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Li T, Zhong S, Wen B, Jiang L, Zhang M. Comparative Analysis of Complete Mitochondrial Genomes of Five Chromodorididae Species (Nudibranchia:Doridina). Biochem Genet 2024:10.1007/s10528-024-10878-3. [PMID: 38954214 DOI: 10.1007/s10528-024-10878-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 06/24/2024] [Indexed: 07/04/2024]
Abstract
Mitochondrial genome is an important molecular marker for exploring the phylogenetic relationships of species and revealing molecular evolution. In the present study, 5 mitogenomes of Chromodorididae (Chromodoris lochi, Chromodoris colemani, Chromodoris elisabethina, Chromodoris annae and Hypselodoris whitei) were systemically investigated. The lengths of the mitogenomes sequences were 14248 bp, 14257 bp, 14252 bp, 14254 bp and 14856 bp, respectively. Most protein-coding genes (PCGs) were initiated with the common ATG codon and terminated with the TAA and TAG. We calculated Ka/Ks values for all 13 PCGs of Chromodorididae species, all ratios were less than 1, indicating selection by purification. Phylogenetic relationships were constructed by Bayesian inference (BI) and maximum likelihood (ML) methods based on all complete genomes of 50 species, primarily from the family Chromodorididae (Doridina) and 2 outgroups. This phylogenetic tree provided further additional references for the classification of the suborder Doridina. Gene rearrangement suggested a more conserved pattern of gene sequences in the superfamily Chromodoridoidea. These results and newly sequenced will contribute to a better understanding of Chromodorididae and provide reference for further phylogenetic studies.
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Affiliation(s)
- Tianyu Li
- National Engineering Research Center of Marine Facilities Aquaculture, College of Fisheries, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Shengping Zhong
- Guangxi Key Laboratory of Marine Drugs, Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, 530200, China
| | - Beihua Wen
- School of Marine Sciences, School of Resources, Environment and Materials, Guangxi University, Nanning, 530004, China
| | - Lihua Jiang
- National Engineering Research Center of Marine Facilities Aquaculture, College of Fisheries, Zhejiang Ocean University, Zhoushan, 316022, China.
| | - Man Zhang
- School of Marine Sciences, School of Resources, Environment and Materials, Guangxi University, Nanning, 530004, China.
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Fuchs LIR, Knobloch J, Wiesenthal AA, Fuss J, Franzenburg S, Torres Oliva M, Müller C, Wheat CW, Hildebrandt JP. A draft genome of the neritid snail Theodoxus fluviatilis. G3 (BETHESDA, MD.) 2024; 14:jkad282. [PMID: 38069680 PMCID: PMC10917513 DOI: 10.1093/g3journal/jkad282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 12/01/2023] [Indexed: 03/08/2024]
Abstract
The neritid snail Theodoxus fluviatilis is found across habitats differing in salinity, from shallow waters along the coast of the Baltic Sea to lakes throughout Europe. Living close to the water surface makes this species vulnerable to changes in salinity in their natural habitat, and the lack of a free-swimming larval stage limits this species' dispersal. Together, these factors have resulted in a patchy distribution of quite isolated populations differing in their salinity tolerances. In preparation for investigating the mechanisms underlying the physiological differences in osmoregulation between populations that cannot be explained solely by phenotypic plasticity, we present here an annotated draft genome assembly for T. fluviatilis, generated using PacBio long reads, Illumina short reads, and transcriptomic data. While the total assembly size (1045 kb) is similar to those of related species, it remains highly fragmented (N scaffolds = 35,695; N50 = 74 kb) though moderately high in complete gene content (BUSCO single copy complete: 74.3%, duplicate: 2.6%, fragmented: 10.6%, missing: 12.5% using metazoa n = 954). Nevertheless, we were able to generate gene annotations of 21,220 protein-coding genes (BUSCO single copy complete: 65.1%, duplicate: 16.7%, fragmented: 9.1%, missing: 9.1% using metazoa n = 954). Not only will this genome facilitate comparative evolutionary studies across Gastropoda, as this is the first genome assembly for the basal snail family Neritidae, it will also greatly facilitate the study of salinity tolerance in this species. Additionally, we discuss the challenges of working with a species where high molecular weight DNA isolation is very difficult.
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Affiliation(s)
- Laura Iris Regina Fuchs
- Animal Physiology and Biochemistry, Zoological Institute and Museum, University of Greifswald, Felix Hausdorff-Strasse 1, D - 17489 Greifswald, Germany
| | - Jan Knobloch
- Animal Physiology and Biochemistry, Zoological Institute and Museum, University of Greifswald, Felix Hausdorff-Strasse 1, D - 17489 Greifswald, Germany
| | - Amanda Alice Wiesenthal
- Animal Physiology and Biochemistry, Zoological Institute and Museum, University of Greifswald, Felix Hausdorff-Strasse 1, D - 17489 Greifswald, Germany
- Marine Biology, University of Rostock, Albert-Einstein-Straße 3, D - 18059 Rostock, Germany
| | - Janina Fuss
- Institute of Clinical Molecular Biology, Kiel University (CAU), University Hospital Schleswig Holstein, Rosalind-Franklin-Strasse 12, D - 24105 Kiel, Germany
| | - Soeren Franzenburg
- Institute of Clinical Molecular Biology, Kiel University (CAU), University Hospital Schleswig Holstein, Rosalind-Franklin-Strasse 12, D - 24105 Kiel, Germany
| | - Montserrat Torres Oliva
- Institute of Clinical Molecular Biology, Kiel University (CAU), University Hospital Schleswig Holstein, Rosalind-Franklin-Strasse 12, D - 24105 Kiel, Germany
| | - Christian Müller
- Animal Physiology and Biochemistry, Zoological Institute and Museum, University of Greifswald, Felix Hausdorff-Strasse 1, D - 17489 Greifswald, Germany
| | - Christopher W Wheat
- Department of Zoology, Stockholm University, Svante Arrheniusväg 18 B, S-10691 Stockholm, Sweden
| | - Jan-Peter Hildebrandt
- Animal Physiology and Biochemistry, Zoological Institute and Museum, University of Greifswald, Felix Hausdorff-Strasse 1, D - 17489 Greifswald, Germany
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Jiang S, Li Z, Li J, Xu K, Ye Y. Analysis of Genetic Diversity and Structure of Eight Populations of Nerita yoldii along the Coast of China Based on Mitochondrial COI Gene. Animals (Basel) 2024; 14:718. [PMID: 38473102 DOI: 10.3390/ani14050718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/14/2024] [Accepted: 01/29/2024] [Indexed: 03/14/2024] Open
Abstract
Nerita yoldii is a euryhaline species commonly found in the intertidal zone. To investigate the genetic diversity of 233 N. yoldii individuals from eight locations along the coast of China, we utilized the mitochondrial COI gene as a molecular marker. A total of 34 haplotypes were detected, exhibiting a mean haplotype diversity (Hd) of 0.5915 and a mean nucleotide diversity (Pi) of 0.0025, indicating high levels of genetic diversity among all populations. An analysis of molecular variance (AMOVA) indicated that the primary source of genetic variation occurs within populations. In addition, neutral tests and mismatch analyses suggested that N. yoldii populations may have experienced bottleneck events. Moderate genetic differentiation was observed between Xiapu and other populations, excluding the Taizhou population, and may be attributed to the ocean currents. Intensively studying the genetic variation and population structure of N. yoldii populations contributes to understanding the current population genetics of N. yoldii in the coastal regions of China. This not only provides a reference for the study of other organisms in the same region but also lays the foundation for the systematic evolution of the Neritidae family.
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Affiliation(s)
- Senping Jiang
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
| | - Zhenhua Li
- Key Laboratory of Sustainable Utilization of Technology Research for Fisheries Resources of Zhejiang Province, Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, Ministry of Agriculture and Rural Affairs of China, Zhejiang Marine Fisheries Research Institute, Zhoushan 316021, China
| | - Jiji Li
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
| | - Kaida Xu
- Key Laboratory of Sustainable Utilization of Technology Research for Fisheries Resources of Zhejiang Province, Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, Ministry of Agriculture and Rural Affairs of China, Zhejiang Marine Fisheries Research Institute, Zhoushan 316021, China
| | - Yingying Ye
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
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Baeza JA, González MT, Sigwart JD, Greve C, Pirro S. Insights into the genome of the 'Loco' Concholepas concholepas (Gastropoda: Muricidae) from low-coverage short-read sequencing: genome size, ploidy, transposable elements, nuclear RNA gene operon, mitochondrial genome, and phylogenetic placement in the family Muricidae. BMC Genomics 2024; 25:77. [PMID: 38243187 PMCID: PMC10797722 DOI: 10.1186/s12864-023-09953-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 12/28/2023] [Indexed: 01/21/2024] Open
Abstract
BACKGROUND The Peruvian 'chanque' or Chilean 'loco' Concholepas concholepas is an economically, ecologically, and culturally important muricid gastropod heavily exploited by artisanal fisheries in the temperate southeastern Pacific Ocean. In this study, we have profited from a set of bioinformatics tools to recover important biological information of C. concholepas from low-coverage short-read NGS datasets. Specifically, we calculated the size of the nuclear genome, ploidy, and estimated transposable elements content using an in silico k-mer approach, we discovered, annotated, and quantified those transposable elements, we assembled and annotated the 45S rDNA RNA operon and mitochondrial genome, and we confirmed the phylogenetic position of C. concholepas within the muricid subfamily Rapaninae based on translated protein coding genes. RESULTS Using a k-mer approach, the haploid genome size estimated for the predicted diploid genome of C. concholepas varied between 1.83 Gbp (with kmer = 24) and 2.32 Gbp (with kmer = 36). Between half and two thirds of the nuclear genome of C. concholepas was composed of transposable elements. The most common transposable elements were classified as Long Interspersed Nuclear Elements and Short Interspersed Nuclear Elements, which were more abundant than DNA transposons, simple repeats, and Long Terminal Repeats. Less abundant repeat elements included Helitron mobile elements, 45S rRNA DNA, and Satellite DNA, among a few others.The 45S rRNA DNA operon of C. concholepas that encodes for the ssrRNA, 5.8S rRNA, and lsrRNA genes was assembled into a single contig 8,090 bp long. The assembled mitochondrial genome of C. concholepas is 15,449 bp long and encodes 13 protein coding genes, two ribosomal genes, and 22 transfer RNAs. CONCLUSION The information gained by this study will inform the assembly of a high quality nuclear genome for C. concholepas and will support bioprospecting and biomonitoring using environmental DNA to advance development of conservation and management plans in this overexploited marine snail.
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Affiliation(s)
- J Antonio Baeza
- Department of Biological Sciences, Clemson University, Clemson, SC, USA.
- Departamento de Biología Marina, Universidad Catolica del Norte, Coquimbo, Chile.
- Smithsonian Marine Station at Fort Pierce, Smithsonian Institution, Fort Pierce, FL, USA.
| | - M Teresa González
- Facultad de Ciencias del Mar y Recursos Biológicos, Instituto de Ciencias Naturales Alexander Von Humboldt, Universidad de Antofagasta, Angamos 601, Antofagasta, Chile
| | - Julia D Sigwart
- Marine Zoology Department, Senckenberg Research Institute and Museum, Frankfurt, Germany
- Institute of Ecology, Evolution & Diversity, Goethe University, Frankfurt, Germany
| | - Carola Greve
- LOEWE -Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, Frankfurt Am Main, Germany
- Senckenberg Forschungsinstitut und Naturmuseum, Frankfurt am Main, Germany
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Jiang X, Miao J, Li J, Ye Y. Characterization of Lophiotoma leucotropis Mitochondrial Genome of Family Turridae and Phylogenetic Considerations within the Neogastropoda. Animals (Basel) 2024; 14:192. [PMID: 38254362 PMCID: PMC11326093 DOI: 10.3390/ani14020192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
Neogastropoda is a group of marine organisms with an extremely wide distribution that is rich in species and economic and ornamental values, the classification of species in this order has been ongoing for a long time, but there is still a great controversy about whether this order is monophyletic. In this study, we obtained the complete mitogenome of Lophiotoma leucotropis by next-generation sequencing and analyzed the basic structural features of the genome, and we found that the number of genes was consistent with that of most of the Neogastropoda snails, containing 37 genes, including 13 protein-coding genes (PCGs), 2 rRNAs, and 22 tRNAs. Analyzing base content, amino acid content, codon usage preference, and tRNA structure, the mitogenomes of eight species of Turridae were selected for analysis of selection pressures, and it was found that the evolution of species in this family was affected by purifying selection. In addition, by analyzing the rearrangement characteristics, it was found that the sequence of L. leucotropis was consistent with the Conoidea consensus order, and four of the eight species involved in the analysis showed rearrangements. Finally, we constructed a phylogenetic tree by combining PCGs of 60 species within Caenogastropoda and found Neogastropoda to be a monophyletic group, validating the results of morphological classification. The results will provide more references for the classification and species evolution of Neogastropoda, as well as phylogenetic analysis.
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Affiliation(s)
- Xinqin Jiang
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
- College of Fisheries, Zhejiang Ocean University, Zhoushan 316022, China
| | - Jing Miao
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
| | - Jiji Li
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
| | - Yingying Ye
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
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Marshall DJ, Mustapha N, Monaco CJ. Conservation of thermal physiology in tropical intertidal snails following an evolutionary transition to a cooler ecosystem: climate change implications. CONSERVATION PHYSIOLOGY 2023; 11:coad056. [PMID: 37533818 PMCID: PMC10393397 DOI: 10.1093/conphys/coad056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 07/04/2023] [Accepted: 07/21/2023] [Indexed: 08/04/2023]
Abstract
Predictions for animal responses to climate warming usually assume that thermal physiology is adapted to present-day environments, and seldom consider the influence of evolutionary background. Little is known about the conservation of warm-adapted physiology following an evolutionary transition to a cooler environment. We used cardiac thermal performance curves (cTPCs) of six neritid gastropod species to study physiological thermal trait variation associated with a lineage transition from warmer rocky shores to cooler mangroves. We distinguished between functional thermal performance traits, related to energy homeostasis (slope gradient, slope curvature, HRmax, maximum cardiac activity and Topt, the temperature that maximizes cardiac activity) and a trait that limits performance (ULT, the upper lethal temperature). Considering the theory of optimal thermal performance, we predicted that the functional traits should be under greater selective pressure to change directionally and in magnitude than the thermal limit, which is redundant in the cooler environment. We found little variation in all traits across species, habitats and ecosystems, despite a ~20°C reduction in maximum habitat temperature in the mangrove species over 50 million years. While slope gradient was significantly lowered in the mangrove species, the effect difference was negated by greater thermal plasticity in the rocky shore species. ULT showed the least variation and suggested thermal specialization in the warmest habitat studied. The observed muted variation of the functional traits among the species may be explained by their limited role in energy acquisition and rather their association with heat tolerance adaptation, which is redundant in the mangrove species. These findings have implications for the conservation of habitat of intertidal gastropods that transition to cooler environments. Furthermore, they highlight the significance of evolutionary history and physiological conservation when predicting species responses to climate change.
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Affiliation(s)
- David J Marshall
- Corresponding author: Environmental and Life Sciences, Faculty of Science, Jalan Tungku Link, Gadong, Universiti Brunei Darussalam, BE1410, Brunei Darussalam. E-mail:
| | - Nurshahida Mustapha
- Environmental and Life Sciences, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Gadong, BE1410, Brunei Darussalam
| | - Cristián J Monaco
- IFREMER, IRD, Institut Louis-Malardé, Univ Polynésie française, Tahiti, Polynésie française, EIO, F-98725 Taravao, France
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Marshall DJ, Tsikouras B. Clay-shielded estuarine gastropods are better protected against environmental acidification than unshielded individuals. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 866:161367. [PMID: 36610628 DOI: 10.1016/j.scitotenv.2022.161367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/23/2022] [Accepted: 12/30/2022] [Indexed: 06/17/2023]
Abstract
The effects of progressive global acidification on the shells of marine organisms is a topic of much current interest. Most studies on molluscan shell resistance to dissolution consider the carbonate mineral component, with less known about the protective role of the outer organic periostracum. Outer-shell resistance would seem especially important to gastropods living in carbonate-undersaturated and calcium-deficient estuarine waters that threaten shell dissolution and constrain CaCO3 production. We tested this prediction using gastropods from an acidified estuarine population (Neripteron violaceum) that form a clay shield outside the periostracum. Specifically, we aimed to show that the carbonate shell component lacks integrity, that the formation of the clay shield is directed by the organism, and that the clay shield functions to protect against shell dissolution. We found no evidence for any specific carbonate dissolution resistance strategy in the thin, predominantly aragonitic shells of these gastropods. Shield formation was directed by an ornamented periostracum which strongly bonded illite elements (e.g., Fe, Al and S), that become available through suspension in the water column. In unshielded individuals, CaCO3 erosion was initiated randomly across the shell (not age-related) and progressed rapidly when the periostracum was breached. A light reflectance technique showed qualitatively that shield consolidation is negatively-related to shell erosion. These findings support a conceptual framework for gastropod outer-shell responses to acidification that considers both environmental and evolutionary constraints on shell construction. We describe a novel strategy for shell protection against dissolution, highlighting the diversity of mechanisms available to gastropods facing extreme coastal acidification.
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Affiliation(s)
- David J Marshall
- Environmental and Life Sciences, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Gadong BE1410, Brunei Darussalam.
| | - Basilios Tsikouras
- Geosciences Programme, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Gadong BE1410, Brunei Darussalam
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Qi L, Xu B, Kong L, Li Q. Improved phylogenetic resolution within Neritidae (Gastropoda, Nertimorpha) with implications for the evolution of shell traits and habitat. ZOOL SCR 2022. [DOI: 10.1111/zsc.12567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Lu Qi
- Key Laboratory of Mariculture, Ministry of Education Ocean University of China Qingdao China
| | - Biyang Xu
- Key Laboratory of Mariculture, Ministry of Education Ocean University of China Qingdao China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education Ocean University of China Qingdao China
- Laboratory for Marine Fisheries Science and Food Production Processes Qingdao National Laboratory for Marine Science and Technology Qingdao China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education Ocean University of China Qingdao China
- Laboratory for Marine Fisheries Science and Food Production Processes Qingdao National Laboratory for Marine Science and Technology Qingdao China
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Insights into the Deep Phylogeny and Novel Divergence Time Estimation of Patellogastropoda from Complete Mitogenomes. Genes (Basel) 2022; 13:genes13071273. [PMID: 35886056 PMCID: PMC9322768 DOI: 10.3390/genes13071273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/13/2022] [Accepted: 07/16/2022] [Indexed: 11/21/2022] Open
Abstract
To further understand the origin and evolution of Patellogastropoda, we determined the mitochondrial genome sequence of Cellana toreuma, and compared its mitogenome characteristics with the other four limpets of Nacellidae. The ratio of Ka and Ks indicated that these Nacellidae species were suffering a purifying selection, with exception of the atp6 gene. The gene sequence is basically consistent among families, while there are great differences among Lottidae species. According to the mitogenome sequences of selected gastropod species, we reconstructed a new phylogenetic tree with two methods. The data complement the mitogenome database of limpets and is a favorable research tool for the phylogenetic analysis of Gastropoda. It is found that there is a long-branch attraction (LBA) artefact in the family Lottiidae of Patellogastropoda. Therefore, the Patellogastropoda was separated by Heterobranchia, and Lottiidae is located at the root of the whole phylogenetic tree. Furthermore, we constructed the divergence time tree according to the Bayesian method and discussed the internal historical dynamics, and divergence differences among the main lineages of 12 Patellogastropoda under an uncorrelated relaxed molecular clock. In turn, we made a more comprehensive discussion on the divergence time of limpets at the molecular level.
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