
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Sato K, Kano Y, Setiamarga DHE, Watanabe HK, Sasaki T. Molecular phylogeny of protobranch bivalves and systematic implications of their shell microstructure. ZOOL SCR 2020. [DOI: 10.1111/zsc.12419] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Kei Sato
- Waseda University Tokyo Japan
- The University Museum The University of Tokyo Tokyo Japan
| | - Yasunori Kano
- Atmosphere and Ocean Research Institute The University of Tokyo Chiba Japan
| | - Davin H. E. Setiamarga
- The University Museum The University of Tokyo Tokyo Japan
- National Institute of Technology Wakayama College Gobo Japan
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Molecular characterization of a whirlin-like protein with biomineralization-related functions from the shell of Mytilus coruscus. PLoS One 2020; 15:e0231414. [PMID: 32267882 PMCID: PMC7141649 DOI: 10.1371/journal.pone.0231414] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 03/23/2020] [Indexed: 11/19/2022] Open
Abstract
Mollusc shells are produced from calcified skeletons and have excellent mechanical properties. Shell matrix proteins (SMPs) have important functions in shell formation. A 16.6 kDa whirlin-like protein (WLP) with a PDZ domain was identified in the shell of Mytilus coruscus as a novel SMP. In this study, the expression, function, and location of WLP were analysed. The WLP gene was highly expressed and specifically located in the adductor muscle and mantle. The expression of recombinant WLP (rWLP) was associated with morphological change, polymorphic change, binding ability, and crystallization rate inhibition of the calcium carbonate crystals in vitro. In addition, an anti-rWLP antibody was prepared, and the results from immunohistochemistry and immunofluorescence analyses revealed the specific location of the WLP in the mantle, adductor muscle, and myostracum layer of the shell, suggesting multiple functions for WLP in biomineralization, muscle-shell attachment, and muscle attraction. Furthermore, results from a pull-down analysis revealed 10 protein partners of WLP in the shell matrices and a possible network of interacting WLPs in the shell. In addition, in this study, one of the WLP partners, actin, was confirmed to have the ability to bind WLP. These results expand the understanding of the functions of PDZ-domain-containing proteins in biomineralization and provide clues for determining the mechanisms of myostracum formation and muscle-shell attachment.
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32
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Calcino AD, de Oliveira AL, Simakov O, Schwaha T, Zieger E, Wollesen T, Wanninger A. The quagga mussel genome and the evolution of freshwater tolerance. DNA Res 2020; 26:411-422. [PMID: 31504356 PMCID: PMC6796509 DOI: 10.1093/dnares/dsz019] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 08/01/2019] [Indexed: 02/06/2023] Open
Abstract
Freshwater dreissenid mussels evolved from marine ancestors during the Miocene ∼30 million years ago and today include some of the most successful and destructive invasive species of freshwater environments. Here, we sequenced the genome of the quagga mussel Dreissena rostriformis to identify adaptations involved in embryonic osmoregulation. We provide evidence that a lophotrochozoan-specific aquaporin water channel, a vacuolar ATPase subunit and a sodium/hydrogen exchanger are involved in osmoregulation throughout early cleavage, during which time large intercellular fluid-filled 'cleavage cavities' repeatedly form, coalesce and collapse, expelling excess water to the exterior. Independent expansions of aquaporins coinciding with at least five freshwater colonization events confirm their role in freshwater adaptation. Repeated aquaporin expansions and the evolution of membrane-bound fluid-filled osmoregulatory structures in diverse freshwater taxa point to a fundamental principle guiding the evolution of freshwater tolerance and provide a framework for future species control efforts.
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Affiliation(s)
- Andrew D Calcino
- Department of Integrative Zoology, University of Vienna, Vienna, Austria
| | | | - Oleg Simakov
- Department of Molecular Evolution and Development, University of Vienna, Vienna, Austria
| | - Thomas Schwaha
- Department of Integrative Zoology, University of Vienna, Vienna, Austria
| | - Elisabeth Zieger
- Department of Integrative Zoology, University of Vienna, Vienna, Austria
| | - Tim Wollesen
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Andreas Wanninger
- Department of Integrative Zoology, University of Vienna, Vienna, Austria
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33
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Lemer S, Bieler R, Giribet G. Resolving the relationships of clams and cockles: dense transcriptome sampling drastically improves the bivalve tree of life. Proc Biol Sci 2020; 286:20182684. [PMID: 30963927 PMCID: PMC6408618 DOI: 10.1098/rspb.2018.2684] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Bivalvia has been the subject of extensive recent phylogenetic work to attempt resolving either the backbone of the bivalve tree using transcriptomic data, or the tips using morpho-anatomical data and up to five genetic markers. Yet the first approach lacked decisive taxon sampling and the second failed to resolve many interfamilial relationships, especially within the diverse clade Imparidentia. Here we combine dense taxon sampling with 108 deep-sequenced Illumina-based transcriptomes to provide resolution in nodes that required additional study. We designed specific data matrices to address the poorly resolved relationships within Imparidentia. Our results support the overall backbone of the bivalve tree, the monophyly of Bivalvia and all its main nodes, although the monophyly of Protobranchia remains less clear. Likewise, the inter-relationships of the six main bivalve clades were fully supported. Within Imparidentia, resolution increases when analysing Imparidentia-specific matrices. Lucinidae, Thyasiridae and Gastrochaenida represent three early branches. Gastrochaenida is sister group to all remaining imparidentians, which divide into six orders. Neoheterodontei is always fully supported, and consists of Sphaeriida, Myida and Venerida, with the latter now also containing Mactroidea, Ungulinoidea and Chamidae, a family particularly difficult to place in earlier work. Overall, our study, by using densely sampled transcriptomes, provides the best-resolved bivalve phylogeny to date.
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Affiliation(s)
- Sarah Lemer
- 1 University of Guam Marine Laboratory , 303 University Drive, UOG Station, Mangilao, GU 96923 , USA.,2 Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University , 26 Oxford Street, Cambridge, MA 02138 , USA
| | - Rüdiger Bieler
- 3 Integrative Research Center, Field Museum of Natural History , 1400 South Lake Shore Drive, Chicago, IL 60605 , USA
| | - Gonzalo Giribet
- 2 Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University , 26 Oxford Street, Cambridge, MA 02138 , USA
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34
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The Tc1-like elements with the spliceosomal introns in mollusk genomes. Mol Genet Genomics 2020; 295:621-633. [DOI: 10.1007/s00438-020-01645-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 01/09/2020] [Indexed: 12/22/2022]
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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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36
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Thai BT, Lee YP, Gan HM, Austin CM, Croft LJ, Trieu TA, Tan MH. Whole Genome Assembly of the Snout Otter Clam, Lutraria rhynchaena, Using Nanopore and Illumina Data, Benchmarked Against Bivalve Genome Assemblies. Front Genet 2019; 10:1158. [PMID: 31824566 PMCID: PMC6880199 DOI: 10.3389/fgene.2019.01158] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 10/22/2019] [Indexed: 12/31/2022] Open
Affiliation(s)
| | - Yin Peng Lee
- Centre of Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia.,Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia
| | - Han Ming Gan
- Centre of Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia.,Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia
| | - Christopher M Austin
- Centre of Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia.,Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia
| | - Laurence J Croft
- Centre of Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia.,Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia
| | - Tuan Anh Trieu
- Faculty of Biology, Ha Noi National University of Education, Ha Noi, Vietnam.,Science and Technique Department, Hung Vuong University, Viet Tri, Vietnam
| | - Mun Hua Tan
- Centre of Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia.,Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia
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Péden R, Poupin P, Sohm B, Flayac J, Giambérini L, Klopp C, Louis F, Pain-Devin S, Potet M, Serre RF, Devin S. Environmental transcriptomes of invasive dreissena, a model species in ecotoxicology and invasion biology. Sci Data 2019; 6:234. [PMID: 31653851 PMCID: PMC6814772 DOI: 10.1038/s41597-019-0252-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 09/11/2019] [Indexed: 11/27/2022] Open
Abstract
Dreissenids are established model species for ecological and ecotoxicological studies, since they are sessile and filter feeder organisms and reflect in situ freshwater quality. Despite this strong interest for hydrosystem biomonitoring, omics data are still scarce. In the present study, we achieved full de novo assembly transcriptomes of digestive glands to gain insight into Dreissena polymorpha and D. rostriformis bugensis molecular knowledge. Transcriptomes were obtained by Illumina RNA sequencing of seventy-nine organisms issued from fifteen populations inhabiting sites that exhibits multiple freshwater contamination levels and different hydrosystem topographies (open or closed systems). Based on a recent de novo assembly algorithm, we carried out a complete, quality-checked and annotated transcriptomes. The power of the present study lies in the completeness of transcriptomes gathering multipopulational organisms sequencing and its full availability through an open access interface that gives a friendly and ready-to-use access to data. The use of such data for proteogenomic and targeted biological pathway investigations purpose is promising as they are first full transcriptomes for this two Dreissena species.
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Affiliation(s)
- Romain Péden
- Université de Lorraine, CNRS, LIEC, F-57000, Metz, France
- Université Reims Champagne Ardenne, UMR-I 02 SEBIO, 51097, Reims, France
| | - Pascal Poupin
- Université de Lorraine, CNRS, LIEC, F-57000, Metz, France
| | - Bénédicte Sohm
- Université de Lorraine, CNRS, LIEC, F-57000, Metz, France
| | - Justine Flayac
- Université de Lorraine, CNRS, LIEC, F-57000, Metz, France
| | | | - Christophe Klopp
- Plate-forme bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRA, 31326, Castanet-Tolosan, France
| | - Fanny Louis
- Université de Lorraine, CNRS, LIEC, F-57000, Metz, France
| | | | - Marine Potet
- Université de Lorraine, CNRS, LIEC, F-57000, Metz, France
| | - Rémy-Félix Serre
- INRA, US 1426, GeT-PlaGe, Genotoul, INRA Auzeville, Castanet Tolosan, Cedex, France
| | - Simon Devin
- Université de Lorraine, CNRS, LIEC, F-57000, Metz, France.
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Charrier NP, Hermouet A, Hervet C, Agoulon A, Barker SC, Heylen D, Toty C, McCoy KD, Plantard O, Rispe C. A transcriptome-based phylogenetic study of hard ticks (Ixodidae). Sci Rep 2019; 9:12923. [PMID: 31501478 PMCID: PMC6733903 DOI: 10.1038/s41598-019-49641-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 08/19/2019] [Indexed: 11/30/2022] Open
Abstract
Hard ticks are widely distributed across temperate regions, show strong variation in host associations, and are potential vectors of a diversity of medically important zoonoses, such as Lyme disease. To address unresolved issues with respect to the evolutionary relationships among certain species or genera, we produced novel RNA-Seq data sets for nine different Ixodes species. We combined this new data with 18 data sets obtained from public databases, both for Ixodes and non-Ixodes hard tick species, using soft ticks as an outgroup. We assembled transcriptomes (for 27 species in total), predicted coding sequences and identified single copy orthologues (SCO). Using Maximum-likelihood and Bayesian frameworks, we reconstructed a hard tick phylogeny for the nuclear genome. We also obtained a mitochondrial DNA-based phylogeny using published genome sequences and mitochondrial sequences derived from the new transcriptomes. Our results confirm previous studies showing that the Ixodes genus is monophyletic and clarify the relationships among Ixodes sub-genera. This work provides a baseline for studying the evolutionary history of ticks: we indeed found an unexpected acceleration of substitutions for mitochondrial sequences of Prostriata, and for nuclear and mitochondrial genes of two species of Rhipicephalus, which we relate with patterns of genome architecture and changes of life-cycle, respectively.
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Affiliation(s)
| | | | | | | | - Stephen C Barker
- Department of Parasitology, School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Qld, Australia
| | - Dieter Heylen
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Wilrijk, Belgium
- Interuniversity Institute for Biostatistics and statistical Bioinformatics, Hasselt University, Diepenbeek, Belgium
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Céline Toty
- Laboratoire MIVEGEC (Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution & Contrôle), Université de Montpellier, Centre National de la Recherche Scientifique (UMR5290), Institut de Recherche pour le Développement (UR224), Montpellier, France
| | - Karen D McCoy
- Laboratoire MIVEGEC (Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution & Contrôle), Université de Montpellier, Centre National de la Recherche Scientifique (UMR5290), Institut de Recherche pour le Développement (UR224), Montpellier, France
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Pfeiffer JM, Breinholt JW, Page LM. Unioverse: A phylogenomic resource for reconstructing the evolution of freshwater mussels (Bivalvia, Unionoida). Mol Phylogenet Evol 2019; 137:114-126. [DOI: 10.1016/j.ympev.2019.02.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 01/25/2019] [Accepted: 02/18/2019] [Indexed: 10/27/2022]
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Sigwart JD, Garbett A. Biodiversity Assessment, DNA Barcoding, and the Minority Majority. Integr Comp Biol 2019; 58:1146-1156. [PMID: 30053016 DOI: 10.1093/icb/icy076] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The majority of species on Earth are in "under-studied" groups, and indeed probably the majority of species remain undiscovered and undescribed. Species are natural units of evolution, and they are formed from branching phylogenetic processes that have a mathematical structure. So it follows that we should be able to develop a set of general principles that describe global patterns of species groups, like genera. Understanding such patterns would lend considerable power to the approach of "taxonomic surrogacy." In environmental assessments, ecology, and paleontology, it is common to substitute genus-level or family-level identification where definitive species identification is impractical. Clarity and confidence in fundamental patterns, based on a robust null model for species and genus level diversity, can accelerate species discovery: there are more species in the tropics, species-poor genera are very common, large genera are rare. Much hope has been placed in DNA barcoding as an effective tool to increase the pace of species discovery, but it is abundantly clear that certain mitochondrial DNA (mtDNA) markers are more or less variable in different clades and universal threshold values are impractical to delimit species. This study further examines the patterns of divergence in one common mtDNA barcode fragment, cytochrome c oxidase subunit 1at the genus level. We compared pairwise divergence in this fragment between two animal clades that have similar species richness but different evolutionary histories: birds and bivalves. We analyzed quality controlled alignments of over 39,000 published sequences in 1223 genera. Median pairwise differences at the genus level are positively correlated with the species richness of a genus, and this is not dependent of the number of sequences sampled. Unsurprisingly, sequence divergence in vertebrates was far more constrained than in evolutionarily more ancient non-vertebrate clades. Differences among the groups examined highlight the need for DNA barcode approaches to be considered in the context of specific biological groups. Vertebrates are better studied, but not necessarily representative of the majority of biodiversity. A technique that provides powerful insights for vertebrate species may be ineffective for the majority of organisms.
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Affiliation(s)
- Julia D Sigwart
- Queen's University Marine Laboratory, 12-13 The Strand, Portaferry BT22 1PF, Northern Ireland
| | - Amy Garbett
- Queen's University Marine Laboratory, 12-13 The Strand, Portaferry BT22 1PF, Northern Ireland
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Phylogenomic analyses and divergence time estimation of Elateroidea (Coleoptera) based on RNA-Seq data. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019; 30:283-289. [PMID: 30991174 DOI: 10.1016/j.cbd.2019.04.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 03/29/2019] [Accepted: 04/02/2019] [Indexed: 02/06/2023]
Abstract
Bioluminescence, the emission of visible light in a living organism, is an intriguing phenomenon observed in different species and environments. In terrestrial organisms, the bioluminescence is observed mainly in beetles of the Elateroidea superfamily (Coleoptera). Several phylogenetic studies have been used different strategies to propose a scenario for the origin and evolution of the bioluminescence within this group, however some of them showed incongruences, mainly about the relationship of the bioluminescent families. In order to increase the number of molecular markers available for Elateroidea species and to propose a more accurate phylogeny, with high supported topology, we employed the Next-Generation Sequencing (NGS) methodology to perform the RNA-Seq analysis of luminescent (Elateridae, Phengodidae, Rhagophthalmidae, and Lampyridae) and non-luminescent (Cantharidae) species of Neotropical beetles. We used the RNA-Seq data to construct a calibrated phylogeny of Elateroidea superfamily using a large number of nuclear molecular markers. The results indicate Lampyridae and Phengodidae/Rhagophthalmidae as sister-groups, suggesting that the bioluminescence evolved later in Elateridae than other families (Lampyridae, Phengodidae, and Rhagophthalmidae), and indicating the Upper Cretaceous as the period for the main diversification of Elateroidea bioluminescent species.
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Johnson LK, Alexander H, Brown CT. Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes. Gigascience 2019; 8:giy158. [PMID: 30544207 PMCID: PMC6481552 DOI: 10.1093/gigascience/giy158] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 09/18/2018] [Accepted: 11/29/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND De novo transcriptome assemblies are required prior to analyzing RNA sequencing data from a species without an existing reference genome or transcriptome. Despite the prevalence of transcriptomic studies, the effects of using different workflows, or "pipelines," on the resulting assemblies are poorly understood. Here, a pipeline was programmatically automated and used to assemble and annotate raw transcriptomic short-read data collected as part of the Marine Microbial Eukaryotic Transcriptome Sequencing Project. The resulting transcriptome assemblies were evaluated and compared against assemblies that were previously generated with a different pipeline developed by the National Center for Genome Research. RESULTS New transcriptome assemblies contained the majority of previous contigs as well as new content. On average, 7.8% of the annotated contigs in the new assemblies were novel gene names not found in the previous assemblies. Taxonomic trends were observed in the assembly metrics. Assemblies from the Dinoflagellata showed a higher number of contigs and unique k-mers than transcriptomes from other phyla, while assemblies from Ciliophora had a lower percentage of open reading frames compared to other phyla. CONCLUSIONS Given current bioinformatics approaches, there is no single "best" reference transcriptome for a particular set of raw data. As the optimum transcriptome is a moving target, improving (or not) with new tools and approaches, automated and programmable pipelines are invaluable for managing the computationally intensive tasks required for re-processing large sets of samples with revised pipelines and ensuring a common evaluation workflow is applied to all samples. Thus, re-assembling existing data with new tools using automated and programmable pipelines may yield more accurate identification of taxon-specific trends across samples in addition to novel and useful products for the community.
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Affiliation(s)
- Lisa K Johnson
- Department of Population Health, and Reproduction, School of Veterinary Medicine, University of California Davis, One Shields Ave, Davis, CA 95616, USA
- Molecular, Cellular, and Integrative Physiology Graduate Group, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Harriet Alexander
- Department of Population Health, and Reproduction, School of Veterinary Medicine, University of California Davis, One Shields Ave, Davis, CA 95616, USA
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - C Titus Brown
- Department of Population Health, and Reproduction, School of Veterinary Medicine, University of California Davis, One Shields Ave, Davis, CA 95616, USA
- Molecular, Cellular, and Integrative Physiology Graduate Group, University of California Davis, One Shields Ave, Davis, CA 95616, USA
- Genome Center, University of California Davis, 451 Health Sciences Dr, Davis, CA 95616, USA
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Strathmann RR, Brante A, Oyarzun FX. Contrasting Metatrochal Behavior of Mollusc and Annelid Larvae and the Regulation of Feeding While Swimming. THE BIOLOGICAL BULLETIN 2019; 236:130-143. [PMID: 30933637 DOI: 10.1086/701730] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Molluscan veliger larvae and some annelid larvae capture particulate food between a preoral prototrochal band of long cilia that create a current for both swimming and feeding and a postoral metatrochal band of shorter cilia that beat toward the prototroch. Larvae encountering satiating or noxious particles must somehow swim without capturing particles or else reject large numbers of captured particles. Because high rates of particle capture are inferred to depend on the beat of both ciliary bands, arrest of the metatroch could be one way to swim while reducing captures. Larvae in eight families of annelids arrest metatrochal cilia frequently during prototrochal beat, often over a large part of the metatrochal band and with the arrested cilia aligned near the beginning of the effective stroke. In contrast, metatrochs of veligers of gastropods and bivalves rarely arrested while the prototroch beat, and those arrests were more localized and variable in position. This difference in metatrochal arrest was unexpected under hypotheses of either a single origin of this feeding mechanism or multiple origins within each phylum. Although different in metatrochal arrests, larvae of both phyla can separate swimming from feeding while both prototroch and metatroch beat. One hypothesis explaining low rates of capture per encounter, without metatrochal arrest, is a change in adhesion of prototrochal cilia with algae. In a few observations, part of the velar edge was retained within the veliger's shell so that exposed prototrochal cilia contributed to swimming while the adjacent metatroch and food groove were sequestered.
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Parks MB, Wickett NJ, Alverson AJ. Signal, Uncertainty, and Conflict in Phylogenomic Data for a Diverse Lineage of Microbial Eukaryotes (Diatoms, Bacillariophyta). Mol Biol Evol 2019; 35:80-93. [PMID: 29040712 PMCID: PMC5850769 DOI: 10.1093/molbev/msx268] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Diatoms (Bacillariophyta) are a species-rich group of eukaryotic microbes diverse in morphology, ecology, and metabolism. Previous reconstructions of the diatom phylogeny based on one or a few genes have resulted in inconsistent resolution or low support for critical nodes. We applied phylogenetic paralog pruning techniques to a data set of 94 diatom genomes and transcriptomes to infer perennially difficult species relationships, using concatenation and summary-coalescent methods to reconstruct species trees from data sets spanning a wide range of thresholds for taxon and column occupancy in gene alignments. Conflicts between gene and species trees decreased with both increasing taxon occupancy and bootstrap cutoffs applied to gene trees. Concordance between gene and species trees was lowest for short internodes and increased logarithmically with increasing edge length, suggesting that incomplete lineage sorting disproportionately affects species tree inference at short internodes, which are a common feature of the diatom phylogeny. Although species tree topologies were largely consistent across many data treatments, concatenation methods appeared to outperform summary-coalescent methods for sparse alignments. Our results underscore that approaches to species-tree inference based on few loci are likely to be misled by unrepresentative sampling of gene histories, particularly in lineages that may have diversified rapidly. In addition, phylogenomic studies of diatoms, and potentially other hyperdiverse groups, should maximize the number of gene trees with high taxon occupancy, though there is clearly a limit to how many of these genes will be available.
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Affiliation(s)
- Matthew B Parks
- Daniel F. and Ada L. Rice Plant Conservation Science Center, Chicago Botanic Garden, Glencoe, IL
| | - Norman J Wickett
- Daniel F. and Ada L. Rice Plant Conservation Science Center, Chicago Botanic Garden, Glencoe, IL
| | - Andrew J Alverson
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR
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Abdelkrim J, Aznar-Cormano L, Fedosov AE, Kantor YI, Lozouet P, Phuong MA, Zaharias P, Puillandre N. Exon-Capture-Based Phylogeny and Diversification of the Venomous Gastropods (Neogastropoda, Conoidea). Mol Biol Evol 2018; 35:2355-2374. [DOI: 10.1093/molbev/msy144] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Jawad Abdelkrim
- Outils et Méthodes de la Systématique Intégrative (OMSI) UMS 2700, Muséum National d’Histoire Naturelle, Paris, France
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP 26, 75005 Paris, France
| | - Laetitia Aznar-Cormano
- Outils et Méthodes de la Systématique Intégrative (OMSI) UMS 2700, Muséum National d’Histoire Naturelle, Paris, France
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP 26, 75005 Paris, France
| | - Alexander E Fedosov
- A.N. Severtzov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninski prospect 33, 119071 Moscow, Russian Federation
| | - Yuri I Kantor
- A.N. Severtzov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninski prospect 33, 119071 Moscow, Russian Federation
| | - Pierre Lozouet
- Muséum National d’Histoire Naturelle, Direction des Collections, 55, rue Buffon, 75005 Paris, France
| | - Mark A Phuong
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - Paul Zaharias
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP 26, 75005 Paris, France
| | - Nicolas Puillandre
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP 26, 75005 Paris, France
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Yurchenko AA, Katolikova N, Polev D, Shcherbakova I, Strelkov P. Transcriptome of the bivalve Limecola balthica L. from Western Pacific: A new resource for studies of European populations. Mar Genomics 2018; 40:58-63. [DOI: 10.1016/j.margen.2018.03.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 03/29/2018] [Accepted: 03/31/2018] [Indexed: 10/17/2022]
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Abstract
Background Quahog Parasite Unknown (QPX) is an opportunistic protistan pathogen of the clam Mercenaria mercenaria. Infections with QPX have caused significant economic losses in the Northeastern United States. Previous research demonstrated a geographic gradient for disease prevalence and intensity, but little information is available on the genetic diversity of the parasite throughout its distribution range. Also, QPX virulence factors are not well understood. This study addresses the occurrence of QPX genetic variants with a particular focus on functions involved in virulence and adaptation to environmental conditions. Results Analyses were performed using transcriptome-wide single-nucleotide polymorphism (SNP) of four QPX isolates cultured from infected clams collected from disparate locations along the Northeastern United States. For contig assembly and mapping, two different genome builds and four transcriptomes of the parasite were examined. Genomic variants appeared at a differential rate relative to sequenced transcripts at 20.18 and 22.55% occurrence under 1000 base pairs upstream and downstream protein domains respectively and at 57.26% rate in protein domain coding sequences. QPX strains shared 30.50% of the mutations and exhibited a preferential nucleotide substitution towards thymine. Sequence identity suggested relatedness between different QPX strains, with the parasite being possibly introduced to Virginia from the Massachusetts region during clam trading, while QPX could have been naturally present in New York. Diversity in virulence, temperature, and salinity domains suggested a common variability between strains, but with a preferential higher variation in local adaptation genes. This could explain differences in disease prevalence noted in different regions. Overall, the results supported views that this opportunistic parasite might be able to adapt to varying environmental conditions. Conclusion Relatedness and mutations between the four QPX strains suggested that variability in environmental-related functions favors parasite survival, potentially promoting resilience against stressful conditions. These findings are in agreement with the widespread presence of QPX in the environment. Although QPX levels are enzootic in most areas, an increase in disease outbreaks were often associated with seasonal changes in environmental conditions. A selection mediated by the parasitic life of QPX remains possible, but the effect of the environment on the biology of the parasite appears more obvious. Electronic supplementary material The online version of this article (10.1186/s12864-018-4866-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sleiman Bassim
- School of Marine and Atmospheric Sciences, Stony Brook University, NY, 11794-5000, USA
| | - Bassem Allam
- School of Marine and Atmospheric Sciences, Stony Brook University, NY, 11794-5000, USA.
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Mann K, Cerveau N, Gummich M, Fritz M, Mann M, Jackson DJ. In-depth proteomic analyses of Haliotis laevigata (greenlip abalone) nacre and prismatic organic shell matrix. Proteome Sci 2018; 16:11. [PMID: 29983641 PMCID: PMC6003135 DOI: 10.1186/s12953-018-0139-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 05/25/2018] [Indexed: 01/12/2023] Open
Abstract
Background The shells of various Haliotis species have served as models of invertebrate biomineralization and physical shell properties for more than 20 years. A focus of this research has been the nacreous inner layer of the shell with its conspicuous arrangement of aragonite platelets, resembling in cross-section a brick-and-mortar wall. In comparison, the outer, less stable, calcitic prismatic layer has received much less attention. One of the first molluscan shell proteins to be characterized at the molecular level was Lustrin A, a component of the nacreous organic matrix of Haliotis rufescens. This was soon followed by the C-type lectin perlucin and the growth factor-binding perlustrin, both isolated from H. laevigata nacre, and the crystal growth-modulating AP7 and AP24, isolated from H. rufescens nacre. Mass spectrometry-based proteomics was subsequently applied to to Haliotis biomineralization research with the analysis of the H. asinina shell matrix and yielded 14 different shell-associated proteins. That study was the most comprehensive for a Haliotis species to date. Methods The shell proteomes of nacre and prismatic layer of the marine gastropod Haliotis laevigata were analyzed combining mass spectrometry-based proteomics and next generation sequencing. Results We identified 297 proteins from the nacreous shell layer and 350 proteins from the prismatic shell layer from the green lip abalone H. laevigata. Considering the overlap between the two sets we identified a total of 448 proteins. Fifty-one nacre proteins and 43 prismatic layer proteins were defined as major proteins based on their abundance at more than 0.2% of the total. The remaining proteins occurred at low abundance and may not play any significant role in shell fabrication. The overlap of major proteins between the two shell layers was 17, amounting to a total of 77 major proteins. Conclusions The H. laevigata shell proteome shares moderate sequence similarity at the protein level with other gastropod, bivalve and more distantly related invertebrate biomineralising proteomes. Features conserved in H. laevigata and other molluscan shell proteomes include short repetitive sequences of low complexity predicted to lack intrinsic three-dimensional structure, and domains such as tyrosinase, chitin-binding, and carbonic anhydrase. This catalogue of H. laevigata shell proteins represents the most comprehensive for a haliotid and should support future efforts to elucidate the molecular mechanisms of shell assembly. Electronic supplementary material The online version of this article (10.1186/s12953-018-0139-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Karlheinz Mann
- 1Abteilung Proteomics und Signaltransduktion, Max-Planck-Institut für Biochemie, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Nicolas Cerveau
- 2Department of Geobiology, Georg-August University of Göttingen, Goldschmidstr. 3, 37077 Göttingen, Germany
| | - Meike Gummich
- 3Universität Bremen, Institut für Biophysik, Otto Hahn Allee NW1, D-28334 Bremen, Germany
| | - Monika Fritz
- 3Universität Bremen, Institut für Biophysik, Otto Hahn Allee NW1, D-28334 Bremen, Germany
| | - Matthias Mann
- 1Abteilung Proteomics und Signaltransduktion, Max-Planck-Institut für Biochemie, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Daniel J Jackson
- 2Department of Geobiology, Georg-August University of Göttingen, Goldschmidstr. 3, 37077 Göttingen, Germany
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Yurchenko OV, Skiteva OI, Voronezhskaya EE, Dyachuk VA. Nervous system development in the Pacific oyster, Crassostrea gigas (Mollusca: Bivalvia). Front Zool 2018; 15:10. [PMID: 29681988 PMCID: PMC5896133 DOI: 10.1186/s12983-018-0259-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Accepted: 03/20/2018] [Indexed: 01/26/2023] Open
Abstract
Background Bivalves comprise a large, highly diverse taxon of invertebrate species. Developmental studies of neurogenesis among species of Bivalvia are limited. Due to a lack of neurogenesis information, it is difficult to infer a ground pattern for Bivalvia. To provide more comprehensive morphogenetic data on bivalve molluscs and relationships among molluscan clades, we investigated neurogenesis in the Pacific oyster, Crassostrea gigas, from the appearance of the first sensory cells to the formation of the larval ganglionic nervous system by co-immunocytochemistry of the neuronal markers FMRFamide or 5-HT and vesicular acetylcholine transporter (VAChT). Results Neurogenesis begins with the emergence of the apical serotonin-immunoreactive (5-HT-ir) sensory cells and paired sensory posttrochal dorsal and ventral FMRFamide-immunoreactive (FMRFamide-ir) cells at the early trochophore stage. Later, at the early veliger stage, the apical organ (AO) includes 5-HT-ir, FMRFamide-ir, and VAChT-ir cells. At the same stage, VAChT-ir cells appear in the posterior region of larvae and send axons towards the AO. Thus, FMRFamide-ir neurites and VAChT-ir processes form scaffolds for longitudinal neurite bundles develop into the paired ventral nerve cords (VNC). Later-appearing axons from the AO/CG neurons join the neurite bundles comprising the VNC. All larval ganglia appear along the VNC as paired or fused (epiathroid) clusters in late veliger and pediveliger larvae. We observed the transformation of the AO into the cerebral ganglia, which abundantly innervated the velum, and the transformation of ventral neurons into the pedal ganglia, innervating the foot, gills, and anterior adductor muscle. The visceral ganglia appear last in the pediveliger oyster and innervate the visceral mass and posterior adductor of premetamorphic larvae. In addition, a local FMRFamide-ir network was detected in the digestive system of pediveliger larvae. We identified VAChT-ir nervous elements in oyster larvae, which have not been observed previously in molluscs. Finally, we performed a morphology-based comparative analysis of neuronal structures among bivalve, conchiferan, and aculiferan species. Conclusions We described the development of the nervous system during the larval development in Crassostrea gigas. These data greatly advance the currently limited understanding of neurodevelopment in bivalves and mollusks, which has hampered the generation of a ground pattern reconstruction of the last common ancestor of Mollusca. Our morphological data support phylogenomic data indicating a closer Bivalvia-Gastropoda sister group relationship than the Bivalvia-Scaphopoda (Diasoma) group relationship. Electronic supplementary material The online version of this article (10.1186/s12983-018-0259-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Olga V Yurchenko
- 1National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, 690041 Russia
| | - Olga I Skiteva
- 2Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Elena E Voronezhskaya
- 3N.K. Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, 119991 Russia.,Department of Pathology, Cell biology and Biochemistry, Central Tuberculosis Research Institute, Moscow, Russian Federation
| | - Vyacheslav A Dyachuk
- 1National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, 690041 Russia.,5Far Eastern Federal University, Vladivostok, 690950 Russia.,6Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
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Breinholt JW, Earl C, Lemmon AR, Lemmon EM, Xiao L, Kawahara AY. Resolving Relationships among the Megadiverse Butterflies and Moths with a Novel Pipeline for Anchored Phylogenomics. Syst Biol 2018; 67:78-93. [PMID: 28472519 DOI: 10.1093/sysbio/syx048] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 04/28/2017] [Indexed: 11/12/2022] Open
Abstract
The advent of next-generation sequencing technology has allowed for thecollection of large portions of the genome for phylogenetic analysis. Hybrid enrichment and transcriptomics are two techniques that leverage next-generation sequencing and have shown much promise. However, methods for processing hybrid enrichment data are still limited. We developed a pipeline for anchored hybrid enrichment (AHE) read assembly, orthology determination, contamination screening, and data processing for sequences flanking the target "probe" region. We apply this approach to study the phylogeny of butterflies and moths (Lepidoptera), a megadiverse group of more than 157,000 described species with poorly understood deep-level phylogenetic relationships. We introduce a new, 855 locus AHE kit for Lepidoptera phylogenetics and compare resulting trees to those from transcriptomes. The enrichment kit was designed from existing genomes, transcriptomes, and expressed sequence tags and was used to capture sequence data from 54 species from 23 lepidopteran families. Phylogenies estimated from AHE data were largely congruent with trees generated from transcriptomes, with strong support for relationships at all but the deepest taxonomic levels. We combine AHE and transcriptomic data to generate a new Lepidoptera phylogeny, representing 76 exemplar species in 42 families. The tree provides robust support for many relationships, including those among the seven butterfly families. The addition of AHE data to an existing transcriptomic dataset lowers node support along the Lepidoptera backbone, but firmly places taxa with AHE data on the phylogeny. Combining taxa sequenced for AHE with existing transcriptomes and genomes resulted in a tree with strong support for (Calliduloidea $+$ Gelechioidea $+$ Thyridoidea) $+$ (Papilionoidea $+$ Pyraloidea $+$ Macroheterocera). To examine the efficacy of AHE at a shallow taxonomic level, phylogenetic analyses were also conducted on a sister group representing a more recent divergence, the Saturniidae and Sphingidae. These analyses utilized sequences from the probe region and data flanking it, nearly doubled the size of the dataset; resulting trees supported new phylogenetics relationships, especially within the Saturniidae and Sphingidae (e.g., Hemarina derived in the latter). We hope that our data processing pipeline, hybrid enrichment gene set, and approach of combining AHE data with transcriptomes will be useful for the broader systematics community.
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Affiliation(s)
- Jesse W Breinholt
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA.,RAPiD Genomics, Gainesville, FL 32601, USA
| | - Chandra Earl
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | | | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Lei Xiao
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Akito Y Kawahara
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
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