1
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Wang H, Wu Z, Li T, Zhao J. Phylogenomics resolves the backbone of Poales and identifies signals of hybridization and polyploidy. Mol Phylogenet Evol 2024; 200:108184. [PMID: 39209045 DOI: 10.1016/j.ympev.2024.108184] [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: 02/19/2024] [Revised: 08/05/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
Poales, as one of the largest orders of angiosperm, holds crucial economic and ecological importance. Nevertheless, achieving a consensus topology has been challenging in previous studies due to limited molecular data and sparse taxon sampling. The uneven distribution of species diversity among families and the factors leading to elevated species richness in certain lineages have also been subjects of ongoing discussion and investigation. In this study, we conducted a comprehensive sampling, including representatives from all 14 families and 85 taxa of Poales, along with five additional outgroups. To reconstruct the phylogeny of Poales, we employed a combination of coalescent and concatenation methods on three nuclear gene sets (1093, 491, 143) and one plastid gene set (53), which were inferenced from genomic data. We also conducted phylogenetic hypothesis analyses to evaluate two major conflicting nodes detected in phylogenetic analyses. As a result, we successfully resolved the backbone of Poales and provided a timeline for its evolutionary history. We recovered the sister relationship between Typhaceae and Bromeliaceae as the earliest diverging families within Poales. The clade consisting of Ecdeiocoleaceae and Joinvilleaceae was recovered as the sister group of Poaceae. Within the xyrid clade, Mayacaceae and Erioaculaceae + Xyridaceae successively diverged along the backbone of Poales. The topology of [Aristidoideae, ((Micrairoideae, Panicoideae), (Arundinoideae, (Chloridoideae, Danthonioideae)))] within the PACMAD clade has received strong support from multiple findings. We also delved into the underlying biological factors that contributed to the conflicting nodes observed in the phylogenetic analysis. Apart from the uncertainty regarding the sister group of Poaceae caused by cytonuclear discordance, frequent hybridization and polyploidy may have contributed to other conflicting nodes. We identified 26 putative whole-genome duplication (WGD) events within Poales. However, apart from the σ-WGD and the ρ-WGD, we did not observe any potential polyploid events that could be directly linked to the species diversification in specific lineages. Furthermore, there was a significant increase in the net diversification rate of Poales following the K-Pg boundary.
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Affiliation(s)
- Huijun Wang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China
| | - Zhigang Wu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China.
| | - Tao Li
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China.
| | - Jindong Zhao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China; State Key Laboratory of Protein and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing, China
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2
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Jiang L, Sun Q, Zhu X, Hu X. Taxonomy and molecular phylogeny of genus Plagiocampa (Ciliophora, Prostomatea), with redescriptions of two poorly known species. Protist 2024; 175:126059. [PMID: 39208765 DOI: 10.1016/j.protis.2024.126059] [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: 03/21/2024] [Revised: 08/09/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024]
Abstract
Prostomateans, as common inhabitants in diverse aquatic environments, are among the simplest ciliate lineages, and serve as trophic links in food webs. However, only a few members are well-known and thoroughly studied, and the diversity of this group remains elusive. The unique genus Plagiocampa has a long history of research, but few studies have been performed using up-to-date methods. In the present work, Plagiocampa longis Kahl, 1927 and Plagiocampa minima Kahl, 1927, collected from Chinese coastal habitats, were investigated based on microscopical observation, protargol staining, and SSU rRNA gene sequencing. Their ciliature and morphometric data as well as gene sequences are documented. Phylogenetic analyses revealed that the family Plagiocampidae is likely monophyletic and has a closer relationship with parasitic Cryptocaryon.
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Affiliation(s)
- Limin Jiang
- College of Fisheries, and Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao 266003, China; Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education), & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Qianhui Sun
- College of Fisheries, and Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao 266003, China; Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education), & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Xiaoxuan Zhu
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education), & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China; College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Xiaozhong Hu
- College of Fisheries, and Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, Qingdao 266003, China; Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education), & Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China.
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3
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Fedosov AE, Zaharias P, Lemarcis T, Modica MV, Holford M, Oliverio M, Kantor YI, Puillandre N. Phylogenomics of Neogastropoda: The Backbone Hidden in the Bush. Syst Biol 2024; 73:521-531. [PMID: 38456663 PMCID: PMC11377187 DOI: 10.1093/sysbio/syae010] [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: 10/12/2022] [Revised: 02/16/2024] [Accepted: 03/06/2024] [Indexed: 03/09/2024] Open
Abstract
The molluskan order Neogastropoda encompasses over 15,000 almost exclusively marine species playing important roles in benthic communities and in the economies of coastal countries. Neogastropoda underwent intensive cladogenesis in the early stages of diversification, generating a "bush" at the base of their evolutionary tree, which has been hard to resolve even with high throughput molecular data. In the present study to resolve the bush, we use a variety of phylogenetic inference methods and a comprehensive exon capture dataset of 1817 loci (79.6% data occupancy) comprising 112 taxa of 48 out of 60 Neogastropoda families. Our results show consistent topologies and high support in all analyses at (super)family level, supporting monophyly of Muricoidea, Mitroidea, Conoidea, and, with some reservations, Olivoidea and Buccinoidea. Volutoidea and Turbinelloidea as currently circumscribed are clearly paraphyletic. Despite our analyses consistently resolving most backbone nodes, 3 prove problematic: First, the uncertain placement of Cancellariidae, as the sister group to either a Ficoidea-Tonnoidea clade or to the rest of Neogastropoda, leaves monophyly of Neogastropoda unresolved. Second, relationships are contradictory at the base of the major "core Neogastropoda" grouping. Third, coalescence-based analyses reject monophyly of the Buccinoidea in relation to Vasidae. We analyzed phylogenetic signal of targeted loci in relation to potential biases, and we propose the most probable resolutions in the latter 2 recalcitrant nodes. The uncertain placement of Cancellariidae may be explained by orthology violations due to differential paralog loss shortly after the whole genome duplication, which should be resolved with a curated set of longer loci.
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Affiliation(s)
- Alexander E Fedosov
- Department of Zoology, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 50, 75005 Paris, France
| | - Paul Zaharias
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 50, 75005 Paris, France
| | - Thomas Lemarcis
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 50, 75005 Paris, France
| | - Maria Vittoria Modica
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 50, 75005 Paris, France
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Mandë Holford
- Department of Chemistry, Hunter College, Belfer Research Building, City University of New York, 413 E. 69th Street, BRB 424, New York, NY 10021, USA
- Department of Invertebrate Zoology, the American Museum of Natural History, New York, NY 10024, USA
- PhD Programs in Biology, Biochemistry, and Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
| | - Marco Oliverio
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 50, 75005 Paris, France
- Department of Biology and Biotechnologies "Charles Darwin," Sapienza University of Rome, Viale dell'Università 32, I-00185 Rome, Italy
| | - Yuri I Kantor
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 50, 75005 Paris, France
- Department of Ecology and Morphology of Marine Invertebrates, A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninsky prospect, 33, 119071 Moscow, Russia
| | - Nicolas Puillandre
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 50, 75005 Paris, France
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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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5
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Roestel JA, Wiersema JH, Jansen RK, Borsch T, Gruenstaeudl M. On the importance of sequence alignment inspections in plastid phylogenomics - an example from revisiting the relationships of the water-lilies. Cladistics 2024. [PMID: 38761095 DOI: 10.1111/cla.12584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 04/27/2024] [Accepted: 04/29/2024] [Indexed: 05/20/2024] Open
Abstract
The water-lily clade represents the second earliest-diverging branch of angiosperms. Most of its species belong to Nymphaeaceae, of which the "core Nymphaeaceae"-comprising the genera Euryale, Nymphaea and Victoria-is the most diverse clade. Despite previous molecular phylogenetic studies on the core Nymphaeaceae, various aspects of their evolutionary relationships have remained unresolved. The length-variable introns and intergenic spacers are known to contain most of the sequence variability within the water-lily plastomes. Despite the challenges with multiple sequence alignment, any new molecular phylogenetic investigation on the core Nymphaeaceae should focus on these noncoding plastome regions. For example, a new plastid phylogenomic study on the core Nymphaeaceae should generate DNA sequence alignments of all plastid introns and intergenic spacers based on the principle of conserved sequence motifs. In this investigation, we revisit the phylogenetic history of the core Nymphaeaceae by employing such an approach. Specifically, we use a plastid phylogenomic analysis strategy in which all coding and noncoding partitions are separated and then undergo software-driven DNA sequence alignment, followed by a motif-based alignment inspection and adjustment. This approach allows us to increase the reliability of the character base compared to the default practice of aligning complete plastomes through software algorithms alone. Our approach produces significantly different phylogenetic tree reconstructions for several of the plastome regions under study. The results of these reconstructions underscore that Nymphaea is paraphyletic in its current circumscription, that each of the five subgenera of Nymphaea is monophyletic, and that the subgenus Nymphaea is sister to all other subgenera of Nymphaea. Our results also clarify many evolutionary relationships within the Nymphaea subgenera Brachyceras, Hydrocallis and Nymphaea. In closing, we discuss whether the phylogenetic reconstructions obtained through our motif-based alignment adjustments are in line with morphological evidence on water-lily evolution.
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Affiliation(s)
- Jessica A Roestel
- Institut für Biologie, Systematische Botanik und Pflanzengeographie, Freie Universität Berlin, Berlin, 14195, Germany
| | - John H Wiersema
- Department of Botany, National Museum of Natural History - Smithsonian Institution, Washington, DC, 37012, USA
| | - Robert K Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Thomas Borsch
- Institut für Biologie, Systematische Botanik und Pflanzengeographie, Freie Universität Berlin, Berlin, 14195, Germany
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, 14195, Berlin, Germany
| | - Michael Gruenstaeudl
- Institut für Biologie, Systematische Botanik und Pflanzengeographie, Freie Universität Berlin, Berlin, 14195, Germany
- Department of Biological Sciences, Fort Hays State University, Hays, KS, 67601, USA
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6
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Wan JN, Wang SW, Leitch AR, Leitch IJ, Jian JB, Wu ZY, Xin HP, Rakotoarinivo M, Onjalalaina GE, Gituru RW, Dai C, Mwachala G, Bai MZ, Zhao CX, Wang HQ, Du SL, Wei N, Hu GW, Chen SC, Chen XY, Wan T, Wang QF. The rise of baobab trees in Madagascar. Nature 2024; 629:1091-1099. [PMID: 38750363 PMCID: PMC11136661 DOI: 10.1038/s41586-024-07447-4] [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: 05/20/2023] [Accepted: 04/19/2024] [Indexed: 05/30/2024]
Abstract
The baobab trees (genus Adansonia) have attracted tremendous attention because of their striking shape and distinctive relationships with fauna1. These spectacular trees have also influenced human culture, inspiring innumerable arts, folklore and traditions. Here we sequenced genomes of all eight extant baobab species and argue that Madagascar should be considered the centre of origin for the extant lineages, a key issue in their evolutionary history2,3. Integrated genomic and ecological analyses revealed the reticulate evolution of baobabs, which eventually led to the species diversity seen today. Past population dynamics of Malagasy baobabs may have been influenced by both interspecific competition and the geological history of the island, especially changes in local sea levels. We propose that further attention should be paid to the conservation status of Malagasy baobabs, especially of Adansonia suarezensis and Adansonia grandidieri, and that intensive monitoring of populations of Adansonia za is required, given its propensity for negatively impacting the critically endangered Adansonia perrieri.
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Affiliation(s)
- Jun-Nan Wan
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Wuhan, China
| | - Sheng-Wei Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Wuhan, China
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | | | - Jian-Bo Jian
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | | | - Hai-Ping Xin
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | | | | | - Robert Wahiti Gituru
- Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Wuhan, China
- Department of Botany, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Can Dai
- School of Resources and Environmental Science, Hubei University, Wuhan, China
| | | | - Ming-Zhou Bai
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | | | | | - Sheng-Lan Du
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Neng Wei
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Wuhan, China
| | - Guang-Wan Hu
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Wuhan, China
| | - Si-Chong Chen
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Wuhan, China
| | - Xiao-Ya Chen
- Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Wuhan, China
- Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Tao Wan
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.
- Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Wuhan, China.
| | - Qing-Feng Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.
- Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Wuhan, China.
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Marlétaz F, Timoshevskaya N, Timoshevskiy VA, Parey E, Simakov O, Gavriouchkina D, Suzuki M, Kubokawa K, Brenner S, Smith JJ, Rokhsar DS. The hagfish genome and the evolution of vertebrates. Nature 2024; 627:811-820. [PMID: 38262590 PMCID: PMC10972751 DOI: 10.1038/s41586-024-07070-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 01/15/2024] [Indexed: 01/25/2024]
Abstract
As the only surviving lineages of jawless fishes, hagfishes and lampreys provide a crucial window into early vertebrate evolution1-3. Here we investigate the complex history, timing and functional role of genome-wide duplications4-7 and programmed DNA elimination8,9 in vertebrates in the light of a chromosome-scale genome sequence for the brown hagfish Eptatretus atami. Combining evidence from syntenic and phylogenetic analyses, we establish a comprehensive picture of vertebrate genome evolution, including an auto-tetraploidization (1RV) that predates the early Cambrian cyclostome-gnathostome split, followed by a mid-late Cambrian allo-tetraploidization (2RJV) in gnathostomes and a prolonged Cambrian-Ordovician hexaploidization (2RCY) in cyclostomes. Subsequently, hagfishes underwent extensive genomic changes, with chromosomal fusions accompanied by the loss of genes that are essential for organ systems (for example, genes involved in the development of eyes and in the proliferation of osteoclasts); these changes account, in part, for the simplification of the hagfish body plan1,2. Finally, we characterize programmed DNA elimination in hagfish, identifying protein-coding genes and repetitive elements that are deleted from somatic cell lineages during early development. The elimination of these germline-specific genes provides a mechanism for resolving genetic conflict between soma and germline by repressing germline and pluripotency functions, paralleling findings in lampreys10,11. Reconstruction of the early genomic history of vertebrates provides a framework for further investigations of the evolution of cyclostomes and jawed vertebrates.
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Affiliation(s)
- Ferdinand Marlétaz
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK.
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.
| | | | | | - Elise Parey
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Oleg Simakov
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
- Department for Neurosciences and Developmental Biology, University of Vienna, Vienna, Austria
| | - Daria Gavriouchkina
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
- UK Dementia Research Institute, University College London, London, UK
| | - Masakazu Suzuki
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Kaoru Kubokawa
- Ocean Research Institute, The University of Tokyo, Tokyo, Japan
| | - Sydney Brenner
- Comparative and Medical Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore, Singapore
| | - Jeramiah J Smith
- Department of Biology, University of Kentucky, Lexington, KY, USA.
| | - Daniel S Rokhsar
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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8
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Xu Y, Wei Y, Zhou Z, Cai X, Boden SA, Umer MJ, Safdar LB, Liu Y, Jin D, Hou Y, Wang Y, Wall SB, Wang K, Yu S, Zhang B, Peng R, Liu F. Widespread incomplete lineage sorting and introgression shaped adaptive radiation in the Gossypium genus. PLANT COMMUNICATIONS 2024; 5:100728. [PMID: 37803827 PMCID: PMC10873890 DOI: 10.1016/j.xplc.2023.100728] [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: 05/11/2023] [Revised: 09/14/2023] [Accepted: 10/02/2023] [Indexed: 10/08/2023]
Abstract
Cotton (Gossypium) stands as a crucial economic crop, serving as the primary source of natural fiber for the textile sector. However, the evolutionary mechanisms driving speciation within the Gossypium genus remain unresolved. In this investigation, we leveraged 25 Gossypium genomes and introduced four novel assemblies-G. harknessii, G. gossypioides, G. trilobum, and G. klotzschianum (Gklo)-to delve into the speciation history of this genus. Notably, we encountered intricate phylogenies potentially stemming from introgression. These complexities are further compounded by incomplete lineage sorting (ILS), a factor likely to have been instrumental in shaping the swift diversification of cotton. Our focus subsequently shifted to the rapid radiation episode during a concise period in Gossypium evolution. For a recently diverged lineage comprising G. davidsonii, Gklo, and G. raimondii, we constructed a finely detailed ILS map. Intriguingly, this analysis revealed the non-random distribution of ILS regions across the reference Gklo genome. Moreover, we identified signs of robust natural selection influencing specific ILS regions. Noteworthy variations pertaining to speciation emerged between the closely related sister species Gklo and G. davidsonii. Approximately 15.74% of speciation structural variation genes and 12.04% of speciation-associated genes were estimated to intersect with ILS signatures. These findings enrich our understanding of the role of ILS in adaptive radiation, shedding fresh light on the intricate speciation history of the Gossypium genus.
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Affiliation(s)
- Yanchao Xu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 40070, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China
| | - Yangyang Wei
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China
| | - Zhongli Zhou
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Xiaoyan Cai
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China
| | - Scott A Boden
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA 5005, Australia
| | - Muhammad Jawad Umer
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Luqman B Safdar
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA 5005, Australia
| | - Yuling Liu
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China
| | - Dingsha Jin
- Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya 572000, China
| | - Yuqing Hou
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Yuhong Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Sarah Brooke Wall
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Kunbo Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Shuxun Yu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858, USA.
| | - Renhai Peng
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China.
| | - Fang Liu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China.
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9
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Morita K, Saito T, Uechi T, Sawada N, Miura O. Out of the ancient lake: Multiple riverine colonizations and diversification of the freshwater snails in the genus Semisulcospira around Lake Biwa. Mol Phylogenet Evol 2024; 191:107987. [PMID: 38081401 DOI: 10.1016/j.ympev.2023.107987] [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: 07/02/2023] [Revised: 11/20/2023] [Accepted: 12/07/2023] [Indexed: 12/18/2023]
Abstract
Ancient lakes are a hotspot of biodiversity. Freshwater species often experience spectacular species radiation after colonizing lakes from riverine habitats. Therefore, the relationship between the fauna of the ancient lakes and the surrounding riverine system has a special significance in understanding their origin and evolutionary history. The study of ancient lake species often focused on the lake colonization of riverine species. In contrast, far less attention has been placed on the reverse direction: the riverine colonization of the lake species, despite its importance in disentangling their complex evolutionary history. The freshwater snails in the genus Semisulcospira involve endemic groups that radiated in the ancient Lake Biwa. Using genetics and fossil records, we inferred that the ancestors of these lake-endemic Semisulcospira snails historically colonized the riverine habitats at least three times during the Middle Pleistocene. Each colonization resulted in the formation of a new lineage that was genetically and morphologically distinct from other lineages. Further, one of these colonizations was followed by hybridization with a cosmopolitan riverine species, which potentially facilitated the population persistence of the colonizers in the new environment. Despite their complex histories, all these colonizers were currently grouped within a single species, Semisulcospira kurodai, suggesting cryptic diversity in this species. This study highlights the significance of the riverine colonizations of the lake species to fully understand the diversification history of freshwater fauna in and around the ancient lakes.
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Affiliation(s)
- Kohei Morita
- Faculty of Agriculture and Marine Science, Kochi University, 200 Monobe, Nankoku, Kochi 783-8502 Japan
| | - Takumi Saito
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Takeru Uechi
- Major in Environmental Management, Graduate School of Agriculture, Kindai University, 3327-204 Nakamachi, Nara 631-8505, Japan
| | - Naoto Sawada
- Department of Zoology, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo, Kyoto, Kyoto 606-8502 Japan
| | - Osamu Miura
- Faculty of Agriculture and Marine Science, Kochi University, 200 Monobe, Nankoku, Kochi 783-8502 Japan.
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10
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Li X, Breinholt JW, Martinez JI, Keegan K, Ellis EA, Homziak NT, Zwick A, Storer CG, McKenna D, Kawahara AY. Large-scale genomic data reveal the phylogeny and evolution of owlet moths (Noctuoidea). Cladistics 2024; 40:21-33. [PMID: 37787424 DOI: 10.1111/cla.12559] [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: 04/21/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 10/04/2023] Open
Abstract
The owlet moths (Noctuoidea; ~43-45K described species) are one of the most ecologically diverse and speciose superfamilies of animals. Moreover, they comprise some of the world's most notorious pests of agriculture and forestry. Despite their contributions to terrestrial biodiversity and impacts on ecosystems and economies, the evolutionary history of Noctuoidea remains unclear because the superfamily lacks a statistically robust phylogenetic and temporal framework. We reconstructed the phylogeny of Noctuoidea using data from 1234 genes (946.4 kb nucleotides) obtained from the genome and transcriptome sequences of 76 species. The relationships among the six families of Noctuoidea were well resolved and consistently recovered based on both concatenation and gene coalescence approaches, supporting the following relationships: Oenosandridae + (Notodontidae + (Erebidae + (Nolidae + (Euteliidae + Noctuidae)))). A Yule tree prior with three unlinked molecular clocks was identified as the preferred BEAST analysis using marginal-likelihood estimations. The crown age of Noctuoidea was estimated at 74.5 Ma, with most families originating before the end of the Paleogene (23 Ma). Our study provides the first statistically robust phylogenetic and temporal framework for Noctuoidea, including all families of owlet moths, based on large-scale genomic data.
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Affiliation(s)
- Xuankun Li
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100193, China
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Department of Biological Sciences, University of Memphis, Memphis, TN, 38152, USA
- Center for Biodiversity Research, University of Memphis, Memphis, TN, 38152, USA
| | - Jesse W Breinholt
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Precision Genomics, Intermountain Healthcare, St George, UT, 84790, USA
| | - Jose I Martinez
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Entomology and Nematology Department, University of Florida, Gainesville, FL, 32608, USA
| | - Kevin Keegan
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06268, USA
- Section of Invertebrate Zoology, Carnegie Museum of Natural History, 4400 Forbes Ave, Pittsburgh, PA, 15213-4080, USA
| | - Emily A Ellis
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Nicholas T Homziak
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Andreas Zwick
- Australian National Insect Collection, CSIRO National Research Collections Australia, Canberra, ACT, 2601, Australia
| | - Caroline G Storer
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Duane McKenna
- Department of Biological Sciences, University of Memphis, Memphis, TN, 38152, USA
- Center for Biodiversity Research, University of Memphis, Memphis, TN, 38152, USA
| | - Akito Y Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Entomology and Nematology Department, University of Florida, Gainesville, FL, 32608, USA
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11
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Liao L, Jiang L, Hu X. Integrative data of a novel ciliate (Alveolata, Ciliophora) propose the establishment of Heterodeviata nantongensis nov. sp. BMC Microbiol 2024; 24:27. [PMID: 38243176 PMCID: PMC10797804 DOI: 10.1186/s12866-024-03190-y] [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: 10/16/2023] [Accepted: 01/09/2024] [Indexed: 01/21/2024] Open
Abstract
BACKGROUND As unicellular eukaryotes, ciliates are an indispensable component of micro-ecosystems that play the role of intermediate nutrition link between bacteria or algae and meiofauna. Recent faunistic studies have revealed many new taxa of hypotrich ciliates, indicating their diversity is greater than previously thought. Here we document an undescribed form isolated from an artificial brackish water pond in East China. Examination of its morphology, ontogenesis and molecular phylogeny suggests that it represents a new species. RESULTS The morphology and morphogenesis of the new brackish-water deviatid ciliate, Heterodeviata nantongensis nov. sp., isolated from Nantong, China, were investigated using live observations and protargol staining. The diagnostic traits of the new species include three frontal cirri, one buccal cirrus, one or two parabuccal cirri, an inconspicuous frontoventral cirral row of four to six frontoventral cirri derived from two anlagen, three left and two right marginal rows, two dorsal kineties, dorsal kinety 1 with 9-14 dikinetids and dorsal kinety 2 with only two dikinetids, and one to three caudal cirri at the rear end of dorsal kinety 1. Its main morphogenetic features are: (i) the old oral apparatus is completely inherited by the proter except undulating membranes, which are reorganized in situ; (ii) anlagen for marginal rows and the left dorsal kinety develop intrakinetally in both proter and opisthe; (iii) dorsal kinety 2 is generated dorsomarginally; (iv) five cirral anlagen are formed in both proter and opisthe; (v) in the proter, anlagen I and II very likely originate from the parental undulating membranes and the buccal cirrus, respectively, anlage III from anterior parabuccal cirrus, anlage IV originates from the parental frontoventral cirri and anlage V from the innermost parental right marginal row; and (vi) anlagen I-IV of the opisthe are all generated from oral primordium, anlage V from the innermost parental right marginal row. Phylogenetic analyses based on SSU rRNA gene sequence data were performed to determine the systematic position of the new taxon. CONCLUSIONS The study on the morphology, and ontogenesis of a new brackish-water taxon increases the overall knowledge about the biodiversity of this ciliate group. It also adds to the genetic data available and further provides a reliable reference for environmental monitoring and resource investigations.
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Affiliation(s)
- Lijian Liao
- College of Fisheries, & Key Laboratory of Evolution and Marine Biodiversity of Ministry of Education, Ocean University of China, Qingdao, 266003, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Limin Jiang
- College of Fisheries, & Key Laboratory of Evolution and Marine Biodiversity of Ministry of Education, Ocean University of China, Qingdao, 266003, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Xiaozhong Hu
- College of Fisheries, & Key Laboratory of Evolution and Marine Biodiversity of Ministry of Education, Ocean University of China, Qingdao, 266003, China.
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
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12
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Du K, Lu Y, Garcia-Olazabal M, Walter RB, Warren WC, Dodge T, Schumer M, Park H, Meyer A, Schartl M. Phylogenomics analyses of all species of Swordtails (Genus Xiphophorus ) highlights hybridization precedes speciation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.30.573732. [PMID: 38260540 PMCID: PMC10802237 DOI: 10.1101/2023.12.30.573732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Hybridization has been recognized as an important driving force for evolution, however studies of the genetic consequence and its cause are still lagging behind in vertebrates due to the lack of appropriate experimental systems. Fish of the central American genus Xiphophorus were proposed to have evolved with multiple ancient and ongoing hybridization events, and served as a valuable research model in evolutionary biology and in biomedical research on human disease for more than a century. Here, we provide the complete genome resource and its annotation of all 26 Xiphophorus species. On this dataset we resolved the so far conflicting phylogeny. Through comparative genomic analyses we investigated the molecular evolution of genes related to melanoma, for a main sexually selected trait and for the genetic control of puberty timing, which are predicted to be involved in pre-and postzygotic isolation and thus to influence the probability of interspecific hybridization in Xiphophorus . We demonstrate dramatic size-variation of some gene families across species, despite the reticulate evolution and short divergence time. Finally, we clarify the hybridization history in the genus Xiphophorus genus, settle the long dispute on the hybridization origin of two Southern swordtails, highlight hybridizations precedes speciation, and reveal the distribution of hybridization ancestry remaining in the fused genome.
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13
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Patané JSL, Martins J, Setubal JC. A Guide to Phylogenomic Inference. Methods Mol Biol 2024; 2802:267-345. [PMID: 38819564 DOI: 10.1007/978-1-0716-3838-5_11] [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: 06/01/2024]
Abstract
Phylogenomics aims at reconstructing the evolutionary histories of organisms taking into account whole genomes or large fractions of genomes. Phylogenomics has significant applications in fields such as evolutionary biology, systematics, comparative genomics, and conservation genetics, providing valuable insights into the origins and relationships of species and contributing to our understanding of biological diversity and evolution. This chapter surveys phylogenetic concepts and methods aimed at both gene tree and species tree reconstruction while also addressing common pitfalls, providing references to relevant computer programs. A practical phylogenomic analysis example including bacterial genomes is presented at the end of the chapter.
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Affiliation(s)
- José S L Patané
- Laboratório de Genética e Cardiologia Molecular, Instituto do Coração/Heart Institute Hospital das Clínicas - Faculdade de Medicina da Universidade de São Paulo São Paulo, São Paulo, SP, Brazil
| | - Joaquim Martins
- Integrative Omics group, Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - João Carlos Setubal
- Departmento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil.
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14
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Nishihara H, Toda Y, Kuramoto T, Kamohara K, Goto A, Hoshino K, Okada S, Kuraku S, Okabe M, Ishimaru Y. A vertebrate-wide catalogue of T1R receptors reveals diversity in taste perception. Nat Ecol Evol 2024; 8:111-120. [PMID: 38093021 PMCID: PMC10781636 DOI: 10.1038/s41559-023-02258-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 10/25/2023] [Indexed: 01/12/2024]
Abstract
Taste is a vital chemical sense for feeding behaviour. In mammals, the umami and sweet taste receptors comprise three members of the taste receptor type 1 (T1R/TAS1R) family: T1R1, T1R2 and T1R3. Because their functional homologues exist in teleosts, only three TAS1R genes generated by gene duplication are believed to have been inherited from the common ancestor of bony vertebrates. Here, we report five previously uncharacterized TAS1R members in vertebrates, TAS1R4, TAS1R5, TAS1R6, TAS1R7 and TAS1R8, based on genome-wide survey of diverse taxa. We show that mammalian and teleost fish TAS1R2 and TAS1R3 genes are paralogues. Our phylogenetic analysis suggests that the bony vertebrate ancestor had nine TAS1Rs resulting from multiple gene duplications. Some TAS1Rs were lost independently in descendent lineages resulting in retention of only three TAS1Rs in mammals and teleosts. Combining functional assays and expression analysis of non-teleost fishes we show that the novel T1Rs form heterodimers in taste-receptor cells and recognize a broad range of ligands such as essential amino acids, including branched-chain amino acids, which have not been previously considered as T1R ligands. This study reveals diversity of taste sensations in both modern vertebrates and their ancestors, which might have enabled vertebrates to adapt to diverse habitats on Earth.
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Affiliation(s)
- Hidenori Nishihara
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara, Japan.
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.
| | - Yasuka Toda
- Department of Agricultural Chemistry, School of Agriculture, Meiji University, Kawasaki, Japan
| | - Tae Kuramoto
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara, Japan
- Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Kota Kamohara
- Department of Agricultural Chemistry, School of Agriculture, Meiji University, Kawasaki, Japan
| | - Azusa Goto
- Department of Agricultural Chemistry, School of Agriculture, Meiji University, Kawasaki, Japan
| | - Kyoko Hoshino
- Department of Agricultural Chemistry, School of Agriculture, Meiji University, Kawasaki, Japan
| | - Shinji Okada
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Shigehiro Kuraku
- Molecular Life History Laboratory, National Institute of Genetics, Mishima, Japan
- Department of Genetics, SOKENDAI (Graduate University for Advanced Studies), Mishima, Japan
| | - Masataka Okabe
- Department of Anatomy, The Jikei University School of Medicine, Tokyo, Japan
| | - Yoshiro Ishimaru
- Department of Agricultural Chemistry, School of Agriculture, Meiji University, Kawasaki, Japan.
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15
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Lian C, Zhao Y, Li P, Zhang T, Al-Rasheid KAS, Stover NA, Wang Y, Shao C. Three closely-related subclasses Phacodiniidia Small & Lynn, 1985, Protohypotrichia Shi et al., 1999, and Euplotia Jankowski, 1979 (Protista, Ciliophora): A new contribution to their phylogeny with reconsiderations on the evolutionary hypotheses. Mol Phylogenet Evol 2023; 189:107936. [PMID: 37778530 DOI: 10.1016/j.ympev.2023.107936] [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: 03/08/2023] [Revised: 09/28/2023] [Accepted: 09/28/2023] [Indexed: 10/03/2023]
Abstract
The huge variety of species and worldwide distribution of ciliated protists in class Spirotrichea continue to make it one of the most complicated and confused groups in Ciliophora, despite significant research interest in the unique molecular genetics of these organisms. In this study, the morphological and molecular information were integrated, and it is inferred from a new perspective for the evolutionary relationship among Phacodiniidia, Protohypotrichia, Hypotrichia and Euplotia. Our results indicate that Kiitricha and Caryotricha, two members in Protohypotrichia, may represent two parallel branches of evolution; Euplotidae and Aspidiscidae represent the most recently diverged taxa within Euplotida, followed by Certesiidae, Gastrocirrhidae, and Uronychidae. Further, representative morphological characters (e.g. fronto-ventral-transverse cirral anlagen, undulating membranes, marginal cirri and caudal cirri) were stochastically mapped on phylogenies to speculate evolutionary path and morphological characters of the evolutionary transition node groups were assumed.
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Affiliation(s)
- Chunyu Lian
- Laboratory of Protozoological Biodiversity and Evolution in Wetland, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Yan Zhao
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Ping Li
- Powerchina Northwest Engineering Corporation Limited, Xi'an 710065, China
| | - Tengteng Zhang
- Laboratory of Protozoological Biodiversity and Evolution in Wetland, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Khaled A S Al-Rasheid
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Naomi A Stover
- Department of Biology, Bradley University, Peoria 61625, USA
| | - Yurui Wang
- Laboratory of Protozoological Biodiversity and Evolution in Wetland, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China.
| | - Chen Shao
- Laboratory of Protozoological Biodiversity and Evolution in Wetland, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China.
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16
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Harada R, Inagaki Y. Gleaning Euglenozoa-specific DNA polymerases in public single-cell transcriptome data. Protist 2023; 174:125997. [PMID: 38039844 DOI: 10.1016/j.protis.2023.125997] [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: 09/15/2023] [Revised: 11/17/2023] [Accepted: 11/22/2023] [Indexed: 12/03/2023]
Abstract
Multiple genes encoding family A DNA polymerases (famA DNAPs), which are evolutionary relatives of DNA polymerase I (PolI) in bacteria and phages, have been found in eukaryotic genomes, and many of these proteins are used mainly in organelles. Among members of the phylum Euglenozoa, distinct types of famA DNAP, PolIA, PolIBCD+, POP, and eugPolA, have been found. It is intriguing how the suite of famA DNAPs had been established during the evolution of Euglenozoa, but the DNAP data have not been sampled from the taxa that sufficiently represent the diversity of this phylum. In particular, little sequence data were available for basal branching species in Euglenozoa until recently. Thanks to the single-cell transcriptome data from symbiontids and phagotrophic euglenids, we have an opportunity to cover the "hole" in the repertory of famA DNAPs in the deep branches in Euglenozoa. The current study identified 16 new famA DNAP sequences in the transcriptome data from 33 phagotrophic euglenids and two symbiontids, respectively. Based on the new famA DNAP sequences, the updated diversity and evolution of famA DNAPs in Euglenozoa are discussed.
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Affiliation(s)
- Ryo Harada
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Japan
| | - Yuji Inagaki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Japan; Center for Computational Sciences, University of Tsukuba, Japan.
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17
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Mahendrarajah TA, Moody ERR, Schrempf D, Szánthó LL, Dombrowski N, Davín AA, Pisani D, Donoghue PCJ, Szöllősi GJ, Williams TA, Spang A. ATP synthase evolution on a cross-braced dated tree of life. Nat Commun 2023; 14:7456. [PMID: 37978174 PMCID: PMC10656485 DOI: 10.1038/s41467-023-42924-w] [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: 04/21/2023] [Accepted: 10/25/2023] [Indexed: 11/19/2023] Open
Abstract
The timing of early cellular evolution, from the divergence of Archaea and Bacteria to the origin of eukaryotes, is poorly constrained. The ATP synthase complex is thought to have originated prior to the Last Universal Common Ancestor (LUCA) and analyses of ATP synthase genes, together with ribosomes, have played a key role in inferring and rooting the tree of life. We reconstruct the evolutionary history of ATP synthases using an expanded taxon sampling set and develop a phylogenetic cross-bracing approach, constraining equivalent speciation nodes to be contemporaneous, based on the phylogenetic imprint of endosymbioses and ancient gene duplications. This approach results in a highly resolved, dated species tree and establishes an absolute timeline for ATP synthase evolution. Our analyses show that the divergence of ATP synthase into F- and A/V-type lineages was a very early event in cellular evolution dating back to more than 4 Ga, potentially predating the diversification of Archaea and Bacteria. Our cross-braced, dated tree of life also provides insight into more recent evolutionary transitions including eukaryogenesis, showing that the eukaryotic nuclear and mitochondrial lineages diverged from their closest archaeal (2.67-2.19 Ga) and bacterial (2.58-2.12 Ga) relatives at approximately the same time, with a slightly longer nuclear stem-lineage.
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Affiliation(s)
- Tara A Mahendrarajah
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, AB Den Burg, The Netherlands
| | - Edmund R R Moody
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, BS8 1TQ, Bristol, UK
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, BS8 1TQ, Bristol, UK
| | - Dominik Schrempf
- Department Biological Physics, Eötvös University, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- MTA-ELTE "Lendulet" Evolutionary Genomics Research Group, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
| | - Lénárd L Szánthó
- Department Biological Physics, Eötvös University, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- MTA-ELTE "Lendulet" Evolutionary Genomics Research Group, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- Institute of Evolution, Centre for Ecological Research, Karolina ut 29, H-1113, Budapest, Hungary
| | - Nina Dombrowski
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, AB Den Burg, The Netherlands
| | - Adrián A Davín
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Davide Pisani
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, BS8 1TQ, Bristol, UK
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, BS8 1TQ, Bristol, UK
| | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, BS8 1TQ, Bristol, UK
| | - Gergely J Szöllősi
- Department Biological Physics, Eötvös University, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- MTA-ELTE "Lendulet" Evolutionary Genomics Research Group, Pázmány P. stny. 1A., H-1117, Budapest, Hungary
- Model-Based Evolutionary Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Tom A Williams
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, BS8 1TQ, Bristol, UK.
| | - Anja Spang
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, AB Den Burg, The Netherlands.
- Department of Evolutionary & Population Biology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands.
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18
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Lu B. Evolutionary Insights into the Relationship of Frogs, Salamanders, and Caecilians and Their Adaptive Traits, with an Emphasis on Salamander Regeneration and Longevity. Animals (Basel) 2023; 13:3449. [PMID: 38003067 PMCID: PMC10668855 DOI: 10.3390/ani13223449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/01/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
The extant amphibians have developed uncanny abilities to adapt to their environment. I compared the genes of amphibians to those of other vertebrates to investigate the genetic changes underlying their unique traits, especially salamanders' regeneration and longevity. Using the well-supported Batrachia tree, I found that salamander genomes have undergone accelerated adaptive evolution, especially for development-related genes. The group-based comparison showed that several genes are under positive selection, rapid evolution, and unexpected parallel evolution with traits shared by distantly related species, such as the tail-regenerative lizard and the longer-lived naked mole rat. The genes, such as EEF1E1, PAFAH1B1, and OGFR, may be involved in salamander regeneration, as they are involved in the apoptotic process, blastema formation, and cell proliferation, respectively. The genes PCNA and SIRT1 may be involved in extending lifespan, as they are involved in DNA repair and histone modification, respectively. Some genes, such as PCNA and OGFR, have dual roles in regeneration and aging, which suggests that these two processes are interconnected. My experiment validated the time course differential expression pattern of SERPINI1 and OGFR, two genes that have evolved in parallel in salamanders and lizards during the regeneration process of salamander limbs. In addition, I found several candidate genes responsible for frogs' frequent vocalization and caecilians' degenerative vision. This study provides much-needed insights into the processes of regeneration and aging, and the discovery of the critical genes paves the way for further functional analysis, which could open up new avenues for exploiting the genetic potential of humans and improving human well-being.
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Affiliation(s)
- Bin Lu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
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Tang J, Zhang G, Guo J, Luo L, Jiang J, Pan H. A new contribution to the raptorial ciliate genus Lacrymaria (Protista: Ciliophora): a brief review and comprehensive descriptions of two new species from Changjiang Estuary. Front Microbiol 2023; 14:1259653. [PMID: 38029185 PMCID: PMC10658195 DOI: 10.3389/fmicb.2023.1259653] [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: 07/16/2023] [Accepted: 10/03/2023] [Indexed: 12/01/2023] Open
Abstract
Ciliates serve as excellent indicators for water quality monitoring. However, their utilization is hindered by various taxonomic confusions. The ciliate genus Lacrymaria Bory de Saint-Vincent, 1824 is commonly found in different aquatic habitats, but its taxonomy has been sparsely investigated using state-of-the-art methods. This study investigated two new Lacrymaria species from Nanhui Wetland, Shanghai, China, using living observation, protargol staining, and molecular phylogeny methods. Lacrymaria songi sp. nov. is 180-340 × 20-25 μm in size and possesses 12-16 somatic kineties, 1 terminal contractile vacuole, 2 macronuclear nodules, and 2 types of rod-shaped extrusomes. Lacrymaria dragescoi sp. nov. is distinguished from its congeners by its cell size of 210-400 × 25-35 μm, 14-17 somatic kineties, 1 terminal contractile vacuole, 1 macronucleus, and 2 types of rod-shaped extrusomes. Phylogenetic analyses based on SSU rRNA gene sequences indicate that Lacrymariidae is monophyletic but Lacrymaria is not. Additionally, a brief review of the genus Lacrymaria is provided in this study. We suggest that L. bulbosa Alekperov, 1984, L. lanceolata Kahl, 1930, and L. ovata Burkovsky, 1970 be removed from the genus and propose Phialina lanceolata nov. comb. and Phialina ovata nov. comb. for the latter two. ZooBank registration: Present work: urn:lsid:zoobank.org:pub:CDFB1EBD-80BD-4533-B391-CEE89F62EDC4 Lacrymaria songi sp. nov.: urn:lsid:zoobank.org:act:417E7C2D-DAEC-4711-90BB-64AB3CD2F7D5 Lacrymaria dragescoi sp. nov.: urn:lsid:zoobank.org:act:8778D6B0-1F2E-473C-BE19-3F685391A40D.
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Affiliation(s)
- Jin Tang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China
| | - Gongaote Zhang
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Junqi Guo
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China
| | - Lingxuan Luo
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Jiamei Jiang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China
| | - Hongbo Pan
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China
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Song W, Jiao H, Yang J, Tang D, Ye T, Li L, Yang L, Li L, Song W, Al-Farraj SA, Hines HN, Liu W, Chen X. New evidence of consistency between phylogeny and morphology for two taxa in ciliated protists, the subclasses Oligotrichia and Choreotrichia (Protista, Ciliophora). Mol Phylogenet Evol 2023; 188:107911. [PMID: 37648182 DOI: 10.1016/j.ympev.2023.107911] [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: 04/20/2023] [Revised: 08/21/2023] [Accepted: 08/27/2023] [Indexed: 09/01/2023]
Abstract
Marine planktonic ciliates are largely oligotrichs and choreotrichs, which are two subclasses of the class Spirotrichea. The current phylogenetic assignments of oligotrichs and choreotrichs are inconsistent with previous results based on morphological features, probably hindered by the limited information from a single gene locus. Here we provide 53 new sequences from small subunit ribosomal RNA (SSU rDNA), ITS1-5.8S rDNA-ITS2, and large subunit ribosomal RNA (LSU rDNA) gene loci in 25 oligotrich and choreotrich species. We also predict RNA secondary structures for the ITS2 regions in 55 species, 48 species of which are reported for the first time. Based on these novel data, we make a more comprehensive phylogenetic reconstruction, revealing consistency between morphological taxonomy and an updated phylogenetic system for oligotrichs and choreotrichs. With the addition of data from ciliature patterns and genes, the phylogenetic analysis of the subclass Oligotrichia suggests three evolutionary trajectories, among which: 1) Novistrombidium asserts an ancestral ciliary pattern in Oligotrichia; 2) the subgenera division of Novistrombidium and Parallelostrombidium are fully supported; 3) the three families (Tontoniidae, Pelagostrombidiidae and Cyrtostrombidiidae) all evolved from the most diverse family Strombidiidae, which explains why strombidiids consistently form polyphyletic clades. In the subclass Choreotrichia, Strombidinopsis likely possesses an ancestral position to other choreotrichs, and both phylogenetic analysis and RNA secondary structure prediction support the hypothesis that tintinnids may have evolved from Strombidinopsis. The results presented here offer an updated hypothesis for the evolutionary history of oligotrichs and choreotrichs based on new evidence obtained by expanding sampling of molecular information across multiple gene loci.
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Affiliation(s)
- Wen Song
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
| | - Huixin Jiao
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
| | - Juan Yang
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
| | - Danxu Tang
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
| | - Tingting Ye
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
| | - Lu Li
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
| | - Lei Yang
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
| | - Lifang Li
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
| | - Weibo Song
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China; Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Laoshan Laboratory, Qingdao 266237, China
| | - Saleh A Al-Farraj
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Hunter N Hines
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, FL, USA
| | - Weiwei Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou 510301, China.
| | - Xiao Chen
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China; Suzhou Research Institute of Shandong University, Suzhou 215123, China.
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21
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Pan Z, Huang S, Zheng W. The complete mitogenome of Anaplectoides virens (Butler, 1878) (Lepidoptera: Noctuidae) and phylogenetic analysis. Mitochondrial DNA B Resour 2023; 8:960-962. [PMID: 37705758 PMCID: PMC10496521 DOI: 10.1080/23802359.2023.2254460] [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: 04/19/2022] [Accepted: 08/28/2023] [Indexed: 09/15/2023] Open
Abstract
Anaplectoides virens (Noctuoidea: Noctuidae) is a polyphagous herbivorous moth, which feeds on a wide variety of crops. Molecular phylogenetic studies of this species are still limited. We presented the first complete mitochondrial genome of the genus Anaplectoides, which was assembled from data generated using a genome skimming method. The assembled mitogenome is 15,358 bp in length and consists of 37 genes, including 13 protein-coding genes, two rRNAs, 22 tRNAs, and a control region. Except for the start codon of cox1 with CGA, other coding genes use ATN as the start codon. Most PCGs use TAA as the stop codon; however, cox1, cox2, and nad4 use T as the termination codon. Phylogenetic analysis revealed that the genera of ((Agrotis + Striacosta) + Anaplectoides) within Noctuinae formed a monophyletic group. Among Noctuidae, the relationship of ((Noctuinae + Hadninae) + Amphipyrinae) was also highly supported.
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Affiliation(s)
- Zhaohui Pan
- Key Laboratory of Forest Ecology in Tibet Plateau, Ministry of Education (Institute of Plateau Ecology, Tibet Agricultural & Animal Husbandry University), Linzhi, China
| | - Sicheng Huang
- Key Laboratory of Forest Ecology in Tibet Plateau, Ministry of Education (Institute of Plateau Ecology, Tibet Agricultural & Animal Husbandry University), Linzhi, China
| | - Weilie Zheng
- Key Laboratory of Forest Ecology in Tibet Plateau, Ministry of Education (Institute of Plateau Ecology, Tibet Agricultural & Animal Husbandry University), Linzhi, China
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Pereira AG, Kohlsdorf T. Repeated evolution of similar phenotypes: Integrating comparative methods with developmental pathways. Genet Mol Biol 2023; 46:e20220384. [PMID: 37486083 PMCID: PMC10364090 DOI: 10.1590/1678-4685-gmb-2022-0384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 05/24/2023] [Indexed: 07/25/2023] Open
Abstract
Repeated phenotypes, often referred to as 'homoplasies' in cladistic analyses, may evolve through changes in developmental processes. Genetic bases of recurrent evolution gained attention and have been studied in the past years using approaches that combine modern analytical phylogenetic tools with the stunning assemblage of new information on developmental mechanisms. In this review, we evaluated the topic under an integrated perspective, revisiting the classical definitions of convergence and parallelism and detailing comparative methods used to evaluate evolution of repeated phenotypes, which include phylogenetic inference, estimates of evolutionary rates and reconstruction of ancestral states. We provide examples to illustrate how a given methodological approach can be used to identify evolutionary patterns and evaluate developmental mechanisms associated with the intermittent expression of a given trait along the phylogeny. Finally, we address why repeated trait loss challenges strict definitions of convergence and parallelism, discussing how changes in developmental pathways might explain the high frequency of repeated trait loss in specific lineages.
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Affiliation(s)
- Anieli Guirro Pereira
- Universidade de São Paulo, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), Departamento de Biologia, Ribeirão Preto, SP, Brazil
| | - Tiana Kohlsdorf
- Universidade de São Paulo, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), Departamento de Biologia, Ribeirão Preto, SP, Brazil
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23
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Wang X, Wanasinghe DN, Zhang J, Ma J, Zhou P, Zhang L, Lu Y, Zhang Z. Insights from the Endophytic Fungi in Amphisphaeria (Sordariomycetes): A. orixae sp. nov. from Orixa japonica and Its Secondary Metabolites. Microorganisms 2023; 11:1268. [PMID: 37317242 DOI: 10.3390/microorganisms11051268] [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: 04/17/2023] [Revised: 05/04/2023] [Accepted: 05/09/2023] [Indexed: 06/16/2023] Open
Abstract
Endophytic fungi are a remarkably diverse group of microorganisms that have imperceptible associations with their hosts for at least a part of their life cycle. The enormous biological diversity and the capability of producing bioactive secondary metabolites such as alkaloids, terpenoids, and polyketides have attracted the attention of different scientific communities, resulting in numerous investigations on these fungal endophytes. During our surveys of plant-root-based fungi in the mountain areas of Qingzhen, Guizhou Province, several isolates of endophytic fungi were identified. In this study, a novel endophytic fungus was discovered in the roots of a medicinal plant (Orixa japonica) in Southern China and introduced as a new species (Amphisphaeria orixae) based on morphological evidence and molecular phylogenetic analysis (combined ITS and LSU sequence data). To the best of our knowledge, A. orixae is the first reported endophyte as well as the first hyphomycetous asexual morph in Amphisphaeria. A new isocoumarin, (R)-4,6,8-trihydroxy-5-methylisochroman-1-one (1), and 12 known compounds (2-13) were isolated from the rice fermentation products of this fungus. Using 1D- and 2D-NMR, mass spectrometry, and ECD studies, their structures were identified. The antitumor activity of these compounds was tested. Unfortunately, none of the compounds tested showed significant antitumor activity.
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Affiliation(s)
- Xiaojie Wang
- School of Liquor and Food Engineering, Guizhou University, Guiyang 550025, China
- Guizhou Academy of Testing and Analysis, Guizhou Academy of Sciences, Guiyang 550014, China
| | - Dhanushka N Wanasinghe
- Centre for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Honghe County 654400, China
| | - Jingyi Zhang
- School of Food and Pharmaceutical Engineering, Guizhou Institute of Technology, Guiyang 550003, China
| | - Jian Ma
- School of Food and Pharmaceutical Engineering, Guizhou Institute of Technology, Guiyang 550003, China
| | - Peifeng Zhou
- School of Liquor and Food Engineering, Guizhou University, Guiyang 550025, China
- Guizhou Academy of Testing and Analysis, Guizhou Academy of Sciences, Guiyang 550014, China
| | - Lijuan Zhang
- School of Food and Pharmaceutical Engineering, Guizhou Institute of Technology, Guiyang 550003, China
| | - Yongzhong Lu
- School of Food and Pharmaceutical Engineering, Guizhou Institute of Technology, Guiyang 550003, China
| | - Zhen Zhang
- Guizhou Academy of Testing and Analysis, Guizhou Academy of Sciences, Guiyang 550014, China
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24
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Raiyemo DA, Tranel PJ. Comparative analysis of dioecious Amaranthus plastomes and phylogenomic implications within Amaranthaceae s.s. BMC Ecol Evol 2023; 23:15. [PMID: 37149567 PMCID: PMC10164334 DOI: 10.1186/s12862-023-02121-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 04/28/2023] [Indexed: 05/08/2023] Open
Abstract
BACKGROUND The genus Amaranthus L. consists of 70-80 species distributed across temperate and tropical regions of the world. Nine species are dioecious and native to North America; two of which are agronomically important weeds of row crops. The genus has been described as taxonomically challenging and relationships among species including the dioecious ones are poorly understood. In this study, we investigated the phylogenetic relationships among the dioecious amaranths and sought to gain insights into plastid tree incongruence. A total of 19 Amaranthus species' complete plastomes were analyzed. Among these, seven dioecious Amaranthus plastomes were newly sequenced and assembled, an additional two were assembled from previously published short reads sequences and 10 other plastomes were obtained from a public repository (GenBank). RESULTS Comparative analysis of the dioecious Amaranthus species' plastomes revealed sizes ranged from 150,011 to 150,735 bp and consisted of 112 unique genes (78 protein-coding genes, 30 transfer RNAs and 4 ribosomal RNAs). Maximum likelihood trees, Bayesian inference trees and splits graphs support the monophyly of subgenera Acnida (7 dioecious species) and Amaranthus; however, the relationship of A. australis and A. cannabinus to the other dioecious species in Acnida could not be established, as it appears a chloroplast capture occurred from the lineage leading to the Acnida + Amaranthus clades. Our results also revealed intraplastome conflict at some tree branches that were in some cases alleviated with the use of whole chloroplast genome alignment, indicating non-coding regions contribute valuable phylogenetic signals toward shallow relationship resolution. Furthermore, we report a very low evolutionary distance between A. palmeri and A. watsonii, indicating that these two species are more genetically related than previously reported. CONCLUSIONS Our study provides valuable plastome resources as well as a framework for further evolutionary analyses of the entire Amaranthus genus as more species are sequenced.
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Affiliation(s)
- Damilola A Raiyemo
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA
| | - Patrick J Tranel
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA.
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25
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Li J, Li S, Su H, Yu M, Xu J, Yi Z. Comprehensive phylogenomic analyses reveal that order Armophorida is most closely related to class Armophorea (Protista, Ciliophora). Mol Phylogenet Evol 2023; 182:107737. [PMID: 36841269 DOI: 10.1016/j.ympev.2023.107737] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 02/12/2023] [Accepted: 02/19/2023] [Indexed: 02/27/2023]
Abstract
Ciliate species within the class Armophorea are widely distributed in various anaerobic environments, hence they are of great interest to researchers studying evolution and adaptation of eukaryotes to extreme habitats. However, phylogenetic relationships within the class remain largely elusive, most especially assignment of the order Armophorida and classification within the family Metopidae. In this study, we newly sequenced transcriptomes and the SSU rDNA of five armophorean species, Sulfonecta cf. uniserialis (order Armophorida), Nyctotheroides sp. (order Clevelandellida), and Metopus major, M. paraes, and Brachonella contorta (order Metopida). Comprehensive phylogenomic analyses revealed that Armophorea was most closely related to Muranotrichea and Parablepharismea. Our results indicate that the order Armophorida either belongs to Armophorea or represents a new class within APM (Armophorea-Parablepharismea-Muranotrichea). Analyses combining ecological niches and molecular trees showed that APM species might descend from an anaerobic free-living ciliate species. Existing molecular phylogenomic/phylogenetic and morphological evidence indicate that the family Metopidae is non-monophyletic and should be further classified with inclusion of additional lines of evidences. Our results provide new insights into the long-debated relationships within Armophorea.
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Affiliation(s)
- Jia Li
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Song Li
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China
| | - Hua Su
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Minjie Yu
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Jiahui Xu
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Zhenzhen Yi
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China.
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Dil S, Ye J, Ma H, Unar A, Khan I, Ali A, Khan K, Menglei Y, Ma A, Shah B, Khan R, Liu Z, Shi Q. Cornichon protein CNIH4 is not essential for mice gametogenesis and fertility. Dev Biol 2023; 496:15-23. [PMID: 36657507 DOI: 10.1016/j.ydbio.2023.01.004] [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: 06/13/2022] [Revised: 01/03/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023]
Abstract
BACKGROUND Cornichon is a functionally conserved transmembrane protein family that generally acts as a cargo-sorting receptor and cycles between the ER and the Golgi. Four Cornichon family members (CNIH1-4) have been identified. The key residues responsible for CNIH1-3 to bind to AMPA receptors are not conserved in CNIH4. Additionally, the function of CNIH1-3 in GPCR signaling is less established, while more established in case of CNIH4 protein that interact with GPCR and control their exportation. Many GPCRs are known for their essential roles in male and female gonad development. But whether CNIH4 plays a role in gametogenesis remains unknown. DESIGN Mice carrying the Cnih4 knockout allele (Cnih4tm1a-/-) were generated by insertion of a LacZ reporter and a polyadenylation site after exon 1. Western blot, Immunofluorescence, computer-aided sperm analysis and other methods were used in the functional analysis. RESULTS We identified that both Cnih4tm1a-/- male and female mice have normal fertility. Though, the sperm count, morphology, and motility of Cnih4tm1a-/- mice were slightly impaired compared to those of wild-type mice, the testes to body weight ratio and testicular histology were similar to those in control mice. Histological examination of Cnih4tm1a-/- ovaries detected follicles from primordial to antral stages and the numbers of follicles at each stage were also comparable to wild-type controls. Normal fertility was noticed after six-month fertility tests. That was likely due to the compensatory role of Chin3, which significantly upregulated in the Cnih4tm1a-/- mice to preserve the fertility role. CONCLUSION Despite CNIH4 showing enriched expression in mouse germ cells, our genetic knockout studies demonstrated that CNIH4 is not essential for gametogenesis and fertility in mice although with a slight reduction in count, motility and morphology of sperm in male mice.
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Affiliation(s)
- Sobia Dil
- Division of Reproduction and Genetics, The First Affiliated Hospital of University of Science and Technology of China, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, 230027, China
| | - Jingwei Ye
- Division of Reproduction and Genetics, The First Affiliated Hospital of University of Science and Technology of China, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, 230027, China
| | - Hui Ma
- Division of Reproduction and Genetics, The First Affiliated Hospital of University of Science and Technology of China, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, 230027, China
| | - Ahsanullah Unar
- Division of Reproduction and Genetics, The First Affiliated Hospital of University of Science and Technology of China, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, 230027, China
| | - Ihsan Khan
- Division of Reproduction and Genetics, The First Affiliated Hospital of University of Science and Technology of China, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, 230027, China
| | - Asim Ali
- Division of Reproduction and Genetics, The First Affiliated Hospital of University of Science and Technology of China, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, 230027, China; Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, Pakistan
| | - Khalid Khan
- Division of Reproduction and Genetics, The First Affiliated Hospital of University of Science and Technology of China, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, 230027, China
| | - Yang Menglei
- Division of Reproduction and Genetics, The First Affiliated Hospital of University of Science and Technology of China, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, 230027, China
| | - Ao Ma
- Division of Reproduction and Genetics, The First Affiliated Hospital of University of Science and Technology of China, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, 230027, China
| | - Basit Shah
- Division of Reproduction and Genetics, The First Affiliated Hospital of University of Science and Technology of China, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, 230027, China; Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, Pakistan
| | - Ranjha Khan
- Division of Reproduction and Genetics, The First Affiliated Hospital of University of Science and Technology of China, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, 230027, China
| | - Zhiwei Liu
- Cambridge-Suda Genomic Research Center, Soochow University, Suzhou, China.
| | - Qinghua Shi
- Division of Reproduction and Genetics, The First Affiliated Hospital of University of Science and Technology of China, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, 230027, China.
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Yasir A, Mahmood Y, Yaqoob MA, Zia UUR, Munoz-Zanzi C, Alam MM, Warraich MA, Hassan Mushtaq M. Epidemiological investigation of norovirus infections in Punjab, Pakistan, through the One Health approach. Front Public Health 2023; 11:1065105. [PMID: 37006581 PMCID: PMC10052407 DOI: 10.3389/fpubh.2023.1065105] [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: 10/09/2022] [Accepted: 02/14/2023] [Indexed: 03/16/2023] Open
Abstract
IntroductionNorovirus, mainly associated with acute gastroenteritis, is very contagious and can affect a vast range of species ranging from cattle, pigs, dogs, mice, cats, sheep, and lions to humans. It is a foodborne pathogen that mainly transmits through the fecal–oral route.MethodsThis is the first-ever study conducted in Lahore and Sheikhupura districts of Punjab, Pakistan, to investigate noroviruses through the One Health approach. From January 2020 to September 2021, 200 fecal samples were collected from clinical cases of hospitalized patients and 200 fecal samples from sick animals at veterinary hospitals and local farms. In addition, 500 food and beverage samples were collected from street vendors and retail stores. A predesigned questionnaire was used to assess the risk factors and clinical characteristics of sick people and animals.Results and discussionOverall, 14% of the human clinical samples were positive by RT-PCR for genogroup GII. All bovine samples were negative. Food and beverage samples were tested in pools, resulting in sugarcane juice samples positive for genogroup GII. Previous contact with acute gastroenteritis patients, sex, and presence of vomiting were found to be significant risk factors (p ≤ 0.05). The substantial number of diarrhea cases associated with noroviruses calls for additional studies to investigate the epidemiology and transmission and to improve surveillance.
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Affiliation(s)
- Ammar Yasir
- Department of Epidemiology and Public Health, University of Veterinary and Animal Sciences, Lahore, Pakistan
- Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, MN, United States
| | - Yasir Mahmood
- Department of Epidemiology and Public Health, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Muhammad Arsalan Yaqoob
- Department of Epidemiology and Public Health, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Ubaid-ur-Rehman Zia
- Department of Epidemiology and Public Health, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Claudia Munoz-Zanzi
- Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, MN, United States
| | | | | | - Muhammad Hassan Mushtaq
- Department of Epidemiology and Public Health, University of Veterinary and Animal Sciences, Lahore, Pakistan
- *Correspondence: Muhammad Hassan Mushtaq
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28
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Feng C, Wang K, Xu W, Yang L, Wanghe K, Sun N, Wu B, Wu F, Yang L, Qiu Q, Gan X, Chen Y, He S. Monsoon boosted radiation of the endemic East Asian carps. SCIENCE CHINA. LIFE SCIENCES 2023; 66:563-578. [PMID: 36166180 DOI: 10.1007/s11427-022-2141-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 04/21/2022] [Indexed: 10/14/2022]
Abstract
Major historical events often trigger the rapid flourishing of a few lineages, which in turn shape established biodiversity patterns. How did this process occur and develop? This study provides a window into this issue. The endemic East Asian carps (EEAC) dominated the ichthyofauna of East Asia and exhibited a high degree of adaptation to monsoonal river-lake ecosystems. A series of evidence, including ecogeography, phylogenetics, and macroevolution, suggests that the EEAC is a lineage that arose with the East Asian monsoon and thrived intimately with subsequent monsoon activities. We further deduce the evolution of the EEAC and find that a range of historical events in the monsoon setting (e.g., marine transgression and regression and glacial-interglacial cycle) have further reshaped the distribution patterns of EEAC's members. Comparative genomics analyses reveal that introgressions during the initial period of EEAC radiation and innovations in the regulation of the brain and nervous system may have aided their adaptation to river-lake ecosystems in a monsoon setting, which boosted radiation. Overall, this study strengthens knowledge of the evolutionary patterns of freshwater fishes in East Asia and provides a model case for understanding the impact of major historical events on the evolution of biota.
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Affiliation(s)
- Chenguang Feng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Kun Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Wenjie Xu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Liandong Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Kunyuan Wanghe
- Key Laboratory of Adaptation and Evolution of Plateau Biota of Chinese Academy of Sciences, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | - Ning Sun
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Baosheng Wu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Feixiang Wu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China
| | - Lei Yang
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Qiang Qiu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Xiaoni Gan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yiyu Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- National Natural Science Foundation of China, Beijing, 100085, China
| | - Shunping He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
- Center for Excellence in Animal Evolution and Genetics, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
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Parey E, Roest Crollius H, Berthelot C. SCORPiOs, a Novel Method to Reconstruct Gene Phylogenies in the Context of a Known WGD Event. Methods Mol Biol 2023; 2545:155-173. [PMID: 36720812 DOI: 10.1007/978-1-0716-2561-3_8] [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: 02/02/2023]
Abstract
Phylogenetic gene trees recapitulate the evolutionary history of genes across species, forming an essential framework for comparative genomic studies. In particular, within the context of whole-genome duplications (WGDs), they serve as a basis to investigate patterns of duplicate gene retention and loss, timing of genome rediploidization, and, more generally, to explore the functional consequences of the duplication in descending species. Yet, despite ever more sophisticated models to describe the evolution of gene sequences, building accurate gene trees remains a challenge in ancient polyploid taxons. WGDs generate complex gene families with many duplicated copies and recurrent gene losses, which complicate this task even more. Here, we describe how to use SCORPiOs, a novel method that leverages synteny conservation to provide more accurate phylogenies in the presence of a known WGD event.
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Affiliation(s)
- Elise Parey
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- INRAE, LPGP, Rennes, France
| | - Hugues Roest Crollius
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Camille Berthelot
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.
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Lyu Z, Ma X, Su J, Hu F, Liu W, Zhao Y, Zhao X, Xing L. Morphology, morphogenesis and molecular phylogeny of Lamtostyla granulifera sinensis subsp. nov. (Ciliophora, Hypotrichia) from a wetland in China. Eur J Protistol 2023; 87:125938. [PMID: 36512884 DOI: 10.1016/j.ejop.2022.125938] [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: 05/01/2022] [Revised: 09/26/2022] [Accepted: 10/24/2022] [Indexed: 12/15/2022]
Abstract
The morphology, morphogenesis and molecular phylogeny of a hypotrichous ciliate, Lamtostyla granulifera sinensis subsp. nov., isolated from northern China, were investigated. This population appeared highly similar in morphology to L. granulifera Foissner, 1997. However, on detailed investigation some non-overlapping features were identified, i.e., the body shape and the arrangement of the cortical granules. These differences suggested the separation at subspecies level. Furthermore, the morphogenesis of the new subspecies is described, which is characterized by: (1) the posterior part of the parental adoral zone of membranelles is renewed; (2) the amphisiellid median cirral row is formed from two anlagen; and (3) the frontoventral-transverse cirral anlagen II to VI generate one transverse cirrus each. Phylogenetic analyses based on SSU rDNA sequence data show that Lamtostyla species are scattered in different clades. The monophyly of the genus Lamtostyla is also rejected by the AU test in this study.
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Affiliation(s)
- Zhao Lyu
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Xiaoqin Ma
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Jian Su
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Fangcheng Hu
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Wanjing Liu
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Yuqing Zhao
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Xi Zhao
- Xijing University, Xi'an 710123, China
| | - Lianxi Xing
- College of Life Sciences, Northwest University, Xi'an 710069, China.
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Liu J, Yang Y, Yan Z, Wang H, Bai M, Shi C, Li J. Analysis of the Mitogenomes of Two Helotid Species Provides New Insights into the Phylogenetic Relationship of the Basal Cucujoidea (Insecta: Coleoptera). BIOLOGY 2023; 12:biology12010135. [PMID: 36671827 PMCID: PMC9855730 DOI: 10.3390/biology12010135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023]
Abstract
Helotid beetles are commonly found in places where sap flows from tree trunks and in crevices in bark. The Helotidae family is a rare and primitive group of Cucujoidea. To date, no complete mitochondrial (mt) genome has been sequenced for this family. To better understand the characteristics of the mt genome and the evolution of Cucujoidea, we sequenced and annotated the complete mt genomes of Helota thoracica (Ritsema, 1895) and Helota yehi Lee, 2017 using next-generation sequencing. These are the first record of Helotidae mt genomes. The RNA secondary structures of both species were also predicted in this study. The mt genomes of H. thoracica and H. yehi are circular, with total lengths of 16,112 bp and 16,401 bp, respectively. After comparing the mt genomes of H. thoracica and H. yehi, we observed the gene arrangement, codon usage patterns, base content, and RNA secondary structures of both species to be similar, which has also been noted in other Coleoptera insects. The nucleotide sequence of the coding regions and the control region has small differences. The phylogenetic analysis indicated that Helotidae and Protocucujidae are sister groups and revealed the relationship between seven families; however, the validity of the two series (Erotylid series and Nitidulid series) as larger groups in the superfamily was not supported. The mt phylogenomic relationships have strong statistical support. Therefore, the division of Cucujoidea into series should be re-examined. Our results will provide a better understanding of the mt genome and phylogeny of Helotidae and Cucujoidea and will provide valuable molecular markers for further genetic studies.
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Affiliation(s)
- Jing Liu
- College of Plant Protection, Hebei Agricultural University, Baoding 071000, China
| | - Yuhang Yang
- College of Plant Protection, Hebei Agricultural University, Baoding 071000, China
| | - Zihan Yan
- College of Plant Protection, Hebei Agricultural University, Baoding 071000, China
| | - Haishan Wang
- College of Plant Protection, Hebei Agricultural University, Baoding 071000, China
| | - Ming Bai
- College of Plant Protection, Hebei Agricultural University, Baoding 071000, China
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Correspondence: (M.B.); (J.L.)
| | - Chengmin Shi
- College of Plant Protection, Hebei Agricultural University, Baoding 071000, China
| | - Jing Li
- College of Plant Protection, Hebei Agricultural University, Baoding 071000, China
- Correspondence: (M.B.); (J.L.)
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Wang C, Jiang L, Pan H, Warren A, Hu X. New contributions to the Cyrtophoria ciliates (Protista, Ciliophora): Establishment of new taxa and phylogenetic analyses using two ribosomal genes. J Eukaryot Microbiol 2023; 70:e12938. [PMID: 35892241 DOI: 10.1111/jeu.12938] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 07/06/2022] [Accepted: 07/22/2022] [Indexed: 01/13/2023]
Abstract
Periphytic ciliates play a vital role in the material cycle and energy flow of microbial food web, however, their taxonomy and biodiversity are inadequately studied given their high species richness. Two new and one little known species, viz. Derouxella lembodes gen. et sp. nov., Cyrtophoron multivacuolatum sp. nov., and Cyrtophoron apsheronica Aliev, 1991, collected from coastal waters of China, were investigated using modern methods. Derouxella gen. nov. can be recognized by having dorsoventrally flattened body, a podite, one fragmented preoral kinety, two parallel circumoral kineties, and somatic kineties progressively shortened from right to left. Morphological classification and phylogenetic analyses based on nuclear small subunit ribosomal RNA (nSSU rRNA) and mitochondrial small subunit ribosomal RNA (mtSSU rRNA) gene sequence data inferred that Derouxella gen. nov. occupies an intermediate position between Hartmannulidae and Dysteriidae. Cyrtophoron multivacuolatum sp. nov. is characterized by large body size, the numbers of somatic kineties and nematodesmal rods, and having numerous contractile vacuoles. The genus Cyrtophoron and the poorly known species C. apsheronica were redefined. Even with the addition of newly obtained nSSU rRNA and mtSSU rRNA gene sequences of Cyrtophoron, the family Chlamydodontidae was still recovered as a monophyletic group, the monophyly of Cyrtophoron was supported too.
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Affiliation(s)
- Congcong Wang
- Key Laboratory of Mariculture, Ministry of Education, College of Fisheries, Ocean University of China, Qingdao, China.,Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Limin Jiang
- Key Laboratory of Mariculture, Ministry of Education, College of Fisheries, Ocean University of China, Qingdao, China.,Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Hongbo Pan
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China.,Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai, China
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London, UK
| | - Xiaozhong Hu
- Key Laboratory of Mariculture, Ministry of Education, College of Fisheries, Ocean University of China, Qingdao, China.,Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
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Rudenko N, Golovchenko M, Horak A, Grubhoffer L, Mongodin EF, Fraser CM, Qiu W, Luft BJ, Morgan RG, Casjens SR, Schutzer SE. Genomic Confirmation of Borrelia garinii, United States. Emerg Infect Dis 2023; 29:64-69. [PMID: 36573553 PMCID: PMC9796223 DOI: 10.3201/eid2901.220930] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Lyme disease is a multisystem disorder primarily caused by Borrelia burgdorferi sensu lato. However, B. garinii, which has been identified on islands off the coast of Newfoundland and Labrador, Canada, is a cause of Lyme disease in Eurasia. We report isolation and whole-genome nucleotide sequencing of a B. garinii isolate from a cotton mouse (Peromyscus gossypinus) in South Carolina, USA. We identified a second B. garinii isolate from the same repository. Phylogenetic analysis does not associate these isolates with the previously described isolates of B. garinii from Canada.
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Lin Q, Braukmann TWA, Soto Gomez M, Mayer JLS, Pinheiro F, Merckx VSFT, Stefanović S, Graham SW. Mitochondrial genomic data are effective at placing mycoheterotrophic lineages in plant phylogeny. THE NEW PHYTOLOGIST 2022; 236:1908-1921. [PMID: 35731179 DOI: 10.1111/nph.18335] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 06/13/2022] [Indexed: 05/03/2023]
Abstract
Fully mycoheterotrophic plants can be difficult to place in plant phylogeny due to elevated substitution rates associated with photosynthesis loss. This potentially limits the effectiveness of downstream analyses of mycoheterotrophy that depend on accurate phylogenetic inference. Although mitochondrial genomic data sets are rarely used in plant phylogenetics, theory predicts that they should be resilient to long-branch artefacts, thanks to their generally slow evolution, coupled with limited rate elevation in heterotrophs. We examined the utility of mitochondrial genomes for resolving contentious higher-order placements of mycoheterotrophic lineages in two test cases: monocots (focusing on Dioscoreales) and Ericaceae. We find Thismiaceae to be distantly related to Burmanniaceae in the monocot order Dioscoreales, conflicting with current classification schemes based on few gene data sets. We confirm that the unusual Afrothismia is related to Taccaceae-Thismiaceae, with a corresponding independent loss of photosynthesis. In Ericaceae we recovered the first well supported relationships among its five major lineages: mycoheterotrophic Ericaceae are not monophyletic, as pyroloids are inferred to be sister to core Ericaceae, and monotropoids to arbutoids. Genes recovered from mitochondrial genomes collectively resolved previously ambiguous mycoheterotroph higher-order relationships. We propose that mitochondrial genomic data should be considered in standardised gene panels for inferring overall plant phylogeny.
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Affiliation(s)
- Qianshi Lin
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
- Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 2Z9, Canada
| | - Thomas W A Braukmann
- Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 2Z9, Canada
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA
| | - Marybel Soto Gomez
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - Juliana Lischka Sampaio Mayer
- Departamento de Biologia Vegetal, Universidade Estadual de Campinas, 255 Rua Monteiro Lobato, Campinas, São Paulo, 13.083-862, Brazil
| | - Fábio Pinheiro
- Departamento de Biologia Vegetal, Universidade Estadual de Campinas, 255 Rua Monteiro Lobato, Campinas, São Paulo, 13.083-862, Brazil
| | - Vincent S F T Merckx
- Naturalis Biodiversity Center, Vondellaan 55, 2332 AA, Leiden, the Netherlands
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, PO Box 94240, 1090 GE, Amsterdam, the Netherlands
| | - Saša Stefanović
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
- Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 2Z9, Canada
| | - Sean W Graham
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
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Lu YZ, Ma J, Xiao XJ, Zhang LJ, Xiao YP, Kang JC. Four new species and three new records of helicosporous hyphomycetes from China and their multi-gene phylogenies. Front Microbiol 2022; 13:1053849. [PMID: 36504835 PMCID: PMC9732463 DOI: 10.3389/fmicb.2022.1053849] [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: 09/26/2022] [Accepted: 10/31/2022] [Indexed: 11/27/2022] Open
Abstract
Helicosporous hyphomycetes have the potential to produce a variety of bioactive compounds. However, the strain resources of this fungal group are relatively scarce, which limits their further exploitation and utilization. In this study, based on phylogenetic analyses of combined ITS, LSU, RPB2, and TEF1α sequence data and the morphology from 11 isolates, we introduce four new species of helicosporous hyphomycetes, viz. Helicoma wuzhishanense, Helicosporium hainanense, H. viridisporum, and Neohelicomyces hainanensis, as well as three new records, viz. Helicoma guttulatum, H. longisporum, and Helicosporium sexuale. Detailed morphological comparisons of the four new species that distinguish them are provided.
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Affiliation(s)
- Yong-Zhong Lu
- Engineering and Research Center for Southwest Bio-Pharmaceutical Resources of National Education Ministry of China, Guizhou University, Guiyang, China
- School of Pharmaceutical Engineering, Guizhou Institute of Technology, Guiyang, China
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, Thailand
- Guizhou Key Laboratory of Agricultural Biotechnology, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Jian Ma
- School of Pharmaceutical Engineering, Guizhou Institute of Technology, Guiyang, China
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, Thailand
- Guizhou Key Laboratory of Agricultural Biotechnology, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Xing-Juan Xiao
- School of Pharmaceutical Engineering, Guizhou Institute of Technology, Guiyang, China
| | - Li-Juan Zhang
- School of Pharmaceutical Engineering, Guizhou Institute of Technology, Guiyang, China
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, Thailand
| | - Yuan-Pin Xiao
- Engineering and Research Center for Southwest Bio-Pharmaceutical Resources of National Education Ministry of China, Guizhou University, Guiyang, China
- School of Pharmaceutical Engineering, Guizhou Institute of Technology, Guiyang, China
| | - Ji-Chuan Kang
- Engineering and Research Center for Southwest Bio-Pharmaceutical Resources of National Education Ministry of China, Guizhou University, Guiyang, China
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Wang T, Li TZ, Chen SS, Yang T, Shu JP, Mu YN, Wang KL, Chen JB, Xiang JY, Yan YH. Untying the Gordian knot of plastid phylogenomic conflict: A case from ferns. FRONTIERS IN PLANT SCIENCE 2022; 13:918155. [PMID: 36507421 PMCID: PMC9730426 DOI: 10.3389/fpls.2022.918155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 10/11/2022] [Indexed: 06/17/2023]
Abstract
Phylogenomic studies based on plastid genome have resolved recalcitrant relationships among various plants, yet the phylogeny of Dennstaedtiaceae at the level of family and genera remains unresolved due to conflicting plastid genes, limited molecular data and incomplete taxon sampling of previous studies. The present study generated 30 new plastid genomes of Dennstaedtiaceae (9 genera, 29 species), which were combined with 42 publicly available plastid genomes (including 24 families, 27 genera, 42 species) to explore the evolution of Dennstaedtiaceae. In order to minimize the impact of systematic errors on the resolution of phylogenetic inference, we applied six strategies to generate 30 datasets based on CDS, intergenic spacers, and whole plastome, and two tree inference methods (maximum-likelihood, ML; and multispecies coalescent, MSC) to comprehensively analyze the plastome-scale data. Besides, the phylogenetic signal among all loci was quantified for controversial nodes using ML framework, and different topologies hypotheses among all datasets were tested. The species trees based on different datasets and methods revealed obvious conflicts at the base of the polypody ferns. The topology of the "CDS-codon-align-rm3" (CDS with the removal of the third codon) matrix was selected as the primary reference or summary tree. The final phylogenetic tree supported Dennstaedtiaceae as the sister group to eupolypods, and Dennstaedtioideae was divided into four clades with full support. This robust reconstructed phylogenetic backbone establishes a framework for future studies on Dennstaedtiaceae classification, evolution and diversification. The present study suggests considering plastid phylogenomic conflict when using plastid genomes. From our results, reducing saturated genes or sites can effectively mitigate tree conflicts for distantly related taxa. Moreover, phylogenetic trees based on amino acid sequences can be used as a comparison to verify the confidence of nucleotide-based trees.
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Affiliation(s)
- Ting Wang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Ting-Zhang Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Si-Si Chen
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
| | - Tuo Yang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
| | - Jiang-Ping Shu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
| | - Yu-Nong Mu
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Kang-Lin Wang
- Green Development Institute, Southwest Forestry University, Kunming, China
| | - Jian-Bing Chen
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
| | - Jian-Ying Xiang
- Yunnan Academy of Biodiversity, Southwest Forestry University, Kunming, China
| | - Yue-Hong Yan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
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Harris BJ, Clark JW, Schrempf D, Szöllősi GJ, Donoghue PCJ, Hetherington AM, Williams TA. Divergent evolutionary trajectories of bryophytes and tracheophytes from a complex common ancestor of land plants. Nat Ecol Evol 2022; 6:1634-1643. [PMID: 36175544 PMCID: PMC9630106 DOI: 10.1038/s41559-022-01885-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 08/12/2022] [Indexed: 11/16/2022]
Abstract
The origin of plants and their colonization of land fundamentally transformed the terrestrial environment. Here we elucidate the basis of this formative episode in Earth history through patterns of lineage, gene and genome evolution. We use new fossil calibrations, a relative clade age calibration (informed by horizontal gene transfer) and new phylogenomic methods for mapping gene family origins. Distinct rooting strategies resolve tracheophytes (vascular plants) and bryophytes (non-vascular plants) as monophyletic sister groups that diverged during the Cambrian, 515-494 million years ago. The embryophyte stem is characterized by a burst of gene innovation, while bryophytes subsequently experienced an equally dramatic episode of reductive genome evolution in which they lost genes associated with the elaboration of vasculature and the stomatal complex. Overall, our analyses reveal that extant tracheophytes and bryophytes are both highly derived from a more complex ancestral land plant. Understanding the origin of land plants requires tracing character evolution across a diversity of modern lineages.
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Affiliation(s)
- Brogan J Harris
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - James W Clark
- School of Biological Sciences, University of Bristol, Bristol, UK
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK
| | - Dominik Schrempf
- Department of Biological Physics, Eötvös Loránd University, Budapest, Hungary
| | - Gergely J Szöllősi
- Department of Biological Physics, Eötvös Loránd University, Budapest, Hungary
- MTA-ELTE 'Lendület' Evolutionary Genomics Research Group, Budapest, Hungary
- Institute of Evolution, Centre for Ecological Research, Budapest, Hungary
| | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK
| | | | - Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol, UK.
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK.
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38
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Lv G, Shi Q, Zhang T, Li J, Kalashova J, Long Y, Sun Y, Li C, Choudhry N, Li H, Yang C, Zhou X, Reddy MC, Anantoju KK, Jupelli R, Zhang S, Zhang J, Allen T, Liu H, Nimishetti N, Yang D. 2-Phenoxy-3, 4′-bipyridine derivatives inhibit AURKB-dependent mitotic processes by disrupting its localization. Eur J Med Chem 2022; 245:114904. [DOI: 10.1016/j.ejmech.2022.114904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/02/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022]
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Zhang T, Wang J, Lyu Z, Wang Y, Al-Rasheid KA, Shao C. Morphology, morphogenesis and phylogeny of a new soil ciliate, Bistichella sinensis n. sp., and morphology of two oxytrichids (Ciliophora, Hypotrichia). Eur J Protistol 2022; 86:125934. [DOI: 10.1016/j.ejop.2022.125934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 09/29/2022] [Accepted: 10/10/2022] [Indexed: 11/03/2022]
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Parey E, Louis A, Montfort J, Guiguen Y, Crollius HR, Berthelot C. An atlas of fish genome evolution reveals delayed rediploidization following the teleost whole-genome duplication. Genome Res 2022; 32:1685-1697. [PMID: 35961774 PMCID: PMC9528989 DOI: 10.1101/gr.276953.122] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/09/2022] [Indexed: 11/25/2022]
Abstract
Teleost fishes are ancient tetraploids descended from an ancestral whole-genome duplication that may have contributed to the impressive diversification of this clade. Whole-genome duplications can occur via self-doubling (autopolyploidy) or via hybridization between different species (allopolyploidy). The mode of tetraploidization conditions evolutionary processes by which duplicated genomes return to diploid meiotic pairing, and subsequent genetic divergence of duplicated genes (cytological and genetic rediploidization). How teleosts became tetraploid remains unresolved, leaving a fundamental gap in the interpretation of their functional evolution. As a result of the whole-genome duplication, identifying orthologous and paralogous genomic regions across teleosts is challenging, hindering genome-wide investigations into their polyploid history. Here, we combine tailored gene phylogeny methodology together with a state-of-the-art ancestral karyotype reconstruction to establish the first high-resolution comparative atlas of paleopolyploid regions across 74 teleost genomes. We then leverage this atlas to investigate how rediploidization occurred in teleosts at the genome-wide level. We uncover that some duplicated regions maintained tetraploidy for more than 60 million years, with three chromosome pairs diverging genetically only after the separation of major teleost families. This evidence suggests that the teleost ancestor was an autopolyploid. Further, we find evidence for biased gene retention along several duplicated chromosomes, contradicting current paradigms that asymmetrical evolution is specific to allopolyploids. Altogether, our results offer novel insights into genome evolutionary dynamics following ancient polyploidizations in vertebrates.
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Affiliation(s)
- Elise Parey
- Institut de Biologie de l'Ecole normale supérieure (IBENS), Département de Biologie, Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
- INRAE, LPGP, 35000, Rennes, France
| | - Alexandra Louis
- Institut de Biologie de l'Ecole normale supérieure (IBENS), Département de Biologie, Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | | | | | - Hugues Roest Crollius
- Institut de Biologie de l'Ecole normale supérieure (IBENS), Département de Biologie, Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Camille Berthelot
- Institut de Biologie de l'Ecole normale supérieure (IBENS), Département de Biologie, Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
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Zhang T, Tang Q, Chen Z, Lian C, Yang X, Song W, Warren A, Shao C. Insights into the phylogeny of the family Deviatidae (Protozoa, Ciliophora, Hypotrichia) based on multi-gene, morphological and ontogenetic information, with the establishment of a new species Deviata multilineae n. sp. Mol Phylogenet Evol 2022; 177:107623. [PMID: 36058509 DOI: 10.1016/j.ympev.2022.107623] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 08/10/2022] [Accepted: 08/29/2022] [Indexed: 11/25/2022]
Abstract
Hitherto, the phylogeny of ciliated protists, an important group of model organisms in many fields, has been mainly based on a single marker gene (SSU rDNA, nuclear small subunit ribosomal RNA gene). However, there is increasing evidence showing this is insufficient to provide robust phylogenies and has resulted in confusing systematics in many ciliates groups. Among these, the phylogenies within family Deviatidae (Spirotrichea, Hypotrichia) are ambiguous due to the dependence on SSU rDNA and undersampling. Here, we provide eight new sequences and conduct phylogenetic analyses based on both multi-gene and single-gene to clarify evolutionary relationships among all deviatids for which gene sequence are available. The results reveal that: (1) the monophyly of Deviatidae is well-supported by both single-gene and concatenated data; (2) the presence of fine cirri and relatively wide spacing of these cirri within all rows are plesiomorphies of Deviatidae; (3) Pseudosincirra longicirrata is closely related to Deviata rositae, which is supported by their shared possession of dorsomarginal kineties; (4) phylogenetic analyses and approximately unbiased test based on multi-gene support a close relationship among taxa lacking dorsomarginal kineties (D. parabacilliformis, D. multilineae nov. spec., D. abbrevescens, D. brasiliensis and Perisincirra paucicirrata); (5) Deviatidae shows a close relationship with Dorsomarginalia and Strongylidium-Hemiamphisiella-Pseudouroleptus assemblage, suggesting the presence/absence of dorsomarginal kineties is phylogenetically informative in this family and presence of them may be a plesiomorphy. Based on the morphological, morphogenetic and phylogenetic data, the evolutionary relationships within Deviatidae are hypothesized, and a new ciliate, Deviata multilineae nov. spec., collected from China, is investigated.
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Affiliation(s)
- Tengteng Zhang
- Laboratory of Protozoological Biodiversity and Evolution in Wetland, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Qiuyue Tang
- Laboratory of Protozoological Biodiversity and Evolution in Wetland, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Zhuofan Chen
- Laboratory of Protozoological Biodiversity and Evolution in Wetland, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Chunyu Lian
- Laboratory of Protozoological Biodiversity and Evolution in Wetland, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Xiaoqing Yang
- Laboratory of Protozoological Biodiversity and Evolution in Wetland, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Weibo Song
- Laboratory of Protozoological Biodiversity and Evolution in Wetland, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
| | - Chen Shao
- Laboratory of Protozoological Biodiversity and Evolution in Wetland, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China.
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Hao T, Li B, Song Y, Warren A, Pan X. Taxonomy and molecular phylogeny of two new Blepharisma species (Ciliophora, Heterotrichea) from northeastern china. Eur J Protistol 2022; 85:125908. [DOI: 10.1016/j.ejop.2022.125908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 11/03/2022]
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Lin Q, Banerjee A, Stefanović S. Mitochondrial phylogenomics of Cuscuta (Convolvulaceae) reveals a potentially functional horizontal gene transfer from the host. Genome Biol Evol 2022; 14:evac091. [PMID: 35700229 PMCID: PMC9234195 DOI: 10.1093/gbe/evac091] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 06/06/2022] [Accepted: 06/09/2022] [Indexed: 11/14/2022] Open
Abstract
Horizontal gene transfers (HGTs) from host or other organisms have been reported in mitochondrial genomes of parasitic plants. Genes transferred in this fashion have usually been found non-functional. Several examples of HGT from the mitochondrial genome of parasitic Cuscuta (Convolvulaceae) to its hosts have been reported, but not vice versa. Here we used 31 protein-coding mitochondrial genes to infer the phylogeny of Cuscuta, and compared it with previous nuclear and plastid phylogenetic estimates. We also investigated the presence of HGTs within these lineages. Unlike in plastid genomes, we did not find extensive gene loss in their mitochondrial counterparts. Our results reveal the first example of organellar HGT from host to Cuscuta. Mitochondrial atp1 genes of South African subgenus Pachystigma were inferred to be transferred from Lamiales, with high support. Moreover, the horizontally transferred atp1 gene has functionally replaced the native, vertically transmitted copy, has an intact open reading frame, and is under strong purifying selection, all of which suggests that this xenolog remains functional. The mitochondrial phylogeny of Cuscuta is generally consistent with previous plastid and nuclear phylogenies, except for the misplacement of Pachystigma when atp1 is included. This incongruence may be caused by the HGT mentioned above. No example of HGT was found within mitochondrial genes of three other, independently evolved parasitic lineages we sampled: Cassytha/Laurales, Krameria/Zygophyllales, and Lennooideae/Boraginales.
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Affiliation(s)
- Qianshi Lin
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
- Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 2Z9, Canada
| | - Arjan Banerjee
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
- Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 2Z9, Canada
| | - Saša Stefanović
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
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Chen LY, Lu B, Morales-Briones DF, Moody ML, Liu F, Hu GW, Huang CH, Chen JM, Wang QF. Phylogenomic Analyses of Alismatales Shed Light into Adaptations to Aquatic Environments. Mol Biol Evol 2022; 39:msac079. [PMID: 35438770 PMCID: PMC9070837 DOI: 10.1093/molbev/msac079] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Land plants first evolved from freshwater algae, and flowering plants returned to water as early as the Cretaceous and multiple times subsequently. Alismatales is the largest clade of aquatic angiosperms including all marine angiosperms, as well as terrestrial plants. We used Alismatales to explore plant adaptations to aquatic environments by analyzing a data set that included 95 samples (89 Alismatales species) covering four genomes and 91 transcriptomes (59 generated in this study). To provide a basis for investigating adaptations, we assessed phylogenetic conflict and whole-genome duplication (WGD) events in Alismatales. We recovered a relationship for the three main clades in Alismatales as (Tofieldiaceae, Araceae) + core Alismatids. We also found phylogenetic conflict among the three main clades that was best explained by incomplete lineage sorting and introgression. Overall, we identified 18 putative WGD events across Alismatales. One of them occurred at the most recent common ancestor of core Alismatids, and three occurred at seagrass lineages. We also found that lineage and life-form were both important for different evolutionary patterns for the genes related to freshwater and marine adaptation. For example, several light- or ethylene-related genes were lost in the seagrass Zosteraceae, but are present in other seagrasses and freshwater species. Stomata-related genes were lost in both submersed freshwater species and seagrasses. Nicotianamine synthase genes, which are important in iron intake, expanded in both submersed freshwater species and seagrasses. Our results advance the understanding of the adaptation to aquatic environments and WGDs using phylogenomics.
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Affiliation(s)
- Ling-Yun Chen
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden/Core Botanical Garden, Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Bei Lu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden/Core Botanical Garden, Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Diego F. Morales-Briones
- Department of Plant and Microbial Biology, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
- Systematics, Biodiversity and Evolution of Plants, Ludwig-Maximilians-Universität München, Menzinger Str. 67, 80638 Munich, Germany
| | - Michael L. Moody
- Department of Biological Sciences, University of Texas at El Paso, 500 West University Ave, El Paso, TX 79968, USA
| | - Fan Liu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden/Core Botanical Garden, Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Guang-Wan Hu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden/Core Botanical Garden, Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Chien-Hsun Huang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Jin-Ming Chen
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden/Core Botanical Garden, Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Qing-Feng Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden/Core Botanical Garden, Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
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45
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Huang W, Zhang L, Columbus JT, Hu Y, Zhao Y, Tang L, Guo Z, Chen W, McKain M, Bartlett M, Huang CH, Li DZ, Ge S, Ma H. A well-supported nuclear phylogeny of Poaceae and implications for the evolution of C 4 photosynthesis. MOLECULAR PLANT 2022; 15:755-777. [PMID: 35093593 DOI: 10.1016/j.molp.2022.01.015] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 06/09/2021] [Accepted: 01/24/2022] [Indexed: 05/11/2023]
Abstract
Poaceae (the grasses) includes rice, maize, wheat, and other crops, and is the most economically important angiosperm family. Poaceae is also one of the largest plant families, consisting of over 11 000 species with a global distribution that contributes to diverse ecosystems. Poaceae species are classified into 12 subfamilies, with generally strong phylogenetic support for their monophyly. However, many relationships within subfamilies, among tribes and/or subtribes, remain uncertain. To better resolve the Poaceae phylogeny, we generated 342 transcriptomic and seven genomic datasets; these were combined with other genomic and transcriptomic datasets to provide sequences for 357 Poaceae species in 231 genera, representing 45 tribes and all 12 subfamilies. Over 1200 low-copy nuclear genes were retrieved from these datasets, with several subsets obtained using additional criteria, and used for coalescent analyses to reconstruct a Poaceae phylogeny. Our results strongly support the monophyly of 11 subfamilies; however, the subfamily Puelioideae was separated into two non-sister clades, one for each of the two previously defined tribes, supporting a hypothesis that places each tribe in a separate subfamily. Molecular clock analyses estimated the crown age of Poaceae to be ∼101 million years old. Ancestral character reconstruction of C3/C4 photosynthesis supports the hypothesis of multiple independent origins of C4 photosynthesis. These origins are further supported by phylogenetic analysis of the ppc gene family that encodes the phosphoenolpyruvate carboxylase, which suggests that members of three paralogous subclades (ppc-aL1a, ppc-aL1b, and ppc-B2) were recruited as functional C4ppc genes. This study provides valuable resources and a robust phylogenetic framework for evolutionary analyses of the grass family.
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Affiliation(s)
- Weichen Huang
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, PA 16802, USA
| | - Lin Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering and State Key Laboratory of Genetic Engineering, Institute of Biodiversity Sciences and Institute of Plant Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - J Travis Columbus
- Rancho Santa Ana Botanic Garden and Claremont Graduate University, 1500 North College Avenue, Claremont, CA 91711, USA
| | - Yi Hu
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, PA 16802, USA
| | - Yiyong Zhao
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, PA 16802, USA; Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering and State Key Laboratory of Genetic Engineering, Institute of Biodiversity Sciences and Institute of Plant Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - Lin Tang
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, PA 16802, USA; College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Zhenhua Guo
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201 China
| | - Wenli Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Michael McKain
- Department of Biological Sciences, University of Alabama, 411 Mary Harmon Bryant Hall, Tuscaloosa, AL 35487, USA
| | - Madelaine Bartlett
- Biology Department, University of Massachusetts Amherst, 611 North Pleasant Street, 221 Morrill 3, Amherst, MA 01003 USA
| | - Chien-Hsun Huang
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, PA 16802, USA; Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering and State Key Laboratory of Genetic Engineering, Institute of Biodiversity Sciences and Institute of Plant Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - De-Zhu Li
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201 China
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Hong Ma
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, PA 16802, USA.
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Nikolaidis M, Papakyriakou A, Chlichlia K, Markoulatos P, Oliver SG, Amoutzias GD. Comparative Analysis of SARS-CoV-2 Variants of Concern, Including Omicron, Highlights Their Common and Distinctive Amino Acid Substitution Patterns, Especially at the Spike ORF. Viruses 2022; 14:707. [PMID: 35458441 PMCID: PMC9025783 DOI: 10.3390/v14040707] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/25/2022] [Accepted: 03/27/2022] [Indexed: 12/13/2022] Open
Abstract
In order to gain a deeper understanding of the recently emerged and highly divergent Omicron variant of concern (VoC), a study of amino acid substitution (AAS) patterns was performed and compared with those of the other four successful variants of concern (Alpha, Beta, Gamma, Delta) and one closely related variant of interest (VoI-Lambda). The Spike ORF consistently emerges as an AAS hotspot in all six lineages, but in Omicron this enrichment is significantly higher. The progenitors of each of these VoC/VoI lineages underwent positive selection in the Spike ORF. However, once they were established, their Spike ORFs have been undergoing purifying selection, despite the application of global vaccination schemes from 2021 onwards. Our analyses reject the hypothesis that the heavily mutated receptor binding domain (RBD) of the Omicron Spike was introduced via recombination from another closely related Sarbecovirus. Thus, successive point mutations appear as the most parsimonious scenario. Intriguingly, in each of the six lineages, we observed a significant number of AAS wherein the new residue is not present at any homologous site among the other known Sarbecoviruses. Such AAS should be further investigated as potential adaptations to the human host. By studying the phylogenetic distribution of AAS shared between the six lineages, we observed that the Omicron (BA.1) lineage had the highest number (8/10) of recurrent mutations.
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Affiliation(s)
- Marios Nikolaidis
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece;
| | - Athanasios Papakyriakou
- Institute of Biosciences & Applications, National Centre for Scientific Research Demokritos, 15341 Agia Paraskevi, Greece;
| | - Katerina Chlichlia
- Laboratory of Molecular Immunology, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus-Dragana, 68100 Alexandroupolis, Greece;
| | - Panayotis Markoulatos
- Microbial Biotechnology-Molecular Bacteriology-Virology Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece;
| | - Stephen G. Oliver
- Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK;
| | - Grigorios D. Amoutzias
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece;
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Morel B, Schade P, Lutteropp S, Williams TA, Szöllősi GJ, Stamatakis A. SpeciesRax: A Tool for Maximum Likelihood Species Tree Inference from Gene Family Trees under Duplication, Transfer, and Loss. Mol Biol Evol 2022; 39:msab365. [PMID: 35021210 PMCID: PMC8826479 DOI: 10.1093/molbev/msab365] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Species tree inference from gene family trees is becoming increasingly popular because it can account for discordance between the species tree and the corresponding gene family trees. In particular, methods that can account for multiple-copy gene families exhibit potential to leverage paralogy as informative signal. At present, there does not exist any widely adopted inference method for this purpose. Here, we present SpeciesRax, the first maximum likelihood method that can infer a rooted species tree from a set of gene family trees and can account for gene duplication, loss, and transfer events. By explicitly modeling events by which gene trees can depart from the species tree, SpeciesRax leverages the phylogenetic rooting signal in gene trees. SpeciesRax infers species tree branch lengths in units of expected substitutions per site and branch support values via paralogy-aware quartets extracted from the gene family trees. Using both empirical and simulated data sets we show that SpeciesRax is at least as accurate as the best competing methods while being one order of magnitude faster on large data sets at the same time. We used SpeciesRax to infer a biologically plausible rooted phylogeny of the vertebrates comprising 188 species from 31,612 gene families in 1 h using 40 cores. SpeciesRax is available under GNU GPL at https://github.com/BenoitMorel/GeneRax and on BioConda.
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Affiliation(s)
- Benoit Morel
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
- Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Paul Schade
- Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Sarah Lutteropp
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Gergely J Szöllősi
- ELTE-MTA “Lendület” Evolutionary Genomics Research Group, Budapest, Hungary
- Department of Biological Physics, Eötvös University, Budapest, Hungary
- Institute of Evolution, Centre for Ecological Research, Budapest, Hungary
| | - Alexandros Stamatakis
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
- Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
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48
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Ma M, Li Y, Maurer-Alcalá XX, Wang Y, Yan Y. Deciphering phylogenetic relationships in class Karyorelictea (Protista, Ciliophora) based on updated multi-gene information with establishment of a new order Wilbertomorphida n. ord. Mol Phylogenet Evol 2022; 169:107406. [PMID: 35031457 DOI: 10.1016/j.ympev.2022.107406] [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: 06/09/2021] [Revised: 12/07/2021] [Accepted: 01/01/2022] [Indexed: 10/19/2022]
Abstract
The class Karyorelictea, a unique assemblage of ciliates, is a key group in deciphering ciliate evolution history. However, the systematic relationships among members of this class remain poorly understood. Here we newly obtained eight small subunit (SSU) rDNA, 24 large subunit (LSU) rDNA, and 25 ITS1-5.8S-ITS2 sequences (covering 25 species, 10 genera and 4 out of 6 families) to analyze the phylogenetic relationships within Karyorelictea. Our results indicate that: (1) considering its unique morphology and early branching position in the SSU rDNA-based tree, the family Wilbertomorphidae represents a new taxon at order level, hence the new order Wilbertomorphida n. ord. is established; (2) all five families with available molecular information are monophyletic, as expected, and the orders Loxodida and Protostomatida show a closer relationship than with Protoheterotrichida; (3) in Trachelocercidae, the compound circumoral kineties is believed to be a plesiomorphic feature while the single circumoral kinety is synapomorphic; and (4) the freshwater genus Loxodes could be derived from the marine Remanella and both share most morphological features. Taken together, these muti-gene analyses provide further insights into the phylogeny of the diverse clades in Karyorelictea.
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Affiliation(s)
- Mingzhen Ma
- Laboratory of Protozoology, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Yuqing Li
- Laboratory of Protozoology, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Xyrus X Maurer-Alcalá
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland; Division of Invertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
| | - Yurui Wang
- Laboratory of Protozoological Biodiversity and Evolution in Wetland, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China.
| | - Ying Yan
- Laboratory of Protozoology, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
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Nikolaidis M, Markoulatos P, Van de Peer Y, Oliver SG, Amoutzias GD. The Neighborhood of the Spike Gene Is a Hotspot for Modular Intertypic Homologous and Nonhomologous Recombination in Coronavirus Genomes. Mol Biol Evol 2022; 39:msab292. [PMID: 34638137 PMCID: PMC8549283 DOI: 10.1093/molbev/msab292] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Coronaviruses (CoVs) have very large RNA viral genomes with a distinct genomic architecture of core and accessory open reading frames (ORFs). It is of utmost importance to understand their patterns and limits of homologous and nonhomologous recombination, because such events may affect the emergence of novel CoV strains, alter their host range, infection rate, tissue tropism pathogenicity, and their ability to escape vaccination programs. Intratypic recombination among closely related CoVs of the same subgenus has often been reported; however, the patterns and limits of genomic exchange between more distantly related CoV lineages (intertypic recombination) need further investigation. Here, we report computational/evolutionary analyses that clearly demonstrate a substantial ability for CoVs of different subgenera to recombine. Furthermore, we show that CoVs can obtain-through nonhomologous recombination-accessory ORFs from core ORFs, exchange accessory ORFs with different CoV genera, with other viruses (i.e., toroviruses, influenza C/D, reoviruses, rotaviruses, astroviruses) and even with hosts. Intriguingly, most of these radical events result from double crossovers surrounding the Spike ORF, thus highlighting both the instability and mobile nature of this genomic region. Although many such events have often occurred during the evolution of various CoVs, the genomic architecture of the relatively young SARS-CoV/SARS-CoV-2 lineage so far appears to be stable.
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Affiliation(s)
- Marios Nikolaidis
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Panayotis Markoulatos
- Microbial Biotechnology-Molecular Bacteriology-Virology Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Stephen G Oliver
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Grigorios D Amoutzias
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
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Harris BJ, Sheridan PO, Davín AA, Gubry-Rangin C, Szöllősi GJ, Williams TA. Rooting Species Trees Using Gene Tree-Species Tree Reconciliation. Methods Mol Biol 2022; 2569:189-211. [PMID: 36083449 DOI: 10.1007/978-1-0716-2691-7_9] [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: 05/24/2023]
Abstract
Interpreting phylogenetic trees requires a root, which provides the direction of evolution and polarizes ancestor-descendant relationships. But inferring the root using genetic data is difficult, particularly in cases where the closest available outgroup is only distantly related, which are common for microbes. In this chapter, we present a workflow for estimating rooted species trees and the evolutionary history of the gene families that evolve within them using probabilistic gene tree-species tree reconciliation. We illustrate the pipeline using a small dataset of prokaryotic genomes, for which the example scripts can be run using modest computer resources. We describe the rooting method used in this work in the context or other rooting strategies and discuss some of the limitations and opportunities presented by probabilistic gene tree-species tree reconciliation methods.
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Affiliation(s)
- Brogan J Harris
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Paul O Sheridan
- School of Biological Sciences, University of Bristol, Bristol, UK
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Adrián A Davín
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | | | - Gergely J Szöllősi
- Dept. of Biological Physics, Eötvös Loránd University, Budapest, Hungary
- MTA-ELTE "Lendület" Evolutionary Genomics Research Group, Budapest, Hungary
- Institute of Evolution, Centre for Ecological Research, Budapest, Hungary
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol, UK.
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