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Kosicka E, Pieńkowska JR, Lesicki A. The complete mitochondrial genome of the terrestrial snail Monachacartusiana (O.F. Müller, 1774) (Gastropoda, Eupulmonata, Hygromiidae). Zookeys 2022; 1130:65-78. [PMID: 36761020 PMCID: PMC9836564 DOI: 10.3897/zookeys.1130.91325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 10/24/2022] [Indexed: 11/18/2022] Open
Abstract
The mitochondrial genome of Monachacartusiana is the first complete mitochondrial sequence described for the pulmonate snail genus Monacha and for the family Hygromiidae. The identified mitogenome has a length of 13,894 bp and encodes 13 proteins, 22 tRNAs, and two rRNAs. A phylogenetic analysis of available mitogenomes from representatives of helicoid families shows a sister group relationship of Hygromiidae and Geomitridae, which have been recently recognised as separate families.
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Affiliation(s)
- Ewa Kosicka
- Department of Cell Biology, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznańskiego 6, 61-614, Poznań, PolandAdam Mickiewicz UniversityPoznańPoland
| | - Joanna R. Pieńkowska
- Department of Cell Biology, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznańskiego 6, 61-614, Poznań, PolandAdam Mickiewicz UniversityPoznańPoland
| | - Andrzej Lesicki
- Department of Cell Biology, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznańskiego 6, 61-614, Poznań, PolandAdam Mickiewicz UniversityPoznańPoland
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Korábek O, Juřičková L, Petrusek A. Diversity of Land Snail Tribe Helicini (Gastropoda: Stylommatophora: Helicidae): Where Do We Stand after 20 Years of Sequencing Mitochondrial Markers? Diversity 2022; 14:24. [DOI: 10.3390/d14010024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Sequences of mitochondrial genes revolutionized the understanding of animal diversity and continue to be an important tool in biodiversity research. In the tribe Helicini, a prominent group of the western Palaearctic land snail fauna, mitochondrial data accumulating since the 2000s helped to newly delimit genera, inform species-level taxonomy and reconstruct past range dynamics. We combined the published data with own unpublished sequences and provide a detailed overview of what they revealed about the diversity of the group. The delimitation of Helix is revised by placing Helix godetiana back in the genus and new synonymies are suggested within the genera Codringtonia and Helix. The spatial distribution of intraspecific mitochondrial lineages of several species is shown for the first time. Comparisons between species reveal considerable variation in distribution patterns of intraspecific lineages, from broad postglacial distributions to regions with a fine-scale pattern of allopatric lineage replacement. To provide a baseline for further research and information for anyone re-using the data, we thoroughly discuss the gaps in the current dataset, focusing on both taxonomic and geographic coverage. Thanks to the wealth of data already amassed and the relative ease with which they can be obtained, mitochondrial sequences remain an important source of information on intraspecific diversity over large areas and taxa.
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Quenu M, Trewick SA, Daly EE, Morgan-Richards M. Generation of large mitochondrial and nuclear nucleotide sequences and phylogenetic analyses using high-throughput short-read datasets for endangered Placostylinae snails of the southwest Pacific. Molluscan Research 2021. [DOI: 10.1080/13235818.2021.1957552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Mathieu Quenu
- Wildlife & Ecology, School of Agriculture & Environment, College of Sciences, Massey University, Palmerston North, New Zealand
| | - Steven A. Trewick
- Wildlife & Ecology, School of Agriculture & Environment, College of Sciences, Massey University, Palmerston North, New Zealand
| | - Elizabeth E. Daly
- Wildlife & Ecology, School of Agriculture & Environment, College of Sciences, Massey University, Palmerston North, New Zealand
| | - Mary Morgan-Richards
- Wildlife & Ecology, School of Agriculture & Environment, College of Sciences, Massey University, Palmerston North, New Zealand
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Guzmán LB, Vogler RE, Beltramino AA. The mitochondrial genome of the semi-slug Omalonyx unguis (Gastropoda: Succineidae) and the phylogenetic relationships within Stylommatophora. PLoS One 2021; 16:e0253724. [PMID: 34170937 PMCID: PMC8232460 DOI: 10.1371/journal.pone.0253724] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 06/10/2021] [Indexed: 11/23/2022] Open
Abstract
Here we report the first complete mitochondrial genome of the semi-slug Omalonyx unguis (d’Orbigny, 1836) (Gastropoda: Succineidae). Sequencing was performed on a specimen from Argentina. Assembly was performed using Sanger data and Illumina next generation sequencing (NGS). The mitogenome was 13,984 bp in length and encoded the 37 typical Metazoan genes. A potential origin for mitochondrial DNA replication was found in a non-coding intergenic spacer (49 bp) located between cox3 and tRNA-Ile genes, and its secondary structure was characterized. Secondary structure models of the tRNA genes of O. unguis largely agreed with those proposed for other mollusks. Secondary structure models for the two rRNA genes were also obtained. To our knowledge, the 12S-rRNA model derived here is the first complete one available for mollusks. Phylogenetic analyses based on the mitogenomes of O. unguis and 37 other species of Stylommatophora were performed using amino acid sequences from the 13 protein-coding genes. Our results located Succineoidea as a sister group of Helicoidea + Urocoptoidea, similar to previous studies based on mitochondrial genomes. The gene arrangement of O. unguis was identical to that reported for another species of Succineoidea. The unique rearrangements observed for this group within Stylommatophora, may constitute synapomorphies for the superfamily.
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Affiliation(s)
- Leila Belén Guzmán
- Grupo de Investigación en Genética de Moluscos (GIGeMol), Instituto de Biología Subtropical (IBS), CONICET–UNaM, Posadas, Misiones, Argentina
- * E-mail: (LBG); (AAB)
| | - Roberto Eugenio Vogler
- Grupo de Investigación en Genética de Moluscos (GIGeMol), Instituto de Biología Subtropical (IBS), CONICET–UNaM, Posadas, Misiones, Argentina
| | - Ariel Aníbal Beltramino
- Grupo de Investigación en Genética de Moluscos (GIGeMol), Instituto de Biología Subtropical (IBS), CONICET–UNaM, Posadas, Misiones, Argentina
- * E-mail: (LBG); (AAB)
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Dayrat B, Goulding TC, Apte D, Aslam S, Bourke A, Comendador J, Khalil M, Ngô XQ, Tan SK, Tan SH. Systematic revision of the genus Peronia Fleming, 1822 (Gastropoda, Euthyneura, Pulmonata, Onchidiidae). Zookeys 2020; 972:1-224. [PMID: 33071542 PMCID: PMC7544732 DOI: 10.3897/zookeys.972.52853] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 08/13/2020] [Indexed: 11/12/2022] Open
Abstract
The genus Peronia Fleming, 1822 includes all the onchidiid slugs with dorsal gills. Its taxonomy is revised for the first time based on a large collection of fresh material from the entire Indo-West Pacific, from South Africa to Hawaii. Nine species are supported by mitochondrial (COI and 16S) and nuclear (ITS2 and 28S) sequences as well as comparative anatomy. All types available were examined and the nomenclatural status of each existing name in the genus is addressed. Of 31 Peronia species-group names available, 27 are regarded as invalid (twenty-one synonyms, sixteen of which are new, five nomina dubia, and one homonym), and four as valid: Peronia peronii (Cuvier, 1804), Peronia verruculata (Cuvier, 1830), Peronia platei (Hoffmann, 1928), and Peronia madagascariensis (Labbé, 1934a). Five new species names are created: P. griffithsi Dayrat & Goulding, sp. nov., P. okinawensis Dayrat & Goulding, sp. nov., P. setoensis Dayrat & Goulding, sp. nov., P. sydneyensis Dayrat & Goulding, sp. nov., and P. willani Dayrat & Goulding, sp. nov. Peronia species are cryptic externally but can be distinguished using internal characters, with the exception of P. platei and P. setoensis. The anatomy of most species is described in detail here for the first time. All the secondary literature is commented on and historical specimens from museum collections were also examined to better establish species distributions. The genus Peronia includes two species that are widespread across the Indo-West Pacific (P. verruculata and P. peronii) as well as endemic species: P. okinawensis and P. setoensis are endemic to Japan, and P. willani is endemic to Northern Territory, Australia. Many new geographical records are provided, as well as a key to the species using morphological traits.
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Affiliation(s)
- Benoît Dayrat
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Tricia C Goulding
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Deepak Apte
- Bombay Natural History Society, Hornbill House, Opp. Lion Gate, Shaheed Bhagat Singh Road, Mumbai 400 001, Maharashtra, India
| | - Sadar Aslam
- Centre of Excellence in Marine Biology, University of Karachi, Karachi 75270, Pakistan
| | - Adam Bourke
- College of Engineering, Information Technology and the Environment, Charles Darwin University, Ellengowan Dr, Casuarina, NT 0810, Australia
| | - Joseph Comendador
- National Museum of the Philippines, Taft Ave, Ermita, Manila, 1000, Metro Manila, Philippines
| | - Munawar Khalil
- Department of Marine Science, Universitas Malikussaleh, Reuleut Main Campus, Kecamatan Muara Batu, North Aceh, Aceh, 24355, Indonesia
| | - Xuân Quảng Ngô
- Institute of Tropical Biology, Vietnam Academy of Science and Technology, 85 Tran Quoc Toan Street, District 3, Ho Chi Minh City, Vietnam.,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Siong Kiat Tan
- Lee Kong Chian Natural History Museum, 2 Conservatory Dr, National University of Singapore, 117377, Singapore
| | - Shau Hwai Tan
- Centre for Marine and Coastal Studies, Universiti Sains Malaysia, 11800, Minden Penang, Malaysia.,Marine Science Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800, Minden Penang, Malaysia
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Klein AH, Ballard KR, Storey KB, Motti CA, Zhao M, Cummins SF. Multi-omics investigations within the Phylum Mollusca, Class Gastropoda: from ecological application to breakthrough phylogenomic studies. Brief Funct Genomics 2020; 18:377-394. [PMID: 31609407 DOI: 10.1093/bfgp/elz017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 07/06/2019] [Accepted: 07/15/2019] [Indexed: 12/22/2022] Open
Abstract
Gastropods are the largest and most diverse class of mollusc and include species that are well studied within the areas of taxonomy, aquaculture, biomineralization, ecology, microbiome and health. Gastropod research has been expanding since the mid-2000s, largely due to large-scale data integration from next-generation sequencing and mass spectrometry in which transcripts, proteins and metabolites can be readily explored systematically. Correspondingly, the huge data added a great deal of complexity for data organization, visualization and interpretation. Here, we reviewed the recent advances involving gastropod omics ('gastropodomics') research from hundreds of publications and online genomics databases. By summarizing the current publicly available data, we present an insight for the design of useful data integrating tools and strategies for comparative omics studies in the future. Additionally, we discuss the future of omics applications in aquaculture, natural pharmaceutical biodiscovery and pest management, as well as to monitor the impact of environmental stressors.
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Affiliation(s)
- Anne H Klein
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Kaylene R Ballard
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Kenneth B Storey
- Institute of Biochemistry & Department of Biology, Carleton University, Ottawa, ON, Canada K1S 5B6
| | - Cherie A Motti
- Australian Institute of Marine Science (AIMS), Cape Ferguson, Townsville Queensland 4810, Australia
| | - Min Zhao
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Scott F Cummins
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
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8
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Doğan Ö, Schrödl M, Chen Z. The complete mitogenome of Arion vulgaris Moquin-Tandon, 1855 (Gastropoda: Stylommatophora): mitochondrial genome architecture, evolution and phylogenetic considerations within Stylommatophora. PeerJ 2020; 8:e8603. [PMID: 32117634 PMCID: PMC7039129 DOI: 10.7717/peerj.8603] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 01/19/2020] [Indexed: 11/27/2022] Open
Abstract
Stylommatophora is one of the most speciose orders of Gastropoda, including terrestrial snails and slugs, some of which are economically important as human food, agricultural pests, vectors of parasites or due to invasiveness. Despite their great diversity and relevance, the internal phylogeny of Stylommatophora has been debated. To date, only 34 stylommatophoran mitogenomes were sequenced. Here, the complete mitogenome of an invasive pest slug, Arion vulgaris Moquin-Tandon, 1855 (Stylommatophora: Arionidae), was sequenced using next generation sequencing, analysed and compared with other stylommatophorans. The mitogenome of A. vulgaris measures 14,547 bp and contains 13 protein-coding, two rRNA, 22 tRNA genes, and one control region, with an A + T content of 70.20%. All protein coding genes (PCGs) are initiated with ATN codons except for COX1, ND5 and ATP8 and all are ended with TAR or T-stop codons. All tRNAs were folded into a clover-leaf secondary structure except for trnC and trnS1 (AGN). Phylogenetic analyses confirmed the position of A. vulgaris within the superfamily Arionoidea, recovered a sister group relationship between Arionoidea and Orthalicoidea, and supported monophyly of all currently recognized superfamilies within Stylommatophora except for the superfamily Helicoidea. Initial diversification time of the Stylommatophora was estimated as 138.55 million years ago corresponding to Early Cretaceous. The divergence time of A. vulgaris and Arion rufus (Linnaeus, 1758) was estimated as 15.24 million years ago corresponding to one of Earth's most recent, global warming events, the Mid-Miocene Climatic Optimum. Furthermore, selection analyses were performed to investigate the role of different selective forces shaping stylommatophoran mitogenomes. Although purifying selection is the predominant selective force shaping stylommatophoran mitogenomes, six genes (ATP8, COX1, COX3, ND3, ND4 and ND6) detected by the branch-specific aBSREL approach and three genes (ATP8, CYTB and ND4L) detected by codon-based BEB, FUBAR and MEME approaches were exposed to diversifying selection. The positively selected substitutions at the mitochondrial PCGs of stylommatophoran species seems to be adaptive to environmental conditions and affecting mitochondrial ATP production or protection from reactive oxygen species effects. Comparative analysis of stylommatophoran mitogenome rearrangements using MLGO revealed conservatism in Stylommatophora; exceptions refer to potential apomorphies for several clades including rearranged orders of trnW-trnY and of trnE-trnQ-rrnS-trnM-trnL2-ATP8-trnN-ATP6-trnR clusters for the genus Arion. Generally, tRNA genes tend to be rearranged and tandem duplication random loss, transitions and inversions are the most basic mechanisms shaping stylommatophoran mitogenomes.
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Affiliation(s)
- Özgül Doğan
- Department of Molecular Biology and Genetics, Faculty of Science, Sivas Cumhuriyet University, Sivas, Turkey
- SNSB-Bavarian State Collection of Zoology, Munich, Germany
| | - Michael Schrödl
- SNSB-Bavarian State Collection of Zoology, Munich, Germany
- Department Biology II, Ludwig-Maximilians-Universität, Munich, Germany
- GeoBio-Center LMU, Munich, Germany
| | - Zeyuan Chen
- SNSB-Bavarian State Collection of Zoology, Munich, Germany
- Department Biology II, Ludwig-Maximilians-Universität, Munich, Germany
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Ayyagari VS, Sreerama K. Molecular phylogeny and evolution of Pulmonata (Mollusca: Gastropoda) on the basis of mitochondrial (16S, COI) and nuclear markers (18S, 28S): an overview. J Genet 2020. [DOI: 10.1007/s12041-020-1177-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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10
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Korábek O. On Helix grisea Linnaeus, 1758 and the Helix species described by Carl Linnaeus and Otto Friedrich Müller. Malacol Bohemoslov 2020. [DOI: 10.5817/mab2020-19-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Helix grisea was described by Linnaeus in 1758, and its identity has been doubtful ever since. The name features in the early taxonomic history of some other species of Helix sensu lato. Here I provide a summary of the history of its use. Mostly, the name was applied for the widespread species now accepted as Cornu aspersum (O. F. Müller, 1774), while a few authors used it for Helix cincta O. F. Müller, 1774. Neither usage is in line with the Linnaeus' account. Based on a figure to which Linnaeus referred, I propose that the name originally applied to a species now known as Helix lucorum Linnaeus, 1758 and as the first reviser, I give precedence to H. lucorum over H. grisea. In respect to C. aspersum, H. grisea cannot take precedence because of reversal of precedence according to Art. 23.9, and is pronounced a nomen oblitum. The case of H. grisea illustrates the importance of Müller's work for the taxonomy of the genus. In this respect it is regrettable that some of his species, including C. aspersum, lack a known and well documented type specimens.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Orábek O, Petrusek A, Rovatsos M. The complete mitogenome of Helixpomatia and the basal phylogeny of Helicinae (Gastropoda, Stylommatophora, Helicidae). Zookeys 2019; 827:19-30. [PMID: 31114424 PMCID: PMC6472302 DOI: 10.3897/zookeys.827.33057] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 01/27/2019] [Indexed: 11/23/2022] Open
Abstract
A complete mitochondrial genome of the Roman snail Helixpomatia Linnaeus, 1758 has been sequenced. The length and gene order correspond to that of other available helicid mitogenomes. We used the mitogenome sequence to reappraise the relationships among the four presumed principal groups of the helicid subfamily Helicinae. The results support the idea that the subfamily is divided between two western Palaearctic diversification centres: Iberian Peninsula and western Maghreb in the west, and Anatolia, the Aegean and Caucasus in the east. One group, the tribe Helicini, diversified in the east and the remaining three currently recognised tribes in the west. However, the exact relationships among lineages of the non-Helicini tribes could not be resolved.
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Affiliation(s)
- Ondřej Orábek
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, CZ-12844 Prague 2, Czechia Charles University Prague Czech Republic
| | - Adam Petrusek
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, CZ-12844 Prague 2, Czechia Charles University Prague Czech Republic
| | - Michail Rovatsos
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, CZ-12844 Prague 2, Czechia Charles University Prague Czech Republic
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Affiliation(s)
| | - E. Duijm
- Naturalis Biodiversity Center, Leiden, The Netherlands
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Gaitán-Espitia JD, González-Wevar CA, Poulin E, Cardenas L. Antarctic and sub-Antarctic Nacella limpets reveal novel evolutionary characteristics of mitochondrial genomes in Patellogastropoda. Mol Phylogenet Evol 2019; 131:1-7. [PMID: 30395937 DOI: 10.1016/j.ympev.2018.10.036] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 07/23/2018] [Accepted: 10/30/2018] [Indexed: 11/22/2022]
Abstract
Mitochondrial genomes (mitogenomes) provide valuable phylogenetic information and genome-level characters that are useful in resolving evolutionary relationships within major lineages of gastropods. However, for more than one decade, these relationships and the phylogenetic position of Patellogastropoda have been inferred based on the genomic architecture as well as the nucleotide and protein sequences of a single representative, the limpet Lottia digitalis. This mitogenome exhibits extensive rearrangements and several repetitive units that may not represent universal features for Patellogastropoda. Here, we sequenced the complete mitogenomes of three Nacella limpets, providing new insights into the dynamics of gene order and phylogenetic relationships of Patellogastropoda. Comparative analyses revealed novel gene rearrangements in Gastropoda, characterised by two main translocations that affect the KARNI and the MYCWQ clusters in Nacella limpets. Our phylogenetic reconstructions using combined sequence datasets of 13 mitochondrial protein-coding genes and two rRNAs, recovered Patellogastropoda, and Gastropoda in general, as non-monophyletic. These findings could be related to the long-branch attraction tendency of these groups, and/or taxon sampling bias. In our novel mitogenome-based phylogenetic hypothesis, L. digitalis is placed in a sister position to Bivalvia and Heterobranchia, whereas Nacella limpets are placed sister to a clade containing Caenogastropoda + Neritimorpha and Vetigastropoda + Neomphalina.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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17
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Raheem D, Breugelmans K, Wade C, Naggs F, Backeljau T. Exploring the shell-based taxonomy of the Sri Lankan land snail Corilla H. and A. Adams, 1855 (Pulmonata: Corillidae) using mitochondrial DNA. Mol Phylogenet Evol 2017; 107:609-18. [DOI: 10.1016/j.ympev.2016.12.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 12/08/2016] [Accepted: 12/20/2016] [Indexed: 11/22/2022]
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Minton RL, Cruz MAM, Farman ML, Perez KE. Two complete mitochondrial genomes from Praticolella mexicana Perez, 2011 (Polygyridae) and gene order evolution in Helicoidea (Mollusca, Gastropoda). Zookeys 2016:137-154. [PMID: 27833437 PMCID: PMC5096375 DOI: 10.3897/zookeys.626.9633] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 10/16/2016] [Indexed: 01/03/2023] Open
Abstract
Helicoidea is a diverse group of land snails with a global distribution. While much is known regarding the relationships of helicoid taxa, comparatively little is known about the evolution of the mitochondrial genome in the superfamily. We sequenced two complete mitochondrial genomes from Praticolellamexicana Perez, 2011 representing the first such data from the helicoid family Polygyridae, and used them in an evolutionary analysis of mitogenomic gene order. We found the mitochondrial genome of Praticolellamexicana to be 14,008 bp in size, possessing the typical 37 metazoan genes. Multiple alternate stop codons are used, as are incomplete stop codons. Mitogenome size and nucleotide content is consistent with other helicoid species. Our analysis of gene order suggested that Helicoidea has undergone four mitochondrial rearrangements in the past. Two rearrangements were limited to tRNA genes only, and two involved protein coding genes.
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Affiliation(s)
- Russell L Minton
- School of Science and Computer Engineering, University of Houston Clear Lake, 2700 Bay Area Boulevard MC 39, Houston, Texas 77058 USA
| | - Marco A Martinez Cruz
- Department of Biology, University of Texas Rio Grande Valley, 1201 West University Drive, Edinburg, Texas 78539 USA
| | - Mark L Farman
- UK Healthcare Genomics, 225 Plant Science Building, 1405 Veteran's Drive, University of Kentucky, Lexington, Kentucky 40546 USA
| | - Kathryn E Perez
- Department of Biology, University of Texas Rio Grande Valley, 1201 West University Drive, Edinburg, Texas 78539 USA
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Price MR, Forsman ZH, Knapp IS, Toonen RJ, Hadfield MG. The complete mitochondrial genome of Achatinella sowerbyana (Gastropoda: Pulmonata: Stylommatophora: Achatinellidae). Mitochondrial DNA B Resour 2016; 1:666-668. [PMID: 33473590 PMCID: PMC7800958 DOI: 10.1080/23802359.2016.1219631] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 07/15/2016] [Accepted: 07/29/2016] [Indexed: 11/25/2022] Open
Abstract
In this study, we report the complete mitochondrial genome sequence of Achatinella sowerbyana, an endangered Hawaiian tree snail. The mitogenome is 15,374 bp in length and has a base composition of A (36.4%), T (42.7%), C (9.1%), and G (11.8%). Similar to other pulmonates, it contains 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. The gene order is the same as its sister species, A. mustelina. To our knowledge, this is the second mitochondrial genome sequenced within the superfamily Achatinelloidea, and will aid in the examination of the genus Achatinella, part of a spectacular radiation in the Hawaiian Islands.
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Affiliation(s)
- Melissa R. Price
- Kewalo Marine Laboratory, Pacific Biosciences Research Center, University of Hawai‘i at Mānoa, Honolulu, HI, USA
- Department of Natural Resources and Environmental Management, University of Hawai‘i at Mānoa, Honolulu, HI, USA
| | - Zac H. Forsman
- Hawai‘i Institute of Marine Biology, University of Hawai‘i at Mānoa, Kane‘ohe, HI, USA
| | - Ingrid S. Knapp
- Hawai‘i Institute of Marine Biology, University of Hawai‘i at Mānoa, Kane‘ohe, HI, USA
| | - Robert J. Toonen
- Hawai‘i Institute of Marine Biology, University of Hawai‘i at Mānoa, Kane‘ohe, HI, USA
| | - Michael G. Hadfield
- Kewalo Marine Laboratory, Pacific Biosciences Research Center, University of Hawai‘i at Mānoa, Honolulu, HI, USA
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21
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Gaitán-Espitia JD, Quintero-Galvis JF, Mesas A, D'Elía G. Mitogenomics of southern hemisphere blue mussels (Bivalvia: Pteriomorphia): Insights into the evolutionary characteristics of the Mytilus edulis complex. Sci Rep 2016; 6:26853. [PMID: 27241855 PMCID: PMC4886515 DOI: 10.1038/srep26853] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 04/26/2016] [Indexed: 11/09/2022] Open
Abstract
Marine blue mussels (Mytilus spp.) are widespread species that exhibit an antitropical distribution with five species occurring in the Northern Hemisphere (M. trossulus, M. edulis, M. galloprovincialis, M. californianus and M. coruscus) and three in the Southern Hemisphere (M. galloprovincialis, M. chilensis and M. platensis). Species limits in this group remain controversial, in particular for those forms that live in South America. Here we investigated structural characteristics of marine mussels mitogenomes, based on published F mtDNA sequences of Northern Hemisphere species and two newly sequenced South American genomes, one from the Atlantic M. platensis and another from the Pacific M. chilensis. These mitogenomes exhibited similar architecture to those of other genomes of Mytilus, including the presence of the Atp8 gene, which is missing in most of the other bivalves. Our evolutionary analysis of mitochondrial genes indicates that purifying selection is the predominant force shaping the evolution of the coding genes. Results of our phylogenetic analyses supported the monophyly of Pteriomorphia and fully resolved the phylogenetic relationships among its five orders. Finally, the low genetic divergence of specimens assigned to M. chilensis and M. platensis suggests that these South American marine mussels represent conspecific variants rather than distinct species.
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Affiliation(s)
- Juan Diego Gaitán-Espitia
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Casilla 567 Valdivia, Chile.,CSIRO Oceans and Atmosphere, GPO Box 1538, Hobart 7001, TAS, Australia
| | - Julian F Quintero-Galvis
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Casilla 567 Valdivia, Chile.,Programa de Doctorado en Ciencias mención Ecología y Evolución, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Andres Mesas
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Casilla 567 Valdivia, Chile.,Programa de Doctorado en Ciencias mención Ecología y Evolución, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Guillermo D'Elía
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Casilla 567 Valdivia, Chile
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22
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Gaitán-Espitia JD, Solano-Iguaran JJ, Tejada-Martinez D, Quintero-Galvis JF. Mitogenomics of electric rays: evolutionary considerations within Torpediniformes (Batoidea; Chondrichthyes). Zool J Linn Soc 2016. [DOI: 10.1111/zoj.12417] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Juan Diego Gaitán-Espitia
- Instituto de Ciencias Ambientales y Evolutivas; Universidad Austral de Chile; Casilla 567 Valdivia Chile
- CSIRO Oceans & Atmosphere; GPO Box 1538 Hobart 7001 TAS Australia
| | - Jaiber J. Solano-Iguaran
- Instituto de Ciencias Ambientales y Evolutivas; Universidad Austral de Chile; Casilla 567 Valdivia Chile
- Programa de Magister en Ciencias mención Genética; Facultad de Ciencias; Universidad Austral de Chile; Valdivia Chile
| | - Daniela Tejada-Martinez
- Instituto de Ciencias Ambientales y Evolutivas; Universidad Austral de Chile; Casilla 567 Valdivia Chile
- Programa de Doctorado en Ciencias mención Ecología y Evolución; Facultad de Ciencias; Universidad Austral de Chile; Valdivia Chile
| | - Julian F. Quintero-Galvis
- Instituto de Ciencias Ambientales y Evolutivas; Universidad Austral de Chile; Casilla 567 Valdivia Chile
- Programa de Magister en Ciencias mención Genética; Facultad de Ciencias; Universidad Austral de Chile; Valdivia Chile
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Price MR, Forsman ZH, Knapp I, Hadfield MG, Toonen RJ. The complete mitochondrial genome of Achatinella mustelina (Gastropoda: Pulmonata: Stylommatophora). Mitochondrial DNA B Resour 2016; 1:175-177. [PMID: 33644335 PMCID: PMC7871653 DOI: 10.1080/23802359.2016.1149787] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this study, we report the complete mitochondrial genome sequence of Achatinella mustelina, an endangered Hawaiian tree snail. The mitogenome is 16 323 bp in length and has a base composition of A (34.7%), T (42.6%), C (12.7%) and G (10.0%). Similar to other Pulmonates, it contains 13 protein-coding genes, 2 rRNA genes and 22 tRNA genes. To our knowledge, this is the first mitochondrial genome sequenced within the Achatinelloidea superfamily, which contains a high number of endangered species. As such, this mitogenome will be useful in conservation genetics studies.
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Affiliation(s)
- Melissa R Price
- Kewalo Marine Laboratory, Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, HI, USA.,Department of Natural Resources and Environmental Management, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - Zac H Forsman
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kane'ohe, HI, USA
| | - Ingrid Knapp
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kane'ohe, HI, USA
| | - Michael G Hadfield
- Kewalo Marine Laboratory, Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - Robert J Toonen
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kane'ohe, HI, USA
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Cabrera-Brandt MA, Gaitán-Espitia JD. Phylogenetic analysis of the complete mitogenome sequence of the raspberry weevil, Aegorhinus superciliosus (Coleoptera: Curculionidae), supports monophyly of the tribe Aterpini. Gene 2015; 571:205-11. [PMID: 26117169 DOI: 10.1016/j.gene.2015.06.059] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 05/29/2015] [Accepted: 06/22/2015] [Indexed: 11/29/2022]
Abstract
The superfamily Curculionoidea is one of the most diverse groups of insects in the world, including many species which are crop pests. Within this group, the native raspberry weevil, Aegorhinus superciliosus (Guérin, 1830), is an important pest in blueberry and raspberry fields in southern South America. Using a 454 sequencing approach, we sequenced and annotated the mitogenome of A. superciliosus, it, providing the first such information for any species in the tribe Aterpini, subfamily Cyclominae. The assembled mitogenome is a circular DNA molecule 15,121bp in length containing all 37 genes normally found in metazoans. Mitogenome organization and transcriptional orientation in A. superciliosus showed the same pattern that characterizes the suborder Polyphaga. Bayesian and Maximum Likelihood phylogenetic analyses supported the monophyly of the tribe Aterpini and the subfamily Cyclominae, recovering this clade in a sister group relationship with Entiminae and Hyperinae. The monophyly of these three subfamilies defines a critical transition to an ectophagous lifestyle in the larvae, from an ancestrally endophagous larval lifestyle in all other lineages. The sequenced mitogenome of A. superciliosus can provide basic data for future studies investigating population history, molecular systematics, stress ecophysiology and phylogeography.
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Affiliation(s)
- Marco A Cabrera-Brandt
- Departamento de Producción Agrícola, Facultad de Ciencias Agrarias, Universidad de Talca, Casilla 747, Talca, Chile; Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Casilla 567, Valdivia, Chile.
| | - Juan D Gaitán-Espitia
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Casilla 567, Valdivia, Chile; CSIRO Oceans and Atmosphere, GPO Box 1538, Hobart 7001, TAS, Australia
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Huang CW, Lin SM, Wu WL. Mitochondrial genome sequences of landsnails Aegista diversifamilia and Dolicheulota formosensis (Gastropoda: Pulmonata: Stylommatophora). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2793-5. [PMID: 26094989 DOI: 10.3109/19401736.2015.1053070] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The first mitochondrial genome sequences of Aegista and Dolicheulota belonging to Bradybaenidae are described in this report. Mitogenomic sequences were generated from Illumina paired-end sequencing. The complete mitogenome of Aegista diversifamilia was 14,039 bp in length and nearly complete mitogenome of Dolicheulota formosensis was 14,237 bp. Both mitogenomes consisted of 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 22 transfer RNA genes. Most genes were overlapped with neighboring genes that the overlapping regions ranged from 2 to 64 bp in A. diversifamilia and from 1 to 45 bp in D. formosensis. Novel gene arrangement, tRNA-Tyr-ND3-tRNA-Trp, was identified in A. diversifamilia, whereas D. formosensis showed identical gene order to other Bradybaenidae mitogenomes. Maximum likelihood phylogenetic tree suggested Aegista as a sister clade to Euhadra and Dolicheulota. Bradybaenidae is monophyly sister clade to Camaenidae.
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Affiliation(s)
- Chih-Wei Huang
- a Department of Life Science , National Taiwan Normal University , Taipei, Taiwan , ROC and
| | - Si-Min Lin
- a Department of Life Science , National Taiwan Normal University , Taipei, Taiwan , ROC and
| | - Wen-Lung Wu
- b Biodiversity Research Center, Academia Sinica , Nankang Dist., Taipei, Taiwan , ROC
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Sevigny JL, Kirouac LE, Thomas WK, Ramsdell JS, Lawlor KE, Sharifi O, Grewal S, Baysdorfer C, Curr K, Naimie AA, Okamoto K, Murray JA, Newcomb JM. The Mitochondrial Genomes of the Nudibranch Mollusks, Melibe leonina and Tritonia diomedea, and Their Impact on Gastropod Phylogeny. PLoS One 2015; 10:e0127519. [PMID: 25996944 PMCID: PMC4440745 DOI: 10.1371/journal.pone.0127519] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 04/15/2015] [Indexed: 01/28/2023] Open
Abstract
The phylogenetic relationships among certain groups of gastropods have remained unresolved in recent studies, especially in the diverse subclass Opisthobranchia, where nudibranchs have been poorly represented. Here we present the complete mitochondrial genomes of Melibe leonina and Tritonia diomedea (more recently named T. tetraquetra), two nudibranchs from the unrepresented Cladobranchia group, and report on the resulting phylogenetic analyses. Both genomes coded for the typical thirteen protein-coding genes, twenty-two transfer RNAs, and two ribosomal RNAs seen in other species. The twelve-nucleotide deletion previously reported for the cytochrome oxidase 1 gene in several other Melibe species was further clarified as three separate deletion events. These deletions were not present in any opisthobranchs examined in our study, including the newly sequenced M. leonina or T. diomedea, suggesting that these previously reported deletions may represent more recently divergent taxa. Analysis of the secondary structures for all twenty-two tRNAs of both M. leonina and T. diomedea indicated truncated d arms for the two serine tRNAs, as seen in some other heterobranchs. In addition, the serine 1 tRNA in T. diomedea contained an anticodon not yet reported in any other gastropod. For phylogenetic analysis, we used the thirteen protein-coding genes from the mitochondrial genomes of M. leonina, T. diomedea, and seventy-one other gastropods. Phylogenetic analyses were performed for both the class Gastropoda and the subclass Opisthobranchia. Both Bayesian and maximum likelihood analyses resulted in similar tree topologies. In the Opisthobranchia, the five orders represented in our study were monophyletic (Anaspidea, Cephalaspidea, Notaspidea, Nudibranchia, Sacoglossa). In Gastropoda, two of the three traditional subclasses, Opisthobranchia and Pulmonata, were not monophyletic. In contrast, four of the more recently named gastropod clades (Vetigastropoda, Neritimorpha, Caenogastropoda, and Heterobranchia) were all monophyletic, and thus appear to be better classifications for this diverse group.
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Affiliation(s)
- Joseph L. Sevigny
- Department of Biology and Health Science, New England College, Henniker, New Hampshire, United States of America
| | - Lauren E. Kirouac
- Department of Biology and Health Science, New England College, Henniker, New Hampshire, United States of America
| | - William Kelley Thomas
- Department of Biological Sciences, University of New Hampshire, Durham, New Hampshire, United States of America
| | - Jordan S. Ramsdell
- Department of Biological Sciences, University of New Hampshire, Durham, New Hampshire, United States of America
| | - Kayla E. Lawlor
- Department of Biology and Health Science, New England College, Henniker, New Hampshire, United States of America
| | - Osman Sharifi
- Department of Biological Sciences, California State University, East Bay, Hayward, California, United States of America
| | - Simarvir Grewal
- Department of Biological Sciences, California State University, East Bay, Hayward, California, United States of America
| | - Christopher Baysdorfer
- Department of Biological Sciences, California State University, East Bay, Hayward, California, United States of America
| | - Kenneth Curr
- Department of Biological Sciences, California State University, East Bay, Hayward, California, United States of America
| | - Amanda A. Naimie
- Department of Biology and Health Science, New England College, Henniker, New Hampshire, United States of America
| | - Kazufusa Okamoto
- Department of Biological Sciences, University of New Hampshire, Durham, New Hampshire, United States of America
| | - James A. Murray
- Department of Biological Sciences, California State University, East Bay, Hayward, California, United States of America
| | - James M. Newcomb
- Department of Biology and Health Science, New England College, Henniker, New Hampshire, United States of America
- * E-mail:
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Cea G, Gaitán-espitia JD, Cárdenas L. Complete mitogenome of the edible sea urchin Loxechinus albus: genetic structure and comparative genomics within Echinozoa. Mol Biol Rep 2015; 42:1081-9. [DOI: 10.1007/s11033-014-3847-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 11/25/2014] [Indexed: 10/24/2022]
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Deng PJ, Wang WM, Huang XC, Wu XP, Xie GL, Ouyang S. The complete mitochondrial genome of Chinese land snail Mastigeulota kiangsinensis (Gastropoda: Pulmonata: Bradybaenidae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:1441-2. [PMID: 25185698 DOI: 10.3109/19401736.2014.953083] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Mastigeulota kiangsinensis is an endemic and widespread land snail in China. The complete mitochondrial genome of M. kiangsinensis was first determined using long PCR reactions and primer walking method (accession number KM083123). The genome has a length of 14,029 bp, containing 37 typical mitochondrial genes (13 protein-coding genes, 22 tRNA genes and 2 rRNA genes). The base composition of the whole heavy strand is A 29.48%, T 37.92%, C 14.38% and G 18.22%. Gene order of M. kiangsinensis is identical to Euhadra herklotsi, but gene rearrangements are found compared with other mitochondrial genomes described in Stylommatophora. tRNA(Thr) is located in COIII, which has not been found in other helicoids so far. This new complete mitochondrial genome can be the basic data for further studies on mitogenome comparison, molecular taxonomy and phylogenetic analysis in land snails and Molluscs at large.
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Affiliation(s)
- Pu-Juan Deng
- a School of Life Sciences, Nanchang University , Nanchang , People's Republic of China and
| | - Wen-Min Wang
- a School of Life Sciences, Nanchang University , Nanchang , People's Republic of China and
| | - Xiao-Chen Huang
- a School of Life Sciences, Nanchang University , Nanchang , People's Republic of China and.,b Center for Watershed Ecology, Institute of Life Science, Nanchang University , Nanchang , People's Republic of China
| | - Xiao-Ping Wu
- a School of Life Sciences, Nanchang University , Nanchang , People's Republic of China and.,b Center for Watershed Ecology, Institute of Life Science, Nanchang University , Nanchang , People's Republic of China
| | - Guang-Long Xie
- a School of Life Sciences, Nanchang University , Nanchang , People's Republic of China and
| | - Shan Ouyang
- a School of Life Sciences, Nanchang University , Nanchang , People's Republic of China and
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Gaitán-Espitia JD, Belén Arias M, Lardies MA, Nespolo RF. Variation in thermal sensitivity and thermal tolerances in an invasive species across a climatic gradient: lessons from the land snail Cornu aspersum. PLoS One 2013; 8:e70662. [PMID: 23940617 PMCID: PMC3734266 DOI: 10.1371/journal.pone.0070662] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 06/21/2013] [Indexed: 11/18/2022] Open
Abstract
The ability of organisms to perform at different temperatures could be described by a continuous nonlinear reaction norm (i.e., thermal performance curve, TPC), in which the phenotypic trait value varies as a function of temperature. Almost any shift in the parameters of this performance curve could highlight the direct effect of temperature on organism fitness, providing a powerful framework for testing thermal adaptation hypotheses. Inter-and intraspecific differences in this performance curve are also reflected in thermal tolerances limits (e.g., critical and lethal limits), influencing the biogeographic patterns of species' distribution. Within this context, here we investigated the intraspecific variation in thermal sensitivities and thermal tolerances in three populations of the invasive snail Cornu aspersum across a geographical gradient, characterized by different climatic conditions. Thus, we examined population differentiation in the TPCs, thermal-coma recovery times, expression of heat-shock proteins and standard metabolic rate (i.e., energetic costs of physiological differentiation). We tested two competing hypotheses regarding thermal adaptation (the "hotter is better" and the generalist-specialist trade-offs). Our results show that the differences in thermal sensitivity among populations of C. aspersum follow a latitudinal pattern, which is likely the result of a combination of thermodynamic constraints ("hotter is better") and thermal adaptations to their local environments (generalist-specialist trade-offs). This finding is also consistent with some thermal tolerance indices such as the Heat-Shock Protein Response and the recovery time from chill-coma. However, mixed responses in the evaluated traits suggest that thermal adaptation in this species is not complete, as we were not able to detect any differences in neither energetic costs of physiological differentiation among populations, nor in the heat-coma recovery.
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