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Song H, Wang B, Zhao G, Lu S, Zhang D, Kong J, Li J, Zhang X, Lyu Y, Liu L. Discovery and biochemical characterization of two hexokinases from Crassostrea gigas. Protein Expr Purif 2024; 215:106408. [PMID: 38008389 DOI: 10.1016/j.pep.2023.106408] [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: 10/18/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 11/28/2023]
Abstract
Hexokinases (HKs) play a vital role in glucose metabolism, which controls the first committed step catalyzing the production of glucose-6-phosphate from glucose. Two HKs (CGIHK1 and CGIHK2) from the Pacific oyster Crassostrea giga were cloned and characterized. CGIHK1 and CGIHK2 were recombinantly expressed in Escherichia coli and successfully purified by the Ni-NTA column. The optimum pH of the two enzymes was pH 8.0 and 8.5, respectively. The optimum temperature of the two enzymes was 42 °C and 50 °C, respectively. Both enzymes showed a clear requirement for divalent magnesium and were strongly inhibited by SDS. CGIHK1 exhibited highly strict substrate specificity to glucose, while CGIHK2 could also catalyze other 11 monosaccharide substrates. This is the first report on the in vitro biosynthesis of glucose-6-phosphate by the hexokinases from Crassostrea gigas. The facile expression and purification procedures combined with different substrate specificities make CGIHK1 and CGIHK2 candidates for the biosynthesis of glucose-6-phosphate and other sugar-phosphates.
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Affiliation(s)
- Huibo Song
- College of Agricultural and Biological Engineering (College of Tree Peony), Heze University, Heze, 274015, China; Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Bo Wang
- College of Agricultural and Biological Engineering (College of Tree Peony), Heze University, Heze, 274015, China
| | - Guihong Zhao
- College of Agricultural and Biological Engineering (College of Tree Peony), Heze University, Heze, 274015, China.
| | - Shihai Lu
- Shandong Bigtree Dreyfus Special Meals Food Co., Ltd, Heze, 274000, China
| | - Dahu Zhang
- Shandong Bigtree Dreyfus Special Meals Food Co., Ltd, Heze, 274000, China
| | - Jianbiao Kong
- Heze Product Inspection and Testing Research Institute, Heze, 274000, China
| | - Jianxin Li
- Heze Institute for Food and Drug Control. Heze, 274000, China
| | - Xiaoyang Zhang
- School of Marine and Bioengineering, Yancheng Institute of Technology, Yancheng, 224051, China
| | - Yongmei Lyu
- School of Marine and Bioengineering, Yancheng Institute of Technology, Yancheng, 224051, China
| | - Li Liu
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
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2
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Goodheart JA, Rio RA, Taraporevala NF, Fiorenza RA, Barnes SR, Morrill K, Jacob MAC, Whitesel C, Masterson P, Batzel GO, Johnston HT, Ramirez MD, Katz PS, Lyons DC. A chromosome-level genome for the nudibranch gastropod Berghia stephanieae helps parse clade-specific gene expression in novel and conserved phenotypes. BMC Biol 2024; 22:9. [PMID: 38233809 PMCID: PMC10795318 DOI: 10.1186/s12915-024-01814-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 01/03/2024] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND How novel phenotypes originate from conserved genes, processes, and tissues remains a major question in biology. Research that sets out to answer this question often focuses on the conserved genes and processes involved, an approach that explicitly excludes the impact of genetic elements that may be classified as clade-specific, even though many of these genes are known to be important for many novel, or clade-restricted, phenotypes. This is especially true for understudied phyla such as mollusks, where limited genomic and functional biology resources for members of this phylum have long hindered assessments of genetic homology and function. To address this gap, we constructed a chromosome-level genome for the gastropod Berghia stephanieae (Valdés, 2005) to investigate the expression of clade-specific genes across both novel and conserved tissue types in this species. RESULTS The final assembled and filtered Berghia genome is comparable to other high-quality mollusk genomes in terms of size (1.05 Gb) and number of predicted genes (24,960 genes) and is highly contiguous. The proportion of upregulated, clade-specific genes varied across tissues, but with no clear trend between the proportion of clade-specific genes and the novelty of the tissue. However, more complex tissue like the brain had the highest total number of upregulated, clade-specific genes, though the ratio of upregulated clade-specific genes to the total number of upregulated genes was low. CONCLUSIONS Our results, when combined with previous research on the impact of novel genes on phenotypic evolution, highlight the fact that the complexity of the novel tissue or behavior, the type of novelty, and the developmental timing of evolutionary modifications will all influence how novel and conserved genes interact to generate diversity.
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Affiliation(s)
- Jessica A Goodheart
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA.
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
| | - Robin A Rio
- Bioengineering Department, Stanford University, Stanford, CA, USA
| | - Neville F Taraporevala
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Department of Wildland Resources, Utah State University, Logan, UT, USA
| | - Rose A Fiorenza
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Seth R Barnes
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Kevin Morrill
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Mark Allan C Jacob
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Carl Whitesel
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Park Masterson
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Grant O Batzel
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Hereroa T Johnston
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - M Desmond Ramirez
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Paul S Katz
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Deirdre C Lyons
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
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David P, Degletagne C, Saclier N, Jennan A, Jarne P, Plénet S, Konecny L, François C, Guéguen L, Garcia N, Lefébure T, Luquet E. Extreme mitochondrial DNA divergence underlies genetic conflict over sex determination. Curr Biol 2022; 32:2325-2333.e6. [PMID: 35483362 DOI: 10.1016/j.cub.2022.04.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/28/2022] [Accepted: 04/06/2022] [Indexed: 01/06/2023]
Abstract
Cytoplasmic male sterility (CMS) is a form of genetic conflict over sex determination that results from differences in modes of inheritance between genomic compartments.1-3 Indeed, maternally transmitted (usually mitochondrial) genes sometimes enhance their transmission by suppressing the male function in a hermaphroditic organism to the detriment of biparentally inherited nuclear genes. Therefore, these hermaphrodites become functionally female and may coexist with regular hermaphrodites in so-called gynodioecious populations.3 CMS has been known in plants since Darwin's times4 but is previously unknown in the animal kingdom.5-8 We relate the first observation of CMS in animals. It occurs in a freshwater snail population, where some individuals appear unable to sire offspring in controlled crosses and show anatomical, physiological, and behavioral characters consistent with a suppression of the male function. Male sterility is associated with a mitochondrial lineage that underwent a spectacular acceleration of DNA substitution rates, affecting the entire mitochondrial genome-this acceleration concerns both synonymous and non-synonymous substitutions and therefore results from increased mitogenome mutation rates. Consequently, mitochondrial haplotype divergence within the population is exceptionally high, matching that observed between snail taxa that diverged 475 million years ago. This result is reminiscent of similar accelerations in mitogenome evolution observed in plant clades where gynodioecy is frequent,9,10 both being consistent with arms-race evolution of genome regions implicated in CMS.11,12 Our study shows that genomic conflicts can trigger independent evolution of similar sex-determination systems in plants and animals and dramatically accelerate molecular evolution.
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Affiliation(s)
- Patrice David
- CEFE, CNRS, University of Montpellier, IRD, EPHE, Montpellier, France.
| | - Cyril Degletagne
- University of Lyon, CNRS, ENTPE, UMR5023 LEHNA, 69622 Villeurbanne, France
| | | | - Aurel Jennan
- University of Lyon, CNRS, ENTPE, UMR5023 LEHNA, 69622 Villeurbanne, France
| | - Philippe Jarne
- CEFE, CNRS, University of Montpellier, IRD, EPHE, Montpellier, France
| | - Sandrine Plénet
- University of Lyon, CNRS, ENTPE, UMR5023 LEHNA, 69622 Villeurbanne, France
| | - Lara Konecny
- University of Lyon, CNRS, ENTPE, UMR5023 LEHNA, 69622 Villeurbanne, France
| | | | - Laurent Guéguen
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France
| | - Noéline Garcia
- University of Lyon, CNRS, ENTPE, UMR5023 LEHNA, 69622 Villeurbanne, France
| | - Tristan Lefébure
- University of Lyon, CNRS, ENTPE, UMR5023 LEHNA, 69622 Villeurbanne, France
| | - Emilien Luquet
- University of Lyon, CNRS, ENTPE, UMR5023 LEHNA, 69622 Villeurbanne, France
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Comparative mitogenomics of freshwater snails of the genus Bulinus, obligatory vectors of Schistosoma haematobium, causative agent of human urogenital schistosomiasis. Sci Rep 2022; 12:5357. [PMID: 35354876 PMCID: PMC8967911 DOI: 10.1038/s41598-022-09305-7] [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: 09/12/2021] [Accepted: 03/10/2022] [Indexed: 02/05/2023] Open
Abstract
AbstractAmong the snail genera most responsible for vectoring human-infecting schistosomes, Bulinus, Biomphalaria, and Oncomelania, the former is in many respects the most important. Bulinid snails host the most common human blood fluke, Schistosoma haematobium, responsible for approximately two-thirds of the estimated 237 million cases of schistosomiasis. They also support transmission of schistosomes to millions of domestic and wild animals. Nonetheless, our basic knowledge of the 37 Bulinus species remains incomplete, especially with respect to genome information, even including mitogenome sequences. We determined complete mitogenome sequences for Bulinus truncatus, B. nasutus, and B. ugandae, and three representatives of B. globosus from eastern, central, and western Kenya. A difference of the location of tRNA-Asp was found between mitogenomes from the three species of the Bulinus africanus group and B. truncatus. Phylogenetic analysis using partial cox1 sequences suggests that B. globosus is a complex comprised of multiple species. We also highlight the status of B. ugandae as a distinct species with unusual interactions with the S. haematobium group parasites deserving of additional investigation. We provide sequence data for potential development of genetic markers for specific or intraspecific Bulinus studies, help elucidate the relationships among Bulinus species, and suggest ways in which mitogenomes may help understand the complex interactions between Schistosoma and Bulinus snails and their relatives.
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Rempel EM, Marcus JM, Detwiler JT. The complete mitochondrial genome of the file ramshorn snail Planorbella pilsbryi (Mollusca: Gastropoda: Hygrophila: Planorbidae). Mitochondrial DNA B Resour 2021; 6:3181-3183. [PMID: 34746397 PMCID: PMC8567931 DOI: 10.1080/23802359.2021.1975508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/27/2021] [Indexed: 11/09/2022] Open
Abstract
The file ramshorn snail Planorbella pilsbryi Baker, 1926 (Gastropoda: Hygrophila: Planorbidae) is a widespread herbivorous North American freshwater snail found in diverse habitats, including standing and moving water bodies. Genome skimming by Illumina sequencing allowed the assembly of a complete nuclear rRNA repeat sequence and a complete circular mitogenome of 13,720 bp from P. pilsbryi consisting of 75.3% AT nucleotides, 22 tRNAs, 13 protein-coding genes, 2 rRNAs and a control region in the typical order found in panpulmonate snails. Planorbella pilsbryi COXI features a rare TTG start codon while COXII, CYTB, ND2, ND3, and ND5 exhibit incomplete stop codons completed by the addition of 3' A residues to the mRNA. Phylogenetic reconstruction of mitochondrial protein-coding gene and rRNA sequences places P. pilsbryi as sister taxon to Planorbella duryi (Planorbidae) within family Planorbidae, which is consistent with previous phylogenetic hypotheses.
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Affiliation(s)
- Emma M. Rempel
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Jeffrey M. Marcus
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Jillian T. Detwiler
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada
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Pantoja C, Faltýnková A, O'Dwyer K, Jouet D, Skírnisson K, Kudlai O. Diversity of echinostomes (Digenea: Echinostomatidae) in their snail hosts at high latitudes. ACTA ACUST UNITED AC 2021; 28:59. [PMID: 34319230 PMCID: PMC8336728 DOI: 10.1051/parasite/2021054] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 06/24/2021] [Indexed: 11/14/2022]
Abstract
The biodiversity of freshwater ecosystems globally still leaves much to be discovered, not least in the trematode parasite fauna they support. Echinostome trematode parasites have complex, multiple-host life-cycles, often involving migratory bird definitive hosts, thus leading to widespread distributions. Here, we examined the echinostome diversity in freshwater ecosystems at high latitude locations in Iceland, Finland, Ireland and Alaska (USA). We report 14 echinostome species identified morphologically and molecularly from analyses of nad1 and 28S rDNA sequence data. We found echinostomes parasitising snails of 11 species from the families Lymnaeidae, Planorbidae, Physidae and Valvatidae. The number of echinostome species in different hosts did not vary greatly and ranged from one to three species. Of these 14 trematode species, we discovered four species (Echinoparyphium sp. 1, Echinoparyphium sp. 2, Neopetasiger sp. 5, and Echinostomatidae gen. sp.) as novel in Europe; we provide descriptions for the newly recorded species and those not previously associated with DNA sequences. Two species from Iceland (Neopetasiger islandicus and Echinoparyphium sp. 2) were recorded in both Iceland and North America. All species found in Ireland are new records for this country. Via an integrative taxonomic approach taken, both morphological and molecular data are provided for comparison with future studies to elucidate many of the unknown parasite life cycles and transmission routes. Our reports of species distributions spanning Europe and North America highlight the need for parasite biodiversity assessments across large geographical areas.
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Affiliation(s)
- Camila Pantoja
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic - Institute of Ecology, Nature Research Centre, Akademijos 2, 08412 Vilnius, Lithuania
| | - Anna Faltýnková
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Katie O'Dwyer
- Marine and Freshwater Research Centre, Galway-Mayo Institute of Technology, H91 T8NW Galway, Ireland
| | - Damien Jouet
- BioSpecT EA7506, Faculty of Pharmacy, University of Reims Champagne-Ardenne, 51 rue Cognacq-Jay, 51096 Reims Cedex, France
| | - Karl Skírnisson
- Laboratory of Parasitology, Institute for Experimental Pathology, Keldur, University of Iceland, IS-112 Reykjavík, Iceland
| | - Olena Kudlai
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic - Institute of Ecology, Nature Research Centre, Akademijos 2, 08412 Vilnius, Lithuania
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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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8
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Adema CM. Sticky problems: extraction of nucleic acids from molluscs. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200162. [PMID: 33813891 DOI: 10.1098/rstb.2020.0162] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Traditional molecular methods and omics-techniques across molluscan taxonomy increasingly inform biology of Mollusca. Recovery of DNA and RNA for such studies is challenged by common biological properties of the highly diverse molluscs. Molluscan biomineralization, adhesive structures and mucus involve polyphenolic proteins and mucopolysaccharides that hinder DNA extraction or copurify to inhibit enzyme-catalysed molecular procedures. DNA extraction methods that employ the detergent hexadecyltrimethylammoniumbromide (CTAB) to remove these contaminants importantly facilitate molecular-level study of molluscs. Molluscan pigments may stain DNA samples and interfere with spectrophotometry, necessitating gel electrophoresis or fluorometry for accurate quantification. RNA can reliably be extracted but the 'hidden break' in 28S rRNA of molluscs (like most protostomes) causes 18S and 28S rRNA fragments to co-migrate electrophoretically. This challenges the standard quality control based on the ratio of 18S and 28S rRNA, developed for deuterostome animals. High-AT content in molluscan rRNA prevents the effective purification of polyadenylated mRNA. Awareness of these matters aids the continuous expansion of molecular malacology, enabling work also with museum specimens and next-generation sequencing, with the latter imposing unprecedented demands on DNA quality. Alternative methods to extract nucleic acids from molluscs are available from literature and, importantly, from communications with others who study the molecular biology of molluscs. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.
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Affiliation(s)
- Coen M Adema
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, NM 87112, USA
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9
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Varney RM, Brenzinger B, Malaquias MAE, Meyer CP, Schrödl M, Kocot KM. Assessment of mitochondrial genomes for heterobranch gastropod phylogenetics. BMC Ecol Evol 2021; 21:6. [PMID: 33514315 PMCID: PMC7853304 DOI: 10.1186/s12862-020-01728-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 11/26/2020] [Indexed: 01/07/2023] Open
Abstract
Background Heterobranchia is a diverse clade of marine, freshwater, and terrestrial gastropod molluscs. It includes such disparate taxa as nudibranchs, sea hares, bubble snails, pulmonate land snails and slugs, and a number of (mostly small-bodied) poorly known snails and slugs collectively referred to as the “lower heterobranchs”. Evolutionary relationships within Heterobranchia have been challenging to resolve and the group has been subject to frequent and significant taxonomic revision. Mitochondrial (mt) genomes can be a useful molecular marker for phylogenetics but, to date, sequences have been available for only a relatively small subset of Heterobranchia. Results To assess the utility of mitochondrial genomes for resolving evolutionary relationships within this clade, eleven new mt genomes were sequenced including representatives of several groups of “lower heterobranchs”. Maximum likelihood analyses of concatenated matrices of the thirteen protein coding genes found weak support for most higher-level relationships even after several taxa with extremely high rates of evolution were excluded. Bayesian inference with the CAT + GTR model resulted in a reconstruction that is much more consistent with the current understanding of heterobranch phylogeny. Notably, this analysis recovered Valvatoidea and Orbitestelloidea in a polytomy with a clade including all other heterobranchs, highlighting these taxa as important to understanding early heterobranch evolution. Also, dramatic gene rearrangements were detected within and between multiple clades. However, a single gene order is conserved across the majority of heterobranch clades. Conclusions Analysis of mitochondrial genomes in a Bayesian framework with the site heterogeneous CAT + GTR model resulted in a topology largely consistent with the current understanding of heterobranch phylogeny. However, mitochondrial genomes appear to be too variable to serve as good phylogenetic markers for robustly resolving a number of deeper splits within this clade.
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Affiliation(s)
- Rebecca M Varney
- Department of Biological Sciences, The University of Alabama, Campus Box 870344, Tuscaloosa, AL, 35487, USA
| | - Bastian Brenzinger
- SNSB-Bavarian State Collection of Zoology, Münchhausenstr. 21, 81247, München, Germany
| | | | - Christopher P Meyer
- National Museum of Natural History, Smithsonian Institution, 10th St. & Constitution Ave. NW, Washington, D.C., 20560, USA
| | - Michael Schrödl
- SNSB-Bavarian State Collection of Zoology, Münchhausenstr. 21, 81247, München, Germany.,BioGeoCenter LMU (Ludwig Maximillion University Munich), University of Munich, Biozentrum, Großhaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | - Kevin M Kocot
- Department of Biological Sciences, The University of Alabama, Campus Box 870344, Tuscaloosa, AL, 35487, USA. .,Alabama Museum of Natural History, Campus Box 870344, Tuscaloosa, AL, 35487, USA.
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10
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Schultz JH, Bu L, Kamel B, Adema CM. RNA-seq: The early response of the snail Physella acuta to the digenetic trematode Echinostoma paraensei. J Parasitol 2021; 106:490-505. [PMID: 32726421 DOI: 10.1645/19-36] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
To analyze the response of the snail Physella acuta to Echinostoma paraensei, a compatible digenetic trematode, Illumina RNA-seq data were collected from snails with early infection (5 snails at 2 days post-exposure [DPE]) and established infection (4 snails, 8 DPE), and 7 control (unexposed) snails. A reference transcriptome (325,563 transcripts, including 98% of eukaryotic universal single-copy orthologs; BUSCO) and a draft P. acuta genome (employing available genomic Illumina reads; 799,945 scaffolds, includes 88% BUSCO genes) were assembled to guide RNA-seq analyses. Parasite exposure of P. acuta led to 10,195 differentially expressed (DE) genes at 2 DPE and 8,876 DE genes at 8 DPE with only 18% of up-regulated and 22% of down-regulated sequences shared between these time points. Gene ontology (GO) analysis yielded functional annotation of only 1.2% of DE genes but did not indicate major changes in biological activities of P. acuta between 2 and 8 DPE. Increased insights were achieved by analysis of expression profiles of 460 immune-relevant DE transcripts, identified by BLAST and InterProScan. Physella acuta has expanded gene families that encode immune-relevant domains, including CD109/TEP, GTPase IMAP, Limulus agglutination factor (dermatopontin), FReD (≥82 sequences with fibrinogen-related domains), and transcripts that combine C-type lectin (C-LECT) and C1q domains, novel among metazoa. Notably, P. acuta expressed sequences from these immune gene families at all time points, but the assemblages of unique transcripts from particular immune gene families differed between 2 and 8 DPE. The shift in profiles of DE immune genes, from early exposure to parasite establishment, suggests that compatible P. acuta initially respond to infection but switch to express immune genes that likely are less effective against E. paraensei but counter other types of (opportunistic) pathogens and parasites. We propose that the latter expression profile is part of an extended phenotype of E. paraensei, imposed upon P. acuta through parasite manipulation of the host, following successful parasite establishment in the snail after 2 DPE.
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Affiliation(s)
- Jonathan H Schultz
- Center for Evolutionary and Theoretical Immunology (CETI), Department of Biology, University of New Mexico, Albuquerque, New Mexico 87131.,Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California 93106
| | - Lijing Bu
- Center for Evolutionary and Theoretical Immunology (CETI), Department of Biology, University of New Mexico, Albuquerque, New Mexico 87131
| | - Bishoy Kamel
- Center for Evolutionary and Theoretical Immunology (CETI), Department of Biology, University of New Mexico, Albuquerque, New Mexico 87131
| | - Coen M Adema
- Center for Evolutionary and Theoretical Immunology (CETI), Department of Biology, University of New Mexico, Albuquerque, New Mexico 87131
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11
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Xie GL, Köhler F, Huang XC, Wu RW, Zhou CH, Ouyang S, Wu XP. A novel gene arrangement among the Stylommatophora by the complete mitochondrial genome of the terrestrial slug Meghimatium bilineatum (Gastropoda, Arionoidea). Mol Phylogenet Evol 2019; 135:177-184. [PMID: 30858078 DOI: 10.1016/j.ympev.2019.03.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 12/12/2018] [Accepted: 03/05/2019] [Indexed: 12/20/2022]
Abstract
Stylommatophora is a main clade of Gastropoda that encompasses approximately 112 gastropod families and may exceed a total of 30,000 species. Twenty-four complete stylommatophoran mitogenomes have been sequenced to date, yet our understanding of mitochondrial evolution in stylommatophorans is still in its infancy. To further expand the set of available mitogenomes, we sequenced the mitogenome of Meghimatium bilineatum (Arionoidea: Philomycidae), a widespread land slug in East Asia. This is the first report on a mitogenome of the superfamily Arionoidea, and indeed on a terrestrial slug. The mitogenome of Meghimatium bilineatum comprises 13,972 bp and exhibits a novel, highly distinctive gene arrangement among the Stylommatophora. Phylogenetic reconstructions based on the sequences of all protein-coding genes consistently recovered Meghimatium bilineatum as sister-group of the Succineidae. A phylogenetic reconstruction based on gene order, however, suggested a highly divergent tree topology, which is less credible when taking into account prior knowledge of stylommatophoran relationships. Our CREx (Common interval Rearrangement Explorer) analysis suggested that three successive events of tandem duplication random loss (TDRL) best explain the evolutionary process of gene order rearrangement in Meghimatium bilineatum from an ancestral stylommatophoran mitogenome. The present example offers new insights into the mechanisms of mitogenome rearrangements in gastropods at large and into the usefulness of mitogenomic gene order as a phylogenetic marker.
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Affiliation(s)
- Guang-Long Xie
- School of Life Sciences, Nanchang University, Nanchang 330031, China; Australian Museum, 1 William Street, Sydney, NSW 2010, Australia
| | - Frank Köhler
- Australian Museum, 1 William Street, Sydney, NSW 2010, Australia
| | - Xiao-Chen Huang
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, 69120 Heidelberg, Germany
| | - Rui-Wen Wu
- School of Life Sciences, Nanchang University, Nanchang 330031, China
| | - Chun-Hua Zhou
- School of Life Sciences, Nanchang University, Nanchang 330031, China
| | - Shan Ouyang
- School of Life Sciences, Nanchang University, Nanchang 330031, China.
| | - Xiao-Ping Wu
- School of Life Sciences, Nanchang University, Nanchang 330031, China.
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12
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Yang H, Zhang JE, Xia J, Yang J, Guo J, Deng Z, Luo M. Comparative Characterization of the Complete Mitochondrial Genomes of the Three Apple Snails (Gastropoda: Ampullariidae) and the Phylogenetic Analyses. Int J Mol Sci 2018; 19:E3646. [PMID: 30463257 PMCID: PMC6274680 DOI: 10.3390/ijms19113646] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 10/31/2018] [Accepted: 11/02/2018] [Indexed: 01/07/2023] Open
Abstract
The apple snails Pomacea canaliculata, Pomacea diffusa and Pomacea maculate (Gastropoda: Caenogastropoda: Ampullariidae) are invasive pests causing massive economic losses and ecological damage. We sequenced and characterized the complete mitochondrial genomes of these snails to conduct phylogenetic analyses based on comparisons with the mitochondrial protein coding sequences of 47 Caenogastropoda species. The gene arrangements, distribution and content were canonically identical and consistent with typical Mollusca except for the tRNA-Gln absent in P. diffusa. An identifiable control region (d-loop) was absent. Bayesian phylogenetic analysis indicated that all the Ampullariidae species clustered on the same branch. The genus Pomacea clustered together and then with the genus Marisa. The orders Architaenioglossa and Sorbeoconcha clustered together and then with the order Hypsogastropoda. Furthermore, the intergenic and interspecific taxonomic positions were defined. Unexpectedly, Ceraesignum maximum, Dendropoma gregarium, Eualetes tulipa and Thylacodes squamigerus, traditionally classified in order Hypsogastropoda, were isolated from the order Hypsogastropoda in the most external branch of the Bayesian inference tree. The divergence times of the Caenogastropoda indicated that their evolutionary process covered four geological epochs that included the Quaternary, Neogene, Paleogene and Cretaceous periods. This study will facilitate further investigation of species identification to aid in the implementation of effective management and control strategies of these invasive species.
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Affiliation(s)
- Huirong Yang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510640, China.
- Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, HI 96822, USA.
| | - Jia-En Zhang
- Institute of Tropical and Subtropical Ecology, South China Agricultural University, Guangzhou 510642, China.
| | - Jun Xia
- Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, HI 96822, USA.
- Xinjiang Acadamy of Animal Sciences, Institute of Veterinary Medicine (Research Center of Animal Clinical), Urumqi 830000, China.
| | - Jinzeng Yang
- Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, HI 96822, USA.
| | - Jing Guo
- Institute of Tropical and Subtropical Ecology, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Engineering Research Center for Modern Eco-Agriculture and Circular Agriculture, Guangzhou 510642, China.
| | - Zhixin Deng
- Institute of Tropical and Subtropical Ecology, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Engineering Research Center for Modern Eco-Agriculture and Circular Agriculture, Guangzhou 510642, China.
| | - Mingzhu Luo
- Institute of Tropical and Subtropical Ecology, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Engineering Research Center for Modern Eco-Agriculture and Circular Agriculture, Guangzhou 510642, China.
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13
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Schultz JH, Bansbach LM, Bremmer JA, Dimmler KE, Forde QA, Gagliano EM, Glenn EM, Greengrass CM, Hayes JP, Kraus AL, Larsen LI, Lucero E, McClendon MT, Mercer HL, Mims KC, Patel KN, Patsalis FI, Peterson DE, Platero JM, Rizvi MM, Serna KI, Steele TE, Turner NL, Bu L, Lu L, Adema CM. The mitochondrial genome of the planorbid snail Planorbella duryi. MITOCHONDRIAL DNA PART B-RESOURCES 2018; 3:972-973. [PMID: 33474384 PMCID: PMC7800533 DOI: 10.1080/23802359.2018.1503939] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The complete mitochondrial genome of a freshwater planorbid snail, Planorbella duryi (Mollusca, Gastropoda) was recovered from de novo assembly of genomic sequences generated with the Illumina NextSeq500 platform. The P. duryi mitogenome (14,217 base pairs) is AT rich (72.69%) and comprises 13 protein-coding genes, two ribosomal subunit genes, and 22 transfer RNAs. The gene order is identical to that of Biomphalaria glabrata and other snail species in the family Planorbidae. This is the first full characterization of a mitochondrial genome of the genus Planorbella.
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Affiliation(s)
| | - Lauren M Bansbach
- Department of Biology, 1 University of New Mexico, Albuquerque, NM, USA
| | - Jarrett A Bremmer
- Department of Biology, 1 University of New Mexico, Albuquerque, NM, USA
| | - Kirsten E Dimmler
- Department of Biology, 1 University of New Mexico, Albuquerque, NM, USA
| | - Quinn A Forde
- Department of Biology, 1 University of New Mexico, Albuquerque, NM, USA
| | - Elisa M Gagliano
- Department of Biology, 1 University of New Mexico, Albuquerque, NM, USA
| | - Elizabeth M Glenn
- Department of Biology, 1 University of New Mexico, Albuquerque, NM, USA
| | | | - Joe P Hayes
- Department of Biology, 1 University of New Mexico, Albuquerque, NM, USA
| | - Aurora L Kraus
- Department of Biology, 1 University of New Mexico, Albuquerque, NM, USA
| | - Lewis I Larsen
- Department of Biology, 1 University of New Mexico, Albuquerque, NM, USA
| | - Erin Lucero
- Department of Biology, 1 University of New Mexico, Albuquerque, NM, USA
| | | | - Heather L Mercer
- Department of Biology, 1 University of New Mexico, Albuquerque, NM, USA
| | - Karen C Mims
- Department of Biology, 1 University of New Mexico, Albuquerque, NM, USA
| | - Kajal N Patel
- Department of Biology, 1 University of New Mexico, Albuquerque, NM, USA
| | - Fotios I Patsalis
- Department of Biology, 1 University of New Mexico, Albuquerque, NM, USA
| | - Dianne E Peterson
- Department of Biology, 1 University of New Mexico, Albuquerque, NM, USA
| | - Jarrod M Platero
- Department of Biology, 1 University of New Mexico, Albuquerque, NM, USA
| | - Mohammed M Rizvi
- Department of Biology, 1 University of New Mexico, Albuquerque, NM, USA
| | - Kassandra I Serna
- Department of Biology, 1 University of New Mexico, Albuquerque, NM, USA
| | - Tyler E Steele
- Department of Biology, 1 University of New Mexico, Albuquerque, NM, USA
| | - Nicholas L Turner
- Department of Biology, 1 University of New Mexico, Albuquerque, NM, USA
| | - Lijing Bu
- Department of Biology, 1 University of New Mexico, Albuquerque, NM, USA
| | - Lijun Lu
- Department of Biology, 1 University of New Mexico, Albuquerque, NM, USA
| | - Coen M Adema
- Department of Biology, 1 University of New Mexico, Albuquerque, NM, USA
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14
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Ebbs ET, Loker ES, Brant SV. Phylogeography and genetics of the globally invasive snail Physa acuta Draparnaud 1805, and its potential to serve as an intermediate host to larval digenetic trematodes. BMC Evol Biol 2018; 18:103. [PMID: 29969987 PMCID: PMC6029401 DOI: 10.1186/s12862-018-1208-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 06/05/2018] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Physa acuta is a globally invasive freshwater snail native to North America. Prior studies have led to conflicting views of how P. acuta populations are connected and genetic diversity is partitioned globally. This study aims to characterize phylogeographic and population genetic structure within the native range of P. acuta, elucidate its invasion history and assess global patterns of genetic diversity. Further, using meta-analytic methods, we test the 'Enemy-Release hypothesis' within the P. acuta - digenetic trematode system. The 'Enemy-Release hypothesis' refers to the loss of native parasites following establishment of their host within an invasive range. Population genetic data is combined with surveys of trematode infections to map range-wide trematode species richness associated with P. acuta, and to identify relevant host-population parameters important in modeling host-parasite invasion. RESULTS Phylogenetic analyses using mtDNA uncovered two major clades (A & B). Clade A occurs globally while clade B was only recovered from the Western USA. All invasive populations sampled grouped within Clade A, where multiple independent source populations were identified from across North America. Significant population genetic structure was found within the native range of P. acuta, with some evidence for contemporary geographic barriers between western and eastern populations. Mito-nuclear discordance was found suggesting historical isolation with secondary contact between the two mitochondrial clades. Trematode species richness was found to differ significantly between native and invasive populations, in concordance with the 'Enemy-Release hypothesis'. Further, our data suggests a positive relationship between nucleotide diversity of invasive populations and trematode prevalence and richness. CONCLUSIONS This study includes a wider geographic sampling of P. acuta within its native range that provides insight into phylogeographic and population genetic structure, range-wide genetic diversity and estimation of the invasion history. Meta-analysis of P. acuta - trematode surveys globally is consistent with the 'Enemy-Release hypothesis'. Additionally, results from this study suggest that host demographic parameters, namely genetic diversity as a proxy for population size, may play an essential role in how parasite communities assemble within invasive host populations. This knowledge can be used to begin to construct a framework to model host-parasite invasion dynamics over time.
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Affiliation(s)
- Erika T. Ebbs
- Department of Biology, Museum of Southwestern Biology Parasite Division, Center for Evolutionary and Theoretical Immunology, University of New Mexico, 167 Castetter MSCO3 2020, Albuquerque, NM 87131 USA
| | - Eric S. Loker
- Department of Biology, Museum of Southwestern Biology Parasite Division, Center for Evolutionary and Theoretical Immunology, University of New Mexico, 167 Castetter MSCO3 2020, Albuquerque, NM 87131 USA
| | - Sara V. Brant
- Department of Biology, Museum of Southwestern Biology Parasite Division, Center for Evolutionary and Theoretical Immunology, University of New Mexico, 167 Castetter MSCO3 2020, Albuquerque, NM 87131 USA
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15
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Zhang SM, Bu L, Laidemitt MR, Lu L, Mutuku MW, Mkoji GM, Loker ES. Complete mitochondrial and rDNA complex sequences of important vector species of Biomphalaria, obligatory hosts of the human-infecting blood fluke, Schistosoma mansoni. Sci Rep 2018; 8:7341. [PMID: 29743617 PMCID: PMC5943310 DOI: 10.1038/s41598-018-25463-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 04/16/2018] [Indexed: 01/24/2023] Open
Abstract
Using high throughput Illumina sequencing technology, we determined complete sequences for the mitochondrial genome (mitogenome) and nuclear ribosomal DNA (rDNA) complex for three African freshwater snail taxa within the genus Biomphalaria, B. pfeifferi, B. sudanica and B. choanomphala, and for two laboratory strains of B. glabrata originating from the Neotropics. Biomphalaria snails are obligate vectors of the blood fluke Schistosoma mansoni, a major etiologic agent of human intestinal schistosomiasis. Our data show that mitogenomes from African and Neotropical Biomphalaria are highly conserved. With respect to rDNA, the two internal transcribed spacers (ITS1 and 2) were found to be highly variable whereas the three ribosomal RNA genes (28S, 5.8S and 18S rRNA) exhibited no or very limited variation. Our analyses reveal that the two taxa inhabiting Lake Victoria, B. sudanica and B. choanomphala, are very similar to one another relative to the similarity either shows to B. pfeifferi or B. glabrata. This new sequence information may prove useful for developing new markers for snail identification, environmental detection/monitoring purposes or for tracking epidemiology and snail dependencies of S. mansoni in endemic areas. It also provides new information pertinent to still unresolved questions in Biomphalaria systematics and nomenclature.
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Affiliation(s)
- Si-Ming Zhang
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerqu, NM, 87131, USA.
| | - Lijing Bu
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerqu, NM, 87131, USA
| | - Martina R Laidemitt
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerqu, NM, 87131, USA
| | - Lijun Lu
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerqu, NM, 87131, USA
| | - Martin W Mutuku
- Centre for Biotechnology Research and Development, Kenya Medical Research Institute (KEMRI), P.O Box, 54840-00200, Nairobi, Kenya
| | - Gerald M Mkoji
- Centre for Biotechnology Research and Development, Kenya Medical Research Institute (KEMRI), P.O Box, 54840-00200, Nairobi, Kenya
| | - Eric S Loker
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerqu, NM, 87131, USA.,Parasitology Division, Museum of Southwestern Biology, University of New Mexico, Albuquerque, 87131, USA
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16
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Mu X, Yang Y, Liu Y, Luo D, Xu M, Wei H, Gu D, Song H, Hu Y. Retraction Note to: The complete mitochondrial genomes of two freshwater snails provide new protein-coding gene rearrangement models and phylogenetic implications. Parasit Vectors 2017; 10:350. [PMID: 28732528 PMCID: PMC5522592 DOI: 10.1186/s13071-017-2287-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 07/13/2017] [Indexed: 12/03/2022] Open
Affiliation(s)
- Xidong Mu
- Key Laboratory of Tropical&Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Xingyu Road1, Guangzhou, 510380, China
| | - Yexin Yang
- Key Laboratory of Tropical&Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Xingyu Road1, Guangzhou, 510380, China
| | - Yi Liu
- Key Laboratory of Tropical&Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Xingyu Road1, Guangzhou, 510380, China
| | - Du Luo
- Key Laboratory of Tropical&Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Xingyu Road1, Guangzhou, 510380, China
| | - Meng Xu
- Key Laboratory of Tropical&Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Xingyu Road1, Guangzhou, 510380, China
| | - Hui Wei
- Key Laboratory of Tropical&Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Xingyu Road1, Guangzhou, 510380, China
| | - Dangen Gu
- Key Laboratory of Tropical&Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Xingyu Road1, Guangzhou, 510380, China
| | - Hongmei Song
- Key Laboratory of Tropical&Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Xingyu Road1, Guangzhou, 510380, China
| | - Yinchang Hu
- Key Laboratory of Tropical&Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Xingyu Road1, Guangzhou, 510380, China.
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17
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Groenenberg DSJ, Harl J, Duijm E, Gittenberger E. The complete mitogenome of Orcula dolium (Draparnaud, 1801); ultra-deep sequencing from a single long-range PCR using the Ion-Torrent PGM. Hereditas 2017; 154:7. [PMID: 28396619 PMCID: PMC5379511 DOI: 10.1186/s41065-017-0028-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 03/23/2017] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND With the increasing capacity of present-day next-generation sequencers the field of mitogenomics is rapidly changing. Enrichment of the mitochondrial fraction, is no longer necessary for obtaining mitogenomic data. Despite the benefits, shotgun sequencing approaches also have disadvantages. They do not guarantee obtaining the complete mitogenome, generally require larger amounts of input DNA and coverage is low compared to sequencing with enrichment strategies. If the mitogenome could be amplified in a single amplification, additional time and costs for sample preparation might outweigh these disadvantages. RESULTS A sequence of the complete mitochondrial genome of the pupilloid landsnail Orcula dolium is presented. The mitogenome was amplified in a single long-range (LR) PCR and sequenced on an Ion Torrent PGM (Life Technologies). The length is 14,063 nt and the average depth of coverage is 1112 X. This is the first published mitogenome for a member of the family Orculidae. It has the typical metazoan makeup of 13 protein coding genes (PCGs), 2 ribosomal RNAs (12S and 16S) and 22 transfer RNAs (tRNAs). Orcula is positioned between Pupilla and the Vertiginidae as the sister-group of Gastrocopta and Vertigo, together. An ancestral gene order reconstruction shows that Orthurethra in contrast to other Stylommatophora, have tRNA-H before tRNA-G and that the gene order in the 'non-achatinoid' clade is identical to that of closely related non-stylommatophoran taxa. CONCLUSIONS We show it is feasible to ultra-deep sequence a mitogenome from a single LR-PCR. This approach is particularly relevant to studies that have low concentrations of input DNA. It results in a more efficient use of NGS capacity (only the targeted fraction is sequenced) and is an effective selection against nuclear mitochondrial inserts (NUMTS). In contrast to previous studies based in particular on 28S, our results indicate that phylogeny reconstructions based on complete mitogenomes might be more suitable to resolve deep relationships within Stylommatophora. Ancestral gene order reconstructions reveal rearrangements that characterize systematic groups.
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Affiliation(s)
| | - J. Harl
- Central Research Laboratories, Museum of Natural History Vienna, Vienna, Austria
- Department of Biology, Shinshu University, Matsumoto, Japan
| | - E. Duijm
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands
| | - E. Gittenberger
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands
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18
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Campbell DC, Clark SA, Lydeard C. Phylogenetic analysis of the Lancinae (Gastropoda, Lymnaeidae) with a description of the U.S. federally endangered Banbury Springs lanx. Zookeys 2017:107-132. [PMID: 28769620 PMCID: PMC5523177 DOI: 10.3897/zookeys.663.11320] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 03/13/2017] [Indexed: 11/22/2022] Open
Abstract
We examined the patelliform snails of the subfamily Lancinae, endemic to northwestern North America, to test whether morphological variation correlated with genetic and anatomical differences. Molecular analyses using cox1, 16S, calmodulin intron, and 28S rDNA partial sequences and anatomical data supported recognition of four species in three genera. The relationships of lancines within Lymnaeidae are not yet well-resolved. The federally endangered Banbury Springs lanx is described as a new genus and species, Idaholanxfresti, confirming its distinctiveness and narrow endemicity.
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Affiliation(s)
- David C Campbell
- Department of Natural Sciences, Gardner-Webb University, PO Box 7260, Boiling Springs, NC, 28017, USA
| | - Stephanie A Clark
- Invertebrate Identification, 6535 N Mozart St, Chicago, IL, 60645, USA.,Invertebrates, Gantz Family Collections Center, Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA
| | - Charles Lydeard
- Department of Biology and Chemistry, Morehead State University, 103 Lappin Hall, Morehead, KY, 40351, USA
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19
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Mu X, Yang Y, Liu Y, Luo D, Xu M, Wei H, Gu D, Song H, Hu Y. The complete mitochondrial genomes of two freshwater snails provide new protein-coding gene rearrangement models and phylogenetic implications. Parasit Vectors 2017; 10:11. [PMID: 28061879 PMCID: PMC5219674 DOI: 10.1186/s13071-016-1956-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 12/23/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mitochondrial (mt) genome sequences are widely used for species identification and to study the phylogenetic relationships among Gastropoda. However, to date, limited data are available as taxon sampling is narrow. In this study we sequenced the complete mt genomes of the freshwater gastropods Radix swinhoei (Lymnaeidae) and Planorbarius corneus (Planorbidae). Based on these sequences, we investigated the gene rearrangement in these two species and the relationships with respect to the ancestral gene order and assessed their phylogenetic relationships. METHODS The complete mt genomes of R. swinhoei and P. corneus were sequenced using Illumina-based paired-end sequencing and annotated by comparing the sequence information with that of related gastropod species. Putative models of mitochondrial gene rearrangements were predicted for both R. swinhoei and P. corneus, using Reishia clavigera mtDNA structure as the ancestral gene order. The phylogenetic relationships were inferred using thirteen protein sequences based on Maximum likelihood and Bayesian inference analyses. RESULTS The complete circular mt genome sequences of R. swinhoei and P. corneus were 14,241 bp and 13,687 bp in length, respectively. Comparison of the gene order demonstrated complex rearrangement events in Gastropoda, both for tRNA genes and protein-coding genes. The phylogenetic analyses showed that the family Lymnaeidae was more closely related to the family Planorbidae, consistent with previous classification. Nevertheless, due to the position recovered for R. swinhoei, the family Lymnaeidae was not monophyletic. CONCLUSION This study provides the complete mt genomes of two freshwater snails, which will aid the development of useful molecular markers for epidemiological, ecological and phylogenetic studies. Additionally, the predicted models for mt gene rearrangement might provide novel insights into mt genome evolution in gastropods.
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Affiliation(s)
- Xidong Mu
- Key Laboratory of Tropical&Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Xingyu Road1, Guangzhou, 510380 China
| | - Yexin Yang
- Key Laboratory of Tropical&Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Xingyu Road1, Guangzhou, 510380 China
| | - Yi Liu
- Key Laboratory of Tropical&Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Xingyu Road1, Guangzhou, 510380 China
| | - Du Luo
- Key Laboratory of Tropical&Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Xingyu Road1, Guangzhou, 510380 China
| | - Meng Xu
- Key Laboratory of Tropical&Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Xingyu Road1, Guangzhou, 510380 China
| | - Hui Wei
- Key Laboratory of Tropical&Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Xingyu Road1, Guangzhou, 510380 China
| | - Dangen Gu
- Key Laboratory of Tropical&Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Xingyu Road1, Guangzhou, 510380 China
| | - Hongmei Song
- Key Laboratory of Tropical&Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Xingyu Road1, Guangzhou, 510380 China
| | - Yinchang Hu
- Key Laboratory of Tropical&Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Xingyu Road1, Guangzhou, 510380 China
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20
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Romero PE, Weigand AM, Pfenninger M. Positive selection on panpulmonate mitogenomes provide new clues on adaptations to terrestrial life. BMC Evol Biol 2016; 16:164. [PMID: 27549326 PMCID: PMC4994307 DOI: 10.1186/s12862-016-0735-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 08/08/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Transitions from marine to intertidal and terrestrial habitats resulted in a significant adaptive radiation within the Panpulmonata (Gastropoda: Heterobranchia). This clade comprises several groups that invaded the land realm independently and in different time periods, e.g., Ellobioidea, Systellomatophora, and Stylommatophora. Thus, mitochondrial genomes of panpulmonate gastropods are promising to screen for adaptive molecular signatures related to land invasions. RESULTS We obtained three complete mitochondrial genomes of terrestrial panpulmonates, i.e., the ellobiid Carychium tridentatum, and the stylommatophorans Arion rufus and Helicella itala. Our dataset consisted of 50 mitogenomes comprising almost all major panpulmonate lineages. The phylogenetic tree based on mitochondrial genes supports the monophyly of the clade Panpulmonata. Terrestrial lineages were sampled from Ellobioidea (1 sp.) and Stylommatophora (9 spp.). The branch-site test of positive selection detected significant non-synonymous changes in the terrestrial branches leading to Carychium (Ellobiodea) and Stylommatophora. These convergent changes occurred in the cob and nad5 genes (OXPHOS complex III and I, respectively). CONCLUSIONS The convergence of the non-synonymous changes in cob and nad5 suggest possible ancient episodes of positive selection related to adaptations to non-marine habitats. The positively selected sites in our data are in agreement with previous results in vertebrates suggesting a general pattern of adaptation to the new metabolic requirements. The demand for energy due to the colonization of land (for example, to move and sustain the body mass in the new habitat) and the necessity to tolerate new conditions of abiotic stress may have changed the physiological constraints in the early terrestrial panpulmonates and triggered adaptations at the mitochondrial level.
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Affiliation(s)
- Pedro E Romero
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany. .,Institute for Ecology, Evolution & Diversity, Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue-Straße 13, 60438, Frankfurt am Main, Germany. .,Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Av. Arenales 1256, Apartado 14-0434, Lima 14, Peru.
| | - Alexander M Weigand
- Aquatic Ecosystem Research, University of Duisburg-Essen, Universitätsstraße 5, 45141, Essen, Germany.,Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße 2, 45117, Essen, Germany
| | - Markus Pfenninger
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,Institute for Ecology, Evolution & Diversity, Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue-Straße 13, 60438, Frankfurt am Main, Germany
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Fraïsse C, Gunnarsson PA, Roze D, Bierne N, Welch JJ. The genetics of speciation: Insights from Fisher's geometric model. Evolution 2016; 70:1450-64. [PMID: 27252049 DOI: 10.1111/evo.12968] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 05/22/2016] [Indexed: 12/13/2022]
Abstract
Research in speciation genetics has uncovered many robust patterns in intrinsic reproductive isolation, and fitness landscape models have been useful in interpreting these patterns. Here, we examine fitness landscapes based on Fisher's geometric model. Such landscapes are analogous to models of optimizing selection acting on quantitative traits, and have been widely used to study adaptation and the distribution of mutational effects. We show that, with a few modifications, Fisher's model can generate all of the major findings of introgression studies (including "speciation genes" with strong deleterious effects, complex epistasis and asymmetry), and the major patterns in overall hybrid fitnesses (including Haldane's Rule, the speciation clock, heterosis, hybrid breakdown, and male-female asymmetry in the F1). We compare our approach to alternative modeling frameworks that assign fitnesses to genotypes by identifying combinations of incompatible alleles. In some cases, the predictions are importantly different. For example, Fisher's model can explain conflicting empirical results about the rate at which incompatibilities accumulate with genetic divergence. In other cases, the predictions are identical. For example, the quality of reproductive isolation is little affected by the manner in which populations diverge.
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Affiliation(s)
- Christelle Fraïsse
- Université Montpellier, Institut des Sciences de l'Évolution, UMR 5554, Montpellier Cedex 05, France.,CNRS, Institut des Sciences de l'Évolution, UMR 5554, OREME Station Marine, Sète, France.,Department of Genetics, University of Cambridge, Downing Street, Cambridge, United Kingdom
| | - P Alexander Gunnarsson
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, United Kingdom
| | - Denis Roze
- CNRS, UMI 3614, Evolutionary Biology and Ecology of Algae, Roscoff, France.,Sorbonne Universités, UPMC University Paris VI, Roscoff, France
| | - Nicolas Bierne
- Université Montpellier, Institut des Sciences de l'Évolution, UMR 5554, Montpellier Cedex 05, France.,CNRS, Institut des Sciences de l'Évolution, UMR 5554, OREME Station Marine, Sète, France
| | - John J Welch
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, United Kingdom.
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