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Du K, Ricci JMB, Lu Y, Garcia-Olazabal M, Walter RB, Warren WC, Dodge TO, Schumer M, Park H, Meyer A, Schartl M. Phylogenomic analyses of all species of swordtail fishes (genus Xiphophorus) show that hybridization preceded speciation. Nat Commun 2024; 15:6609. [PMID: 39098897 PMCID: PMC11298535 DOI: 10.1038/s41467-024-50852-6] [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: 12/31/2023] [Accepted: 07/16/2024] [Indexed: 08/06/2024] Open
Abstract
Hybridization has been recognized to play important roles in evolution, however studies of the genetic consequence are still lagging behind in vertebrates due to the lack of appropriate experimental systems. Fish of the genus Xiphophorus are proposed to have evolved with multiple ancient and ongoing hybridization events. They have served as an informative research model in evolutionary biology and in biomedical research on human disease for more than a century. Here, we provide the complete genomic resource including annotations for all described 26 Xiphophorus species and three undescribed taxa and resolve all uncertain phylogenetic relationships. We investigate the molecular evolution of genes related to cancers such as melanoma and for the genetic control of puberty timing, focusing on genes that are predicted to be involved in pre-and postzygotic isolation and thus affect hybridization. We discovered dramatic size-variation of some gene families. These persisted despite reticulate evolution, rapid speciation and short divergence time. Finally, we clarify the hybridization history in the entire genus settling disputed hybridization history of two Southern swordtails. Our comparative genomic analyses revealed hybridization ancestries that are manifested in the mosaic fused genomes and show that hybridization often preceded speciation.
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Affiliation(s)
- Kang Du
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, TX, USA
| | | | - Yuan Lu
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, TX, USA
| | - Mateo Garcia-Olazabal
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, TX, USA
| | - Ronald B Walter
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, TX, USA
| | - Wesley C Warren
- Department of Animal Sciences, Department of Surgery, Institute for Data Science and Informatics, University of Missouri, Bond Life Sciences Center, Columbia, MI, USA
| | - Tristram O Dodge
- Department of Biology & Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Molly Schumer
- Department of Biology & Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Hyun Park
- Division of Biotechnology, College of Life Science and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany.
| | - Manfred Schartl
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, TX, USA.
- Developmental Biochemistry, Biocenter, University of Wuerzburg, Am Hubland, Wuerzburg, Germany.
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria.
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2
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Zhu S, Zhang N, Zhang J, Shao X, Guo Y, Cai D. Ancient Mitochondrial Genomes Provide New Clues in the History of the Akhal-Teke Horse in China. Genes (Basel) 2024; 15:790. [PMID: 38927726 PMCID: PMC11203007 DOI: 10.3390/genes15060790] [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: 05/14/2024] [Revised: 06/11/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
This study analyzed ancient DNA from the remains of horses unearthed from the Shihuyao tombs. These were found to date from the Han and Tang Dynasties in Xinjiang (approximately 2200 to 1100 years ago). Two high-quality mitochondrial genomes were acquired and analyzed using next-generation sequencing. The genomes were split into two maternal haplogroups, B and D, according to a study that included ancient and contemporary samples from Eurasia. A close genetic affinity was observed between the horse of the Tang Dynasty and Akhal-Teke horses according to the primitive horse haplotype G1. Historical evidence suggests that the ancient Silk Road had a vital role in their dissemination. Additionally, the matrilineal history of the Akhal-Teke horse was accessed and suggested that the early domestication of the breed was for military purposes.
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Affiliation(s)
- Siqi Zhu
- Department of Archaeology, School of History, Wuhan University, Wuhan 430072, China;
| | - Naifan Zhang
- Research Center for Chinese Frontier Archaeology of Jilin University, Changchun 130012, China; (N.Z.); (Y.G.)
- National Centre for Archaeology, Beijing 100013, China
| | - Jie Zhang
- Xinjiang Institute of Cultural Relics and Archaeology, Ürümqi 830011, China;
| | - Xinyue Shao
- Department of Archaeology, University of Southampton, Avenue Campus, Southampton SO17 1BF, UK;
| | - Yaqi Guo
- Research Center for Chinese Frontier Archaeology of Jilin University, Changchun 130012, China; (N.Z.); (Y.G.)
| | - Dawei Cai
- Research Center for Chinese Frontier Archaeology of Jilin University, Changchun 130012, China; (N.Z.); (Y.G.)
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Carcauzon V, Herrera JP, Kaufman K, Baudino F, Wickenkamp N, Randriamoria TM, Soarimalala V, Goodman SM, Nunn CL, Lebarbenchon C, Tortosa P. Astroviruses in terrestrial Malagasy mammals. PLoS Negl Trop Dis 2024; 18:e0012263. [PMID: 38875307 PMCID: PMC11262628 DOI: 10.1371/journal.pntd.0012263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/22/2024] [Accepted: 06/01/2024] [Indexed: 06/16/2024] Open
Abstract
Small terrestrial mammals are major hosts of infectious agents responsible for zoonotic diseases. Astroviruses (AstVs)-the cause of non-bacterial gastroenteritis mainly affecting young children-have been detected in a wide array of mammalian and avian host species. However, understanding the factors that influence AstV infection within and across hosts is limited. Here, we investigated the impact of land use changes on AstVs in terrestrial small mammals in rural northeastern Madagascar. We sampled 515 small mammals, representing seven endemic and four introduced species. Twenty-two positive samples were identified, all but one of which were found in the introduced species Mus musculus and Rattus rattus (family Muridae), with a positivity rate of 7.7% (6/78) and 5.6% (15/266), respectively. The non-introduced rodent case was from an endemic shrew-tenrec (family Tenrecidae). We found the highest positivity rate of AstVs infection in brushy regrowth (17.5%, 7/40) as compared to flooded rice fields (4.60%, 8/174), secondary forest (4.1%, 3/74), agroforest (3.6%, 1/28), village (2.61%, 3/115), and semi-intact forest (0%, 0/84). A phylogenetic analysis revealed an association between AstVs and their rodent host species. None of the viruses were phylogenetically related to AstVs previously described in Malagasy bats. This study supports AstV circulation in synanthropic animals in agricultural habitats of Madagascar and highlights the need to assess the spillover risk to human populations in rural areas.
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Affiliation(s)
- Victoria Carcauzon
- Université de La Réunion, Unité Mixte de Recherche Processus Infectieux en Milieu Insulaire Tropical (UMR PIMIT), CNRS 9192, INSERM 1187, IRD 249, Plateforme Technologique CYROI, Sainte Clotilde, La Réunion, France
| | - James P. Herrera
- Evolutionary Anthropology, Duke University, Durham, North Carolina, United States of America
- Duke Lemur Center SAVA Conservation, Durham, North Carolina, United States of America
| | - Kayla Kaufman
- Evolutionary Anthropology, Duke University, Durham, North Carolina, United States of America
- University of California Santa Barbara, Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, California, United States of America
| | - Fiona Baudino
- Université de La Réunion, Unité Mixte de Recherche Processus Infectieux en Milieu Insulaire Tropical (UMR PIMIT), CNRS 9192, INSERM 1187, IRD 249, Plateforme Technologique CYROI, Sainte Clotilde, La Réunion, France
| | - Natalie Wickenkamp
- Evolutionary Anthropology, Duke University, Durham, North Carolina, United States of America
| | | | | | - Steven M. Goodman
- Association Vahatra, Antananarivo, Madagascar
- Field Museum of Natural History, Chicago, Illinois, United States of America
| | - Charles L. Nunn
- Evolutionary Anthropology, Duke University, Durham, North Carolina, United States of America
- Duke Global Health Institute, Durham, North Carolina, United States of America
| | - Camille Lebarbenchon
- Université de La Réunion, Unité Mixte de Recherche Processus Infectieux en Milieu Insulaire Tropical (UMR PIMIT), CNRS 9192, INSERM 1187, IRD 249, Plateforme Technologique CYROI, Sainte Clotilde, La Réunion, France
| | - Pablo Tortosa
- Université de La Réunion, Unité Mixte de Recherche Processus Infectieux en Milieu Insulaire Tropical (UMR PIMIT), CNRS 9192, INSERM 1187, IRD 249, Plateforme Technologique CYROI, Sainte Clotilde, La Réunion, France
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Nosková E, Svobodová V, Hypská V, Cerezo-Echevarria A, Kurucová T, Ilík V, Modrý D, Pafčo B. High-throughput sequencing of Strongyloides stercoralis - a fatal disseminated infection in a dog. Parasitology 2024:1-7. [PMID: 38800868 DOI: 10.1017/s0031182024000568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
The rhabditid nematode Strongyloides stercoralis is known worldwide as the causative agent of strongyloidiasis in humans. In addition to public health concerns, S. stercoralis also infects dogs, which represent a possible reservoir for potentially zoonotic transmissions. We describe the first confirmed case of fatal disseminated infection in a dog in the Czech Republic. The microscopic and histological results were supported by a complex genotyping approach. Using high-throughput sequencing of the hypervariable region (HVR-IV) of 18S rDNA and Sanger sequencing of the partial cytochrome c oxidase subunit 1 gene (cox1), the potentially zoonotic haplotype/lineage A of S. stercoralis was confirmed, while the solely canine haplotype/lineage B was not found. The development of the disease is mainly associated with immunodeficiency, and in this case, it was triggered by inappropriate treatment, in particular the use of corticosteroids.
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Affiliation(s)
- Eva Nosková
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
- Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, 603 00 Brno, Czech Republic
| | - Vlasta Svobodová
- Department of Pathology and Parasitology, University of Veterinary Sciences Brno, Palackého třída 1946/1, 612 42, Brno, Czech Republic
| | - Vilma Hypská
- Veterinary centrum VIVA, Medkova 6, 500 02 Hradec Králové, Czech Republic
| | | | - Terézia Kurucová
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Vladislav Ilík
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
- Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, 603 00 Brno, Czech Republic
| | - David Modrý
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
- Department of Veterinary Sciences, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague, Czech Republic
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Barbora Pafčo
- Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, 603 00 Brno, Czech Republic
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Foučková M, Uhrová K, Kubánková A, Pánek T, Čepička I. Lighting lantern above Psalteriomonadidae: Unveiling novel diversity within the genus Psalteriomonas (Discoba: Heterolobosea). Eur J Protistol 2024; 93:126052. [PMID: 38302295 DOI: 10.1016/j.ejop.2024.126052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/09/2024] [Accepted: 01/09/2024] [Indexed: 02/03/2024]
Abstract
Psalteriomonadidae are a small family of anaerobic free-living protists belonging to Heterolobosea, Discoba. We cultured 74 new strains of mostly amoeboid Psalteriomonadidae obtained from mainly freshwater habitats and sequenced their 18S rRNA gene. Based on the phylogenetic analysis and genetic distances, we report multiple novel species, four of which we formally describe based on the light-microscopic morphology (Psalteriomonas minuta, P. australis, P. fimbriata, and P. parva). We also examined the ultrastructure of two Psalteriomonas species using transmission electron microscopy. We transfer Sawyeria marylandensis into the genus Psalteriomonas and synonymize Sawyeria with Psalteriomonas. In addition, we studied the flagellate stage of P. marylandensis comb. nov. for the first time, using light and scanning electron microscopy.
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Affiliation(s)
- Martina Foučková
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, Prague 128 00, Czech Republic
| | - Kristýna Uhrová
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, Prague 128 00, Czech Republic
| | - Aneta Kubánková
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, Prague 128 00, Czech Republic
| | - Tomáš Pánek
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, Prague 128 00, Czech Republic
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, Prague 128 00, Czech Republic.
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Gómez-Palacio A, Cruz-Saavedra L, Van den Broeck F, Geerts M, Pita S, Vallejo GA, Carranza JC, Ramírez JD. High-throughput analysis of the Trypanosoma cruzi minicirculome (mcDNA) unveils structural variation and functional diversity. Sci Rep 2024; 14:5578. [PMID: 38448494 PMCID: PMC10917808 DOI: 10.1038/s41598-024-56076-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 03/01/2024] [Indexed: 03/08/2024] Open
Abstract
Trypanosoma cruzi causes Chagas disease and has a unique extranuclear genome enclosed in a structure called the kinetoplast, which contains circular genomes known as maxi- and minicircles. While the structure and function of maxicircles are well-understood, many aspects of minicircles remain to be discovered. Here, we performed a high-throughput analysis of the minicirculome (mcDNA) in 50 clones isolated from Colombia's diverse T. cruzi I populations. Results indicate that mcDNA comprises four diverse subpopulations with different structures, lengths, and numbers of interspersed semi-conserved (previously termed ultra-conserved regions mHCV) and hypervariable (mHVPs) regions. Analysis of mcDNA ancestry and inter-clone differentiation indicates the interbreeding of minicircle sequence classes is placed along diverse strains and hosts. These results support evidence of the multiclonal dynamics and random bi-parental segregation. Finally, we disclosed the guide RNA repertoire encoded by mcDNA at a clonal scale, and several attributes of its abundance and function are discussed.
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Affiliation(s)
- Andrés Gómez-Palacio
- Laboratorio de Investigación en Genética Evolutiva, Universidad Pedagógica y Tecnológica de Colombia, Boyacá, Colombia
| | - Lissa Cruz-Saavedra
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Frederik Van den Broeck
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000, Leuven, Belgium
- Department of Biomedical Sciences, Institute of Tropical Medicine, 2000, Antwerp, Belgium
| | - Manon Geerts
- Fish Eco-Evo-Devo and Conservation, KU Leuven, 3000, Leuven, Belgium
- Directorate Taxonomy and Phylogeny, Royal Belgian Institute for Natural Sciences, 1000, Brussels, Belgium
| | - Sebastián Pita
- Sección Genética Evolutiva, Facultad de Ciencias, Universidad de La República, Montevideo, Uruguay
| | - Gustavo A Vallejo
- Laboratorio de Investigación en Parasitología Tropical, Facultad de Ciencias, Universidad del Tolima, Ibagué, Colombia
| | - Julio C Carranza
- Laboratorio de Investigación en Parasitología Tropical, Facultad de Ciencias, Universidad del Tolima, Ibagué, Colombia
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia.
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY, 10029, USA.
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Ferreiro D, Branco C, Arenas M. Selection among site-dependent structurally constrained substitution models of protein evolution by approximate Bayesian computation. Bioinformatics 2024; 40:btae096. [PMID: 38374231 PMCID: PMC10914458 DOI: 10.1093/bioinformatics/btae096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 01/15/2024] [Accepted: 02/16/2024] [Indexed: 02/21/2024] Open
Abstract
MOTIVATION The selection among substitution models of molecular evolution is fundamental for obtaining accurate phylogenetic inferences. At the protein level, evolutionary analyses are traditionally based on empirical substitution models but these models make unrealistic assumptions and are being surpassed by structurally constrained substitution (SCS) models. The SCS models often consider site-dependent evolution, a process that provides realism but complicates their implementation into likelihood functions that are commonly used for substitution model selection. RESULTS We present a method to perform selection among site-dependent SCS models, also among empirical and site-dependent SCS models, based on the approximate Bayesian computation (ABC) approach and its implementation into the computational framework ProteinModelerABC. The framework implements ABC with and without regression adjustments and includes diverse empirical and site-dependent SCS models of protein evolution. Using extensive simulated data, we found that it provides selection among SCS and empirical models with acceptable accuracy. As illustrative examples, we applied the framework to analyze a variety of protein families observing that SCS models fit them better than the corresponding best-fitting empirical substitution models. AVAILABILITY AND IMPLEMENTATION ProteinModelerABC is freely available from https://github.com/DavidFerreiro/ProteinModelerABC, can run in parallel and includes a graphical user interface. The framework is distributed with detailed documentation and ready-to-use examples.
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Affiliation(s)
- David Ferreiro
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, Universidade de Vigo, 36310 Vigo, Spain
| | - Catarina Branco
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, Universidade de Vigo, 36310 Vigo, Spain
| | - Miguel Arenas
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, Universidade de Vigo, 36310 Vigo, Spain
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Tang F, Jiao B, Zhang M, He M, Su R, Luo K, Lan T. PtoMYB031, the R2R3 MYB transcription factor involved in secondary cell wall biosynthesis in poplar. FRONTIERS IN PLANT SCIENCE 2024; 14:1341245. [PMID: 38298604 PMCID: PMC10828011 DOI: 10.3389/fpls.2023.1341245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 12/26/2023] [Indexed: 02/02/2024]
Abstract
Introduction The biosynthesis of the secondary cell wall (SCW) is orchestrated by an intricate hierarchical transcriptional regulatory network. This network is initiated by first-layer master switches, SCW-NAC transcription factors, which in turn activate the second-layer master switches MYBs. These switches play a crucial role in regulating xylem specification and differentiation during SCW formation. However, the roles of most MYBs in woody plants are yet to be fully understood. Methods In this study, we identified and isolated the R2R3-MYB transcription factor, PtoMYB031, from Populus tomentosa. We explored its expression, mainly in xylem tissues, and its role as a transcriptional repressor in the nucleus. We used overexpression and RNA interference techniques in poplar, along with Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays, to analyze the regulatory effects of PtoMYB031. Results Overexpression of PtoMYB031 in poplar significantly reduced lignin, cellulose, and hemicellulose content, and inhibited vascular development in stems, resulting in decreased SCW thickness in xylem tissues. Gene expression analysis showed that structural genes involved in SCW biosynthesis were downregulated in PtoMYB031-OE lines. Conversely, RNA interference of PtoMYB031 increased these compounds. Additionally, PtoMYB031 was found to recruit the repressor PtoZAT11, forming a transcriptional inhibition complex. Discussion Our findings provide new insights into how PtoMYB031, through its interaction with PtoZAT11, forms a complex that can suppress the expression of key regulatory genes, PtoWND1A and PtoWND2B, in SCW biosynthesis. This study enhances our understanding of the transcriptional regulation involved in SCW formation in poplar, highlighting the significant role of PtoMYB031.
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Affiliation(s)
- Feng Tang
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, China
| | - Bo Jiao
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, China
- Hebei Key Laboratory of Plant Genetic Engineering, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Meng Zhang
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, China
| | - Minghui He
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, China
| | - Ruiying Su
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, China
| | - Keming Luo
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, China
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Ting Lan
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, China
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Lin Y, Pascall DJ. Characterisation of putative novel tick viruses and zoonotic risk prediction. Ecol Evol 2024; 14:e10814. [PMID: 38259958 PMCID: PMC10800298 DOI: 10.1002/ece3.10814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 11/02/2023] [Accepted: 11/24/2023] [Indexed: 01/24/2024] Open
Abstract
Tick-associated viruses remain a substantial zoonotic risk worldwide, so knowledge of the diversity of tick viruses has potential health consequences. Despite their importance, large amounts of sequences in public data sets from tick meta-genomic and -transcriptomic projects remain unannotated, sequence data that could contain undocumented viruses. Through data mining and bioinformatic analysis of more than 37,800 public meta-genomic and -transcriptomic data sets, we found 83 unannotated contigs exhibiting high identity with known tick viruses. These putative viral contigs were classified into three RNA viral families (Alphatetraviridae, Orthomyxoviridae and Chuviridae) and one DNA viral family (Asfarviridae). After manual checking of quality and dissimilarity towards other sequences in the data set, these 83 contigs were reduced to five contigs in the Alphatetraviridae from four putative viruses, four in the Orthomyxoviridae from two putative viruses and one in the Chuviridae which clustered with known tick-associated viruses, forming a separate clade within the viral families. We further attempted to assess which previously known tick viruses likely represent zoonotic risks and thus deserve further investigation. We ranked the human infection potential of 133 known tick-associated viruses using a genome composition-based machine learning model. We found five high-risk tick-associated viruses (Langat virus, Lonestar tick chuvirus 1, Grotenhout virus, Taggert virus and Johnston Atoll virus) that have not been known to infect human and two viral families (Nairoviridae and Phenuiviridae) that contain a large proportion of potential zoonotic tick-associated viruses. This adds to the knowledge of tick virus diversity and highlights the importance of surveillance of newly emerging tick-associated diseases.
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Affiliation(s)
- Yuting Lin
- MRC Biostatistics UnitUniversity of CambridgeCambridgeUK
- Royal Veterinary CollegeUniversity of LondonLondonUK
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Mino S, Fukazawa S, Tsuchiya J, McNichol JC, Sievert SM, Yamaki S, Ando Y, Sawabe T. Hydrogenimonas cancrithermarum sp. nov., a hydrogen- and thiosulfate-oxidizing mesophilic chemolithoautotroph isolated from diffuse-flow fluids on the East Pacific Rise, and an emended description of the genus Hydrogenimonas. Int J Syst Evol Microbiol 2023; 73. [PMID: 37921642 DOI: 10.1099/ijsem.0.006132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023] Open
Abstract
A novel mesophilic, hydrogen- and thiosulfate-oxidizing bacterium, strain ISO32T, was isolated from diffuse-flow hydrothermal fluids from the Crab Spa vent on the East Pacific Rise. Cells of ISO32T were rods, being motile by means of a single polar flagellum. The isolate grew at a temperature range between 30 and 55 °C (optimum, 43 °C), at a pH range between 5.3 and 7.6 (optimum, pH 5.8) and in the presence of 2.0-4.0 % NaCl (optimum, 2.5 %). The isolate was able to grow chemolithoautotrophically with molecular hydrogen, thiosulfate or elemental sulfur as the sole electron donor. Thiosulfate, elemental sulfur, nitrate and molecular oxygen were each used as a sole electron acceptor. Phylogenetic analysis of 16S rRNA gene sequences placed ISO32T in the genus Hydrogenimonas of the class Epsilonproteobacteria, with Hydrogenimonas thermophila EP1-55-1 %T as its closest relative (95.95 % similarity). On the basis of the phylogenetic, physiological and genomic characteristics, it is proposed that the organism represents a novel species within the genus Hydrogenimonas, Hydrogenimonas cancrithermarum sp. nov. The type strain is ISO32T (=JCM 39185T =KCTC 25252T). Furthermore, the genomic properties of members of the genus Hydrogenimonas are distinguished from those of members of other thermophilic genera in the orders Campylobacterales (Nitratiruptor and Nitrosophilus) and Nautiliales (Caminibacter, Nautilia and Lebetimonas), with larger genome sizes and lower 16S rRNA G+C content values. Comprehensive metabolic comparisons based on genomes revealed that genes responsible for the Pta-AckA pathway were observed exclusively in members of mesophilic genera in the order Campylobacterales and of the genus Hydrogenimonas. Our results indicate that the genus Hydrogenimonas contributes to elucidating the evolutionary history of Epsilonproteobacteria in terms of metabolism and transition from a thermophilic to a mesophilic lifestyle.
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Affiliation(s)
- Sayaka Mino
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - So Fukazawa
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Jiro Tsuchiya
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Jesse C McNichol
- Biology Department, Woods Hole Oceanographic Institution, MA, USA
- Department of Biology, St. Francis Xavier University, NS, Canada
| | - Stefan M Sievert
- Biology Department, Woods Hole Oceanographic Institution, MA, USA
| | - Shogo Yamaki
- Laboratory of Marine Food Science and Technology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Yasuhiro Ando
- Laboratory of Marine Bioresources Chemistry, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Tomoo Sawabe
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
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11
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Liang J, Wu Z, Zhang X, Du X, Wang S, Yang Y, Wang Y, Wang Y, Yang H. Study on the Interactions of Cyclins with CDKs Involved in Auxin Signal during Leaf Development by WGCNA in Populus alba. Int J Mol Sci 2023; 24:13445. [PMID: 37686248 PMCID: PMC10487486 DOI: 10.3390/ijms241713445] [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: 06/30/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Cell division plays an indispensable role in leaf morphogenesis, which is regulated via the complexes formed by cyclin and cyclin-dependent kinase (CDK). In this study, gene family analysis, exogenous auxin stimulation, RNA-seq and WGCNA analysis were all used to investigate the molecular mechanisms by which cell-cycle-related factors participated in the auxin signaling pathway on leaf morphogenesis. Sixty-three cyclin members and seventeen CDK members in Populus alba were identified and systematically analyzed. During the evolution, WGD was the main reason that resulted in the expansion of cyclin and CDK genes. Firstly, after a short time treating with auxin to matured leaves of seedlings, genes related to cell division including GRF and ARGOS were both upregulated to restart the transition of cells from G1-to-S phase. Secondly, with three days of continuous auxin stimulation to leaves at different developmental stages, leaves area variation, transcriptomes and hormones were analyzed. By PCA, PCoA and WGCNA analyses, the turquoise module was both positively related to leaf development and auxin. Based on the co-expression analysis and Y2H experiment, PoalbCYCD1;4, PoalbCYCD3;3 and PoalbCYCD3;5 were supposed to interact with PoalbCDKA;1, which could be the trigger to promote the G1-to-S phase transition. The ARF transcription factor might play the key role of connecting the auxin signaling pathway and cell division in leaf morphogenesis by affecting CYC-CDK complexes.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Hailing Yang
- State Key Laboratory of Tree Genetics and Breeding, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100107, China; (J.L.); (Z.W.); (X.Z.); (X.D.); (S.W.); (Y.Y.); (Y.W.); (Y.W.)
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12
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Xu N, Du X, Zhang XX, Yang HL. The complete chloroplast genome of Salix lindleyana (salicaceae), a plateau plant species. Mitochondrial DNA B Resour 2023; 8:877-881. [PMID: 37614527 PMCID: PMC10443960 DOI: 10.1080/23802359.2023.2246675] [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: 03/06/2023] [Accepted: 08/04/2023] [Indexed: 08/25/2023] Open
Abstract
Salix lindleyana Wallich ex Andersson 1851 is a species of genus Salix which mainly grows on mountains above 3000 m at sea level in Qinghai-Tibetan Plateau (including the Himalayas and Hengduan Mountains). To determine its phylogenetic position within Salix, we reconstructed S. lindleyana complete chloroplast (cp) genome sequence by de novo assembly using whole-genome sequencing data. The completed chloroplast genome was 155,304 bp, with a total GC content of 36.7%. It had a very typical tetrad structure, including a large single-copy (LSC) region of 84,539 bp, a small single-copy (SSC) region of 16,161 bp, and two inverted repeats (IR) regions of 27,302 bp. A total of 132 functional genes were distributed in the chloroplast genome, including 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis showed that S. lindleyana was clustered with Salix dasyclados Wimmer 1849 and Salix variegata Franchet 1887. The complete chloroplast genome of S. lindleyana provides potential genetic resources for further phylogenetic studies.
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Affiliation(s)
- Nan Xu
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration; Institute of Tree Development and Genome Editing, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Xin Du
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration; Institute of Tree Development and Genome Editing, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Xiu-Xing Zhang
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration; Institute of Tree Development and Genome Editing, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Hai-Ling Yang
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration; Institute of Tree Development and Genome Editing, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
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13
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Brazão JM, Foster PG, Cox CJ. Data-specific substitution models improve protein-based phylogenetics. PeerJ 2023; 11:e15716. [PMID: 37576497 PMCID: PMC10416777 DOI: 10.7717/peerj.15716] [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: 02/17/2023] [Accepted: 06/16/2023] [Indexed: 08/15/2023] Open
Abstract
Calculating amino-acid substitution models that are specific for individual protein data sets is often difficult due to the computational burden of estimating large numbers of rate parameters. In this study, we tested the computational efficiency and accuracy of five methods used to estimate substitution models, namely Codeml, FastMG, IQ-TREE, P4 (maximum likelihood), and P4 (Bayesian inference). Data-specific substitution models were estimated from simulated alignments (with different lengths) that were generated from a known simulation model and simulation tree. Each of the resulting data-specific substitution models was used to calculate the maximum likelihood score of the simulation tree and simulated data that was used to calculate the model, and compared with the maximum likelihood scores of the known simulation model and simulation tree on the same simulated data. Additionally, the commonly-used empirical models, cpREV and WAG, were assessed similarly. Data-specific models performed better than the empirical models, which under-fitted the simulated alignments, had the highest difference to the simulation model maximum-likelihood score, clustered further from the simulation model in principal component analysis ordination, and inferred less accurate trees. Data-specific models and the simulation model shared statistically indistinguishable maximum-likelihood scores, indicating that the five methods were reasonably accurate at estimating substitution models by this measure. Nevertheless, tree statistics showed differences between optimal maximum likelihood trees. Unlike other model estimating methods, trees inferred using data-specific models generated with IQ-TREE and P4 (maximum likelihood) were not significantly different from the trees derived from the simulation model in each analysis, indicating that these two methods alone were the most accurate at estimating data-specific models. To show the benefits of using data-specific protein models several published data sets were reanalysed using IQ-TREE-estimated models. These newly estimated models were a better fit to the data than the empirical models that were used by the original authors, often inferred longer trees, and resulted in different tree topologies in more than half of the re-analysed data sets. The results of this study show that software availability and high computation burden are not limitations to generating better-fitting data-specific amino-acid substitution models for phylogenetic analyses.
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Affiliation(s)
- João M. Brazão
- Centro de Ciências do Mar, Universidade do Algarve, Faro, Algarve, Portugal
| | - Peter G. Foster
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Cymon J. Cox
- Centro de Ciências do Mar, Universidade do Algarve, Faro, Algarve, Portugal
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14
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Poláková K, Bourland WA, Čepička I. Anaerocyclidiidae fam. nov. (Oligohymenophorea, Scuticociliatia): A newly recognized major lineage of anaerobic ciliates hosting prokaryotic symbionts. Eur J Protistol 2023; 90:126009. [PMID: 37562169 DOI: 10.1016/j.ejop.2023.126009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 06/21/2023] [Accepted: 07/15/2023] [Indexed: 08/12/2023]
Abstract
The research on anaerobic ciliates, to date, has mainly been focused on representatives of obligately anaerobic classes such as Armophorea or Plagiopylea. In this study, we focus on the anaerobic representatives of the subclass Scuticociliatia, members of the class Oligohymenophorea, which is mainly composed of aerobic ciliates. Until now, only a single anaerobic species, Cyclidium porcatum (here transferred to the genus Anaerocyclidium gen. nov.), has been described both molecularly and morphologically. Our broad sampling of anoxic sediments together with cultivation and single cell sequencing approaches have shown that scuticociliates are common and diversified in anoxic environments. Our results show that anaerobic scuticociliates represent a distinctive evolutionary lineage not closely related to the family Cyclidiidae (order Pleuronematida), as previously suggested. However, the phylogenetic position of the newly recognized lineage within the subclass Scuticociliatia remains unresolved. Based on molecular and morphological data, we establish the family Anaerocyclidiidae fam. nov. to accommodate members of this clade. We further provide detailed morphological descriptions and 18S rRNA gene sequences for six new Anaerocyclidium species and significantly broaden the described diversity of anaerobic scuticociliates.
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Affiliation(s)
- Kateřina Poláková
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 00 Prague, Czech Republic.
| | - William A Bourland
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 00 Prague, Czech Republic
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 00 Prague, Czech Republic
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15
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Nejat F, Benovics M, Řehulková E, Vukić J, Šanda R, Kaya C, Tarkan AS, Abdoli A, Aksu S, Šimková A. Diversity, phylogeny and intraspecific variability of Paradiplozoon species (Monogenea: Diplozoidae) parasitizing endemic cyprinoids in the Middle East. Parasitology 2023; 150:705-722. [PMID: 37157105 PMCID: PMC10410381 DOI: 10.1017/s0031182023000446] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 04/23/2023] [Accepted: 04/24/2023] [Indexed: 05/10/2023]
Abstract
Diplozoidae are common monogenean ectoparasites of cyprinoid fish, with the genus Paradiplozoon being the most diversified. Despite recent studies on Diplozoidae from Europe, Africa and Asia, the diversity, distribution and phylogeny of this parasite group appears to be still underestimated in the Middle East. The objective of this study was to investigate the diversity, endemism and host specificity of diplozoids parasitizing cyprinoid fish from the Middle East, considering this region as an important historical interchange of fish fauna, and to elucidate the phylogenetic position of Middle Eastern Paradiplozoon species within Diplozoidae. Four Paradiplozoon species were collected from 48 out of 94 investigated cyprinoid species. Three known species, Paradiplozoon homoion, Paradiplozoon bliccae and Paradiplozoon bingolensis, were recorded on new cyprinoid host species, and a new species, Paradiplozoon koubkovae n. sp., was recorded on Luciobarbus capito and Capoeta capoeta from the Caspian Sea basin in Iran and Turkey. Paradiplozoon bliccae, exhibiting a wide host range in the Middle East, expressed both morphological and genetic intraspecific variabilities. The four Paradiplozoon species collected in the Middle East were placed in divergent clades, showing the rich evolutionary history of diplozoid parasites in the Middle East. Our study also revealed that two lineages of African diplozoids have a Middle Eastern origin. We stress the importance of applying an integrative approach combining morphological, ecological and molecular methods to reveal the real diversity of diplozoids.
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Affiliation(s)
- Farshad Nejat
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Michal Benovics
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Eva Řehulková
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Jasna Vukić
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague 2 128 44, Czech Republic
| | - Radek Šanda
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague 2 128 44, Czech Republic
- Department of Zoology, National Museum, Václavské náměstí 68, Prague 1 110 00, Czech Republic
| | - Cüneyt Kaya
- Faculty of Fisheries, Recep Tayyip Erdogan University, 53100 Rize, Turkey
| | - Ali Serhan Tarkan
- Department of Basic Sciences, Faculty of Fisheries, Muğla Sıtkı Koçman University, 48000 Menteşe, Muğla, Turkey
| | - Asghar Abdoli
- Department of Biodiversity and Ecosystem Management, Environmental Science Research Institute, Shahid Beheshti University, Shahid Shahriari Sq. Velenjak, 1983969411 Tehran, Iran
| | - Sadi Aksu
- Vocational School of Health Services, Eskişehir Osmangazi University, Büyükdere Meşelik Yerleşkesi, 26040 Eskişehir, Turkey
| | - Andrea Šimková
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
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16
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Kumar L, Ahlawat B, Kumar S, Mushrif-Tripathy V, Rai N. Maternal Ancestry of First Parsi Settlers of India Using Ancient Mitogenome. Mitochondrion 2023:S1567-7249(23)00055-7. [PMID: 37379890 DOI: 10.1016/j.mito.2023.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/18/2023] [Accepted: 06/25/2023] [Indexed: 06/30/2023]
Abstract
The rich cultural and genetic diversity of South Asia emerged from multiple migrations and cultural assimilation of multiple waves of migrants. The Parsi community of North-western India were one of those who migrated from West Eurasia in the aftermath of 7th century CE and assimilated into the local cultural framework. Earlier genetic studies further strengthened this notion with the finding that they harbour both Middle Eastern and South Asian genetic components. Although these studies covered both autosomal and uniparental markers, still maternal ancestry was not covered in depth and with good resolution of mitochondrial markers. Hence in our current study, we have first time generated a complete mitogenome of 19 ancient samples of the first Parsi settlers excavated from the archaeological site of Sanjan and performed detailed phylogenetic analysis to infer their maternal genetic affinity. In our analysis, we found that the Parsi mitogenome with mtDNA haplogroup M3a1+204 shares clade with both Middle Eastern and South Asian modern individuals in both the Maximum Likelihood tree and Bayesian phylogenetic tree. This haplogroup was also prevalent among the medieval Swat valley population of present-day Northern Pakistan and was also observed in two Roopkund A individuals. In the phylogenetic network this sample share haplotype with both South Asian and Middle Eastern samples. So conclusively, the first Parsi settlers' maternal ancestry encompasses both South Asian and Middle Eastern genetic composition.
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Affiliation(s)
- Lomous Kumar
- Birbal Sahni Institute of Palaeosciences, Lucknow, 226007, India
| | - Bhavna Ahlawat
- Birbal Sahni Institute of Palaeosciences, Lucknow, 226007, India; Department of Anthropology, Panjab University, Chandigarh, 160014, India
| | - Sachin Kumar
- Birbal Sahni Institute of Palaeosciences, Lucknow, 226007, India
| | - Veena Mushrif-Tripathy
- Department of Archaeology, Deccan College Post-Graduate and Research Institute, Pune, Maharashtra, 411006, India
| | - Niraj Rai
- Birbal Sahni Institute of Palaeosciences, Lucknow, 226007, India.
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17
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Guan Y, Chang G, Zhao J, Wang Q, Qin J, Tang M, Wang S, Ma L, Ma J, Sun G, Zhou Y, Huang J. Parallel evolution of two AIM24 protein subfamilies and their conserved functions in ER stress tolerance in land plants. PLANT COMMUNICATIONS 2023; 4:100513. [PMID: 36578211 DOI: 10.1016/j.xplc.2022.100513] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 11/25/2022] [Accepted: 12/23/2022] [Indexed: 05/11/2023]
Abstract
Despite decades of efforts in genome sequencing and functional characterization, some important protein families remain poorly understood. In this study, we report the classification, evolution, and functions of the largely uncharacterized AIM24 protein family in plants, including the identification of a novel subfamily. We show that two AIM24 subfamilies (AIM24-A and AIM24-B) are commonly distributed in major plant groups. These two subfamilies not only have modest sequence similarities and different gene structures but also are of independent bacterial ancestry. We performed comparative functional investigations on the two AIM24 subfamilies using three model plants: the moss Physcomitrium patens, the liverwort Marchantia polymorpha, and the flowering plant Arabidopsis thaliana. Intriguingly, despite their significant differences in sequence and gene structure, both AIM24 subfamilies are involved in ER stress tolerance and the unfolded protein response (UPR). In addition, transformation of the AIM24-A gene from P. patens into the AIM24-B null mutant of A. thaliana could at least partially rescue ER stress tolerance and the UPR. We also discuss the role of AIM24 genes in plant development and other cellular activities. This study provides a unique example of parallel evolution in molecular functions and can serve as a foundation for further investigation of the AIM24 family in plants.
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Affiliation(s)
- Yanlong Guan
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Guanxiao Chang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Jinjie Zhao
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Qia Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Jiali Qin
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Mengmeng Tang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Shuanghua Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Lan Ma
- Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Jianchao Ma
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Guiling Sun
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Yun Zhou
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Jinling Huang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China; Department of Biology, East Carolina University, Greenville, NC 27858, USA.
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18
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Nosková E, Modrý D, Baláž V, Červená B, Jirků-Pomajbíková K, Zechmeisterová K, Leowski C, Petrželková KJ, Pšenková I, Vodička R, Kessler SE, Ngoubangoye B, Setchell JM, Pafčo B. Identification of potentially zoonotic parasites in captive orangutans and semi-captive mandrills: Phylogeny and morphological comparison. Am J Primatol 2023; 85:e23475. [PMID: 36776131 DOI: 10.1002/ajp.23475] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 12/12/2022] [Accepted: 01/23/2023] [Indexed: 02/14/2023]
Abstract
Cysts and trophozoites of vestibuliferid ciliates and larvae of Strongyloides were found in fecal samples from captive orangutans Pongo pygmaeus and P. abelii from Czech and Slovak zoological gardens. As comparative material, ciliates from semi-captive mandrills Mandrillus sphinx from Gabon were included in the study. Phylogenetic analysis of the detected vestibuliferid ciliates using ITS1-5.8s-rRNA-ITS2 and partial 18S ribosomal deoxyribonucleic acid (rDNA) revealed that the ciliates from orangutans are conspecific with Balantioides coli lineage A, while the ciliates from mandrills clustered with Buxtonella-like ciliates from other primates. Morphological examination of the cysts and trophozoites using light microscopy did not reveal differences robust enough to identify the genera of the ciliates. Phylogenetic analysis of detected L1 larvae of Strongyloides using partial cox1 revealed Strongyloides stercoralis clustering within the cox1 lineage A infecting dogs, humans, and other primates. The sequences of 18S rDNA support these results. As both B. coli and S. stercoralis are zoonotic parasites and the conditions in captive and semi-captive settings may facilitate transmission to humans, prophylactic measures should reflect the findings.
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Affiliation(s)
- Eva Nosková
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary Sciences, Brno, Czech Republic
| | - David Modrý
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Department of Veterinary Sciences, Faculty of Agrobiology, Food and Natural Resources/CINeZ, Czech University of Life Sciences , Prague, Czech Republic
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Vojtech Baláž
- Department of Ecology and Diseases of Zoo Animals, Game, Fish and Bees, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences, Brno, Czech Republic
| | - Barbora Červená
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary Sciences, Brno, Czech Republic
| | | | | | - Clotilde Leowski
- Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary Sciences, Brno, Czech Republic
| | - Klára J Petrželková
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Liberec Zoo, Liberec, Czech Republic
| | | | | | - Sharon E Kessler
- Department of Psychology, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland
| | - Barthélémy Ngoubangoye
- Centre de Primatologie, Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
- Department of Anthropology, and Behaviour, Ecology and Evolution Research Centre, Durham University, Durham, UK
| | - Joanna M Setchell
- Centre de Primatologie, Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
- Department of Anthropology, and Behaviour, Ecology and Evolution Research Centre, Durham University, Durham, UK
| | - Barbora Pafčo
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
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19
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Leal CV, Salani S, de Moraes FC, de Moura RL, Thompson FL, Hajdu E. Lost characters and lost taxonomists: Coelocarteriidae fam. nov., Poecilosclerida with and without chelae, to accommodate supposed phloeodictyids (Haplosclerida). INVERTEBR SYST 2023. [DOI: 10.1071/is22017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Abstract
The taxonomic study of Great Amazon Reef System sponges yielded three Oceanapia-like (Phloeodictyidae, Haplosclerida) species of similar gross morphology, two preliminarily identified as O. bartschi and another as Coelocarteria (Poecilosclerida), due to the presence of common palmate isochelae. The remarkable overall similarity of all three species in gross morphology necessitated an integrative assessment of the phylogenetic affinities. A selection of haplosclerid and poecilosclerid sequences (18S and 28S rRNA) was gathered from Genbank and compared to sequences mapped to reference from metagenome of two Oceanapia-like species from the Amazon River mouth, one of which matched O. bartschi. Both Brazilian species clustered with Coelocarteria singaporensis (Singapore). These species nest in the Poecilosclerida, far from Oceanapia (sp. and isodictyiformis) and other haplosclerids (Amphimedon, Petrosia, Siphonodictyon and Xestospongia) but also far from the poecilosclerid Isodictya that is currently classified in the same family as Coelocarteria, the Isodictyidae. Specimens with chelae are named Coelocarteria alcoladoi sp. nov. herein, while those without chelae represent the other two species. One matched Inflatella bartschi (O. bartchi’s holotype, here re-examined), thereby supporting the transfer of this species to Coelocarteria. The other is proposed as C. amadoi sp. nov. and is the second known lipochelous species in this genus. The 28S phylogenies recovered Coelocarteria bartschi comb. nov. (formerly Oceanapia bartschi) in the Poecilosclerida clade that clustered with Coelocarteria spp., including the type species of this genus, C. singaporensis, with 100% support. Coelocarteria alcoladoi sp. nov., also without chelae, grouped in the same clade, thereby corroborating the classification in this genus. The clade composed of Coelocarteria spp. grouped with Cornulella sp., suggesting an affinity between these genera. Coelocarteria is currently situated within Isodictyidae and Cornulella in Acarnidae. Isodictya (Isodictyidae) grouped with Amphilectus (Esperiopsidae) with high support and is only distantly related to Coelocarteria. Acarnus (Acarnidae) grouped with Clathria, also with high support, far from Coelocarteria and Cornulella. These results suggest the polyphyletic nature of Isodictyidae and Acarnidae, for which reason we preferred to propose a new, currently monotypic family for Coelocarteria spp., Coelocarteriidae fam. nov. ZooBank: urn:lsid:zoobank.org:pub:71FDB6FD-4A5F-4180-8DA7-79EA4CB615D1
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Han J, Wang X, Niu S. Genome-Wide Identification of 2-Oxoglutarate and Fe (II)-Dependent Dioxygenase (2ODD-C) Family Genes and Expression Profiles under Different Abiotic Stresses in Camellia sinensis (L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:1302. [PMID: 36986990 PMCID: PMC10051519 DOI: 10.3390/plants12061302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 02/27/2023] [Accepted: 03/11/2023] [Indexed: 06/19/2023]
Abstract
The 2-oxoglutarate and Fe (II)-dependent dioxygenase (2ODD-C) family of 2-oxoglutarate-dependent dioxygenases potentially participates in the biosynthesis of various metabolites under various abiotic stresses. However, there is scarce information on the expression profiles and roles of 2ODD-C genes in Camellia sinensis. We identified 153 Cs2ODD-C genes from C. sinensis, and they were distributed unevenly on 15 chromosomes. According to the phylogenetic tree topology, these genes were divided into 21 groups distinguished by conserved motifs and an intron/exon structure. Gene-duplication analyses revealed that 75 Cs2ODD-C genes were expanded and retained after WGD/segmental and tandem duplications. The expression profiles of Cs2ODD-C genes were explored under methyl jasmonate (MeJA), polyethylene glycol (PEG), and salt (NaCl) stress treatments. The expression analysis showed that 14, 13, and 49 Cs2ODD-C genes displayed the same expression pattern under MeJA and PEG treatments, MeJA and NaCl treatments, and PEG and NaCl treatments, respectively. A further analysis showed that two genes, Cs2ODD-C36 and Cs2ODD-C21, were significantly upregulated and downregulated after MeJA, PEG, and NaCl treatments, indicating that these two genes played positive and negative roles in enhancing the multi-stress tolerance. These results provide candidate genes for the use of genetic engineering technology to modify plants by enhancing multi-stress tolerance to promote phytoremediation efficiency.
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Genome-wide identification, expression profile and evolutionary relationships of TPS genes in the neotropical fruit tree species Psidium cattleyanum. Sci Rep 2023; 13:3930. [PMID: 36894661 PMCID: PMC9998390 DOI: 10.1038/s41598-023-31061-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 03/06/2023] [Indexed: 03/11/2023] Open
Abstract
Terpenoids are essential for plant growth, development, defense, and adaptation mechanisms. Psidium cattleyanum (Myrtaceae) is a fleshy fruit tree species endemics from Atlantic Forest, known for its pleasant fragrance and sweet taste, attributed to terpenoids in its leaves and fruits. In this study, we conducted genome-wide identification, evolutionary and expression analyses of the terpene synthase gene (TPS) family in P. cattleyanum red guava (var. cattleyanum), and yellow guava (var. lucidum Hort.) morphotypes. We identified 32 full-length TPS in red guava (RedTPS) and 30 in yellow guava (YlwTPS). We showed different expression patterns of TPS paralogous in the two morphotypes, suggesting the existence of distinct gene regulation mechanisms and their influence on the final essential oil content in both morphotypes. Moreover, the oil profile of red guava was dominated by 1,8-cineole and linalool and yellow guava was enriched in α-pinene, coincident in proportion to TPS-b1 genes, which encode enzymes that produce cyclic monoterpenes, suggesting a lineage-specific subfamily expansion of this family. Finally, we identified amino acid residues near the catalytic center and functional areas under positive selection. Our findings provide valuable insights into the terpene biosynthesis in a Neotropical Myrtaceae species and their potential involvement in adaptation mechanisms.
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Méndez-Sánchez D, Pomahač O, Rotterová J, Bourland WA, Čepička I. Morphology and phylogenetic position of three anaerobic ciliates from the classes Odontostomatea and Muranotrichea (Ciliophora). J Eukaryot Microbiol 2023; 70:e12965. [PMID: 36727275 DOI: 10.1111/jeu.12965] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 12/17/2022] [Accepted: 01/27/2023] [Indexed: 02/03/2023]
Abstract
The diversity of the classes Odontostomatea and Muranotrichea, which contain solely obligate anaerobes, is poorly understood. We studied two populations of Mylestoma sp., one of Saprodinium dentatum (Odontostomatea), two of Muranothrix felix sp. nov., and one of Muranothrix sp. (Muranotrichea) employing live observation, protargol impregnation, scanning electron microscopy, and 18S rRNA gene sequencing. Conspecificity of Mylestoma sp., described here, with a previously described species of this genus cannot be excluded since no species have been studied with modern methods. Phylogenetically, the genus Mylestoma is closely related to the odontostomatid Discomorphella pedroeneasi, although the phylogenetic position of class Odontostomatea itself remains unresolved. The newly described muranotrichean species, Muranothrix felix sp. nov., is morphologically similar to M. gubernata but can be distinguished by its fewer macronuclear nodules and fewer adoral membranelles; moreover, it is clearly distinguished from M. gubernata by its 18S rRNA gene sequence. Another population, designated here as Muranothrix sp., most likely represents a separate species.
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Affiliation(s)
- Daniel Méndez-Sánchez
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Ondřej Pomahač
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Johana Rotterová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.,Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, USA
| | - William A Bourland
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
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Guerra Y, Armijos‐Jaramillo V, Pons T, Tejera E, Berry C. Canonical or noncanonical? Structural plasticity of serine protease-binding loops in Kunitz-STI protease inhibitors. Protein Sci 2023; 32:e4570. [PMID: 36660780 PMCID: PMC9885459 DOI: 10.1002/pro.4570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 12/08/2022] [Accepted: 01/13/2023] [Indexed: 01/21/2023]
Abstract
The Kunitz-Soybean Trypsin Inhibitor (Kunitz-STI) family is a large family of proteins with most of its members being protease inhibitors. The versatility of the inhibitory profile and the structural plasticity of these proteins, make this family a promising scaffold for designing new multifunctional proteins. Historically, Kunitz-STI inhibitors have been classified as canonical serine protease inhibitors, but new inhibitors with novel inhibition mechanisms have been described in recent years. Different inhibition mechanisms could be the result of different evolutionary pathways. In the present work, we performed a structural analysis of all the crystallographic structures available for Kunitz-STI inhibitors to characterize serine protease-binding loop structural features and locations. Our study suggests a relationship between the conformation of serine protease-binding loops and the inhibition mechanism, their location in the β-trefoil fold, and the plant source of the inhibitors. The classical canonical inhibitors of this family are restricted to plants from the Fabales order and bind their targets via the β4-β5 loop, whereas serine protease-binding loops in inhibitors from other plants lie mainly in the β5-β6 and β9-β10 loops. In addition, we found that the β5-β6 loop is used to inhibit two different families of serine proteases through a steric blockade inhibition mechanism. This work will help to change the general perception that all Kunitz-STI inhibitors are canonical inhibitors and proteins with protease-binding loops adopting noncanonical conformations are exceptions. Additionally, our results will help in the identification of protease-binding loops in uncharacterized or newly discovered inhibitors, and in the design of multifunctional proteins.
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Affiliation(s)
- Yasel Guerra
- Ingeniería en Biotecnología, Facultad de Ingeniería y Ciencias AplicadasUniversidad de Las AméricasQuitoEcuador
- Grupo de Bio‐QuimioinformáticaUniversidad de Las AméricasQuitoEcuador
| | - Vinicio Armijos‐Jaramillo
- Ingeniería en Biotecnología, Facultad de Ingeniería y Ciencias AplicadasUniversidad de Las AméricasQuitoEcuador
- Grupo de Bio‐QuimioinformáticaUniversidad de Las AméricasQuitoEcuador
| | - Tirso Pons
- Department of Immunology and OncologyNational Centre for Biotechnology (CNB‐CSIC)MadridSpain
| | - Eduardo Tejera
- Ingeniería en Biotecnología, Facultad de Ingeniería y Ciencias AplicadasUniversidad de Las AméricasQuitoEcuador
- Grupo de Bio‐QuimioinformáticaUniversidad de Las AméricasQuitoEcuador
| | - Colin Berry
- Cardiff School of BiosciencesCardiff UniversityCardiffUK
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Pratylenchus Araucensis (Rhabditida: Pratylenchidae) a Widely Distributed Nematode in Musa Spp. from Colombia. J Nematol 2023; 54:20220057. [PMID: 36742266 PMCID: PMC9871600 DOI: 10.2478/jofnem-2022-0057] [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: 09/16/2022] [Indexed: 01/09/2023] Open
Abstract
Pratylenchus is one of the most limiting nematodes of Musaceae production in the world. Knowledge of the nematode species is one of the requirements for its management in the field. This study aimed to identify up to the species level Pratylenchus populations associated with plantain and banana crops in the states of Caldas, Quindío, and Valle del Cauca in Colombia. In these regions, Pratylenchus has been reported to affect these crops in the past, but with records of the nematode only up to the genus level. For this purpose, five populations of Pratylenchus extracted from samples composed of roots and rhizospheric soil, four from plantain and one from banana, were identified through morphological, morphometric, and molecular analysis (sequencing of the D2-D3 of rRNA and cytochrome oxidase subunit I of mtDNA). All populations were identified as P. araucensis, a species reported previously in eastern Colombia, and one that the present study found in the center and southwest of the country, indicating that this species of nematode is widely distributed in the Musaceae-producing areas of Colombia. The present study reports the first COI mtDNA sequences for this species of nematode.
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25
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Bakalin VA, Vilnet AA, Maltseva YD, Klimova KG, Bakalin DA, Choi SS. Hidden Diversity within Tetralophozia filiformis (Marchantiophyta, Anastrophyllaceae) in East Asia. PLANTS (BASEL, SWITZERLAND) 2022; 11:3121. [PMID: 36432850 PMCID: PMC9698241 DOI: 10.3390/plants11223121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/07/2022] [Accepted: 11/11/2022] [Indexed: 06/16/2023]
Abstract
Tetralophozia filiformis s.l. is known from a number of localities mostly in amphi-oceanic areas in Northern Hemisphere, including Atlantic Europe, amphi-Pacific Asia, South Siberia, and western North America. The newly obtained collections of this 'species' show strong variation in morphology of the taxon across amphi-Pacific Asia although connected by some 'intergrading' modifications. This implies the genetic diversity within this unit earlier recognized as a single taxon. Authors used molecular-genetic, morphological, and chorological methods to understand if the geographically correlated morphological variation also correlates with genetic differences and if it is possible to distinguish some additional taxa within the series of specimens originating from the various areas in amphi-Pacific Asia. It was found that Tetralophozia filiformis is a complex of at least three morphologically similar species, including one long forgotten name (Chandonanthus pusillus) that should be reinstated as separate species and one taxon (Tetralophozia sibirica) that should be described as new. Tetralophozia filiformis and Chandonanthus pusillus are lectotypified, and the new combination is provided for the latter. The three accepted taxa distinctly differ one from another in distribution patterns, preferable climate characteristics, and genetic distances, besides minor differentiations in morphology. The main morphological distinguishing features are the leaf cell size, height of undivided part in leaf lamina, and leaf dentation characteristics. Taking into account the robust correlation between the climate-based and molecular-genetic-based clusters, one more (fourth) taxon could be probably segregated from Tetralophozia filiformis.
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Affiliation(s)
- Vadim A. Bakalin
- Laboratory of Cryptogamic Biota, Botanical Garden-Institute FEB RAS, Makovskogo Street 142, 690024 Vladivostok, Russia
| | - Anna A. Vilnet
- Polar-Alpine Botanical Garden-Institute of the Russian Academy of Sciences, Fersmana Street, 18A, Apatity, 184209 Murmansk, Russia
| | - Yulia D. Maltseva
- Laboratory of Cryptogamic Biota, Botanical Garden-Institute FEB RAS, Makovskogo Street 142, 690024 Vladivostok, Russia
| | - Ksenia G. Klimova
- Laboratory of Cryptogamic Biota, Botanical Garden-Institute FEB RAS, Makovskogo Street 142, 690024 Vladivostok, Russia
| | - Daniil A. Bakalin
- AXiiO Oy Company, Hämeentie, 135 A, Helsinki XR Center, 00560 Helsinki, Finland
| | - Seung Se Choi
- Team of National Ecosystem Survey, National Institute of Ecology, Seocheon 33657, Republic of Korea
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Hypo-Osmoregulatory Roles of Vasotocinergic and Isotocinergic Systems in the Intestines of Two European Sea Bass Lineages. Int J Mol Sci 2022; 23:ijms232113636. [PMID: 36362422 PMCID: PMC9655083 DOI: 10.3390/ijms232113636] [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: 10/04/2022] [Revised: 10/25/2022] [Accepted: 10/31/2022] [Indexed: 11/09/2022] Open
Abstract
European sea bass (Dicentrarchus labrax) are a major aquaculture species that live in habitats with fluctuating salinities that are sometimes higher than in seawater (SW). Atlantic and West-Mediterranean genetic lineages were compared regarding intestinal neuropeptide receptor expression in SW (36%) and following a two-week transfer to hypersalinity (HW, 55%). Phylogenetic analysis revealed seven neuropeptide receptors belonging to the arginine vasotocine (AVTR) family and two isotocin receptors (ITR). Among AVTR paralogs, the highest mRNA levels were recorded for v1a2, with a two- to fourfold upregulation in the European sea bass intestinal sections after transfer of fish to HW. Principal component analysis in posterior intestines showed that v1a2 expression grouped together with the expression and activity of main ion transporters and channels involved in solute-coupled water uptake, indicating a possible role of this receptor in triggering water absorption. v1a1 expression, however, was decreased or did not change after transfer to hypersaline water. Among ITR paralogs, itr1 was the most expressed paralog in the intestine and opposite expression patterns were observed following salinity transfer, comparing intestinal sections. Overall, different expression profiles were observed between genetic lineages for several analyzed genes which could contribute to different osmotic stress-related responses in D. labrax lineages.
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27
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Study on the interaction preference between CYCD subclass and CDK family members at the poplar genome level. Sci Rep 2022; 12:16805. [PMID: 36207355 PMCID: PMC9547009 DOI: 10.1038/s41598-022-20800-9] [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: 05/16/2022] [Accepted: 09/19/2022] [Indexed: 12/31/2022] Open
Abstract
Cyclin-dependent kinases (CDKs) control the progression of the cell cycle. D-type cyclin (CYCD) is generally believed to form a complex with CDK and control the G1/S transition. In plants, CYCD and CDK gene families can be divided into 6 (D1-D7) and 7 (CDKA-CDKG) subclasses, respectively. Different subclasses in the CYCD and CDK families have different numbers, structures and functions. In some heterologous woody plants, the functions of these subclass family members remain unclear. In this study, 43 CYCD and 27 CDK gene family members were identified in the allodiploid Populus tomentosa Carr. Phylogenetic analysis suggested that these CYCDs and CDKs were divided into 6 and 7 subclasses, respectively, which were the same as other species. The analysis of protein properties, gene structure, motifs, domains, cis-acting elements and tissue-specific expression of all members of these CYCDs and CDKs showed that the differences between members of different subclasses varied widely, but members of the same subclass especially in the CDK gene family were very similar. These findings also demonstrated a strong correlation between CYCD and CDK gene family members in response to hormones and specific expression. The collinear analysis of P. tomentosa, Populus trichocarpa and Arabidopsis thaliana showed that the expansion patterns of CYCD and CDK gene families were predominantly whole genome duplications (WGD). The protein interaction prediction results of different subclasses of CYCD and CDKs showed that the interaction between different subclasses of CYCD and CDKs was significantly different. Our previous study found that transgenic PtoCYCD2;1 and PtoCYCD3;3 poplars exhibited opposite phenotypes. Y2H and BIFC results showed that the interaction between PtoCYCD2;1 and PtoCYCD3;3 was significantly different with CDKs. This finding might suggest that the functional differences of different CYCD subclasses in plant growth and development were closely related to the different interactions between CYCD and CDK. Our results provide a good idea and direction for the functional study of CYCD and CDK proteins in woody plants.
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28
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Ezzedine JA, Scheifler M, Desdevises Y, Jacquet S. A Comparative Study of the Dynamics and Diversity of Bdellovibrio and Like Organisms in Lakes Annecy and Geneva. Microorganisms 2022; 10:microorganisms10101960. [PMID: 36296236 PMCID: PMC9610775 DOI: 10.3390/microorganisms10101960] [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: 08/23/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 12/02/2022] Open
Abstract
Bdellovibrio and like organisms (BALOs) are obligate bacterial predators of other Gram-negative bacteria. Here, we used quantitative PCR (qPCR) and recently developed specific primers which target the 16S rRNA gene to explore the abundance and distribution of three families of BALO belonging to the Oligoflexia class (i.e., Bdellovibrionaceae, Peredibacteraceae and Bacteriovoracaceae) over one year in the epilimnion and hypolimnion of Lakes Annecy and Geneva. Peredibacteraceae was the dominant group at all sampling points except at the bottom of Lake Geneva, where Bdellovibrionaceae was found in higher number. In addition, the abundance of BALOs increased significantly during the warmer months. Using high-throughput sequencing (Illumina Miseq), hundreds of OTUs were identified for Bdellovibrionaceae and Peredibacteraceae. Phylogenetic analysis suggests that Bdellovibrionaceae are more diverse than Peredibacteraceae and that some OTUs belong to new species of Bdellovibrionaceae. We also found that dominant OTUs were present simultaneously in the two lakes, while some others were specific to each lake, suggesting an adaptive pattern. Finally, both abundance and diversity of BALOs were poorly associated with abiotic factors except temperature, suggesting the importance of studying biotic relationships, assumed to play a greater role than physico-chemical variables in BALOs' dynamics and distribution.
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Affiliation(s)
- Jade A. Ezzedine
- Université Savoie Mont-Blanc, INRAE, CARRTEL, 74200 Thonon les Bains, France
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, INRAE, IRIG, Université Grenoble Alpes, 38058 Grenoble, France
| | - Mathilde Scheifler
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Yves Desdevises
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Stéphan Jacquet
- Université Savoie Mont-Blanc, INRAE, CARRTEL, 74200 Thonon les Bains, France
- Correspondence:
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29
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Fan ZF, Ma CL. Comparative chloroplast genome and phylogenetic analyses of Chinese Polyspora. Sci Rep 2022; 12:15984. [PMID: 36163343 PMCID: PMC9512918 DOI: 10.1038/s41598-022-16290-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 07/07/2022] [Indexed: 11/09/2022] Open
Abstract
Polyspora Sweet (Theaceae) are winter ornamental landscape plants native to southern and southeastern Asia, some of which have medicinal value. The chloroplast (cp) genome data of Polyspora are scarce, and the gene evolution and interspecific relationship are still unclear. In this study, we sequenced and annotated Polyspora chrysandra cp genome and combined it with previously published genomes for other Chinese Polyspora species. The results showed that cp genomes of six Chinese Polyspora varied in length between 156,452 bp (P. chrysandra) and 157,066 bp (P. speciosa), but all contained 132 genes, with GC content of 37.3%, and highly similar genes distribution and codon usage. A total of eleven intergenic spacer regions were found having the highest levels of divergence, and eight divergence hotspots were identified as molecular markers for Phylogeography and genetic diversity studies in Polyspora. Gene selection pressure suggested that five genes were subjected to positive selection. Phylogenetic relationships among Polyspora species based on the complete cp genomes were supported strongly, indicating that the cp genomes have the potential to be used as super barcodes for further analysis of the phylogeny of the entire genus. The cp genomes of Chinese Polyspora species will provide valuable information for species identification, molecular breeding and evolutionary analysis of genus Polyspora.
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Affiliation(s)
- Zhi-Feng Fan
- Southwest Research Center for Engineering Technology of Landscape Architecture (State Forestry and Grassland Administration), College of Landscape Architecture and Horticulture Sciences, Southwest Forestry University, Kunming, 650224, People's Republic of China.,Kunming University of Science and Technology, Kunming, 650500, People's Republic of China
| | - Chang-Le Ma
- Southwest Research Center for Engineering Technology of Landscape Architecture (State Forestry and Grassland Administration), College of Landscape Architecture and Horticulture Sciences, Southwest Forestry University, Kunming, 650224, People's Republic of China.
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Karamycheva S, Wolf YI, Persi E, Koonin EV, Makarova KS. Analysis of lineage-specific protein family variability in prokaryotes combined with evolutionary reconstructions. Biol Direct 2022; 17:22. [PMID: 36042479 PMCID: PMC9425974 DOI: 10.1186/s13062-022-00337-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 08/13/2022] [Indexed: 12/24/2022] Open
Abstract
Background Evolutionary rate is a key characteristic of gene families that is linked to the functional importance of the respective genes as well as specific biological functions of the proteins they encode. Accurate estimation of evolutionary rates is a challenging task that requires precise phylogenetic analysis. Here we present an easy to estimate protein family level measure of sequence variability based on alignment column homogeneity in multiple alignments of protein sequences from Clade-Specific Clusters of Orthologous Genes (csCOGs). Results We report genome-wide estimates of variability for 8 diverse groups of bacteria and archaea and investigate the connection between variability and various genomic and biological features. The variability estimates are based on homogeneity distributions across amino acid sequence alignments and can be obtained for multiple groups of genomes at minimal computational expense. About half of the variance in variability values can be explained by the analyzed features, with the greatest contribution coming from the extent of gene paralogy in the given csCOG. The correlation between variability and paralogy appears to originate, primarily, not from gene duplication, but from acquisition of distant paralogs and xenologs, introducing sequence variants that are more divergent than those that could have evolved in situ during the lifetime of the given group of organisms. Both high-variability and low-variability csCOGs were identified in all functional categories, but as expected, proteins encoded by integrated mobile elements as well as proteins involved in defense functions and cell motility are, on average, more variable than proteins with housekeeping functions. Additionally, using linear discriminant analysis, we found that variability and fraction of genomes carrying a given gene are the two variables that provide the best prediction of gene essentiality as compared to the results of transposon mutagenesis in Sulfolobus islandicus. Conclusions Variability, a measure of sequence diversity within an alignment relative to the overall diversity within a group of organisms, offers a convenient proxy for evolutionary rate estimates and is informative with respect to prediction of functional properties of proteins. In particular, variability is a strong predictor of gene essentiality for the respective organisms and indicative of sub- or neofunctionalization of paralogs. Supplementary Information The online version contains supplementary material available at 10.1186/s13062-022-00337-7.
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Affiliation(s)
- Svetlana Karamycheva
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA
| | - Erez Persi
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA.
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Ip YK, Leong CWQ, Boo MV, Wong WP, Lam SH, Chew SF. Evidence for the involvement of branchial Vacuolar-type H +-ATPase in the acidification of the external medium by the West African lungfish, Protopterus annectens, exposed to ammonia-loading conditions. Comp Biochem Physiol A Mol Integr Physiol 2022; 273:111297. [PMID: 35987338 DOI: 10.1016/j.cbpa.2022.111297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 10/31/2022]
Abstract
African lungfishes are obligatory air-breathers with exceptionally high environmental ammonia tolerance. They can lower the pH of the external medium during exposure to ammonia-loading conditions. This study aimed to demonstrate the possible involvement of branchial vacuolar-type H+-ATPase (Vha) in the ammonia-induced acidification of the external medium by the West African lungfish, Protopterus annectens, and to examine whether its capacity to acidify the medium could be augmented after exposure to 100 mmol l-1 NH4Cl for six days. Two full coding cDNA sequences of Vha subunit B (atp6v1b), atp6v1b1 and atp6v1b2, were obtained from the internal gills of P. annectens. The sequence of atp6v1b1 comprised 1548 bp, encoding 515 amino acids (57.4 kDa), while that of atp6v1b2 comprised 1536 bp, encoding 511 amino acids (56.6 kDa). Using a custom-made antibody reactive to both isoforms, immunofluorescence microscopy revealed the collective localization of Atp6v1b (atp6v1b1 and atp6v1b2) at the apical or the basolateral membrane of two different types of branchial Na+/K+-ATPase-immunoreactive ionocyte. The ionocytes labelled apically with Atp6v1b presumably expressed Atp6v1b1 containing a PDZ-binding domain, indicating that the apical Vha was positioned to transport H+ to the external medium. The expression of Atp6v1b was regulated post-transcriptionally, as the protein abundance of Atp6v1b and Vha activity increased significantly in the gills of fish exposed to 100 mmol l-1 NH4Cl for six days. Correspondingly, the fish exposed to ammonia had a greater capacity to acidify the external medium, presumably to decrease the ratio of [NH3] to [NH4+] in order to reduce the influx of exogenous NH3.
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Affiliation(s)
- Yuen K Ip
- Department of Biological Sciences, National University of Singapore, Kent Ridge, Singapore 117543, Republic of Singapore.
| | - Charmaine W Q Leong
- Department of Biological Sciences, National University of Singapore, Kent Ridge, Singapore 117543, Republic of Singapore
| | - Mel V Boo
- Department of Biological Sciences, National University of Singapore, Kent Ridge, Singapore 117543, Republic of Singapore
| | - Wai P Wong
- Department of Biological Sciences, National University of Singapore, Kent Ridge, Singapore 117543, Republic of Singapore
| | - Siew H Lam
- Department of Biological Sciences, National University of Singapore, Kent Ridge, Singapore 117543, Republic of Singapore
| | - Shit F Chew
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, 1 Nanyang Walk, Singapore 637616, Republic of Singapore
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Xiaokaiti X, Hashiguchi Y, Ota H, Kumazawa Y. Evolution of the Noncoding Features of Sea Snake Mitochondrial Genomes within Elapidae. Genes (Basel) 2022; 13:genes13081470. [PMID: 36011381 PMCID: PMC9407768 DOI: 10.3390/genes13081470] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/12/2022] [Accepted: 08/13/2022] [Indexed: 02/07/2023] Open
Abstract
Mitochondrial genomes of four elapid snakes (three marine species [Emydocephalus ijimae, Hydrophis ornatus, and Hydrophis melanocephalus], and one terrestrial species [Sinomicrurus japonicus]) were completely sequenced by a combination of Sanger sequencing, next-generation sequencing and Nanopore sequencing. Nanopore sequencing was especially effective in accurately reading through long tandem repeats in these genomes. This led us to show that major noncoding regions in the mitochondrial genomes of those three sea snakes contain considerably long tandem duplications, unlike the mitochondrial genomes previously reported for same and other sea snake species. We also found a transposition of the light-strand replication origin within a tRNA gene cluster for the three sea snakes. This change can be explained by the Tandem Duplication—Random Loss model, which was further supported by remnant intervening sequences between tRNA genes. Mitochondrial genomes of true snakes (Alethinophidia) have been shown to contain duplicate major noncoding regions, each of which includes the control region necessary for regulating the heavy-strand replication and transcription from both strands. However, the control region completely disappeared from one of the two major noncoding regions for two Hydrophis sea snakes, posing evolutionary questions on the roles of duplicate control regions in snake mitochondrial genomes. The timing and molecular mechanisms for these changes are discussed based on the elapid phylogeny.
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Affiliation(s)
- Xiakena Xiaokaiti
- Department of Information and Basic Science and Research Center for Biological Diversity, Graduate School of Science, Nagoya City University, Nagoya 467-8501, Japan
| | - Yasuyuki Hashiguchi
- Department of Biology, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Takatsuki 569-0801, Japan
| | - Hidetoshi Ota
- Institute of Natural and Environmental Sciences, University of Hyogo, and Museum of Nature and Human Activities, Sanda 669-1546, Japan
| | - Yoshinori Kumazawa
- Department of Information and Basic Science and Research Center for Biological Diversity, Graduate School of Science, Nagoya City University, Nagoya 467-8501, Japan
- Correspondence: ; Tel.: +81-52-872-5844
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Bakalin VA, Vilnet AA, Mamontov YS, Schäfer-Verwimp A, Maltseva YD, Klimova KG, Nguyen VS, Choi SS. Stolonicaulon: A Section-Puzzle within Marsupella (Gymnomitriaceae, Marchantiophyta). PLANTS 2022; 11:plants11121596. [PMID: 35736747 PMCID: PMC9230718 DOI: 10.3390/plants11121596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/11/2022] [Accepted: 06/13/2022] [Indexed: 11/16/2022]
Abstract
Marsupella sect. Stolonicaulon is not speciose and is a commonly neglected section within the genus, which currently includes three species with somewhat similar morphologies (wiry shoots with distanced leaves) and distributions in the mountains of tropical and subtropical regions (SE (Southeast) Asia, the Venezuelan Andes, and the high mountains of SE Brazil). After studying materials that were found to be dissimilar to the “traditional” Marsupella that were collected in the last decade by the authors of this article, it was found that these plants belong to three new-for-science species, and all of these species should be included in Marsupella sect. Stolonicaulon. The newly described species have expanded the boundaries of morphological variability, not only for the section itself, but also for the genus based on two findings: (1) the leaves of Marsupella sect. Stolonicaulon can be either appressed and entire or spaced and deeply divided (thus, the plants could occasionally be similar to Cephaloziella or Anastrophyllum); (2) some species of the section possess regular underleaf production. The first discovery of regular underleaves in Marsupella, as noted in two of the three newly described taxa, is the main morphological novelty described in this paper. The development of regular underleaves is a presumable relict character that brings Marsupella closer to Nardia, which was recently transferred to the Gymnomitriaceae and occupies an isolated position within its own subfamily, Nardioideae.
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Affiliation(s)
- Vadim A. Bakalin
- Laboratory of Cryptogamic Biota, Botanical Garden-Institute FEB RAS, Makovskogo Street 142, Vladivostok 690024, Russia; (Y.D.M.); (K.G.K.)
- Correspondence: (V.A.B.); (S.S.C.)
| | - Anna A. Vilnet
- Laboratory of Flora and Vegetation, Polar-Alpine Botanical Garden-Institute of the Russian Academy of Sciences, Akademgorodok, 18A, Apatity 184209, Russia; (A.A.V.); (Y.S.M.)
| | - Yuriy S. Mamontov
- Laboratory of Flora and Vegetation, Polar-Alpine Botanical Garden-Institute of the Russian Academy of Sciences, Akademgorodok, 18A, Apatity 184209, Russia; (A.A.V.); (Y.S.M.)
- Herbarium, Tsitsin Main Botanical Garden RAS, Botanicheskaya 4, Moscow 127276, Russia
| | | | - Yulia D. Maltseva
- Laboratory of Cryptogamic Biota, Botanical Garden-Institute FEB RAS, Makovskogo Street 142, Vladivostok 690024, Russia; (Y.D.M.); (K.G.K.)
| | - Ksenia G. Klimova
- Laboratory of Cryptogamic Biota, Botanical Garden-Institute FEB RAS, Makovskogo Street 142, Vladivostok 690024, Russia; (Y.D.M.); (K.G.K.)
| | - Van Sinh Nguyen
- Institute of Ecology and Biological Resources, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Ha Noi 10072, Vietnam;
| | - Seung Se Choi
- Team of National Ecosystem Survey, National Institute of Ecology, Seocheon 33657, Korea
- Correspondence: (V.A.B.); (S.S.C.)
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Liang D, McManus GB, Wang Q, Sun X, Liu Z, Lin S, Yang Y. Genetic differentiation and phylogeography of rotifer
Polyarthra dolichoptera
and
P. vulgaris
populations between Southeastern China and eastern North America: High intercontinental differences. Ecol Evol 2022; 12:e8912. [PMID: 35592069 PMCID: PMC9101598 DOI: 10.1002/ece3.8912] [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: 06/20/2021] [Revised: 04/18/2022] [Accepted: 04/21/2022] [Indexed: 11/26/2022] Open
Abstract
Genetic differentiations and phylogeographical patterns of small organisms may be shaped by spatial isolation, environmental gradients, and gene flow. However, knowledge about genetic differentiation of rotifers at the intercontinental scale is still limited. Polyarthra dolichoptera and P. vulgaris are cosmopolitan rotifers that are tolerant to environmental changes, offering an excellent model to address the research gap. Here, we investigated the populations in Southeastern China and eastern North America and evaluated the phylogeographical patterns from their geographical range sizes, geographic–genetic distance relationships and their responses to spatial‐environmental factors. Using the mitochondrial cytochrome c oxidase subunit I gene as the DNA marker, we analyzed a total of 170 individuals. Our results showed that some putative cryptic species, also known as entities were widely distributed, but most of them were limited to single areas. The divergence of P. dolichoptera and P. vulgaris indicated that gene flow between continents was limited while that within each continent was stronger. Oceanographic barriers do affect the phylogeographic pattern of rotifers in continental waters and serve to maintain genetic diversity in nature. The genetic distance of P. dolichoptera and P. vulgaris populations showed significant positive correlation with geographic distance. This might be due to the combined effects of habitat heterogeneity, long‐distance colonization, and oceanographic barriers. Furthermore, at the intercontinental scale, spatial distance had a stronger influence than environmental variables on the genetic differentiations of both populations. Wind‐ and animal‐mediated transport and even historical events of continental plate tectonics are potential factors for phylogeography of cosmopolitan rotifers.
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Affiliation(s)
- Diwen Liang
- Department of Ecology Key Laboratory of Philosophy and Social Science in Guangdong Province Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Jinan University Guangzhou P. R. China
- State Environmental Protection Key Laboratory of Urban Ecological Simulation and Protection South China Institute of Environmental Sciences MEE Guangzhou China
- Department of Marine Sciences University of Connecticut Groton Connecticut USA
| | - George B. McManus
- Department of Marine Sciences University of Connecticut Groton Connecticut USA
| | - Qing Wang
- Department of Ecology Key Laboratory of Philosophy and Social Science in Guangdong Province Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Jinan University Guangzhou P. R. China
| | - Xian Sun
- School of Marine Science Sun Yat‐Sen University Guangzhou P. R. China
| | - Zhiwei Liu
- School of Marine Science Sun Yat‐Sen University Guangzhou P. R. China
| | - Senjie Lin
- Department of Marine Sciences University of Connecticut Groton Connecticut USA
| | - Yufeng Yang
- Department of Ecology Key Laboratory of Philosophy and Social Science in Guangdong Province Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Jinan University Guangzhou P. R. China
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35
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Cai D, Zhu S, Gong M, Zhang N, Wen J, Liang Q, Sun W, Shao X, Guo Y, Cai Y, Zheng Z, Zhang W, Hu S, Wang X, Tian H, Li Y, Liu W, Yang M, Yang J, Wu D, Orlando L, Jiang Y. Radiocarbon and genomic evidence for the survival of Equus Sussemionus until the late Holocene. eLife 2022; 11:73346. [PMID: 35543411 PMCID: PMC9142152 DOI: 10.7554/elife.73346] [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: 08/25/2021] [Accepted: 05/11/2022] [Indexed: 12/02/2022] Open
Abstract
The exceptionally rich fossil record available for the equid family has provided textbook examples of macroevolutionary changes. Horses, asses, and zebras represent three extant subgenera of Equus lineage, while the Sussemionus subgenus is another remarkable Equus lineage ranging from North America to Ethiopia in the Pleistocene. We sequenced 26 archaeological specimens from Northern China in the Holocene that could be assigned morphologically and genetically to Equus ovodovi, a species representative of Sussemionus. We present the first high-quality complete genome of the Sussemionus lineage, which was sequenced to 13.4× depth of coverage. Radiocarbon dating demonstrates that this lineage survived until ~3500 years ago, despite continued demographic collapse during the Last Glacial Maximum and the great human expansion in East Asia. We also confirmed the Equus phylogenetic tree and found that Sussemionus diverged from the ancestor of non-caballine equids ~2.3–2.7 million years ago and possibly remained affected by secondary gene flow post-divergence. We found that the small genetic diversity, rather than enhanced inbreeding, limited the species’ chances of survival. Our work adds to the growing literature illustrating how ancient DNA can inform on extinction dynamics and the long-term resilience of species surviving in cryptic population pockets.
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Affiliation(s)
- Dawei Cai
- Bioarchaeology Laboratory, Jilin University, Changchun, China
| | - Siqi Zhu
- Bioarchaeology Laboratory, Jilin University, Changchun, China
| | - Mian Gong
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Naifan Zhang
- Bioarchaeology Laboratory, Jilin University, Changchuin, China
| | - Jia Wen
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Qiyao Liang
- Bioarchaeology Laboratory, Jilin University, Changchun, China
| | - Weilu Sun
- Bioarchaeology Laboratory, Jilin University, Changchun, China
| | - Xinyue Shao
- Bioarchaeology Laboratory, Jilin University, Changchun, China
| | - Yaqi Guo
- Bioarchaeology Laboratory, Jilin University, Changchun, China
| | - Yudong Cai
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zhuqing Zheng
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Wei Zhang
- Heilongjiang Provincial Institute of Cultural Relics and Archaeology, Harbin, China
| | - Songmei Hu
- Shaanxi Provincial Institute of Archaeology, Xi'an, China
| | - Xiaoyang Wang
- Ningxia Institute of Cultural Relics and Archaeology, Yinchuan, China
| | - He Tian
- Heilongjiang Provincial Institute of Cultural Relics and Archaeology, Harbin, China
| | - Youqian Li
- Heilongjiang Provincial Institute of Cultural Relics and Archaeology, Harbin, China
| | - Wei Liu
- Heilongjiang Provincial Institute of Cultural Relics and Archaeology, Harbin, China
| | - Miaomiao Yang
- Shaanxi Provincial Institute of Archaeology, Xi'an, China
| | - Jian Yang
- Ningxia Institute of Cultural Relics and Archaeology, Yinchuan, China
| | - Duo Wu
- College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, China
| | - Ludovic Orlando
- 7Centre d'Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, CNRS UMR 5288, Toulouse, France
| | - Yu Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
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36
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Salabao L, Plevoets T, Frédérich B, Lepoint G, Kochzius M, Schön I. Describing novel mitochondrial genomes of Antarctic amphipods. Mitochondrial DNA B Resour 2022; 7:810-818. [PMID: 35573593 PMCID: PMC9103263 DOI: 10.1080/23802359.2022.2073837] [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] [Indexed: 11/03/2022] Open
Abstract
To date, only one mitogenome from an Antarctic amphipod has been published. Here, novel complete mitochondrial genomes (mitogenomes) of two morphospecies are assembled, namely, Charcotia amundseni and Eusirus giganteus. For the latter species, we have assembled two mitogenomes from different genetic clades of this species. The lengths of Eusirus and Charcotia mitogenomes range from 15,534 to 15,619 base pairs and their mitogenomes are composed of 13 protein coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and 1 putative control region CR. Some tRNAs display aberrant structures suggesting that minimalization is also ongoing in amphipod mitogenomes. The novel mitogenomes of the two Antarctic species have features distinguishing them from other amphipod mitogenomes such as a lower AT-richness in the whole mitogenomes and a negative GC- skew in both strands of protein coding genes. The genetically most variable mitochondrial regions of amphipods are nad6 and atp8, while cox1 shows low nucleotide diversity among closely and more distantly related species. In comparison to the pancrustacean mitochondrial ground pattern, E. giganteus shows a translocation of the nad1 gene, while cytb and nad6 genes are translocated in C. amundseni. Phylogenetic analysis based on mitogenomes illustrates that Eusirus and Charcotia cluster together with other species belonging to the same amphipod superfamilies. In the absence of reference nuclear genomes, mitogenomes can be useful to develop markers for studying population genetics or evolutionary relationships at higher taxonomic levels.
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Affiliation(s)
- Louraine Salabao
- Laboratory of Functional and Evolutionary Morphology, FOCUS, University of Liège, Liège, Belgium
- Centre for Environmental Sciences, Zoology: Toxicology and Biodiversity, Diepenbeek, Belgium
| | - Tim Plevoets
- Unit Animal Sciences - ILVO Marine Research, Flanders Research Institute for Agriculture, Fisheries and Food, Oostende, Belgium
| | - Bruno Frédérich
- Laboratory of Functional and Evolutionary Morphology, FOCUS, University of Liège, Liège, Belgium
| | - Gilles Lepoint
- Laboratory of Trophic and Isotopes Ecology, FOCUS, University of Liège, Liège, Belgium
| | - Marc Kochzius
- Marine Biology, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Isa Schön
- Centre for Environmental Sciences, Zoology: Toxicology and Biodiversity, Diepenbeek, Belgium
- OD Nature, Freshwater Biology, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
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37
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Xu H, Li Z, Jiang PF, Zhao L, Qu C, Van de Peer Y, Liu YJ, Zeng QY. Divergence of active site motifs among different classes of Populus glutaredoxins results in substrate switches. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:129-146. [PMID: 34981873 DOI: 10.1111/tpj.15660] [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: 11/08/2020] [Revised: 12/27/2021] [Accepted: 12/28/2021] [Indexed: 06/14/2023]
Abstract
Enzymes are essential components of all biological systems. The key characteristics of proteins functioning as enzymes are their substrate specificities and catalytic efficiencies. In plants, most genes encoding enzymes are members of large gene families. Within such families, the contributions of active site motifs to the functional divergence of duplicate genes have not been well elucidated. In this study, we identified 41 glutaredoxin (GRX) genes in the Populus trichocarpa genome. GRXs are ubiquitous enzymes in plants that play important roles in developmental and stress tolerance processes. In poplar, GRX genes were divided into four classes based on clear differences in gene structure and expression pattern, subcellular localization, enzymatic activity, and substrate specificity of the encoded proteins. Using site-directed mutagenesis, this study revealed that the divergence of the active site motif among different classes of GRX proteins resulted in substrate switches and thus provided new insights into the molecular evolution of these important plant enzymes.
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Affiliation(s)
- Hui Xu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Peng-Fei Jiang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Li Zhao
- Department of Ecology and Environmental Science, Umeå University, Umeå, SE-90187, Sweden
| | - Chang Qu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0028, South Africa
| | - Yan-Jing Liu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Qing-Yin Zeng
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
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38
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Zhang P, Xin Y, He Y, Tang X, Shen C, Wang Q, Lv N, Li Y, Hu Q, Xu J. Exploring a blue-light-sensing transcription factor to double the peak productivity of oil in Nannochloropsis oceanica. Nat Commun 2022; 13:1664. [PMID: 35351909 PMCID: PMC8964759 DOI: 10.1038/s41467-022-29337-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 03/08/2022] [Indexed: 12/19/2022] Open
Abstract
Oleaginous microalgae can produce triacylglycerol (TAG) under stress, yet the underlying mechanism remains largely unknown. Here, we show that, in Nannochloropsis oceanica, a bZIP-family regulator NobZIP77 represses the transcription of a type-2 diacylgycerol acyltransferase encoding gene NoDGAT2B under nitrogen-repletion (N+), while nitrogen-depletion (N−) relieves such inhibition and activates NoDGAT2B expression and synthesis of TAG preferably from C16:1. Intriguingly, NobZIP77 is a sensor of blue light (BL), which reduces binding of NobZIP77 to the NoDGAT2B-promoter, unleashes NoDGAT2B and elevates TAG under N−. Under N+ and white light, NobZIP77 knockout fully preserves cell growth rate and nearly triples TAG productivity. Moreover, exposing the NobZIP77-knockout line to BL under N− can double the peak productivity of TAG. These results underscore the potential of coupling light quality to oil synthesis in feedstock or bioprocess development. Microalgae are promising feedstock for oil production. The authors report that a transcription factor NobZIP77 can regulate oil synthesis by sensing the blue light, and explore these findings to greatly enhance oil productivity via genetic and process engineering in Nannochloropsis oceanica.
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39
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Jiang PF, Lin XY, Bian XY, Zeng QY, Liu YJ. Ectopic expression of Populus MYB10 promotes secondary cell wall thickening and inhibits anthocyanin accumulation. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 172:24-32. [PMID: 35016103 DOI: 10.1016/j.plaphy.2022.01.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 12/16/2021] [Accepted: 01/03/2022] [Indexed: 06/14/2023]
Abstract
Secondary cell wall (SCW) formation is regulated by a multilevel transcriptional regulatory network, in which MYB transcription factors (TFs) play key roles. In woody plants, hundreds of MYB TFs have been identified, most of which have unknown functions in wood SCW biosynthesis. Here, we characterized the function of a Populus MYB gene, PtoMYB10. PtoMYB10 was found to encode an R2R3-MYB TF and exhibit dominant expression in xylem tissues. PtoMYB10 was determined to be located in the nucleus with the ability to activate transcription. Overexpression of PtoMYB10 in Populus resulted in a drastic increase in SCW thickening in xylem fiber cells as well as ectopic deposition of lignin in cortex cells. The expression of genes associated with lignin biosynthesis was induced in PtoMYB10 overexpressing plants, whereas repressed gene expression was found with the anthocyanin biosynthesis pathway. Lignin and anthocyanin are both produced from metabolites of the phenylpropanoid pathway. Accordingly, the anthocyanin content of Populus overexpressing PtoMYB10 decreased by more than 68%. These results indicate that PtoMYB10 can positively regulate xylary fiber SCW thickening, accompanied by the reprogramming of phenylpropanoid metabolism, which redirects metabolic flux from anthocyanin biosynthesis to monolignol biosynthesis.
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Affiliation(s)
- Peng-Fei Jiang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xiao-Yang Lin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xiu-Yan Bian
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Qing-Yin Zeng
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yan-Jing Liu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China.
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40
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Lan T, Yang X, Chen J, Tian P, Shi L, Yu Y, Liu L, Gao L, Mo B, Chen X, Tang G. Mechanism for the genomic and functional evolution of the MIR2118 family in the grass lineage. THE NEW PHYTOLOGIST 2022; 233:1915-1930. [PMID: 34878652 DOI: 10.1111/nph.17910] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 12/01/2021] [Indexed: 06/13/2023]
Abstract
The MIR2118 family has undergone tremendous expansion in the grass lineage, in which the miRNA targets numerous noncoding PHAS loci to produce 21-nt phased small interfering RNAs (phasiRNAs) involved in male fertility. However, the evolutionary trajectory of the grass MIR2118 genes and the functions of phasiRNAs have not yet been fully elucidated. We conducted comparative genomic, molecular evolution, expression and parallel analysis of RNA ends (PARE) analyses of MIR2118 and the miR2118-mediated regulatory pathway in grasses, focusing on Oryza sativa. In total, 617 MIR2118 and eight MIR1859 novel members were identified. Phylogenetic analyses showed that grass MIR2118 genes form a distinct clade from the MIR482/2118 genes of nongrass species. We reconstructed hypothetical evolutionary histories of the grass MIR2118 clusters and its MIR1859 variants, and examined the polycistronic composition and the differential expression of the osa-MIR2118 clusters. PARE data showed that osa-miR2118 might also direct the cleavage of some protein-coding gene transcripts. Importantly, we found that PARE analysis is inherently prone to false-positive target predictions when a large number of small RNAs, such as phasiRNAs, are analysed. Our results revealed the evolution and diversification of the MIR2118 family, and provide new insights into the functions of phasiRNAs in the grasses.
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Affiliation(s)
- Ting Lan
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Xiaoyu Yang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, China
| | - Jiwei Chen
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Peng Tian
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Lina Shi
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yu Yu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Lin Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Lei Gao
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Beixin Mo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Guiliang Tang
- Department of Biological Sciences, Life Science and Technology Institute, Michigan Technological University, Houghton, MI, 49931, USA
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41
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Genome-Wide Comprehensive Analysis of PtLACs: Prediction and Verification of the Functional Divergence of Tandem-Duplicated Genes. FORESTS 2022. [DOI: 10.3390/f13020157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Laccases (EC 1.10.3.2) have been widely considered to participate in the metabolic processes of lignin synthesis, osmotic stress response, and flavonoid oxidation in higher plants. The research into Populus trichocarpa laccase focused on the synthesis of lignin in the past few years. In this study, for the first time, a comprehensive analysis of 53 laccase copies in the P. trichocarpa genome was conducted. Positive selection analysis using the branch-site model indicated that LAC genes in terrestrial plants have undergone selective pressure for adaptive evolution. On the basis of the phylogenetic relationship, we reconstructed the evolutionary process of terrestrial plant laccase and found that this gene family began to expand during the evolution of angiosperms. Tandem duplication is the main form of expansion of the PtLAC gene family. The analysis of the sequence characteristics, gene structure, expression pattern, and gene synonymous mutation rate of PtLACs provided a theoretical basis for the functional divergence of tandem duplicated genes. The synonymous mutation rate was used to quantify the divergence time of 11 tandem duplicated gene clusters. Cluster 2, with the earliest divergence time and lower share of sequence similarity, and cluster 5, with the latest divergence time and higher share of similarity, were selected in this study to explore the functional divergence of tandem-duplicated gene clusters. Tobacco subcellular localization and Arabidopsis transgenes verified the functional differentiation of PtLAC genes in cluster 2 and the functional non-differentiation of PtLAC genes in cluster 5. The results of this study provide a reference for the functional differentiation of tandem-duplicated PtLAC.
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de Azevedo-Martins AC, Ocaña K, de Souza W, de Vasconcelos ATR, Teixeira MMG, Camargo EP, Alves JMP, Motta MCM. The Importance of Glycerophospholipid Production to the Mutualist Symbiosis of Trypanosomatids. Pathogens 2021; 11:pathogens11010041. [PMID: 35055989 PMCID: PMC8779180 DOI: 10.3390/pathogens11010041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 12/23/2021] [Accepted: 12/28/2021] [Indexed: 12/12/2022] Open
Abstract
The symbiosis in trypanosomatids is a mutualistic relationship characterized by extensive metabolic exchanges between the bacterium and the protozoan. The symbiotic bacterium can complete host essential metabolic pathways, such as those for heme, amino acid, and vitamin production. Experimental assays indicate that the symbiont acquires phospholipids from the host trypanosomatid, especially phosphatidylcholine, which is often present in bacteria that have a close association with eukaryotic cells. In this work, an in-silico study was performed to find genes involved in the glycerophospholipid (GPL) production of Symbiont Harboring Trypanosomatids (SHTs) and their respective bacteria, also extending the search for trypanosomatids that naturally do not have symbionts. Results showed that most genes for GPL synthesis are only present in the SHT. The bacterium has an exclusive sequence related to phosphatidylglycerol production and contains genes for phosphatidic acid production, which may enhance SHT phosphatidic acid production. Phylogenetic data did not indicate gene transfers from the bacterium to the SHT nucleus, proposing that enzymes participating in GPL route have eukaryotic characteristics. Taken together, our data indicate that, differently from other metabolic pathways described so far, the symbiont contributes little to the production of GPLs and acquires most of these molecules from the SHT.
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Affiliation(s)
- Allan C. de Azevedo-Martins
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 20000-000, RJ, Brazil; (A.C.d.A.-M.); (W.d.S.)
| | - Kary Ocaña
- Laboratório Nacional de Computação Científica, Petropolis 25600-000, RJ, Brazil; (K.O.); (A.T.R.d.V.)
| | - Wanderley de Souza
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 20000-000, RJ, Brazil; (A.C.d.A.-M.); (W.d.S.)
- Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagens, Rio de Janeiro 20000-000, RJ, Brazil
| | | | - Marta M. G. Teixeira
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Sao Paulo 05508-000, SP, Brazil; (M.M.G.T.); (E.P.C.)
| | - Erney P. Camargo
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Sao Paulo 05508-000, SP, Brazil; (M.M.G.T.); (E.P.C.)
| | - João M. P. Alves
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Sao Paulo 05508-000, SP, Brazil; (M.M.G.T.); (E.P.C.)
- Correspondence: (J.M.P.A.); (M.C.M.M.)
| | - Maria Cristina M. Motta
- Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 20000-000, RJ, Brazil; (A.C.d.A.-M.); (W.d.S.)
- Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagens, Rio de Janeiro 20000-000, RJ, Brazil
- Correspondence: (J.M.P.A.); (M.C.M.M.)
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Del Amparo R, Arenas M. HIV Protease and Integrase Empirical Substitution Models of Evolution: Protein-Specific Models Outperform Generalist Models. Genes (Basel) 2021; 13:61. [PMID: 35052404 PMCID: PMC8774313 DOI: 10.3390/genes13010061] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 12/22/2021] [Accepted: 12/22/2021] [Indexed: 12/24/2022] Open
Abstract
Diverse phylogenetic methods require a substitution model of evolution that should mimic, as accurately as possible, the real substitution process. At the protein level, empirical substitution models have traditionally been based on a large number of different proteins from particular taxonomic levels. However, these models assume that all of the proteins of a taxonomic level evolve under the same substitution patterns. We believe that this assumption is highly unrealistic and should be relaxed by considering protein-specific substitution models that account for protein-specific selection processes. In order to test this hypothesis, we inferred and evaluated four new empirical substitution models for the protease and integrase of HIV and other viruses. We found that these models more accurately fit, compared with any of the currently available empirical substitution models, the evolutionary process of these proteins. We conclude that evolutionary inferences from protein sequences are more accurate if they are based on protein-specific substitution models rather than taxonomic-specific (generalist) substitution models. We also present four new empirical substitution models of protein evolution that could be useful for phylogenetic inferences of viral protease and integrase.
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Affiliation(s)
- Roberto Del Amparo
- Centro de Investigacións Biomédicas (CINBIO), University of Vigo, 36310 Vigo, Spain;
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
| | - Miguel Arenas
- Centro de Investigacións Biomédicas (CINBIO), University of Vigo, 36310 Vigo, Spain;
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), 36310 Vigo, Spain
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Velandia O, Mestizo Y, Medina HC, Riascos-Ortiz D, De Agudelo FV, Sarria GA. Characterization of Pterotylenchus cecidogenus in Desmodium ovalifolium cover crop from oil palm plantations in central Colombia. J Nematol 2021; 53:e2021-99. [PMID: 34881369 PMCID: PMC8634294 DOI: 10.21307/jofnem-2021-099] [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: 11/16/2020] [Indexed: 11/11/2022] Open
Abstract
Until recently, the stem gall nematode Pterotylenchus cecidogenus was only registered in eastern Colombia. However, the disease has recently been observed in central Colombian oil palm plantations that use Desmodium ovalifolium as a cover crop. Soil, root, stem, and leaf samples were collected from D. ovalifolium. Plants showed foliar yellowing, leaf drying, and galls within stem nodes. Nematodes were identified, and the distribution, population density, and relative importance of different genera were determined. We performed morphometric and molecular identification of nematodes associated with gall symptoms. The D2-D3 segment of the large subunit-28S of ribosomal ribonucleic acid (RNA) and internal transcribed spacer (ITS) was sequenced, and phylogenetic analysis was performed. P. cecidogenus mainly occurred in the galls and to a lesser extent in the roots and soil. Nematodes were not found in leaf or inflorescence tissue. Morphological and morphometric data confirm the presence of P. cecidogenus in the stems of D. ovalifolium with gall symptoms. This study is the first to report deoxyribonucleic acid (DNA) sequences of P. cecidogenus. Based on D2-D3 and ITS partial sequences, P. cecidogenus is a sister species of the leaf-galling nematode Ditylenchus phyllobius (Sinm. Orrina phyllobia).
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Affiliation(s)
- Oscar Velandia
- Pests and Diseases Program, Cenipalma. Experimental Field Palmar de La Vizcaína, Km 132 Vía Puerto Araujo-La Lizama, Barrancabermeja, Santander, 111611, Colombia
| | - Yuri Mestizo
- Pests and Diseases Program, Cenipalma. Experimental Field Palmar de La Vizcaína, Km 132 Vía Puerto Araujo-La Lizama, Barrancabermeja, Santander, 111611, Colombia
| | - Héctor Camilo Medina
- Pests and Diseases Program, Cenipalma. Experimental Field Palmar de La Vizcaína, Km 132 Vía Puerto Araujo-La Lizama, Barrancabermeja, Santander, 111611, Colombia
| | - Donald Riascos-Ortiz
- Facultad de Agronomía de la Universidad del Pacífico, Buenaventura, Valle del Cauca, Campus universitario, Km 13 vía al aeropuerto, Barrio el Triunfo
| | - Francia Varón De Agudelo
- Pests and Diseases Program, Cenipalma. Experimental Field Palmar de La Vizcaína, Km 132 Vía Puerto Araujo-La Lizama, Barrancabermeja, Santander, 111611, Colombia
| | - Greicy Andrea Sarria
- Pests and Diseases Program, Cenipalma. Experimental Field Palmar de La Vizcaína, Km 132 Vía Puerto Araujo-La Lizama, Barrancabermeja, Santander, 111611, Colombia
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Pires WMM, Barros MC, Fraga EC. DNA Barcoding unveils cryptic lineages of Hoplias malabaricus from Northeastern Brazil. BRAZ J BIOL 2021; 81:917-927. [PMID: 33053129 DOI: 10.1590/1519-6984.231598] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 04/29/2020] [Indexed: 11/22/2022] Open
Abstract
The trahira or wolf fish - Hoplias malabaricus- is a valid species, although recent cytogenetic and molecular studies have indicated the existence of a species complex. In this context, the present study analyzed the mitochondrial COI marker to determine the levels of genetic diversity of specimens from the Brazilian state of Maranhão, and verify the occurrence of distinct lineages within the study area. Samples were collected from the basins of the Turiaçu, Pindaré, Mearim, Itapecuru, and Parnaíba rivers. A 630-bp fragment was obtained from 211 specimens, with 484 conserved and 108 variable sites, and 60 haplotypes (Hd = 0,947; π = 0,033). The phylogenetic analyses indicated the existence of three distinct lineages of H. malabaricus from Maranhão. Genetic distances of 1.5-8.2% were found between all the populations analyzed, while the variation between haplogroups ranged from 2.1% to 7.7%. The AMOVA indicated that most of the molecular variation was found among groups, with high FST values. The high levels of genetic variability found in the present study are supported by the available cytogenetic data. These findings reinforce the need for the development of effective programs of conservation and management independently for each river basin, in order to preserve the genetic variability found in this taxon.
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Affiliation(s)
- W M M Pires
- Universidade Estadual do Maranhão - UEMA, Programa de Pós- Graduação em Biodiversidade Ambiente e Saúde, Laboratório de Genética e Biologia Molecular, Caxias, MA, Brasil.,Universidade Estadual do Maranhão - UEMA, Laboratório de Genética e Biologia Molecular - GENBIMOL, Caxias, MA, Brasil
| | - M C Barros
- Universidade Estadual do Maranhão - UEMA, Laboratório de Genética e Biologia Molecular - GENBIMOL, Caxias, MA, Brasil.,Universidade Estadual do Maranhão - UEMA, Departamento de Química e Biologia, Caxias, MA, Brasil
| | - E C Fraga
- Universidade Estadual do Maranhão - UEMA, Laboratório de Genética e Biologia Molecular - GENBIMOL, Caxias, MA, Brasil.,Universidade Estadual do Maranhão - UEMA, Departamento de Química e Biologia, Caxias, MA, Brasil
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Wang X, Liu X, An YQC, Zhang H, Meng D, Jin Y, Huo H, Yu L, Zhang J. Identification of Glutathione Peroxidase Gene Family in Ricinus communis and Functional Characterization of RcGPX4 in Cold Tolerance. FRONTIERS IN PLANT SCIENCE 2021; 12:707127. [PMID: 34804079 PMCID: PMC8602854 DOI: 10.3389/fpls.2021.707127] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 09/30/2021] [Indexed: 06/13/2023]
Abstract
Glutathione peroxidases (GPXs) protect cells against damage caused by reactive oxygen species (ROS) and play key roles in regulating many biological processes. Here, five GPXs were identified in the Ricinus communis genome. Phylogenetic analysis displayed that the GPXs were categorized into five groups. Conserved domain and gene structure analyses showed that the GPXs from different plant species harbored four highly similar motifs and conserved exon-intron arrangement patterns, indicating that their structure and function may have been conserved during evolution. Several abiotic stresses and hormone-responsive cis-acting elements existed in the promoters of the RcGPXs. The expression profiles indicated that the RcGPXs varied substantially, and some RcGPXs were coordinately regulated under abiotic stresses. Overexpression of RcGPX4 in Arabidopsis enhanced cold tolerance at seed germination but reduced freezing tolerance at seedlings. The expression of abscisic acid (ABA) signaling genes (AtABI4 and AtABI5), ABA catabolism genes (AtCYP707A1 and AtCYP707A2), gibberellin acid (GA) catabolism gene (AtGA2ox7), and cytokinin (CTK)-inducible gene (AtARR6) was regulated in the seeds of transgenic lines under cold stress. Overexpression of RcGPX4 can disturb the hydrogen peroxide (H2O2) homeostasis through the modulation of some antioxidant enzymes and compounds involved in the GSH-ascorbate cycle in transgenic plants. Additionally, RcGPX4 depended on the MAPK3-ICE1-C-repeat-binding factor (CBF)-COR signal transduction pathway and ABA-dependent pathway to negatively regulate the freezing tolerance of transgenic plants. This study provides valuable information for understanding the potential function of RcGPXs in regulating the abiotic stress responses of castor beans.
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Affiliation(s)
- Xiaoyu Wang
- College of Life Science and Food Engineering, Inner Mongolia Minzu University, Tongliao, China
- Horqin Plant Stress Biology Research Institute of Inner Mongolia Minzu University, Tongliao, China
| | - Xuming Liu
- College of Life Science and Food Engineering, Inner Mongolia Minzu University, Tongliao, China
- Horqin Plant Stress Biology Research Institute of Inner Mongolia Minzu University, Tongliao, China
| | - Yong-qiang Charles An
- U.S. Department of Agriculture-Agricultural Research Service, Plant Genetics Research Unit, Donald Danforth Plant Science Center, Saint Louis, MO, United States
| | - Hongyu Zhang
- College of Life Science and Food Engineering, Inner Mongolia Minzu University, Tongliao, China
- Horqin Plant Stress Biology Research Institute of Inner Mongolia Minzu University, Tongliao, China
| | - Di Meng
- College of Life Science and Food Engineering, Inner Mongolia Minzu University, Tongliao, China
- Horqin Plant Stress Biology Research Institute of Inner Mongolia Minzu University, Tongliao, China
| | - Yanan Jin
- College of Life Science and Food Engineering, Inner Mongolia Minzu University, Tongliao, China
- Horqin Plant Stress Biology Research Institute of Inner Mongolia Minzu University, Tongliao, China
| | - Hongyan Huo
- College of Life Science and Food Engineering, Inner Mongolia Minzu University, Tongliao, China
- Horqin Plant Stress Biology Research Institute of Inner Mongolia Minzu University, Tongliao, China
| | - Lili Yu
- College of Life Science and Food Engineering, Inner Mongolia Minzu University, Tongliao, China
| | - Jixing Zhang
- College of Life Science and Food Engineering, Inner Mongolia Minzu University, Tongliao, China
- Horqin Plant Stress Biology Research Institute of Inner Mongolia Minzu University, Tongliao, China
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Singh VK, Joshi BD, Bhat GJ, Singh SK, Chandra K, Sharma LK, Thakur M. Population genetics of Sambar (Rusa unicolor) from the Western Himalayas: preliminary findings. Mol Biol Rep 2021; 49:811-816. [PMID: 34668102 DOI: 10.1007/s11033-021-06845-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 10/15/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND The sambar (Rusa unicolor) is one of the largest deer distributed across diverse habitats of India and threatened due to habitat loss, changes in the land-use patterns, illegal poaching, and anthropogenic disturbances. Here, we report the first population genetics account of sambar deer from the Western Himalayas. METHODS AND RESULTS We observed relatively compromised genetic diversity (π = 0.0008 ± 0.0006 at mtDNA and Ho = 0.499 ± 0.056 at nDNA). We identified 60 unique individuals using a select panel of seven loci (PID sib cum 1.60E-03). Bayesian skyline plot showed a stable demographic history since the past 8 kyr with a decline in recent years. The population lacked genetic structuring, likely due to the contiguous distribution and large dispersal patterns of sambar. CONCLUSION The preliminary findings are valuable in exploring the utility of genetic diversity in monitoring the sambar population, estimating density following capture-recapture analysis, and aid to the conservation planning of sambar in large landscapes.
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Affiliation(s)
- Vinaya Kumar Singh
- Zoological Survey of India, New Alipore, Kolkata, 700053, West Bengal, India
| | - Bheem Dutt Joshi
- Zoological Survey of India, New Alipore, Kolkata, 700053, West Bengal, India
| | - Gul Jabin Bhat
- Zoological Survey of India, New Alipore, Kolkata, 700053, West Bengal, India
| | - Sujeet Kumar Singh
- Zoological Survey of India, New Alipore, Kolkata, 700053, West Bengal, India.,Amity Institute of Forestry and Wildlife, Amity University, Sector-125, Noida, 201303, India
| | - Kailash Chandra
- Zoological Survey of India, New Alipore, Kolkata, 700053, West Bengal, India
| | - Lalit Kumar Sharma
- Zoological Survey of India, New Alipore, Kolkata, 700053, West Bengal, India
| | - Mukesh Thakur
- Zoological Survey of India, New Alipore, Kolkata, 700053, West Bengal, India.
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Phuangphong S, Tsunoda J, Wada H, Morino Y. Duplication of spiralian-specific TALE genes and evolution of the blastomere specification mechanism in the bivalve lineage. EvoDevo 2021; 12:11. [PMID: 34663437 PMCID: PMC8524836 DOI: 10.1186/s13227-021-00181-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/04/2021] [Indexed: 12/24/2022] Open
Abstract
Background Despite the conserved pattern of the cell-fate map among spiralians, bivalves display several modified characteristics during their early development, including early specification of the D blastomere by the cytoplasmic content, as well as the distinctive fate of the 2d blastomere. However, it is unclear what changes in gene regulatory mechanisms led to such changes in cell specification patterns. Spiralian-TALE (SPILE) genes are a group of spiralian-specific transcription factors that play a role in specifying blastomere cell fates during early development in limpets. We hypothesised that the expansion of SPILE gene repertoires influenced the evolution of the specification pattern of blastomere cell fates. Results We performed a transcriptome analysis of early development in the purplish bifurcate mussel and identified 13 SPILE genes. Phylogenetic analysis of the SPILE gene in molluscs suggested that duplications of SPILE genes occurred in the bivalve lineage. We examined the expression patterns of the SPILE gene in mussels and found that some SPILE genes were expressed in quartet-specific patterns, as observed in limpets. Furthermore, we found that several SPILE genes that had undergone gene duplication were specifically expressed in the D quadrant, C and D quadrants or the 2d blastomere. These expression patterns were distinct from the expression patterns of SPILE in their limpet counterparts. Conclusions These results suggest that, in addition to their ancestral role in quartet specification, certain SPILE genes in mussels contribute to the specification of the C and D quadrants. We suggest that the expansion of SPILE genes in the bivalve lineage contributed to the evolution of a unique cell fate specification pattern in bivalves. Supplementary Information The online version contains supplementary material available at 10.1186/s13227-021-00181-2.
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Affiliation(s)
- Supanat Phuangphong
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan.
| | - Jumpei Tsunoda
- College of Biological Sciences, School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Hiroshi Wada
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Yoshiaki Morino
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan.
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Wang Y, Zhao Y, Pan Q. Advances, challenges and opportunities of phylogenetic and social network analysis using COVID-19 data. Brief Bioinform 2021; 23:6380452. [PMID: 34601563 DOI: 10.1093/bib/bbab406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/04/2021] [Accepted: 09/03/2021] [Indexed: 11/15/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) has attracted research interests from all fields. Phylogenetic and social network analyses based on connectivity between either COVID-19 patients or geographic regions and similarity between syndrome coronavirus 2 (SARS-CoV-2) sequences provide unique angles to answer public health and pharmaco-biological questions such as relationships between various SARS-CoV-2 mutants, the transmission pathways in a community and the effectiveness of prevention policies. This paper serves as a systematic review of current phylogenetic and social network analyses with applications in COVID-19 research. Challenges in current phylogenetic network analysis on SARS-CoV-2 such as unreliable inferences, sampling bias and batch effects are discussed as well as potential solutions. Social network analysis combined with epidemiology models helps to identify key transmission characteristics and measure the effectiveness of prevention and control strategies. Finally, future new directions of network analysis motivated by COVID-19 data are summarized.
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Affiliation(s)
- Yue Wang
- School of Mathematical and Natural Science, Arizona State University, 4701 W Thunderbird Rd, 85306, Arizona, USA
| | - Yunpeng Zhao
- School of Mathematical and Natural Science, Arizona State University, 4701 W Thunderbird Rd, 85306, Arizona, USA
| | - Qing Pan
- Department of Statistics, George Washington University, 801 22nd St. NW, 20052, Washington DC, USA
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Emelianova K, Martínez Martínez A, Campos-Dominguez L, Kidner C. Multi-tissue transcriptome analysis of two Begonia species reveals dynamic patterns of evolution in the chalcone synthase gene family. Sci Rep 2021; 11:17773. [PMID: 34493743 PMCID: PMC8423730 DOI: 10.1038/s41598-021-96854-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 08/17/2021] [Indexed: 02/07/2023] Open
Abstract
Begonia is an important horticultural plant group, as well as one of the most speciose Angiosperm genera, with over 2000 described species. Genus wide studies of genome size have shown that Begonia has a highly variable genome size, and analysis of paralog pairs has previously suggested that Begonia underwent a whole genome duplication. We address the contribution of gene duplication to the generation of diversity in Begonia using a multi-tissue RNA-seq approach. We chose to focus on chalcone synthase (CHS), a gene family having been shown to be involved in biotic and abiotic stress responses in other plant species, in particular its importance in maximising the use of variable light levels in tropical plants. We used RNA-seq to sample six tissues across two closely related but ecologically and morphologically divergent species, Begonia conchifolia and B. plebeja, yielding 17,012 and 19,969 annotated unigenes respectively. We identified the chalcone synthase gene family members in our Begonia study species, as well as in Hillebrandia sandwicensis, the monotypic sister genus to Begonia, Cucumis sativus, Arabidopsis thaliana, and Zea mays. Phylogenetic analysis suggested the CHS gene family has high duplicate turnover, all members of CHS identified in Begonia arising recently, after the divergence of Begonia and Cucumis. Expression profiles were similar within orthologous pairs, but we saw high inter-ortholog expression variation. Sequence analysis showed relaxed selective constraints on some ortholog pairs, with substitutions at conserved sites. Evidence of pseudogenisation and species specific duplication indicate that lineage specific differences are already beginning to accumulate since the divergence of our study species. We conclude that there is evidence for a role of gene duplication in generating diversity through sequence and expression divergence in Begonia.
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Affiliation(s)
- Katie Emelianova
- grid.426106.70000 0004 0598 2103Royal Botanic Gardens Edinburgh, 20a Inverleith Row, Edinburgh, EH3 5LR UK ,grid.4305.20000 0004 1936 7988Dementia Research Institute at the University of Edinburgh, Edinburgh, UK
| | - Andrea Martínez Martínez
- grid.426106.70000 0004 0598 2103Royal Botanic Gardens Edinburgh, 20a Inverleith Row, Edinburgh, EH3 5LR UK ,grid.4305.20000 0004 1936 7988School of Biological Sciences, University of Edinburgh, King’s Buildings, Mayfield Rd, Edinburgh, EH9 3JU UK
| | - Lucia Campos-Dominguez
- grid.426106.70000 0004 0598 2103Royal Botanic Gardens Edinburgh, 20a Inverleith Row, Edinburgh, EH3 5LR UK ,grid.4305.20000 0004 1936 7988School of Biological Sciences, University of Edinburgh, King’s Buildings, Mayfield Rd, Edinburgh, EH9 3JU UK
| | - Catherine Kidner
- grid.426106.70000 0004 0598 2103Royal Botanic Gardens Edinburgh, 20a Inverleith Row, Edinburgh, EH3 5LR UK ,grid.4305.20000 0004 1936 7988School of Biological Sciences, University of Edinburgh, King’s Buildings, Mayfield Rd, Edinburgh, EH9 3JU UK
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