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Pasanen TM, Helske J, Högmander H, Ketola T. Spatio-temporal modeling of co-dynamics of smallpox, measles, and pertussis in pre-healthcare Finland. PeerJ 2024; 12:e18155. [PMID: 39346083 PMCID: PMC11439382 DOI: 10.7717/peerj.18155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 09/01/2024] [Indexed: 10/01/2024] Open
Abstract
Infections are known to interact as previous infections may have an effect on risk of succumbing to a new infection. The co-dynamics can be mediated by immunosuppression or modulation, shared environmental or climatic drivers, or competition for susceptible hosts. Research and statistical methods in epidemiology often concentrate on large pooled datasets, or high quality data from cities, leaving rural areas underrepresented in literature. Data considering rural populations are typically sparse and scarce, especially in the case of historical data sources, which may introduce considerable methodological challenges. In order to overcome many obstacles due to such data, we present a general Bayesian spatio-temporal model for disease co-dynamics. Applying the proposed model on historical (1820-1850) Finnish parish register data, we study the spread of infectious diseases in pre-healthcare Finland. We observe that measles, pertussis, and smallpox exhibit positively correlated dynamics, which could be attributed to immunosuppressive effects or, for example, the general weakening of the population due to recurring infections or poor nutritional conditions.
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Affiliation(s)
- Tiia-Maria Pasanen
- Department of Mathematics and Statistics, University of Jyväskylä, Jyväskylä, Finland
| | - Jouni Helske
- Department of Mathematics and Statistics, University of Jyväskylä, Jyväskylä, Finland
- INVEST Research Flagship Centre, University of Turku, Turku, Finland
| | - Harri Högmander
- Department of Mathematics and Statistics, University of Jyväskylä, Jyväskylä, Finland
| | - Tarmo Ketola
- Department of Forestry, University of Helsinki, Helsinki, Finland
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
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2
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Lecocq de Pletincx N, Cerdà X, Kiran K, Karaman C, Taheri A, Aron S. Ecological diversification preceded geographical expansion during the evolutionary radiation of Cataglyphis desert ants. iScience 2024; 27:109852. [PMID: 38779477 PMCID: PMC11109030 DOI: 10.1016/j.isci.2024.109852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 03/20/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024] Open
Abstract
Biological diversity often arises as organisms adapt to new ecological conditions (i.e., ecological opportunities) or colonize suitable areas (i.e., spatial opportunities). Cases of geographical expansion followed by local ecological divergence are well described; they result in clades comprising ecologically heterogeneous subclades. Here, we show that the desert ant genus Cataglyphis likely originated in open grassland habitats in the Middle East ∼18 million years ago and became a taxon of diverse species specializing in prey of different masses. The genus then colonized the Mediterranean Basin around 9 million years ago. The result was the rapid accumulation of species, and the appearance of local assemblages containing species from different lineages that still displayed ancestral foraging specialties. These findings highlight that, in Cataglyphis, ecological diversification preceded geographical expansion, resulting in a clade composed of ecologically homogeneous subclades.
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Affiliation(s)
- Nathan Lecocq de Pletincx
- Evolutionary Biology and Ecology, Faculty of Sciences, Université Libre de Bruxelles, CP 160/12, av. FD Roosevelt, 1050 Brussels, Belgium
| | - Xim Cerdà
- Department of Ethology and Biodiversity Conservation, Estación Biológica de Doñana, CSIC, Sevilla, Spain
| | - Kadri Kiran
- Department of Biology, Faculty of Sciences, Trakya University, Edirne 22030, Türkiye
| | - Celal Karaman
- Department of Biology, Faculty of Sciences, Trakya University, Edirne 22030, Türkiye
| | - Ahmed Taheri
- Laboratory of Plant Biotechnology, Ecology and Ecosystem Valorization, Faculty of Sciences of El Jadida, University Chouaïb Doukkali, El Jadida, Morocco
| | - Serge Aron
- Evolutionary Biology and Ecology, Faculty of Sciences, Université Libre de Bruxelles, CP 160/12, av. FD Roosevelt, 1050 Brussels, Belgium
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3
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Wang B, Jin Y, Hu M, Zhao Y, Wang X, Yue J, Ren H. Detecting genetic gain and loss events in terms of protein domain: Method and implementation. Heliyon 2024; 10:e32103. [PMID: 38867972 PMCID: PMC11168390 DOI: 10.1016/j.heliyon.2024.e32103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/08/2024] [Accepted: 05/28/2024] [Indexed: 06/14/2024] Open
Abstract
Continuous gain and loss of genes are the primary driving forces of bacterial evolution and environmental adaptation. Studying bacterial evolution in terms of protein domain, which is the fundamental function and evolutionary unit of proteins, can provide a more comprehensive understanding of bacterial differentiation and phenotypic adaptation processes. Therefore, we proposed a phylogenetic tree-based method for detecting genetic gain and loss events in terms of protein domains. Specifically, the method focuses on a single domain to trace its evolution process or on multiple domains to investigate their co-evolution principles. This novel method was validated using 122 Shigella isolates. We found that the loss of a significant number of domains was likely the main driving force behind the evolution of Shigella, which could reduce energy expenditure and preserve only the most essential functions. Additionally, we observed that simultaneously gained and lost domains were often functionally related, which can facilitate and accelerate phenotypic evolutionary adaptation to the environment. All results obtained using our method agree with those of previous studies, which validates our proposed method.
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Affiliation(s)
- Boqian Wang
- Beijing Institute of Biotechnology, State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Yuan Jin
- Beijing Institute of Biotechnology, State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Mingda Hu
- Beijing Institute of Biotechnology, State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Yunxiang Zhao
- Beijing Institute of Biotechnology, State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Xin Wang
- Beijing Institute of Biotechnology, State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Junjie Yue
- Beijing Institute of Biotechnology, State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Hongguang Ren
- Beijing Institute of Biotechnology, State Key Laboratory of Pathogen and Biosecurity, Beijing, China
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4
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Pham PH, Antropov AV, Nguyen HV. Description of Trypoxylonsicklum sp. nov. from Vietnam and a key to species in the Trypoxylonfulvocollare group (Hymenoptera, Crabronidae). Biodivers Data J 2024; 12:e114333. [PMID: 38812885 PMCID: PMC11134051 DOI: 10.3897/bdj.12.e114333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 04/24/2024] [Indexed: 05/31/2024] Open
Abstract
Background Trypoxylon Latreille, 1796 (Hymenoptera, Crabronidae) consists of 633 known species worldwide and the genus is divided into numerous species groups. In Vietnam, 19 species of Trypoxylon have been recorded to date. In this study, a new species, Trypoxylonsicklum Pham and Antropov sp. nov. is described and illustrated from Vinh Phuc Province, Vietnam. The new species is the second member of the Trypoxylonfulvocollare species group. A key to species in the Trypoxylonfulvocollaris group is presented. New information Trypoxylonsicklum Pham and Antropov sp. nov., is described as a new species and is the second member of the Trypoxylonfulvocollare species group. A key to species in the Trypoxylonfulvocollaris group is presented.
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Affiliation(s)
- Phong Huy Pham
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, VietnamInstitute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau GiayHanoiVietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, VietnamGraduate University of Science and Technology, Vietnam Academy of Science and TechnologyHanoiVietnam
| | - Alexander V. Antropov
- Zoological Museum of Moscow, Lomonosov State University, Bolshaya Nikitskaya str. 2, Moscow, 125009, Moscow, RussiaZoological Museum of Moscow, Lomonosov State University, Bolshaya Nikitskaya str. 2, Moscow, 125009MoscowRussia
| | - Hieu Van Nguyen
- Faculty of Biology and Agricultural Engineering, Hanoi Pedagogical University 2, 32 Nguyen Van Linh Street, Xuan Hoa, Phuc Yen, Vinh Phuc, VietnamFaculty of Biology and Agricultural Engineering, Hanoi Pedagogical University 2, 32 Nguyen Van Linh Street, Xuan Hoa, Phuc YenVinh PhucVietnam
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5
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Hegarty BE, Gruenhagen GW, Johnson ZV, Baker CM, Streelman JT. Spatially resolved cell atlas of the teleost telencephalon and deep homology of the vertebrate forebrain. Commun Biol 2024; 7:612. [PMID: 38773256 PMCID: PMC11109250 DOI: 10.1038/s42003-024-06315-1] [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: 05/10/2024] [Indexed: 05/23/2024] Open
Abstract
The telencephalon has undergone remarkable diversification and expansion throughout vertebrate evolution, exhibiting striking variations in structural and functional complexity. Nevertheless, fundamental features are shared across vertebrate taxa, such as the presence of distinct regions including the pallium, subpallium, and olfactory structures. Teleost fishes have a uniquely "everted" telencephalon, which has confounded comparisons of their brain regions to other vertebrates. Here we combine spatial transcriptomics and single nucleus RNA-sequencing to generate a spatially-resolved transcriptional atlas of the Mchenga conophorus cichlid fish telencephalon. We then compare cell-types and anatomical regions in the cichlid telencephalon with those in amphibians, reptiles, birds, and mammals. We uncover striking transcriptional similarities between cell-types in the fish telencephalon and subpallial, hippocampal, and cortical cell-types in tetrapods, and find support for partial eversion of the teleost telencephalon. Ultimately, our work lends new insights into the organization and evolution of conserved cell-types and regions in the vertebrate forebrain.
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Affiliation(s)
- Brianna E Hegarty
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - George W Gruenhagen
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
- Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
| | - Zachary V Johnson
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, 30329, USA
| | - Cristina M Baker
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Kavli Institute for Systems Neuroscience, Norwegian University of Science and Technology, Trondheim, Norway
| | - Jeffrey T Streelman
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
- Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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6
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Wang S, Wang C, Lv F, Chu P, Jin H. Genome-wide identification of the OMT gene family in Cucumis melo L. and expression analysis under abiotic and biotic stress. PeerJ 2023; 11:e16483. [PMID: 38107581 PMCID: PMC10725674 DOI: 10.7717/peerj.16483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 10/27/2023] [Indexed: 12/19/2023] Open
Abstract
Background O-methyltransferase (OMT)-mediated O-methylation is a frequent modification that occurs during natural product biosynthesis, and it increases the diversity and stability of secondary metabolites. However, detailed genome-wide identification and expression analyses of OMT gene family members have not been performed in melons. In this study, we aimed to perform the genome-wide identification of OMT gene family members in melon to identify and clarify their actions during stress. Methods Genome-wide identification of OMT gene family members was performed using data from the melon genome database. The Cucumis melo OMT genes (CmOMTs) were then compared with the genes from two representative monocotyledons and three representative dicotyledons. The basic information, cis-regulatory elements in the promoter, predicted 3-D-structures, and GO enrichment results of the 21 CmOMTs were analyzed. Results In our study, 21 CmOMTs (named CmOMT1-21) were obtained by analyzing the melon genome. These genes were located on six chromosomes and divided into three groups composed of nine, six, and six CmOMTs based on phylogenetic analysis. Gene structure and motif descriptions were similar within the same classes. Each CmOMT gene contains at least one cis-acting element associated with hormone transport regulation. Analysis of cis-acting elements illustrated the potential role of CmOMTs in developmental regulation and adaptations to various abiotic and biotic stresses. The RNA-seq and quantitative real-time PCR (qRT-PCR) results indicated that NaCl stress significantly induced CmOMT6/9/14/18 and chilling and high temperature and humidity (HTH) stresses significantly upregulated CmOMT14/18. Furthermore, the expression pattern of CmOMT18 may be associated with Fusarium oxysporum f. sp. melonis race 1.2 (FOM1.2) and powdery mildew resistance. Our study tentatively explored the biological functions of CmOMT genes in various stress regulation pathways and provided a conceptual basis for further detailed studies of the molecular mechanisms.
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Affiliation(s)
| | - Chuang Wang
- Liaocheng Vocational & Technical College, Liaocheng, China
| | - Futang Lv
- Liaocheng University, Liaocheng, China
| | | | - Han Jin
- Liaocheng University, Liaocheng, China
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7
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Wang Y, Zhao Z, Miao X, Wang Y, Qian X, Chen L, Wang C, Li S. eSMC: a statistical model to infer admixture events from individual genomics data. BMC Genomics 2022; 23:827. [PMCID: PMC9748406 DOI: 10.1186/s12864-022-09033-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 11/21/2022] [Indexed: 12/15/2022] Open
Abstract
Abstract
Background
Inferring historical population admixture events yield essential insights in understanding a species demographic history. Methods are available to infer admixture events in demographic history with extant genetic data from multiple sources. Due to the deficiency in ancient population genetic data, there lacks a method for admixture inference from a single source. Pairwise Sequentially Markovian Coalescent (PSMC) estimates the historical effective population size from lineage genomes of a single individual, based on the distribution of the most recent common ancestor between the diploid’s alleles. However, PSMC does not infer the admixture event.
Results
Here, we proposed eSMC, an extended PSMC model for admixture inference from a single source. We evaluated our model’s performance on both in silico data and real data. We simulated population admixture events at an admixture time range from 5 kya to 100 kya (5 years/generation) with population admix ratio at 1:1, 2:1, 3:1, and 4:1, respectively. The root means the square error is $$\pm 7.61$$
±
7.61
kya for all experiments. Then we implemented our method to infer the historical admixture events in human, donkey and goat populations. The estimated admixture time for both Han and Tibetan individuals range from 60 kya to 80 kya (25 years/generation), while the estimated admixture time for the domesticated donkeys and the goats ranged from 40 kya to 60 kya (8 years/generation) and 40 kya to 100 kya (6 years/generation), respectively. The estimated admixture times were concordance to the time that domestication occurred in human history.
Conclusion
Our eSMC effectively infers the time of the most recent admixture event in history from a single individual’s genomics data. The source code of eSMC is hosted at https://github.com/zachary-zzc/eSMC.
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Castillo R, Wurdack M, Pauli T, Keller A, Feldhaar H, Polidori C, Niehuis O, Schmitt T. Evidence for a chemical arms race between cuckoo wasps of the genus Hedychrum and their distantly related host apoid wasps. BMC Ecol Evol 2022; 22:138. [PMID: 36443667 PMCID: PMC9703671 DOI: 10.1186/s12862-022-02093-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 11/14/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Brood parasites can exert strong selection pressure on their hosts. Many brood parasites escape their detection by mimicking sensory cues of their hosts. However, there is little evidence whether or not the hosts are able to escape the parasites' mimicry by changing these cues. We addressed this question by analyzing cuticular hydrocarbon (CHC) profiles of Cerceris and Philanthus wasps and their brood parasites, cuckoo wasps mimicking the CHC profiles of their hosts. Some of these hosts use hydrocarbons to preserve their prey against fungal infestation and thus, they cannot significantly change their CHC composition in response to chemical mimicry by Hedychrum brood parasites. RESULTS We found that the CHC overlap between brood parasites and their hosts was lower in case of host wasps not preserving their prey than in case of prey-preserving host wasps, whose CHC evolution is constrained. Furthermore, the CHC profiles in non-preserving host wasps is more strongly diversified in females than in males, thus in the sex that is chemically mimicked by brood parasites. CONCLUSION Our results provide evidence for a chemical arms race between those hosts that are liberated from stabilizing selection on their chemical template and their parasites.
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Affiliation(s)
- Ruth Castillo
- grid.8379.50000 0001 1958 8658Department of Animal Ecology and Tropical Biology, Biocentre, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Mareike Wurdack
- grid.8379.50000 0001 1958 8658Department of Animal Ecology and Tropical Biology, Biocentre, University of Würzburg, Am Hubland, 97074 Würzburg, Germany ,grid.5963.9Department of Evolutionary Biology and Ecology, University of Freiburg, Hauptstraße 1, 79104 Freiburg, Germany
| | - Thomas Pauli
- grid.5963.9Department of Evolutionary Biology and Ecology, University of Freiburg, Hauptstraße 1, 79104 Freiburg, Germany ,grid.7708.80000 0000 9428 7911Institute of Medical Bioinformatics and Systems Medicine, Medical Center, University of Freiburg, Breisacher Straße 153, 79110 Freiburg, Germany
| | - Alexander Keller
- grid.5252.00000 0004 1936 973XCellular and Organismic Networks, Faculty of Biology, Ludwig-Maximilians-University München, 82152 Planegg-Martinsried, Germany
| | - Heike Feldhaar
- grid.7384.80000 0004 0467 6972Animal Population Ecology, Department of Animal Ecology I, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, 95440 Bayreuth, Germany
| | - Carlo Polidori
- grid.4708.b0000 0004 1757 2822Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, via Celoria 26, 20133 Milan, Italy
| | - Oliver Niehuis
- grid.5963.9Department of Evolutionary Biology and Ecology, University of Freiburg, Hauptstraße 1, 79104 Freiburg, Germany
| | - Thomas Schmitt
- grid.8379.50000 0001 1958 8658Department of Animal Ecology and Tropical Biology, Biocentre, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
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9
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Barten R, van Workum DJM, de Bakker E, Risse J, Kleisman M, Navalho S, Smit S, Wijffels RH, Nijveen H, Barbosa MJ. Genetic mechanisms underlying increased microalgal thermotolerance, maximal growth rate, and yield on light following adaptive laboratory evolution. BMC Biol 2022; 20:242. [PMID: 36303154 PMCID: PMC9615354 DOI: 10.1186/s12915-022-01431-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 10/03/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Adaptive laboratory evolution (ALE) is a powerful method for strain optimization towards abiotic stress factors and for identifying adaptation mechanisms. In this study, the green microalga Picochlorum sp. BPE23 was cultured under supra-optimal temperature to force genetic adaptation. The robustness and adaptive capacity of Picochlorum strains turned them into an emerging model for evolutionary studies on abiotic stressors such as temperature, salinity, and light. RESULTS Mutant strains showed an expanded maximal growth temperature of 44.6 °C, whereas the maximal growth temperature of the wild-type strain was 42 °C. Moreover, at the optimal growth temperature of 38 °C, the biomass yield on light was 22.3% higher, and the maximal growth rate was 70.5% higher than the wild type. Genome sequencing and transcriptome analysis were performed to elucidate the mechanisms behind the improved phenotype. A de novo assembled phased reference genome allowed the identification of 21 genic mutations involved in various processes. Moreover, approximately half of the genome contigs were found to be duplicated or even triplicated in all mutants, suggesting a causal role in adaptation. CONCLUSIONS The developed tools and mutant strains provide a strong framework from whereupon Picochlorum sp. BPE23 can be further developed. Moreover, the extensive strain characterization provides evidence of how microalgae evolve to supra-optimal temperature and to photobioreactor growth conditions. With this study, microalgal evolutionary mechanisms were identified by combining ALE with genome sequencing.
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Affiliation(s)
- Robin Barten
- Bioprocess Engineering & AlgaePARC, Wageningen University and Research, PO Box 16, Wageningen, 6700 AA, The Netherlands.
| | - Dirk-Jan M van Workum
- Bioinformatics Group, Wageningen University and Research, PO Box 633, Wageningen, 6700 AP, The Netherlands
| | - Emma de Bakker
- Bioprocess Engineering & AlgaePARC, Wageningen University and Research, PO Box 16, Wageningen, 6700 AA, The Netherlands
| | - Judith Risse
- Bioinformatics Group, Wageningen University and Research, PO Box 633, Wageningen, 6700 AP, The Netherlands
| | - Michelle Kleisman
- Bioinformatics Group, Wageningen University and Research, PO Box 633, Wageningen, 6700 AP, The Netherlands
| | - Sofia Navalho
- Bioprocess Engineering & AlgaePARC, Wageningen University and Research, PO Box 16, Wageningen, 6700 AA, The Netherlands
| | - Sandra Smit
- Bioinformatics Group, Wageningen University and Research, PO Box 633, Wageningen, 6700 AP, The Netherlands
| | - Rene H Wijffels
- Bioprocess Engineering & AlgaePARC, Wageningen University and Research, PO Box 16, Wageningen, 6700 AA, The Netherlands.,Biosciences and Aquaculture, Nord University, N-8049, Bodø, Norway
| | - Harm Nijveen
- Bioinformatics Group, Wageningen University and Research, PO Box 633, Wageningen, 6700 AP, The Netherlands
| | - Maria J Barbosa
- Bioprocess Engineering & AlgaePARC, Wageningen University and Research, PO Box 16, Wageningen, 6700 AA, The Netherlands
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10
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Jeon HB, Song HY, Suk HY, Bang IC. Phylogeography of the Korean endemic Coreoleuciscus (Cypriniformes: Gobionidae): the genetic evidence of colonization through Eurasian continent to the Korean Peninsula during Late Plio-Pleistocene. Genes Genomics 2022; 44:709-719. [PMID: 35438462 PMCID: PMC9120112 DOI: 10.1007/s13258-022-01243-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 03/12/2022] [Indexed: 11/30/2022]
Abstract
Background Freshwater endemism is thought to have been formed through the vicariance of connected water systems or the process by which ancestral populations colonized specific areas. The Korean Peninsula is well recognized for its high level of freshwater endemism with about 40% of freshwater fish species being endemic. Objective In this study, we attempted to reconstruct the process of speciation and phylogenetic dispersal of Coreoleuciscus species, which is endemic in the Korean Peninsula. Methods We used fossil-calibrated divergence time estimation and ancestral distributional reconstruction to infer phylogeographic reconstruction of Coreoleuciscus based on mitochondrial cytochrome c oxidate subunit I (COI) sequences (1551 bp). Results Our phylogeographic analysis based on a total of 626 individuals revealed that the two Coreoleuciscus species have originated from the independent colonization of different lineages in the ancestral populations, probably during the Late Plio-Pleistocene. The full-scale expansion of Coreoleuciscus populations appears to have taken place after major river structures were completed on the Korean Peninsula. We also provided evidence that the common ancestors of Coreoleuciscus was distributed in Eastern Eurasian continent and subsequently dispersed into the tip of East Asia. High genetic diversity was mainly concentrated in large drainage populations, while small populations showed an monomorphism, which could give important implications for planning the conservation and management of Coreoleuciscus. Conclusions The phylogenetic background of the rheophilic Coreoleuciscus species can be explained by the colonizer hypothesis that the endemic freshwater fish originated from the common ancestor in continental region. Supplementary Information The online version contains supplementary material available at 10.1007/s13258-022-01243-y.
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Affiliation(s)
- Hyung-Bae Jeon
- Department of Biology, Concordia University, Montreal, Canada
| | - Ha Youn Song
- Inland Fisheries Research Institute, National Institute of Fisheries Science, Busan, South Korea
| | - Ho Young Suk
- Department of Life Sciences, Yeungnam University, Gyeongsan, South Korea
| | - In-Chul Bang
- Department of Life Sciences, Soonchunhyang University, Asan, South Korea.
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11
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Gruenhagen GW, Mubeen T, Patil C, Stockert J, Streelman JT. Single Cell RNA Sequencing Reveals Deep Homology of Dental Cell Types Across Vertebrates. FRONTIERS IN DENTAL MEDICINE 2022; 3. [DOI: 10.3389/fdmed.2022.845449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023] Open
Abstract
Like most mammals, humans replace their teeth once throughout their lives and have limited regenerative capabilities. In contrast, mice continually renew tissues lost due to gnawing through a well characterized population of stem cells on the labial surface of the incisor. Most non-mammalian vertebrates replace teeth throughout life; the cellular and molecular mechanisms of successional tooth replacement are largely unknown. Here we use single nuclei RNA sequencing (snRNA-seq) of replacement teeth and adjacent oral lamina in Lake Malawi cichlids, species with lifelong whole–tooth replacement, to make two main discoveries. First, despite hundreds of millions of years of evolution, we demonstrate conservation of cell type gene expression across vertebrate teeth (fish, mouse, human). Second, we used an approach that combines marker gene expression and developmental potential of dental cells to uncover the transcriptional signature of stem-like cells in regenerating teeth. Our work underscores the importance of a comparative framework in the study of vertebrate oral and regenerative biology.
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12
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Ayadi ZEM, Tazerouti F, Gastineau R, Justine JL. Redescription, complete mitochondrial genome and phylogenetic relationships of Hexostoma thynni (Delaroche, 1811) Rafinesque, 1815 (Monogenea, Hexostomatidae). Parasite 2022; 29:29. [PMID: 35604345 PMCID: PMC9126124 DOI: 10.1051/parasite/2022030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/11/2022] [Indexed: 11/17/2022] Open
Abstract
Specimens of Hexostoma thynni (Delaroche, 1811) Rafinesque, 1815 were collected from their type-host, the bluefin tuna Thunnus thynnus, caught off Algeria, i.e. close to the type-locality, off Mallorca, which is also in the Mediterranean. The species is briefly redescribed and compared to previous descriptions, under the same name or as its synonym Plagiopeltis duplicata Diesing, 1858, to ascertain identity of specimens. The three genera within the Hexostomatidae (Hexostoma Rafinesque, 1815, Neohexostoma Price, 1961 and Homostoma Unnithan, 1965) are briefly discussed, with comments on the fragility of characters used to distinguish them. Using next-generation sequencing, the complete mitogenome and the cluster of ribosomal genes (SSU, LSU, ITS1, ITS2, 5.8S) were obtained. The mitogenome is 14,649 bp long and codes for 12 protein-coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes; its size is similar to other mitogenomes obtained from polyopisthocotylean monogeneans. A phylogeny based on concatenated mitogenome protein-coding genes from nine species of polyopisthocotylean monogeneans produced a tree in which the Hexostomatidae H. thynni was associated with other Mazocraeidea, such as Chauhaneidae and Diclidophoridae. This invalidates the hypothesis of Boeger & Kritsky (1993) of Hexostomatidae as sister-group to the Mazocraeidea and suggests the demise of the suborder Hexostomatinea Boeger & Kritsky, 1993. We insist on the usefulness of depositing parts of specimens used for molecular analyses, prepared on permanent slides, in a curated collection.
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Affiliation(s)
- Zouhour El Mouna Ayadi
- Université des Sciences et de la Technologie Houari Boumediene, Faculté des Sciences Biologiques, Laboratoire de Biodiversité et Environnement : Interactions – Génomes (LBEIG) BP 32 El Alia, Bab Ezzouar Alger Algeria
| | - Fadila Tazerouti
- Université des Sciences et de la Technologie Houari Boumediene, Faculté des Sciences Biologiques, Laboratoire de Biodiversité et Environnement : Interactions – Génomes (LBEIG) BP 32 El Alia, Bab Ezzouar Alger Algeria
| | - Romain Gastineau
- Institute of Marine and Environmental Sciences, University of Szczecin Szczecin Poland
| | - Jean-Lou Justine
- ISYEB, Institut de Systématique, Évolution, Biodiversité (UMR7205 CNRS, EPHE, MNHN, UPMC, Université des Antilles), Muséum National d’Histoire Naturelle CP 51 55 rue Buffon 75231 Paris Cedex 05 France
- Corresponding author:
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Antigen Presentation and Autophagy in Teleost Adaptive Immunity. Int J Mol Sci 2022; 23:ijms23094899. [PMID: 35563287 PMCID: PMC9103719 DOI: 10.3390/ijms23094899] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 01/27/2023] Open
Abstract
Infectious diseases are a burden for aquaculture. Antigen processing and presentation (APP) to the immune effector cells that fight pathogens is key in the adaptive immune response. At the core of the adaptive immunity that appeared in lower vertebrates during evolution are the variable genes encoding the major histocompatibility complex (MHC). MHC class I molecules mainly present peptides processed in the cytosol by the proteasome and transported to the cell surface of all cells through secretory compartments. Professional antigen-presenting cells (pAPC) also express MHC class II molecules, which normally present peptides processed from exogenous antigens through lysosomal pathways. Autophagy is an intracellular self-degradation process that is conserved in all eukaryotes and is induced by starvation to contribute to cellular homeostasis. Self-digestion during autophagy mainly occurs by the fusion of autophagosomes, which engulf portions of cytosol and fuse with lysosomes (macroautophagy) or assisted by chaperones (chaperone-mediated autophagy, CMA) that deliver proteins to lysosomes. Thus, during self-degradation, antigens can be processed to be presented by the MHC to immune effector cells, thus, linking autophagy to APP. This review is focused on the essential components of the APP that are conserved in teleost fish and the increasing evidence related to the modulation of APP and autophagy during pathogen infection.
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Fu MJ, Wu HY, Jia DR, Tian B. Evolutionary history of a desert perennial Arnebia szechenyi (Boraginaceae): Intraspecific divergence, regional expansion and asymmetric gene flow. PLANT DIVERSITY 2021; 43:462-471. [PMID: 35024515 PMCID: PMC8720688 DOI: 10.1016/j.pld.2021.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 04/07/2021] [Accepted: 04/09/2021] [Indexed: 05/20/2023]
Abstract
The complex interactions of historical, geological and climatic events on plant evolution have been an important research focus for many years. However, the role of desert formation and expansion in shaping the genetic structures and demographic histories of plants occurring in arid areas has not been well explored. In the present study, we investigated the phylogeography of Arnebia szechenyi, a desert herb showing a near-circular distribution surrounding the Tengger Desert in Northwest China. We measured genetic diversity of populations using three maternally inherited chloroplast DNA (cpDNA) fragments and seven bi-paternally inherited nuclear DNA (nDNA) loci that were sequenced from individuals collected from 16 natural populations across its range and modelled current and historical potential habitats of the species. Our data indicated a considerably high level of genetic variation within A. szechenyi and noteworthy asymmetry in historical migration from the east to the west. Moreover, two nuclear genetic groups of populations were revealed, corresponding to the two geographic regions separated by the Tengger Desert. However, analysis of cpDNA data did not show significant geographic structure. The most plausible explanation for the discrepancy between our findings based on cpDNA and nDNA data is that A. szechenyi populations experienced long periods of geographic isolation followed by range expansion, which would have promoted generalized recombination of the nuclear genome. Our findings further highlight the important role that the Tengger Desert, together with the Helan Mountains, has played in the evolution of desert plants and the preservation of biodiversity in arid Northwest China.
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Affiliation(s)
- Meng-Jiao Fu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China
| | - Hai-Yang Wu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China
| | - Dong-Rui Jia
- School of Ecology and Environmental Science & Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, Yunnan University, Kunming 650091, China
- Corresponding author.
| | - Bin Tian
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China
- CAS Key Laboratory for Plant Diversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
- Corresponding author. Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China.
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Patil C, Sylvester JB, Abdilleh K, Norsworthy MW, Pottin K, Malinsky M, Bloomquist RF, Johnson ZV, McGrath PT, Streelman JT. Genome-enabled discovery of evolutionary divergence in brains and behavior. Sci Rep 2021; 11:13016. [PMID: 34155279 PMCID: PMC8217251 DOI: 10.1038/s41598-021-92385-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 06/08/2021] [Indexed: 02/05/2023] Open
Abstract
Lake Malawi cichlid fishes exhibit extensive divergence in form and function built from a relatively small number of genetic changes. We compared the genomes of rock- and sand-dwelling species and asked which genetic variants differed among the groups. We found that 96% of differentiated variants reside in non-coding sequence but these non-coding diverged variants are evolutionarily conserved. Genome regions near differentiated variants are enriched for craniofacial, neural and behavioral categories. Following leads from genome sequence, we used rock- vs. sand-species and their hybrids to (i) delineate the push-pull roles of BMP signaling and irx1b in the specification of forebrain territories during gastrulation and (ii) reveal striking context-dependent brain gene expression during adult social behavior. Our results demonstrate how divergent genome sequences can predict differences in key evolutionary traits. We highlight the promise of evolutionary reverse genetics-the inference of phenotypic divergence from unbiased genome sequencing and then empirical validation in natural populations.
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Affiliation(s)
- Chinar Patil
- School of Biological Sciences and Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA.
| | - Jonathan B Sylvester
- School of Biological Sciences and Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Biology, Georgia State University, Atlanta, GA, USA
| | - Kawther Abdilleh
- School of Biological Sciences and Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
| | - Michael W Norsworthy
- Catalog Technologies Inc., Boston, MA, USA
- Freedom of Form Foundation, Inc., Cambridge, MA, USA
| | - Karen Pottin
- Laboratoire de Biologie du Dévelopement (IBPS-LBD, UMR7622), CNRS, Institut de Biologie Paris Seine, Sorbonne Université, Paris, France
| | - Milan Malinsky
- Department of Environmental Sciences, Zoological Institute, University of Basel, Basel, Switzerland
- Wellcome Trust Sanger Institute, Cambridge, UK
| | - Ryan F Bloomquist
- School of Biological Sciences and Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Oral Biology and Diagnostic Sciences, Department of Restorative Sciences, Dental College of Georgia, Augusta University, Augusta, GA, USA
| | - Zachary V Johnson
- School of Biological Sciences and Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
| | - Patrick T McGrath
- School of Biological Sciences and Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
| | - Jeffrey T Streelman
- School of Biological Sciences and Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
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16
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Zhang J, Miao G, Hu S, Sun Q, Ding H, Ji Z, Guo P, Yan S, Wang C, Kan X, Nie L. Quantification and evolution of mitochondrial genome rearrangement in Amphibians. BMC Ecol Evol 2021; 21:19. [PMID: 33563214 PMCID: PMC7871395 DOI: 10.1186/s12862-021-01755-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 01/28/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rearrangement is an important topic in the research of amphibian mitochondrial genomes ("mitogenomes" hereafter), whose causes and mechanisms remain enigmatic. Globally examining mitogenome rearrangements and uncovering their characteristics can contribute to a better understanding of mitogenome evolution. RESULTS Here we systematically investigated mitogenome arrangements of 232 amphibians including four newly sequenced Dicroglossidae mitogenomes. The results showed that our new sequenced mitogenomes all possessed a trnM tandem duplication, which was not exclusive to Dicroglossidae. By merging the same arrangements, the mitogenomes of ~ 80% species belonged to the four major patterns, the major two of which were typical vertebrate arrangement and typical neobatrachian arrangement. Using qMGR for calculating rearrangement frequency (RF) (%), we found that the control region (CR) (RF = 45.04) and trnL2 (RF = 38.79) were the two most frequently rearranged components. Forty-seven point eight percentage of amphibians possessed rearranged mitogenomes including all neobatrachians and their distribution was significantly clustered in the phylogenetic trees (p < 0.001). In addition, we argued that the typical neobatrachian arrangement may have appeared in the Late Jurassic according to possible occurrence time estimation. CONCLUSION It was the first global census of amphibian mitogenome arrangements from the perspective of quantity statistics, which helped us to systematically understand the type, distribution, frequency and phylogenetic characteristics of these rearrangements.
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Affiliation(s)
- Jifeng Zhang
- School of Biological Engineering, Huainan Normal University, Huainan, Anhui, 232001, People's Republic of China.
- College of Life Science, Anhui Normal University, Wuhu, Anhui, 241000, People's Republic of China.
- Anhui Key Laboratory of Low Temperature Co-Fired Materials, Huainan Normal University, Huainan, 232001, People's Republic of China.
- Key Laboratory of Industrial Dust Prevention and Control and Occupational Health and Safety, Ministry of Education, Huainan, 232001, People's Republic of China.
- Anhui Shanhe Pharmaceutical Excipients Co., Ltd., Huainan, 232001, People's Republic of China.
| | - Guopen Miao
- School of Biological Engineering, Huainan Normal University, Huainan, Anhui, 232001, People's Republic of China
| | - Shunjie Hu
- School of Biological Engineering, Huainan Normal University, Huainan, Anhui, 232001, People's Republic of China
| | - Qi Sun
- School of Biological Engineering, Huainan Normal University, Huainan, Anhui, 232001, People's Republic of China
| | - Hengwu Ding
- College of Life Science, Anhui Normal University, Wuhu, Anhui, 241000, People's Republic of China
| | - Zhicheng Ji
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Pen Guo
- Life Science and Food Engineering College, Yibin University, Yibin, Sichuan, 644000, People's Republic of China
| | - Shoubao Yan
- School of Biological Engineering, Huainan Normal University, Huainan, Anhui, 232001, People's Republic of China
| | - Chengrun Wang
- School of Biological Engineering, Huainan Normal University, Huainan, Anhui, 232001, People's Republic of China
| | - Xianzhao Kan
- College of Life Science, Anhui Normal University, Wuhu, Anhui, 241000, People's Republic of China.
| | - Liuwang Nie
- College of Life Science, Anhui Normal University, Wuhu, Anhui, 241000, People's Republic of China.
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Zhang K, Zhu K, Liu Y, Zhang H, Gong L, Jiang L, Liu L, Lü Z, Liu B. Novel gene rearrangement in the mitochondrial genome of Muraenesox cinereus and the phylogenetic relationship of Anguilliformes. Sci Rep 2021; 11:2411. [PMID: 33510193 PMCID: PMC7844273 DOI: 10.1038/s41598-021-81622-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 12/30/2020] [Indexed: 01/30/2023] Open
Abstract
The structure and gene sequence of the fish mitochondrial genome are generally considered to be conservative. However, two types of gene arrangements are found in the mitochondrial genome of Anguilliformes. In this paper, we report a complete mitogenome of Muraenesox cinereus (Anguilliformes: Muraenesocidae) with rearrangement phenomenon. The total length of the M. cinereus mitogenome was 17,673 bp, and it contained 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNA genes, and two identical control regions (CRs). The mitochondrial genome of M. cinereus was obviously rearranged compared with the mitochondria of typical vertebrates. The genes ND6 and the conjoint trnE were translocated to the location between trnT and trnP, and one of the duplicated CR was translocated to the upstream of the ND6. The tandem duplication and random loss is most suitable for explaining this mitochondrial gene rearrangement. The Anguilliformes phylogenetic tree constructed based on the whole mitochondrial genome well supports Congridae non-monophyly. These results provide a basis for the future Anguilliformes mitochondrial gene arrangement characteristics and further phylogenetic research.
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Affiliation(s)
- Kun Zhang
- grid.443668.b0000 0004 1804 4247National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, Zhejiang 316022 People’s Republic of China ,grid.443668.b0000 0004 1804 4247National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 People’s Republic of China
| | - Kehua Zhu
- grid.443668.b0000 0004 1804 4247National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, Zhejiang 316022 People’s Republic of China ,grid.443668.b0000 0004 1804 4247National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 People’s Republic of China
| | - Yifan Liu
- grid.443668.b0000 0004 1804 4247National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, Zhejiang 316022 People’s Republic of China ,grid.443668.b0000 0004 1804 4247National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 People’s Republic of China
| | - Hua Zhang
- grid.9227.e0000000119573309Key Laboratory of Tropical Marine Bio-Resources and Ecology, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Li Gong
- grid.443668.b0000 0004 1804 4247National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, Zhejiang 316022 People’s Republic of China ,grid.443668.b0000 0004 1804 4247National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 People’s Republic of China
| | - Lihua Jiang
- grid.443668.b0000 0004 1804 4247National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, Zhejiang 316022 People’s Republic of China ,grid.443668.b0000 0004 1804 4247National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 People’s Republic of China
| | - Liqin Liu
- grid.443668.b0000 0004 1804 4247National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, Zhejiang 316022 People’s Republic of China ,grid.443668.b0000 0004 1804 4247National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 People’s Republic of China
| | - Zhenming Lü
- grid.443668.b0000 0004 1804 4247National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, Zhejiang 316022 People’s Republic of China ,grid.443668.b0000 0004 1804 4247National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 People’s Republic of China
| | - Bingjian Liu
- grid.443668.b0000 0004 1804 4247National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No. 1, Haida South Road, Zhoushan, Zhejiang 316022 People’s Republic of China ,grid.9227.e0000000119573309Key Laboratory of Tropical Marine Bio-Resources and Ecology, Chinese Academy of Sciences, Beijing, People’s Republic of China ,grid.443668.b0000 0004 1804 4247National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022 People’s Republic of China
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Hou H, Ye H, Wang Z, Wu J, Gao Y, Han W, Na D, Sun G, Wang Y. Demographic history and genetic differentiation of an endemic and endangered Ulmus lamellosa (Ulmus). BMC PLANT BIOLOGY 2020; 20:526. [PMID: 33203402 PMCID: PMC7672979 DOI: 10.1186/s12870-020-02723-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 10/26/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND Ulmus lamellosa (one of the ancient species of Ulmus) is an endemic and endangered plant that has undergone climatic oscillations and geographical changes. The elucidation of its demographic history and genetic differentiation is critical for understanding the evolutionary process and ecological adaption to forests in Northern China. RESULTS Polymorphic haplotypes were detected in most populations of U. lamellosa via DNA sequencing. All haplotypes were divided into three phylogeographic clades fundamentally corresponding to their geographical distribution, namely THM (Taihang Mountains), YM (Yinshan Mountains), and YSM (Yanshan Mountains) groups. The YSM group, which is regarded as ancestral, possessed higher genetic diversity and significant genetic variability in contrast to the YSM and YM groups. Meanwhile, the divergence time of intraspecies haplotypes occurred during the Miocene-Pliocene, which was associated with major Tertiary geological and/or climatic events. Different degrees of gene exchanges were identified between the three groups. During glaciation, the YSM and THM regions might have served as refugia for U. lamellosa. Based on ITS data, range expansion was not expected through evolutionary processes, except for the THM group. A series of mountain uplifts (e.g., Yanshan Mountains and Taihang Mountains) following the Miocene-Pliocene, and subsequently quaternary climatic oscillations in Northern China, further promoted divergence between U. lamellosa populations. CONCLUSIONS Geographical topology and climate change in Northern China played a critical role in establishing the current phylogeographic structural patterns of U. lamellosa. These results provide important data and clues that facilitate the demographic study of tree species in Northern China.
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Affiliation(s)
- Huimin Hou
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Hang Ye
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Zhi Wang
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Jiahui Wu
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Yue Gao
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Wei Han
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Dongchen Na
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
| | - Genlou Sun
- Saint Mary’s University, Halifax, Canada
| | - Yiling Wang
- School of Life Science, Shanxi Normal University, Linfen, 041000 P. R. China
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Behavior-dependent cis regulation reveals genes and pathways associated with bower building in cichlid fishes. Proc Natl Acad Sci U S A 2018; 115:E11081-E11090. [PMID: 30397142 PMCID: PMC6255178 DOI: 10.1073/pnas.1810140115] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Many behaviors are associated with heritable genetic variation [Kendler and Greenspan (2006) Am J Psychiatry 163:1683-1694]. Genetic mapping has revealed genomic regions or, in a few cases, specific genes explaining part of this variation [Bendesky and Bargmann (2011) Nat Rev Gen 12:809-820]. However, the genetic basis of behavioral evolution remains unclear. Here we investigate the evolution of an innate extended phenotype, bower building, among cichlid fishes of Lake Malawi. Males build bowers of two types, pits or castles, to attract females for mating. We performed comparative genome-wide analyses of 20 bower-building species and found that these phenotypes have evolved multiple times with thousands of genetic variants strongly associated with this behavior, suggesting a polygenic architecture. Remarkably, F1 hybrids of a pit-digging and a castle-building species perform sequential construction of first a pit and then a castle bower. Analysis of brain gene expression in these hybrids showed that genes near behavior-associated variants display behavior-dependent allele-specific expression with preferential expression of the pit-digging species allele during pit digging and of the castle-building species allele during castle building. These genes are highly enriched for functions related to neurodevelopment and neural plasticity. Our results suggest that natural behaviors are associated with complex genetic architectures that alter behavior via cis-regulatory differences whose effects on gene expression are specific to the behavior itself.
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