51
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Wang L, Zhang S, Li H, Wang S. The complete plastome and phylogenetic analysis of Commelina benghalensis L.1753 (Commelinaceae). Mitochondrial DNA B Resour 2024; 9:610-615. [PMID: 38737392 PMCID: PMC11086016 DOI: 10.1080/23802359.2024.2347508] [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: 11/11/2023] [Accepted: 04/19/2024] [Indexed: 05/14/2024] Open
Abstract
Commelina benghalensis L. 1753, a member of the Commelinaceae family, holds significant medicinal and culinary value. This study represents the first documentation of the sequencing and assembly of the entire plastome of C. benghalensis. The genome spans a total length of 160,663 bp, exhibiting a conventional quadripartite architecture that comprises a large single-copy (LSC) region (87,750 bp), a small single-copy (SSC) region (18,417 bp), and two inverted repeats (IR) regions (both 27,248 bp). In its entirety, the C. benghalensis plastome encompasses 129 genes (with 108 being unique), incorporating 77 individual protein-coding genes, 37 unique tRNA genes, and four unique rRNA genes. Phylogenetic analysis revealed a close resemblance between C. benghalensis and C. communis. The sequencing of this plastome stands to expedite the development of molecular markers and significantly contribute to genetic assays involving this distinctive plant.
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Affiliation(s)
- Liqiang Wang
- College of Pharmacy, Heze University, Heze, Shandong Province, P. R. China
| | - Shuming Zhang
- College of Pharmacy, Heze University, Heze, Shandong Province, P. R. China
| | - Hongqin Li
- College of Pharmacy, Heze University, Heze, Shandong Province, P. R. China
| | - Shu Wang
- College of Pharmacy, Heze University, Heze, Shandong Province, P. R. China
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Jensen RO, Schulz F, Roux S, Klingeman DM, Mitchell WP, Udwary D, Moraïs S, Reynoso V, Winkler J, Nagaraju S, De Tissera S, Shapiro N, Ivanova N, Reddy TBK, Mizrahi I, Utturkar SM, Bayer EA, Woyke T, Mouncey NJ, Jewett MC, Simpson SD, Köpke M, Jones DT, Brown SD. Phylogenomics and genetic analysis of solvent-producing Clostridium species. Sci Data 2024; 11:432. [PMID: 38693191 PMCID: PMC11063209 DOI: 10.1038/s41597-024-03210-6] [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: 10/15/2023] [Accepted: 04/02/2024] [Indexed: 05/03/2024] Open
Abstract
The genus Clostridium is a large and diverse group within the Bacillota (formerly Firmicutes), whose members can encode useful complex traits such as solvent production, gas-fermentation, and lignocellulose breakdown. We describe 270 genome sequences of solventogenic clostridia from a comprehensive industrial strain collection assembled by Professor David Jones that includes 194 C. beijerinckii, 57 C. saccharobutylicum, 4 C. saccharoperbutylacetonicum, 5 C. butyricum, 7 C. acetobutylicum, and 3 C. tetanomorphum genomes. We report methods, analyses and characterization for phylogeny, key attributes, core biosynthetic genes, secondary metabolites, plasmids, prophage/CRISPR diversity, cellulosomes and quorum sensing for the 6 species. The expanded genomic data described here will facilitate engineering of solvent-producing clostridia as well as non-model microorganisms with innately desirable traits. Sequences could be applied in conventional platform biocatalysts such as yeast or Escherichia coli for enhanced chemical production. Recently, gene sequences from this collection were used to engineer Clostridium autoethanogenum, a gas-fermenting autotrophic acetogen, for continuous acetone or isopropanol production, as well as butanol, butanoic acid, hexanol and hexanoic acid production.
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Affiliation(s)
| | - Frederik Schulz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | | | - Daniel Udwary
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sarah Moraïs
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | | | | | | | | | - Nicole Shapiro
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Natalia Ivanova
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - T B K Reddy
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Itzhak Mizrahi
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - Sagar M Utturkar
- Institute for Cancer Research, Purdue University, West Lafayette, IN, USA
| | - Edward A Bayer
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Tanja Woyke
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- University of California Merced, Life and Environmental Sciences, Merced, CA, USA
| | - Nigel J Mouncey
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michael C Jewett
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | | | | | - David T Jones
- Department of Microbiology, University of Otago, Dunedin, New Zealand.
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53
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Hacioglu S, Ozkul A. Do birds play a role in the transmission of Toscana virus? Initial isolation results from birds in northernmost Türkiye. Zoonoses Public Health 2024; 71:225-235. [PMID: 38041213 DOI: 10.1111/zph.13100] [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: 03/25/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 12/03/2023]
Abstract
AIMS Recent research has prioritized emerging and re-emerging diseases that affect human and animal health, particularly to describe how these diseases enter countries and determine their transmission cycles. Given that migratory birds play a significant role in spreading infections, the present study analysed their migration paths and specimens to investigate Orthoflavivirus, Orthonairovirus, Alphavirus and Phlebovirus in birds in Samsun province, Türkiye. METHODS AND RESULTS For these viruses, 312 samples from 56 birds were analysed using RT-PCR and qRT-PCR. Toscana virus (TOSV) was identified in 14 birds (four mallards, five partridges, four quails and one pigeon), representing 25% of the birds sampled. Genotype B was reported in all 14 birds. After inoculating the positive tissues in cell cultures, TOSV was isolated from the organs of pigeons, mallards and partridges. CONCLUSIONS This is the first time TOSV has been isolated in cell culture from birds and indicates that they may play a role in spreading TOSV in Türkiye. The results also suggest that TOSV might be carried between countries by migratory birds.
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Affiliation(s)
- Sabri Hacioglu
- Virological Diagnostic Laboratory, Veterinary Control Central Research Institute, Ankara, Turkey
| | - Aykut Ozkul
- Department of Virology, Faculty of Veterinary Medicine, Ankara University, Ankara, Turkey
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54
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Stiller J, Feng S, Chowdhury AA, Rivas-González I, Duchêne DA, Fang Q, Deng Y, Kozlov A, Stamatakis A, Claramunt S, Nguyen JMT, Ho SYW, Faircloth BC, Haag J, Houde P, Cracraft J, Balaban M, Mai U, Chen G, Gao R, Zhou C, Xie Y, Huang Z, Cao Z, Yan Z, Ogilvie HA, Nakhleh L, Lindow B, Morel B, Fjeldså J, Hosner PA, da Fonseca RR, Petersen B, Tobias JA, Székely T, Kennedy JD, Reeve AH, Liker A, Stervander M, Antunes A, Tietze DT, Bertelsen MF, Lei F, Rahbek C, Graves GR, Schierup MH, Warnow T, Braun EL, Gilbert MTP, Jarvis ED, Mirarab S, Zhang G. Complexity of avian evolution revealed by family-level genomes. Nature 2024; 629:851-860. [PMID: 38560995 PMCID: PMC11111414 DOI: 10.1038/s41586-024-07323-1] [Citation(s) in RCA: 63] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 03/15/2024] [Indexed: 04/04/2024]
Abstract
Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species sampled, phylogenetic method and the choice of genomic regions1-3. Here we address these issues by analysing the genomes of 363 bird species4 (218 taxonomic families, 92% of total). Using intergenic regions and coalescent methods, we present a well-supported tree but also a marked degree of discordance. The tree confirms that Neoaves experienced rapid radiation at or near the Cretaceous-Palaeogene boundary. Sufficient loci rather than extensive taxon sampling were more effective in resolving difficult nodes. Remaining recalcitrant nodes involve species that are a challenge to model due to either extreme DNA composition, variable substitution rates, incomplete lineage sorting or complex evolutionary events such as ancient hybridization. Assessment of the effects of different genomic partitions showed high heterogeneity across the genome. We discovered sharp increases in effective population size, substitution rates and relative brain size following the Cretaceous-Palaeogene extinction event, supporting the hypothesis that emerging ecological opportunities catalysed the diversification of modern birds. The resulting phylogenetic estimate offers fresh insights into the rapid radiation of modern birds and provides a taxon-rich backbone tree for future comparative studies.
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Affiliation(s)
- Josefin Stiller
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Shaohong Feng
- Center for Evolutionary & Organismal Biology, Liangzhu Laboratory & Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Department of General Surgery, Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, China
| | - Al-Aabid Chowdhury
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | | | - David A Duchêne
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Qi Fang
- BGI Research, Shenzhen, China
| | - Yuan Deng
- BGI Research, Shenzhen, China
- BGI Research, Wuhan, China
| | - Alexey Kozlov
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Alexandros Stamatakis
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
- Institute of Computer Science, Foundation for Research and Technology Hellas, Heraklion, Greece
- Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Santiago Claramunt
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada
| | - Jacqueline M T Nguyen
- College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
- Australian Museum Research Institute, Sydney, New South Wales, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Brant C Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
| | - Julia Haag
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Peter Houde
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
| | - Joel Cracraft
- Department of Ornithology, American Museum of Natural History, New York, NY, USA
| | - Metin Balaban
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Uyen Mai
- Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Guangji Chen
- BGI Research, Wuhan, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Rongsheng Gao
- BGI Research, Wuhan, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | | | - Yulong Xie
- Center for Evolutionary & Organismal Biology, Liangzhu Laboratory & Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zijian Huang
- Center for Evolutionary & Organismal Biology, Liangzhu Laboratory & Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhen Cao
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Zhi Yan
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Huw A Ogilvie
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Luay Nakhleh
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Bent Lindow
- Natural History Museum Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Benoit Morel
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
- Institute of Computer Science, Foundation for Research and Technology Hellas, Heraklion, Greece
| | - Jon Fjeldså
- Natural History Museum Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Peter A Hosner
- Natural History Museum Denmark, University of Copenhagen, Copenhagen, Denmark
- Center for Global Mountain Biodiversity, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Rute R da Fonseca
- Center for Global Mountain Biodiversity, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Bent Petersen
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery, Faculty of Applied Sciences, AIMST University, Bedong, Malaysia
| | - Joseph A Tobias
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, UK
| | - Tamás Székely
- Milner Centre for Evolution, University of Bath, Bath, UK
- ELKH-DE Reproductive Strategies Research Group, University of Debrecen, Debrecen, Hungary
| | - Jonathan David Kennedy
- Center for Macroecology, Evolution, and Climate, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Andrew Hart Reeve
- Natural History Museum Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Andras Liker
- HUN-REN-PE Evolutionary Ecology Research Group, University of Pannonia, Veszprém, Hungary
- Behavioural Ecology Research Group, Center for Natural Sciences, University of Pannonia, Veszprém, Hungary
| | | | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | | | - Mads F Bertelsen
- Centre for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksberg, Denmark
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Carsten Rahbek
- Center for Global Mountain Biodiversity, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Macroecology, Evolution, and Climate, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Institute of Ecology, Peking University, Beijing, China
- Danish Institute for Advanced Study, University of Southern Denmark, Odense, Denmark
| | - Gary R Graves
- Center for Macroecology, Evolution, and Climate, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | | | - Tandy Warnow
- University of Illinois Urbana-Champaign, Champaign, IL, USA
| | - Edward L Braun
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
| | - Erich D Jarvis
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, Durham, NC, USA
| | | | - Guojie Zhang
- Center for Evolutionary & Organismal Biology, Liangzhu Laboratory & Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, China.
- BGI Research, Wuhan, China.
- Villum Center for Biodiversity Genomics, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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55
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Dong X, Zhang T, Wu W, Peng Y, Liu X, Han Y, Chen X, Gao Z, Xia J, Shao Z, Greening C. A vast repertoire of secondary metabolites potentially influences community dynamics and biogeochemical processes in cold seeps. SCIENCE ADVANCES 2024; 10:eadl2281. [PMID: 38669328 PMCID: PMC11051675 DOI: 10.1126/sciadv.adl2281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 03/27/2024] [Indexed: 04/28/2024]
Abstract
In deep-sea cold seeps, microbial communities thrive on the geological seepage of hydrocarbons and inorganic compounds, differing from photosynthetically driven ecosystems. However, their biosynthetic capabilities remain largely unexplored. Here, we analyzed 81 metagenomes, 33 metatranscriptomes, and 7 metabolomes derived from nine different cold seep areas to investigate their secondary metabolites. Cold seep microbiomes encode diverse and abundant biosynthetic gene clusters (BGCs). Most BGCs are affiliated with understudied bacteria and archaea, including key mediators of methane and sulfur cycling. The BGCs encode diverse antimicrobial compounds that potentially shape community dynamics and various metabolites predicted to influence biogeochemical cycling. BGCs from key players are widely distributed and highly expressed, with their abundance and expression levels varying with sediment depth. Sediment metabolomics reveals unique natural products, highlighting uncharted chemical potential and confirming BGC activity in these sediments. Overall, these results demonstrate that cold seep sediments serve as a reservoir of hidden natural products and sheds light on microbial adaptation in chemosynthetically driven ecosystems.
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Affiliation(s)
- Xiyang Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China
| | - Tianxueyu Zhang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200030, China
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310005, China
| | - Weichao Wu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Science, Shanghai Ocean University, Shanghai 201306, China
| | - Yongyi Peng
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China
| | - Xinyue Liu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Yingchun Han
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Xiangwei Chen
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Zhizeng Gao
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China
| | - Jinmei Xia
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
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56
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Zhang T, Huang W, Zhang L, Li DZ, Qi J, Ma H. Phylogenomic profiles of whole-genome duplications in Poaceae and landscape of differential duplicate retention and losses among major Poaceae lineages. Nat Commun 2024; 15:3305. [PMID: 38632270 PMCID: PMC11024178 DOI: 10.1038/s41467-024-47428-9] [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: 07/13/2023] [Accepted: 04/02/2024] [Indexed: 04/19/2024] Open
Abstract
Poaceae members shared a whole-genome duplication called rho. However, little is known about the evolutionary pattern of the rho-derived duplicates among Poaceae lineages and implications in adaptive evolution. Here we present phylogenomic/phylotranscriptomic analyses of 363 grasses covering all 12 subfamilies and report nine previously unknown whole-genome duplications. Furthermore, duplications from a single whole-genome duplication were mapped to multiple nodes on the species phylogeny; a whole-genome duplication was likely shared by woody bamboos with possible gene flow from herbaceous bamboos; and recent paralogues of a tetraploid Oryza are implicated in tolerance of seawater submergence. Moreover, rho duplicates showing differential retention among subfamilies include those with functions in environmental adaptations or morphogenesis, including ACOT for aquatic environments (Oryzoideae), CK2β for cold responses (Pooideae), SPIRAL1 for rapid cell elongation (Bambusoideae), and PAI1 for drought/cold responses (Panicoideae). This study presents a Poaceae whole-genome duplication profile with evidence for multiple evolutionary mechanisms that contribute to gene retention and losses.
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Affiliation(s)
- Taikui Zhang
- Department of Biology, the Eberly College of Science, and the 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, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Weichen Huang
- Department of Biology, the Eberly College of Science, and the 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, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Ji Qi
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China.
| | - Hong Ma
- Department of Biology, the Eberly College of Science, and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, State College, PA, 16802, USA.
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57
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Zhu L, Bau T. Species clarification of fairy inkcap (" Coprinellus disseminatus") in China. Mycology 2024; 15:424-470. [PMID: 39247893 PMCID: PMC11376300 DOI: 10.1080/21501203.2024.2309901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 01/20/2024] [Indexed: 09/10/2024] Open
Abstract
Coprinellus disseminatus and other morphologically similar species are widely dispersed worldwide and are commonly referred to as "fairy inkcap". Based on the molecular phylogenetic study and morphological observation, a thorough investigation was carried out utilising 74 collections of related species that were gathered from seventeen provinces and five Chinese fungaria between 1998 and 2023 and revealed 11 lineages of "fairy inkcap", nine of which were found in China, and which belonged to the two genera Coprinellus and Tulosesus. In sect. Disseminati, genetic diversities (π), and fixation index (Fst) amongst lineages were computed, and a haplotype-based network was established to ascertain the relationships amongst each clade. A new section of Coprinellus, sect. Aureodisseminati, were discovered. In addition, four new species (C. aureodisseminatus, C. austrodisseminatus, C. parcus, and C. velutipes), a new subspecies of C. disseminatus, a new combination (Tulosesus pseudodisseminatus), the first discovery of epigamous type of C. magnoliae and a new record to China (T. subdisseminatus) were also identified and thoroughly described with accompanying illustrations. Their differences in macro- and micro-features, as well as their character sequence, were discussed.
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Affiliation(s)
- Liyang Zhu
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
- Key Laboratory of Edible Fungi Resources and Utilization (North), Ministry of Agriculture, Changchun, China
| | - Tolgor Bau
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
- Key Laboratory of Edible Fungi Resources and Utilization (North), Ministry of Agriculture, Changchun, China
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58
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Tang W, Li X, Ye B, Shi B, Zhang H, Dang Z, Sun Y, Danqu L, Xia C, Quzhen D, Zhao X, Chui W, Huang F. Characterization of the complete mitochondrial genome and phylogenetic analyses of Haemaphysalis tibetensis Hoogstraal, 1965 (Acari: Ixodidae). Ticks Tick Borne Dis 2024; 15:102311. [PMID: 38262211 DOI: 10.1016/j.ttbdis.2024.102311] [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: 05/06/2023] [Revised: 01/11/2024] [Accepted: 01/13/2024] [Indexed: 01/25/2024]
Abstract
Ticks are specialized ectoparasites that feed on blood, causing physical harm to the host and facilitating pathogen transmission. The genus Haemaphysalis contains vectors for numerous infectious agents. These agents cause various diseases in humans and animals. Mitochondrial genome sequences serve as reliable molecular markers, forming a crucial basis for evolutionary analyses, studying species origins, and exploring molecular phylogeny. We extracted mitochondrial genome from the enriched mitochondria of Haemaphysalis tibetensis and obtained a 14,714-bp sequence. The mitochondrial genome consists of 13 protein-coding genes (PCGs), two ribosomal RNA, 22 transfer RNAs (tRNAs), and two control regions. The nucleotide composition of H. tibetensis mitochondrial genome was 38.38 % for A, 9.61 % for G, 39.32 % for T, and 12.69 % for C. The A + T content of H. tibetensis mitochondrial genome was 77.7 %, significantly higher than the G + C content. The repeat units of H. tibetensis exhibited two identical repeat units of 33 bp in length, positioned downstream of nad1 and rrnL genes. Furthermore, phylogenetic analyses based on the 13 PCGs indicated that Haemaphysalis tibetensis (subgenus Allophysalis) formed a monophyletic clade with Haemaphysalis nepalensis (subgenus Herpetobia) and Haemaphysalis danieli (subgenus Allophysalis). Although the species Haemaphysalis inermis, Haemaphysalis kitaokai, Haemaphysalis kolonini, and Haemaphysalis colasbelcouri belong to the subgenus Alloceraea, which were morphologically primitive hemaphysalines just like H. tibetensis, these four tick species cannot form a single clade with H. tibetensis. In this study, the whole mitochondrial genome sequence of H. tibetensis from Tibet was obtained, which enriched the mitochondrial genome data of ticks and provided genetic markers to study the population heredity and molecular evolution of the genus Haemaphysalis.
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Affiliation(s)
- Wenqiang Tang
- Institute of Animal Science, Tibet Academy of Agriculture and Animal Husbandry Sciences, Tibet Lhasa 850009, China; State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Lhasa 850002, China
| | - Xin Li
- School of Life Science and Engineering, Foshan University, Guangdong Foshan 528225, China
| | - Bijin Ye
- School of Life Science and Engineering, Foshan University, Guangdong Foshan 528225, China
| | - Bin Shi
- Institute of Animal Science, Tibet Academy of Agriculture and Animal Husbandry Sciences, Tibet Lhasa 850009, China; State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Lhasa 850002, China
| | - Haoji Zhang
- School of Life Science and Engineering, Foshan University, Guangdong Foshan 528225, China
| | - Zhisheng Dang
- National Institute of Parasitic Diseases at China CDC/Chinese Center for Tropical Diseases Research, WHO Collaborating Centre for Tropical Diseases, NHC Key Laboratory for Parasite and Vector Biology, Shanghai 200025, China
| | - Yuexiang Sun
- School of Life Science and Engineering, Foshan University, Guangdong Foshan 528225, China
| | - Lamu Danqu
- Institute of Animal Science, Tibet Academy of Agriculture and Animal Husbandry Sciences, Tibet Lhasa 850009, China; State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Lhasa 850002, China
| | - Chenyang Xia
- Institute of Animal Science, Tibet Academy of Agriculture and Animal Husbandry Sciences, Tibet Lhasa 850009, China; State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Lhasa 850002, China
| | - Danzeng Quzhen
- Institute of Animal Science, Tibet Academy of Agriculture and Animal Husbandry Sciences, Tibet Lhasa 850009, China; State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Lhasa 850002, China
| | - Xialing Zhao
- Institute of Animal Science, Tibet Academy of Agriculture and Animal Husbandry Sciences, Tibet Lhasa 850009, China
| | - Wenting Chui
- Animal Disease Prevention and Control Center of Qinghai Province, China
| | - Fuqiang Huang
- School of Life Science and Engineering, Foshan University, Guangdong Foshan 528225, China.
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59
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Punacha G, Adiga R. Feature selection for effective prediction of SARS-COV-2 using machine learning. Genes Genomics 2024; 46:341-354. [PMID: 37985549 DOI: 10.1007/s13258-023-01467-6] [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: 05/06/2023] [Accepted: 10/01/2023] [Indexed: 11/22/2023]
Abstract
BACKGROUND With rise in variants of SARS-CoV-2, it is necessary to classify the emerging SARS-CoV-2 for early detection and thereby reduce human transmission. Genomic and proteomic information have less frequently been used for classifying in a machine learning (ML) approach for detection of SARS-CoV-2. OBJECTIVE With this aim we used nucleoprotein and viral proteomic evolutionary information of SARS-CoV-2 along with the charge and basicity distribution of amino acids from various strains of SARS-CoV-2 to generate a disease severity model based on ML. METHODS All sequence and clinical data were obtained from GISAID. Proteomic level calculations were added to comprise the dataset. The training set was used for feature selection. Select K- Best feature selection method was employed which was cross validated with testing set and performance evaluated. Delong's test was also done. We also employed BIRCH clustering on SARS-CoV-2 for clustering the strains. RESULTS Out of six ML models four were successful in training and testing. Extra Trees algorithm generated a micro-averaged F1-score of 74.2% and a weighted averaged area under the receiver operating characteristic curve (AUC-ROC) score of 73.7% with multi-class option. The feature selection set to 5, enhanced the ROC AUC from 73.7 to 76.4%. Accuracy of the selected model of 86.9% was achieved. CONCLUSION The unique features identified in the ML approach was able to classify disease severity into classes and had potential for predicting risk in newer variants.
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Affiliation(s)
- Gagan Punacha
- Nitte (Deemed to be University), Department of Molecular Genetics & Cancer, Nitte University Centre for Science Education & Research (NUCSER), Mangalore, Karnataka, India
| | - Rama Adiga
- Nitte (Deemed to be University), Department of Molecular Genetics & Cancer, Nitte University Centre for Science Education & Research (NUCSER), Mangalore, Karnataka, India.
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60
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Casimiro‐Soriguer CS, Perez‐Florido J, Lara M, Camacho‐Martinez P, Merino‐Diaz L, Pupo‐Ledo I, de Salazar A, Fuentes A, Viñuela L, Chueca N, Martinez‐Martinez L, Lorusso N, Lepe JA, Dopazo J, Garcia F. Molecular and phylogenetic characterization of the monkeypox outbreak in the South of Spain. Health Sci Rep 2024; 7:e1965. [PMID: 38524774 PMCID: PMC10957719 DOI: 10.1002/hsr2.1965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 01/22/2024] [Accepted: 02/22/2024] [Indexed: 03/26/2024] Open
Abstract
Background and Aim Until the May 2022 Monkeypox (MPXV) outbreak, which spread rapidly to many non-endemic countries, the virus was considered a viral zoonosis limited to some African countries. The Andalusian circuit of genomic surveillance was rapidly applied to characterize the MPXV outbreak in the South of Spain. Methods Whole genome sequencing was used to obtain the genomic profiles of samples collected across the south of Spain, representative of all the provinces of Andalusia. Phylogenetic analysis was used to study the relationship of the isolates and the available sequences of the 2022 outbreak. Results Whole genome sequencing of a total of 160 MPXV viruses from the different provinces that reported cases were obtained. Interestingly, we report the sequences of MPXV viruses obtained from two patients who died. While one of the isolates bore no noteworthy mutations that explain a potential heightened virulence, in another patient the second consecutive genome sequence, performed after the administration of tecovirimat, uncovered a mutation within the A0A7H0DN30 gene, known to be a prime target for tecovirimat in its Vaccinia counterpart. In general, a low number of mutations were observed in the sequences reported, which were very similar to the reference of the 2022 outbreak (OX044336), as expected from a DNA virus. The samples likely correspond to several introductions of the circulating MPXV viruses from the last outbreak. The virus sequenced from one of the two patients that died presented a mutation in a gene that bears potential connections to drug resistance. This mutation was absent in the initial sequencing before treatment.
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Affiliation(s)
- Carlos S. Casimiro‐Soriguer
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health‐FPSSevillaSpain
- Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Rocío/CSIC/University of SevilleSevilleSpain
| | - Javier Perez‐Florido
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health‐FPSSevillaSpain
- Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Rocío/CSIC/University of SevilleSevilleSpain
| | - Maria Lara
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health‐FPSSevillaSpain
| | - Pedro Camacho‐Martinez
- Servicio de Microbiología, Unidad Clínica Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen del RocíoSevillaSpain
| | - Laura Merino‐Diaz
- Servicio de Microbiología, Unidad Clínica Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen del RocíoSevillaSpain
| | - Inmaculada Pupo‐Ledo
- Servicio de Microbiología, Unidad Clínica Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen del RocíoSevillaSpain
| | - Adolfo de Salazar
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), ISCIIIMadridSpain
- Servicio de Microbiología, Hospital Universitario San CecilioGranadaSpain
- Instituto de Investigación Biosanitaria, ibs.GRANADAGranadaSpain
| | - Ana Fuentes
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), ISCIIIMadridSpain
- Instituto de Investigación Biosanitaria, ibs.GRANADAGranadaSpain
| | - Laura Viñuela
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), ISCIIIMadridSpain
- Servicio de Microbiología, Hospital Universitario San CecilioGranadaSpain
| | - Natalia Chueca
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), ISCIIIMadridSpain
- Instituto de Investigación Biosanitaria, ibs.GRANADAGranadaSpain
| | - Luis Martinez‐Martinez
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), ISCIIIMadridSpain
- Unit of Microbiology, University Hospital Reina SofiaCordobaSpain
- Departamento de Química AgrícolaEdafología y Microbiología, Universidad de CórdobaCórdobaSpain
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC)CórdobaSpain
| | - Nicola Lorusso
- Dirección General de Salud Pública, Consejería de Salud y Familias, Junta de AndalucíaSevillaSpain
| | - Jose A. Lepe
- Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Rocío/CSIC/University of SevilleSevilleSpain
- Servicio de Microbiología, Unidad Clínica Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen del RocíoSevillaSpain
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), ISCIIIMadridSpain
| | - Joaquín Dopazo
- Computational Medicine Platform, Andalusian Public Foundation Progress and Health‐FPSSevillaSpain
- Institute of Biomedicine of Seville, IBiS, University Hospital Virgen del Rocío/CSIC/University of SevilleSevilleSpain
- FPS/ELIXIR‐ES, Andalusian Public Foundation Progress and Health‐FPSSevillaSpain
| | - Federico Garcia
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), ISCIIIMadridSpain
- Servicio de Microbiología, Hospital Universitario San CecilioGranadaSpain
- Instituto de Investigación Biosanitaria, ibs.GRANADAGranadaSpain
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Mine J, Takadate Y, Kumagai A, Sakuma S, Tsunekuni R, Miyazawa K, Uchida Y. Genetics of H5N1 and H5N8 High-Pathogenicity Avian Influenza Viruses Isolated in Japan in Winter 2021-2022. Viruses 2024; 16:358. [PMID: 38543724 PMCID: PMC10975693 DOI: 10.3390/v16030358] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/21/2024] [Accepted: 02/24/2024] [Indexed: 05/23/2024] Open
Abstract
In winter 2021-2022, H5N1 and H5N8 high-pathogenicity avian influenza (HPAI) viruses (HPAIVs) caused serious outbreaks in Japan: 25 outbreaks of HPAI at poultry farms and 107 cases in wild birds or in the environment. Phylogenetic analyses divided H5 HPAIVs isolated in Japan in the winter of 2021-2022 into three groups-G2a, G2b, and G2d-which were disseminated at different locations and times. Full-genome sequencing analyses of these HPAIVs revealed a strong relationship of multiple genes between Japan and Siberia, suggesting that they arose from reassortment events with avian influenza viruses (AIVs) in Siberia. The results emphasize the complex of dissemination and reassortment events with the movement of migratory birds, and the importance of continual monitoring of AIVs in Japan and Siberia for early alerts to the intrusion of HPAIVs.
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Affiliation(s)
- Junki Mine
- National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba 305-0856, Ibaraki, Japan (A.K.); (S.S.); (R.T.); (K.M.); (Y.U.)
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Xu RJ, Li JF, Zhou DQ, Boonmee S, Zhao Q, Chen YY. Three novel species of Aquapteridospora (Distoseptisporales, Aquapteridosporaceae) from freshwater habitats in Tibetan Plateau, China. MycoKeys 2024; 102:183-200. [PMID: 38434108 PMCID: PMC10907956 DOI: 10.3897/mycokeys.102.112905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 10/17/2023] [Indexed: 03/05/2024] Open
Abstract
During an investigation of lignicolous freshwater fungi in the Tibetan Plateau, three Aquapteridospora taxa were collected from freshwater habitats in Xizang, China. The new species possess polyblastic, sympodial, denticles conidiogenous cells and fusiform, septate, with or without sheath conidial, that fit within the generic concept of Aquapteridospora, and multi-gene phylogeny placed these species within Aquapteridospora. Detailed morphological observations clearly demarcate three of these from extant species and are hence described as new taxa. The multi-gene phylogeny of the combined LSU, TEF1-α, and ITS sequence data to infer phylogenetic relationships and discuss phylogenetic affinities with morphologically similar species. Based on morphological characteristics and phylogenetic analyses, three new species viz. A.linzhiensis, A.yadongensis, and A.submersa are introduced. Details of asexual morphs are described, and justifications for establishing these new species are also provided in this study.
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Affiliation(s)
- Rong-Ju Xu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Yunnan Key Laboratory of Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Guizhou Provincial Institute of Crop Germplasm Resources, Guiyang 550006, China
| | - Jun-Fu Li
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - De-Qun Zhou
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Yunnan Key Laboratory of Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Saranyaphat Boonmee
- Guizhou Provincial Institute of Crop Germplasm Resources, Guiyang 550006, China
| | - Qi Zhao
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Yunnan Key Laboratory of Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Ya-Ya Chen
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Centre for Mountain Futures (CMF), Kunming Institute of Botany, Kunming, Yunnan 650201, China
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63
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Zhou Z, Pi Z, Wang Y, Guo S, Guo N, Yang J, Zhang X, Zhang C, Cai J. The complete mitochondrial genome of Sarcophaga angarosinica (Diptera: Sarcophagidae). Mitochondrial DNA B Resour 2024; 9:242-246. [PMID: 38317664 PMCID: PMC10840587 DOI: 10.1080/23802359.2023.2233740] [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: 02/23/2023] [Accepted: 06/30/2023] [Indexed: 02/07/2024] Open
Abstract
Sarcophaga (Liosarcophaga) angarosinica (Rohdendorf, 1937) (Diptera: Sarcophagidae) is a species of both medical and ecological significance. In this study, the complete mitochondrial genome (mitogenome) of S. angarosinica was sequenced and characterized. The mitogenome has a total length of 15,215 bp, including 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and an adenine and thymine-rich region. This mitogenome comprises 39.5% adenine, 9.4% guanine, 14.4% cytosine, and 36.8% thymine. Phylogenetic analysis revealed that S. angarosinica is closely related to Sarcophaga similis. This study enriches the genetic data on S. angarosinica and will contribute to establishing the phylogenetic relationships among flesh flies.
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Affiliation(s)
- Ziqi Zhou
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Zhiyun Pi
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Yuanxing Wang
- Public Security Forensic Center of Haidian, Beijing, China
| | - Shaojiang Guo
- Public Security Forensic Center of Haidian, Beijing, China
| | - Nan Guo
- Public Security Forensic Center of Haidian, Beijing, China
| | - Junbo Yang
- Public Security Forensic Center of Haidian, Beijing, China
| | - Xiangyan Zhang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Changquan Zhang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Jifeng Cai
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
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64
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Tang Y, Ma W, Chen X, Nie G, Zhou C. Four new complete mitochondrial genomes of Gobioninae fishes (Teleostei: Cyprinidae) and their phylogenetic implications. PeerJ 2024; 12:e16632. [PMID: 38259668 PMCID: PMC10802160 DOI: 10.7717/peerj.16632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 11/17/2023] [Indexed: 01/24/2024] Open
Abstract
The subfamily Gobioninae is one of the most diverse fish groups within Cyprinidae. Their taxonomy and phylogenetic relationships are not completely resolved. In this study, the complete mitochondrial genomes (mitogenome) of four Gobioninae species (Microphysogobio elongatus, Microphysogobio chinssuensis, Gobio rivuloides and Rhinogobio nasutus) were sequenced and compared. The mitogenomes of four species ranges from 16603 bp to 16609 bp in length, consisting of 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a control region. Most PCGs had significant codon usage bias. Except for the tRNASer (GCT), all the nucleotide substitutions of tRNA loops higher than the stems could fold into a stable secondary structure. The nucleotide compositions of Gobioninae mitogenome were biased toward A/T, and NAD4 was subjected to low purification selection and had a faster evolution rate among 13 PCGs. Bayesian inference and maximum likelihood phylogenetic analyses showed the consistent results. The four sequenced species clustered together with their congener species. However, more samples and mitogenome data are needed to untangle the phylogenetic relationships among genera Microphysogobio, Romanogobio, Hugobio, Biwia and Platysmacheilus.
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Affiliation(s)
- Yongtao Tang
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, Henan province, The People’s Republic of China
| | - Wenwen Ma
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, Henan province, The People’s Republic of China
| | - Xin Chen
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, Henan province, The People’s Republic of China
| | - Guoxing Nie
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, Henan province, The People’s Republic of China
| | - Chuanjiang Zhou
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, Henan province, The People’s Republic of China
- College of Life Sciences, Henan Normal University, Xinxiang, Henan Province, China
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65
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Kwon T, Hovde BT. Global characterization of biosynthetic gene clusters in non-model eukaryotes using domain architectures. Sci Rep 2024; 14:1534. [PMID: 38233413 PMCID: PMC10794256 DOI: 10.1038/s41598-023-50095-3] [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: 08/09/2023] [Accepted: 12/15/2023] [Indexed: 01/19/2024] Open
Abstract
The majority of pharmaceuticals are derived from natural products, bioactive compounds naturally synthesized by organisms to provide evolutionary advantages. Although the rich evolutionary history of eukaryotic algal species implicates a high potential for natural product-based drug discovery, it remains largely untouched. This study investigates 2762 putative biosynthetic gene clusters (BGCs) from 212 eukaryotic algal genomes. To analyze a vast set of structurally diverse BGCs, we employed comparative analysis based on the vectorization of biosynthetic domains, referred to as biosynthetic domain architecture (BDA). By characterizing core biosynthetic machineries through BDA, we identified key BDAs of modular BGCs in diverse eukaryotes and introduced 16 candidate modular BGCs with similar BDAs to previously validated BGCs. This study provides a global characterization of eukaryotic algal BGCs, offering an alternative to laborious manual curation for BGC prioritization.
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Affiliation(s)
- Taehyung Kwon
- Genomics and Bioanalytics Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Blake T Hovde
- Genomics and Bioanalytics Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
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Wang S, Jiang L, Zhao Z, Chen Z, Wang J, Alain K, Cui L, Zhong Y, Peng Y, Lai Q, Dong X, Shao Z. Chemolithoautotrophic diazotrophs dominate dark nitrogen fixation in mangrove sediments. THE ISME JOURNAL 2024; 18:wrae119. [PMID: 38916247 PMCID: PMC11474244 DOI: 10.1093/ismejo/wrae119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 02/21/2024] [Accepted: 06/22/2024] [Indexed: 06/26/2024]
Abstract
Diazotrophic microorganisms regulate marine productivity by alleviating nitrogen limitation. So far chemolithoautotrophic bacteria are widely recognized as the principal diazotrophs in oligotrophic marine and terrestrial ecosystems. However, the contribution of chemolithoautotrophs to nitrogen fixation in organic-rich habitats remains unclear. Here, we utilized metagenomic and metatranscriptomic approaches integrated with cultivation assays to investigate the diversity, distribution, and activity of diazotrophs residing in Zhangzhou mangrove sediments. Physicochemical assays show that the studied mangrove sediments are typical carbon-rich, sulfur-rich, nitrogen-limited, and low-redox marine ecosystems. These sediments host a wide phylogenetic variety of nitrogenase genes, including groups I-III and VII-VIII. Unexpectedly diverse chemolithoautotrophic taxa including Campylobacteria, Gammaproteobacteria, Zetaproteobacteria, and Thermodesulfovibrionia are the predominant and active nitrogen fixers in the 0-18 cm sediment layer. In contrast, the 18-20 cm layer is dominated by active diazotrophs from the chemolithoautotrophic taxa Desulfobacterota and Halobacteriota. Further analysis of MAGs shows that the main chemolithoautotrophs can fix nitrogen by coupling the oxidation of hydrogen, reduced sulfur, and iron, with the reduction of oxygen, nitrate, and sulfur. Culture experiments further demonstrate that members of chemolithoautotrophic Campylobacteria have the nitrogen-fixing capacity driven by hydrogen and sulfur oxidation. Activity measurements confirm that the diazotrophs inhabiting mangrove sediments preferentially drain energy from diverse reduced inorganic compounds other than from organics. Overall, our results suggest that chemolithoautotrophs rather than heterotrophs are dominant nitrogen fixers in mangrove sediments. This study underscores the significance of chemolithoautotrophs in carbon-dominant ecosystems.
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Affiliation(s)
- Shasha Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Keey Laboratory of Marine Genetic Resources; Sino-French Laboratory of Deep-Sea Microbiology (MicrobSea), Xiamen 361005, PR China
| | - Lijing Jiang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Keey Laboratory of Marine Genetic Resources; Sino-French Laboratory of Deep-Sea Microbiology (MicrobSea), Xiamen 361005, PR China
| | - Zhuoming Zhao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Keey Laboratory of Marine Genetic Resources; Sino-French Laboratory of Deep-Sea Microbiology (MicrobSea), Xiamen 361005, PR China
| | - Zhen Chen
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Keey Laboratory of Marine Genetic Resources; Sino-French Laboratory of Deep-Sea Microbiology (MicrobSea), Xiamen 361005, PR China
| | - Jun Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Keey Laboratory of Marine Genetic Resources; Sino-French Laboratory of Deep-Sea Microbiology (MicrobSea), Xiamen 361005, PR China
| | - Karine Alain
- Univ Brest, CNRS, Ifremer, EMR6002 BIOMEX, Biologie Interactions et adaptations des Organismes en Milieu EXtrême, IRP 1211 MicrobSea, F-29280 Plouzané, France
| | - Liang Cui
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Keey Laboratory of Marine Genetic Resources; Sino-French Laboratory of Deep-Sea Microbiology (MicrobSea), Xiamen 361005, PR China
| | - Yangsheng Zhong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Keey Laboratory of Marine Genetic Resources; Sino-French Laboratory of Deep-Sea Microbiology (MicrobSea), Xiamen 361005, PR China
| | - Yongyi Peng
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Keey Laboratory of Marine Genetic Resources; Sino-French Laboratory of Deep-Sea Microbiology (MicrobSea), Xiamen 361005, PR China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Keey Laboratory of Marine Genetic Resources; Sino-French Laboratory of Deep-Sea Microbiology (MicrobSea), Xiamen 361005, PR China
| | - Xiyang Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Keey Laboratory of Marine Genetic Resources; Sino-French Laboratory of Deep-Sea Microbiology (MicrobSea), Xiamen 361005, PR China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, PR China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Keey Laboratory of Marine Genetic Resources; Sino-French Laboratory of Deep-Sea Microbiology (MicrobSea), Xiamen 361005, PR China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, PR China
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Alzahrani DA, Abba A, Yaradua SS, Albokhari EJ. An insight on the complete chloroplast genome of Gomphocarpus siniacus and Duvalia velutina, Asclepiadoideae (Apocynaceae). BRAZ J BIOL 2024; 84:e257145. [DOI: 10.1590/1519-6984.257145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 07/20/2022] [Indexed: 12/23/2022] Open
Abstract
Abstract We studied the complete chloroplast genome of Gomphocarpus siniacus and Duvalia velutina from Asclepiadoideae subfamily; due to their medicinal importance and distribution worldwide their interest became high. In this study we analyzed the complete chloroplast genomes of G. siniacus and D. velutina using Illumina sequencing technology. The sequences were compared with the other species from Apocynaceae family. The complete genome of G. siniacus is 162,570 bp while D. velutina has154, 478 bp in length. Both genomes consist of 119 genes; encode 31 tRNA genes, and eight rRNA genes. Comparative studies of the two genomes showed variations in SSR markers in which G. siniacus possesses 223 while D. velutina has 186. This could be used for barcoding in order to aid in easy identification of the species. Phylogenetic analysis on the other hand reaffirms the tribal position of G. siniacus in Asclepiadeae and D. velutina in Ceropegieae. These findings could be used in subsequent research studies of angiosperms identification, genetic engineering, herb genomics and phylogenomic studies of Apocynaceae family.
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Affiliation(s)
| | - A. Abba
- King Abdulaziz University, Saudi Arabia; Federal University Lokoja, Nigeria
| | - S. S. Yaradua
- King Abdulaziz University, Saudi Arabia; Umaru Musa Yaradua University, Nigeria
| | - E. J. Albokhari
- King Abdulaziz University, Saudi Arabia; Umm Al-Qura University, Saudi Arabia
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68
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Thureborn O, Wikström N, Razafimandimbison SG, Rydin C. Phylogenomics and topological conflicts in the tribe Anthospermeae (Rubiaceae). Ecol Evol 2024; 14:e10868. [PMID: 38274863 PMCID: PMC10809029 DOI: 10.1002/ece3.10868] [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: 06/10/2023] [Revised: 11/15/2023] [Accepted: 12/05/2023] [Indexed: 01/27/2024] Open
Abstract
Genome skimming (shallow whole-genome sequencing) offers time- and cost-efficient production of large amounts of DNA data that can be used to address unsolved evolutionary questions. Here we address phylogenetic relationships and topological incongruence in the tribe Anthospermeae (Rubiaceae), using phylogenomic data from the mitochondrion, the nuclear ribosomal cistron, and the plastome. All three genomic compartments resolve relationships in the Anthospermeae; the tribe is monophyletic and consists of three major subclades. Carpacoce Sond. is sister to the remaining clade, which comprises an African subclade and a Pacific subclade. Most results, from all three genomic compartments, are statistically well supported; however, not fully consistent. Intergenomic topological incongruence is most notable in the Pacific subclade but present also in the African subclade. Hybridization and introgression followed by organelle capture may explain these conflicts but other processes, such as incomplete lineage sorting (ILS), can yield similar patterns and cannot be ruled out based on the results. Whereas the null hypothesis of congruence among all sequenced loci in the individual genomes could not be rejected for nuclear and mitochondrial data, it was rejected for plastid data. Phylogenetic analyses of three subsets of plastid loci identified using the hierarchical likelihood ratio test demonstrated statistically supported intragenomic topological incongruence. Given that plastid genes are thought to be fully linked, this result is surprising and may suggest modeling or sampling error. However, biological processes such as biparental inheritance and inter-plastome recombination have been reported and may be responsible for the observed intragenomic incongruence. Mitochondrial insertions into the plastome are rarely documented in angiosperms. Our results indicate that a mitochondrial insertion event in the plastid trnS GGA - rps4 IGS region occurred in the common ancestor of the Pacific clade of Anthospermeae. Exclusion/inclusion of this locus in phylogenetic analyses had a strong impact on topological results in the Pacific clade.
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Affiliation(s)
- Olle Thureborn
- Department of Ecology, Environment and Plant SciencesStockholm UniversityStockholmSweden
| | - Niklas Wikström
- Department of Ecology, Environment and Plant SciencesStockholm UniversityStockholmSweden
- The Bergius FoundationThe Royal Academy of SciencesStockholmSweden
| | | | - Catarina Rydin
- Department of Ecology, Environment and Plant SciencesStockholm UniversityStockholmSweden
- The Bergius FoundationThe Royal Academy of SciencesStockholmSweden
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69
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Little AS, Younker IT, Schechter MS, Bernardino PN, Méheust R, Stemczynski J, Scorza K, Mullowney MW, Sharan D, Waligurski E, Smith R, Ramaswamy R, Leiter W, Moran D, McMillin M, Odenwald MA, Iavarone AT, Sidebottom AM, Sundararajan A, Pamer EG, Eren AM, Light SH. Dietary- and host-derived metabolites are used by diverse gut bacteria for anaerobic respiration. Nat Microbiol 2024; 9:55-69. [PMID: 38177297 PMCID: PMC11055453 DOI: 10.1038/s41564-023-01560-2] [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: 01/11/2023] [Accepted: 11/14/2023] [Indexed: 01/06/2024]
Abstract
Respiratory reductases enable microorganisms to use molecules present in anaerobic ecosystems as energy-generating respiratory electron acceptors. Here we identify three taxonomically distinct families of human gut bacteria (Burkholderiaceae, Eggerthellaceae and Erysipelotrichaceae) that encode large arsenals of tens to hundreds of respiratory-like reductases per genome. Screening species from each family (Sutterella wadsworthensis, Eggerthella lenta and Holdemania filiformis), we discover 22 metabolites used as respiratory electron acceptors in a species-specific manner. Identified reactions transform multiple classes of dietary- and host-derived metabolites, including bioactive molecules resveratrol and itaconate. Products of identified respiratory metabolisms highlight poorly characterized compounds, such as the itaconate-derived 2-methylsuccinate. Reductase substrate profiling defines enzyme-substrate pairs and reveals a complex picture of reductase evolution, providing evidence that reductases with specificities for related cinnamate substrates independently emerged at least four times. These studies thus establish an exceptionally versatile form of anaerobic respiration that directly links microbial energy metabolism to the gut metabolome.
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Affiliation(s)
- Alexander S Little
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Isaac T Younker
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Matthew S Schechter
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Paola Nol Bernardino
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Raphaël Méheust
- Génomique Métabolique, CEA, Genoscope, Institut François Jacob, Université d'Évry, Université Paris-Saclay, CNRS, Evry, France
| | - Joshua Stemczynski
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Kaylie Scorza
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | | | - Deepti Sharan
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Emily Waligurski
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Rita Smith
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | | | - William Leiter
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - David Moran
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Mary McMillin
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Matthew A Odenwald
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Section of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Anthony T Iavarone
- QB3/Chemistry Mass Spectrometry Facility, University of California, Berkeley, Berkeley, CA, USA
| | | | | | - Eric G Pamer
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
- Section of Infectious Diseases & Global Health, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - A Murat Eren
- Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenbug, Germany
| | - Samuel H Light
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA.
- Department of Microbiology, University of Chicago, Chicago, IL, USA.
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70
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Yang F, Long L. Complete mitochondrial genome and phylogenetic analysis of the marine microalga Symbiochlorum hainanensis (Ulvophyceae, Chlorophyta). Mitochondrial DNA B Resour 2023; 8:1377-1380. [PMID: 38130734 PMCID: PMC10732211 DOI: 10.1080/23802359.2023.2290353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 11/28/2023] [Indexed: 12/23/2023] Open
Abstract
Symbiochlorum hainanensis Gong et al. (2018). is a unicellular green alga belonging to Ulvophyceae, Chlorophyta, and considered as an important species in coral-algae symbiont areas. In this study, we revealed firstly the mitochondrial genome sequence of the S. hainanensis. This mitochondrial genome was a circular DNA molecule of 59,508 bp, including 24 transfer RNA genes, 3 ribosomal RNA genes, and 31 protein-coding genes. The GC content of the genome was 35.4%. The phylogenetic tree suggested that S. hainandiae was a sister to the OUU clade within the class Ulvophyceae. The mitochondrial genome structure and gene content of S. hainanensis supported that S. hainanensis was a new unidentified green alga in Ulvophyceae.
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Affiliation(s)
- Fangfang Yang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Lijuan Long
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
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71
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Li R, Hu Y, Xu Y, Zhou J, Li Y, Liu Q, Yu B. Safety assessment, whole genome sequence, and metabolome analysis of Streptococcus thermophilus CICC 20372 for bone cement fermentation. Arch Microbiol 2023; 206:21. [PMID: 38095705 DOI: 10.1007/s00203-023-03737-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/03/2023] [Accepted: 11/06/2023] [Indexed: 12/18/2023]
Abstract
Bone is a kind of meat processing by-product with high nutritional value but low in calorie, which is a typical food in China and parts of East Asian countries. Microbial fermentation by lactic acid bacteria showed remarkable advantages to increase the absorption of nutrients from bone cement by human body. Streptococcus thermophilus CICC 20372 is proven to be a good starter for bone cement fermentation. No genes encoding virulence traits or virulence factors were found in the genome of S. thermophilus CICC 20372 by a thorough genomic analysis. Its notable absence of antibiotic resistance further solidifies the safety. Furthermore, the genomic analysis identified four types of gene clusters responsible for the synthesis of antimicrobial metabolites. A comparative metabolomic analysis was performed by cultivating the strain in bone cement at 37 °C for 72 h, with the culture in de Man, Rogosa, and Sharpe (MRS) medium as control. Metabolome analysis results highlighted the upregulation of pathways involved in 2-oxocarboxylic acid metabolism, ATP-binding cassette (ABC) transporters, amino acid synthesis, and nucleotide metabolism during bone cement fermentation. S. thermophilus CICC 20372 produces several metabolites with health-promoting function during bone cement fermentation, including indole-3-lactic acid, which is demonstrated ameliorative effects on intestinal inflammation, tumor growth, and gut dysbiosis. In addition, lots of nucleotide and organic acids were accumulated at higher levels, which enriched the fermented bone cement with a variety of nutrients. Collectively, these features endow S. thermophilus CICC 20372 a great potential strain for bone food processing.
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Affiliation(s)
- Rongshan Li
- Inner Mongolia Peptide (Mengtai) Biological Engineering Co., Ltd, Hohhot, 011500, China
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yangfan Hu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yang Xu
- Inner Mongolia Peptide (Mengtai) Biological Engineering Co., Ltd, Hohhot, 011500, China
| | - Jinlong Zhou
- Inner Mongolia Peptide (Mengtai) Biological Engineering Co., Ltd, Hohhot, 011500, China
| | - Yunfang Li
- Inner Mongolia Peptide (Mengtai) Biological Engineering Co., Ltd, Hohhot, 011500, China
| | - Qing Liu
- General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Bo Yu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
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72
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Huang F, Li X, Ye B, Zhou Y, Dang Z, Tang W, Wang L, Zhang H, Chui W, Kui J. Characterization of the Complete Mitochondrial Genome and Phylogenetic Analyses of Eurytrema coelomaticum (Trematoda: Dicrocoeliidae). Genes (Basel) 2023; 14:2199. [PMID: 38137020 PMCID: PMC10743053 DOI: 10.3390/genes14122199] [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: 11/20/2023] [Revised: 12/06/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
Eurytrema coelomaticum, a pancreatic fluke, is recognized as a causative agent of substantial economic losses in ruminants. This infection, commonly referred to as eurytrematosis, is a significant concern due to its detrimental impact on livestock production. However, there is a paucity of knowledge regarding the mitochondrial genome of E. coelomaticum. In this study, we performed the initial sequencing of the complete mitochondrial genome of E. coelomaticum. Our findings unveiled that the mitochondrial genome of E. coelomaticum spans a length of 15,831 bp and consists of 12 protein-coding genes, 22 tRNA genes, two rRNA genes, and two noncoding regions. The A+T content constituted 62.49% of the genome. Moreover, all 12 protein-coding genes of E. coelomaticum exhibit the same arrangement as those of E. pancreaticum and other published species belonging to the family Dicrocoeliidae. The presence of a short string of additional amino acids (approximately 20~23 aa) at the N-terminal of the cox1 protein in both E. coelomaticum and E. pancreaticum mitochondrial genomes has contributed to the elongation of the cox1 gene in genus Eurytrema, surpassing that of all previously sequenced Dicrocoeliidae. The phylogenetic analysis displayed a close relationship between E. coelomaticum and E. pancreaticum, along with a genus-level association between Eurytrema and Lyperosomum. These findings underscore the importance of mitochondrial genomic data for comparative studies of Dicrocoeliidae and even Digenea, offering valuable DNA markers for future investigations in the systematic, epidemiological, and population genetic studies of this parasite and other digenean trematodes.
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Affiliation(s)
- Fuqiang Huang
- School of Life Science and Engineering, Foshan University, Foshan 528225, China; (X.L.)
| | - Xin Li
- School of Life Science and Engineering, Foshan University, Foshan 528225, China; (X.L.)
| | - Bijin Ye
- School of Life Science and Engineering, Foshan University, Foshan 528225, China; (X.L.)
| | - Yule Zhou
- School of Life Science and Engineering, Foshan University, Foshan 528225, China; (X.L.)
| | - Zhisheng Dang
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), Key Laboratory of Parasite and Vector Biology, National Health Commission of the People’s Republic of China (NHC), World Health Organization (WHO) Collaborating Center for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai 200025, China
| | - Wenqiang Tang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa 850002, China
- Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa 850009, China
| | - Long Wang
- School of Life Science and Engineering, Foshan University, Foshan 528225, China; (X.L.)
| | - Haoji Zhang
- School of Life Science and Engineering, Foshan University, Foshan 528225, China; (X.L.)
| | - Wenting Chui
- Animal Disease Prevention and Control Center of Qinghai Province, Xining 810003, China
| | - Jun Kui
- Huangzhong District Animal Husbandry and Veterinary Station, Xining 811600, China
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73
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Martínez-Aquino A, García-Teh JG, Ceccarelli FS, Aguirre-Macedo ML, Vidal-Martínez VM. Integrative taxonomy of Serrasentis gibsoni n. sp. (Acanthocephala: Isthmosacanthidae) from flatfishes in the Gulf of Mexico. J Helminthol 2023; 97:e96. [PMID: 38073427 DOI: 10.1017/s0022149x23000822] [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] [Indexed: 12/18/2023]
Abstract
The Isthmosacanthidae acanthocephalan species of the genus Serrasentis are parasites of marine teleosts and an elasmobranch. In this study, Serrasentis gibsoni n. sp. is described from the intestines of four flatfish species (Paralichthyidae), namely Ancyclopsetta quadrocellata, Cyclopsetta chittendeni, Syacium gunteri, and S. papillosum from 10 oceanic sites in the Gulf of Mexico (GoM). Twenty sequences of the 'barcoding' region of cytochrome C oxidase subunit I gene were obtained from 20 adults of Serrasentis gibsoni n. sp. Additionally, five sequences of the barcoding region were obtained from five adults of rhadinorhynchid Gorgorhynchus lepidus from C. chittendeni, S. papillosum and one species of Haemulidae, Haemulom aurolineatum, from five oceanic sites from the GoM. Two phylogenetic approaches were followed: Bayesian inference and maximum likelihood. In both phylogenetic reconstructions, the sequences of Serrasentis gibsoni n. sp. were recovered as a monophyletic group within the genus Serrasentis and placed as a sister group to G. lepidus. However, due to the lack of molecular data for species of the Isthmosacanthidae and Rhadinorhynchidea, these phylogenetic inferences must be taken with caution. Serrasentis gibsoni n. sp. is the first species of Serrasentis described from Paralichthyidae flatfish species from marine waters of the Americas and from the GoM. Based on the barcoding data set analyzed, Serrasentis gibsoni n. sp. appears to have high intraspecific genetic variation; thus, it is necessary to continue exploring the genetic diversity of this species to infer its intraspecific evolutionary patterns.
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Affiliation(s)
- A Martínez-Aquino
- Laboratorio de Biología Evolutiva de Parásitos, Facultad de Ciencias, Universidad Autónoma de Baja California, Carretera Transpeninsular 3917, Fraccionamiento Playitas, Ensenada, Baja California, 22860, Mexico
| | - J G García-Teh
- Laboratorio de Patología Acuática, Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Mérida, Cordemex, Carretera Antigua a Progreso Km. 6, Mérida, Yucatán, 97310, Mexico
| | - F S Ceccarelli
- Departamento de Biología de la Conservación, Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Ensenada-Tijuana, Ensenada, Baja California, 22860, Mexico
| | - M L Aguirre-Macedo
- Laboratorio de Patología Acuática, Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Mérida, Cordemex, Carretera Antigua a Progreso Km. 6, Mérida, Yucatán, 97310, Mexico
| | - V M Vidal-Martínez
- Laboratorio de Patología Acuática, Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Mérida, Cordemex, Carretera Antigua a Progreso Km. 6, Mérida, Yucatán, 97310, Mexico
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74
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Yang F, Huang Y, Long L. Characterization of the chloroplast genome of the marine microalga Tetraselmis marina (Cienkowski) R.E.Norris, Hori & Chihara 1980. Mitochondrial DNA B Resour 2023; 8:1347-1350. [PMID: 38196789 PMCID: PMC10776064 DOI: 10.1080/23802359.2023.2288892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 11/24/2023] [Indexed: 01/11/2024] Open
Abstract
Tetraselmis marina (Cienkowski) R.E.Norris, Hori & Chihara 1980, a costal green microalga, is considered as a promising animal feed in aquaculture due to the high content of fatty acids and carotenoid. Furthermore, T. marina plays important roles in bioremediation. In this study, we assembled the complete chloroplast genome of T. marina. Results showed that the full length of the complete chloroplast genome was 96,151 bp, containing a large single-copy region of 62,574 bp, a small single-copy region of 1261 bp, and a pair of inverted repeat regions of 16,158 bp. The GC content of the genome was 36.6%. A total of 125 genes were annotated, including 81 protein coding genes, 38 tRNA genes, and six rRNA genes. Phylogenetic analysis based on 22 chloroplast genomes suggested that T. marina was closely related to Tetraselmis sp. CCMP 881.
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Affiliation(s)
- Fangfang Yang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Yi Huang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Lijuan Long
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
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75
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Singleton M, Eisen M. Leveraging genomic redundancy to improve inference and alignment of orthologous proteins. G3 (BETHESDA, MD.) 2023; 13:jkad222. [PMID: 37770067 PMCID: PMC10700111 DOI: 10.1093/g3journal/jkad222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/11/2023] [Accepted: 09/19/2023] [Indexed: 10/03/2023]
Abstract
Identifying protein sequences with common ancestry is a core task in bioinformatics and evolutionary biology. However, methods for inferring and aligning such sequences in annotated genomes have not kept pace with the increasing scale and complexity of the available data. Thus, in this work, we implemented several improvements to the traditional methodology that more fully leverage the redundancy of closely related genomes and the organization of their annotations. Two highlights include the application of the more flexible k-clique percolation algorithm for identifying clusters of orthologous proteins and the development of a novel technique for removing poorly supported regions of alignments with a phylogenetic hidden Markov model (phylo-HMM). In making the latter, we wrote a fully documented Python package Homomorph that implements standard HMM algorithms and created a set of tutorials to promote its use by a wide audience. We applied the resulting pipeline to a set of 33 annotated Drosophila genomes, generating 22,813 orthologous groups and 8,566 high-quality alignments.
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Affiliation(s)
- Marc Singleton
- Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA 94720, USA
| | - Michael Eisen
- Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
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76
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Hehenberger E, Guo J, Wilken S, Hoadley K, Sudek L, Poirier C, Dannebaum R, Susko E, Worden AZ. Phosphate Limitation Responses in Marine Green Algae Are Linked to Reprogramming of the tRNA Epitranscriptome and Codon Usage Bias. Mol Biol Evol 2023; 40:msad251. [PMID: 37987557 PMCID: PMC10735309 DOI: 10.1093/molbev/msad251] [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] [Revised: 11/14/2023] [Accepted: 11/16/2023] [Indexed: 11/22/2023] Open
Abstract
Marine algae are central to global carbon fixation, and their productivity is dictated largely by resource availability. Reduced nutrient availability is predicted for vast oceanic regions as an outcome of climate change; however, there is much to learn regarding response mechanisms of the tiny picoplankton that thrive in these environments, especially eukaryotic phytoplankton. Here, we investigate responses of the picoeukaryote Micromonas commoda, a green alga found throughout subtropical and tropical oceans. Under shifting phosphate availability scenarios, transcriptomic analyses revealed altered expression of transfer RNA modification enzymes and biased codon usage of transcripts more abundant during phosphate-limiting versus phosphate-replete conditions, consistent with the role of transfer RNA modifications in regulating codon recognition. To associate the observed shift in the expression of the transfer RNA modification enzyme complement with the transfer RNAs encoded by M. commoda, we also determined the transfer RNA repertoire of this alga revealing potential targets of the modification enzymes. Codon usage bias was particularly pronounced in transcripts encoding proteins with direct roles in managing phosphate limitation and photosystem-associated proteins that have ill-characterized putative functions in "light stress." The observed codon usage bias corresponds to a proposed stress response mechanism in which the interplay between stress-induced changes in transfer RNA modifications and skewed codon usage in certain essential response genes drives preferential translation of the encoded proteins. Collectively, we expose a potential underlying mechanism for achieving growth under enhanced nutrient limitation that extends beyond the catalog of up- or downregulated protein-encoding genes to the cell biological controls that underpin acclimation to changing environmental conditions.
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Affiliation(s)
- Elisabeth Hehenberger
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research, 24148 Kiel, DE
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, CZ
| | - Jian Guo
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Susanne Wilken
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Kenneth Hoadley
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research, 24148 Kiel, DE
| | - Lisa Sudek
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Camille Poirier
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research, 24148 Kiel, DE
| | - Richard Dannebaum
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Edward Susko
- Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, CA
| | - Alexandra Z Worden
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research, 24148 Kiel, DE
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA
- Max Planck Institute for Evolutionary Biology, 24306 Plön, DE
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77
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Thomé PC, Irisarri I, Wolinska J, Monaghan MT, Strassert JFH. Single-cell genomics reveals new rozellid lineages and supports their sister relationship to Microsporidia. Biol Lett 2023; 19:20230398. [PMID: 38087939 PMCID: PMC10716661 DOI: 10.1098/rsbl.2023.0398] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
The phylum Rozellomycota has been proposed for a group of early-branching holomycotan lineages representing obligate parasites and hyperparasites of zoosporic fungi, oomycotes or phytoplankton. Given their predominantly intracellular lifestyle, rozellids are typically known from environmental ribosomal DNA data, except for the well-studied Rozella species. To date, the phylogenetic relationship between rozellids and microsporidians (Microsporidia) is not fully understood and most reliable hypotheses are based on phylogenomic analyses that incorporate the only publicly available rozellid genome of Rozella allomycis. Here, we provide genomic data of three new rozellid lineages obtained by single-cell sequencing from environmental samples and show with a phylogenomic approach that rozellids form a monophyletic group that is sister to microsporidians, corroborating the previously proposed phylum Rozellomycota. Whereas no mitochondrial genes coding for the respiratory Complex I could be found, we discovered a gene coding for a nucleotide phosphate transporter in one of the three draft genomes. The scattered absence of Complex I genes and scattered presence of nucleotide transporter genes across diverse microsporidian and rozellid lineages suggest that these adaptations to a parasitic lifestyle, which reduce the parasite's capability to synthesize ATP but enables it to steal ATP from its host, evolved independently in microsporidians and rozellids.
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Affiliation(s)
- Pauline C. Thomé
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Iker Irisarri
- Section Phylogenomics, Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Museum of Nature Hamburg, Hamburg, Germany
| | - Justyna Wolinska
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
- Institut für Biologie, Freie Universität Berlin, Berlin, Germany
| | - Michael T. Monaghan
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
- Institut für Biologie, Freie Universität Berlin, Berlin, Germany
| | - Jürgen F. H. Strassert
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
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Qu Y, Wang B, Deng J, Feng Y, Pi Z, Ren L, Cai J. Geographical Distribution and Multimethod Species Identification of Forensically Important Necrophagous Flies on Hainan Island. INSECTS 2023; 14:898. [PMID: 37999097 PMCID: PMC10672153 DOI: 10.3390/insects14110898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 11/12/2023] [Accepted: 11/16/2023] [Indexed: 11/25/2023]
Abstract
Forensic entomology offers unique advantages for the minimum postmortem interval (PMImin) estimation of decomposed corpses in forensic investigations. Accurate species identification and up-to-date locality information are essential. Hainan Island has a tropical rainforest climate and a vast territory. In this study, the community structure of necrophagous flies on Hainan Island was investigated in detail according to geographical environment. The results showed that the dominant species included C. megacephala, S. peregrina, C. rufifacies, S. misera, H. ligurriens, S. sericea, S. cinerea, S. dux, C. pinguis, and M. domestica. Furthermore, C. rufifacies and C. villeneuvi were found only in the high-altitude areas of Wuzhi Mountain, while S. cinerea was distributed only in coastal areas; the latter is a representative species of Hainan Island and has not been reported before. Furthermore, a GenBank database of forensically important flies was established, whilst a high-resolution melt (HRM) curve analysis was applied to identify the common species of Hainan Island for the first time. This study enriches the database of forensically important flies in tropical rainforest regions.
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Affiliation(s)
- Yihong Qu
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha 410017, China; (Y.Q.); (Z.P.)
- Hainan Equity Judicial Expertise Center, Hainan Vocational College of Political Science and Law, Haikou 570100, China
| | - Bo Wang
- Hainan Provincial Academician Workstation, Haikou 570100, China; (B.W.); (J.D.)
| | - Jianqiang Deng
- Hainan Provincial Academician Workstation, Haikou 570100, China; (B.W.); (J.D.)
| | - Yakai Feng
- Department of Forensic Medicine, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi 830011, China;
| | - Zhiyun Pi
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha 410017, China; (Y.Q.); (Z.P.)
| | - Lipin Ren
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha 410017, China; (Y.Q.); (Z.P.)
- Shanghai Key Lab of Forensic Medicine, Key Lab of Forensic Science, Ministry of Justice, Academy of Forensic Science, Shanghai 570100, China
| | - Jifeng Cai
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha 410017, China; (Y.Q.); (Z.P.)
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79
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Montes MM, Barneche J, Legunda N, Ferrari W, Aguilar-Aguilar R, Martorelli SR. Systematic assessment of nymphs of Diesingiinae (Pentastomida: Sebekidae) parasitizing Palloceros harpagos (Cyprinodontiformes: Poeciliidae) from Parque Nacional Iguazú, Argentina: filling gaps in an incomplete phylogenetic framework. AN ACAD BRAS CIENC 2023; 95:e20200668. [PMID: 37991102 DOI: 10.1590/0001-3765202320200668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 09/13/2020] [Indexed: 11/23/2023] Open
Abstract
During a search for parasites in fishes from Iguazu River, Argentina, a nymph of pentastomid was found encysted on mesenteries of Phalloceros harpagos. The 28S rDNA and COI mt-DNA were used to compare with the sequences deposited in the GenBank. Pentastomid nymphs belong to the subfamily Diesingiinae (Sebekidae) for having chloride cell pores distributed in a single row per annulus; also, the hooks and rows of spines of our material differ to other genera. Present specimens are most likely Diesingia sp., having 63-74 annuli, a U shaped oral cadre with fibers closing anteriorly and a peg like extension of the oral cadre. The 28S rDNA analysis places our samples into a sister group of Alofia sp., but the COI mt-DNA situate them on the base of the clade. In conclusion, our pentastomid positively belongs to Diesingia sp., however, indisputable assignation requires a reliable description of the nymph, or the availability of sequences linking nymphs and adults, which even could provide evidence of a new hitherto undescribed genus. Aditionally, the systematic position of Sebekia oxycephala previously described by P. harpagos is discussed on the basis of our results, allowing us to suggest a re-assignation of such specimens to the genus Diesingia.
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Affiliation(s)
- Martín Miguel Montes
- Centro de Estudios Parasitológicos y Vectores (CEPAVE-UNLP-CONICET-), Boulevard 120 s/n e/60 y 64, C.P. 1900, La Plata, Buenos Aires, Argentina
| | - Jorge Barneche
- Centro de Estudios Parasitológicos y Vectores (CEPAVE-UNLP-CONICET-), Boulevard 120 s/n e/60 y 64, C.P. 1900, La Plata, Buenos Aires, Argentina
| | - Nicolas Legunda
- Centro de Estudios Parasitológicos y Vectores (CEPAVE-UNLP-CONICET-), Boulevard 120 s/n e/60 y 64, C.P. 1900, La Plata, Buenos Aires, Argentina
| | - Walter Ferrari
- Centro de Estudios Parasitológicos y Vectores (CEPAVE-UNLP-CONICET-), Boulevard 120 s/n e/60 y 64, C.P. 1900, La Plata, Buenos Aires, Argentina
| | - Rogelio Aguilar-Aguilar
- Departamento de Biología Comparada, Facultad de Ciencias, Universidad Nacional Autónoma de México, Circuito Exterior s/n, C.P. 04510, Ciudad Universitaria, Mexico
| | - Sergio Roberto Martorelli
- Centro de Estudios Parasitológicos y Vectores (CEPAVE-UNLP-CONICET-), Boulevard 120 s/n e/60 y 64, C.P. 1900, La Plata, Buenos Aires, Argentina
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80
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Li H, Wang L, Ma C. The complete plastome of Campsis radicans (L.) Bureau 1864 and its phylogenetic analysis. Mitochondrial DNA B Resour 2023; 8:1200-1204. [PMID: 38239913 PMCID: PMC10796121 DOI: 10.1080/23802359.2023.2275827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/21/2023] [Indexed: 01/22/2024] Open
Abstract
Campsis radicans (L.) Bureau 1864, a species of Bignoniaceae, has a widespread paleotropical distribution and is utilized for horticultural and traditional Chinese medicinal purposes. Despite the plant's significance, its genetic diversity must be better understood. In this study, we have successfully assembled and characterized the complete plastome of C. radicans, marking a significant advancement toward comprehending its genetic composition. The plastome is 153,630 bp long and harbors 130 genes, including 86 protein-coding genes, 36 tRNA genes, and eight rRNA genes. Our phylogenomic analysis of the representative species of Bignoniaceae indicated that C. radicans formed a monophyletic sister clade of Campsis with C. grandiflora. These findings are crucial for conserving and utilizing this important plant species. They also highlight the potential for future research into the evolution and preservation of C. radicans, which could be advantageous in pharmaceutical applications.
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Affiliation(s)
- Hongqin Li
- College of Pharmacy, Heze University, Heze, P. R. China
| | - Liqiang Wang
- College of Pharmacy, Heze University, Heze, P. R. China
| | - Changhao Ma
- Inspection Department Three, Shandong Center for Food and Drug Evaluation and Inspection, Jinan, P. R. China
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81
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Choquet M, Lenner F, Cocco A, Toullec G, Corre E, Toullec JY, Wallberg A. Comparative Population Transcriptomics Provide New Insight into the Evolutionary History and Adaptive Potential of World Ocean Krill. Mol Biol Evol 2023; 40:msad225. [PMID: 37816123 PMCID: PMC10642690 DOI: 10.1093/molbev/msad225] [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: 05/01/2023] [Revised: 08/31/2023] [Accepted: 09/25/2023] [Indexed: 10/12/2023] Open
Abstract
Genetic variation is instrumental for adaptation to changing environments but it is unclear how it is structured and contributes to adaptation in pelagic species lacking clear barriers to gene flow. Here, we applied comparative genomics to extensive transcriptome datasets from 20 krill species collected across the Atlantic, Indian, Pacific, and Southern Oceans. We compared genetic variation both within and between species to elucidate their evolutionary history and genomic bases of adaptation. We resolved phylogenetic interrelationships and uncovered genomic evidence to elevate the cryptic Euphausia similis var. armata into species. Levels of genetic variation and rates of adaptive protein evolution vary widely. Species endemic to the cold Southern Ocean, such as the Antarctic krill Euphausia superba, showed less genetic variation and lower evolutionary rates than other species. This could suggest a low adaptive potential to rapid climate change. We uncovered hundreds of candidate genes with signatures of adaptive evolution among Antarctic Euphausia but did not observe strong evidence of adaptive convergence with the predominantly Arctic Thysanoessa. We instead identified candidates for cold-adaptation that have also been detected in Antarctic fish, including genes that govern thermal reception such as TrpA1. Our results suggest parallel genetic responses to similar selection pressures across Antarctic taxa and provide new insights into the adaptive potential of important zooplankton already affected by climate change.
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Affiliation(s)
- Marvin Choquet
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Felix Lenner
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Arianna Cocco
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Gaëlle Toullec
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Erwan Corre
- CNRS, Sorbonne Université, FR 2424, ABiMS Platform, Station Biologique de Roscoff, Roscoff, France
| | - Jean-Yves Toullec
- CNRS, UMR 7144, AD2M, Sorbonne Université, Station Biologique de Roscoff, Roscoff, France
| | - Andreas Wallberg
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
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82
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Cortés-Hernández MÁ, López-Castaño JA, Milani N, DoNascimiento C. A new cryptic species of Imparfinis (Siluriformes: Heptapteridae) from the Orinoco River basin, revealed by an iterative approach. JOURNAL OF FISH BIOLOGY 2023; 103:1015-1030. [PMID: 37395669 DOI: 10.1111/jfb.15495] [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: 04/17/2023] [Revised: 06/26/2023] [Accepted: 06/29/2023] [Indexed: 07/04/2023]
Abstract
An iterative analysis of Imparfinis, combining phylogenetic analysis based on cytochrome oxidase gene and multivariate morphometrics, revealed a new cryptic species from the Andean tributaries of the Orinoco River basin, which is described here. The new species is sister to a clade constituted by Imparfinis hasemani and Imparfinis pijpersi, both from the river basins of the Guiana Shield, being also the most geographically proximate species. Nonetheless, the new species is most similar in general appearance to Imparfinis guttatus from the Madeira and Paraguay River drainages, being almost undistinguishable by conventional characters of external morphology, differing only by morphometric attributes overall. The new species can be distinguished from the remaining congeners by a unique combination of characters, including lower lobe of caudal fin darker than upper lobe, maxillary barbel reaching or surpassing pelvic-fin insertion, 12-15 gill rakers on first gill arch, 40-42 total vertebrae and 9-10 ribs. The new species constitutes the only representative from the Orinoco River basin belonging to Imparfinis sensu stricto.
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Affiliation(s)
- Miguel Ángel Cortés-Hernández
- Grupo de Investigación Evaluación, Manejo y Conservación de Recursos Hidrobiológicos y Pesqueros, Universidad de los Llanos, Villavicencio, Colombia
- Museo de Historia Natural de la Universidad de los Llanos, Villavicencio, Colombia
- Grupo de Investigación Cuencas, Fundación Neotropical Cuencas, Arauca, Colombia
| | - Jeisson Alexis López-Castaño
- Grupo de Investigación Evaluación, Manejo y Conservación de Recursos Hidrobiológicos y Pesqueros, Universidad de los Llanos, Villavicencio, Colombia
| | - Nadia Milani
- Centro Museo de Biología, Instituto de Zoología y Ecología Tropical, Facultad de Ciencias, Universidad Central de Venezuela, Caracas, Venezuela
| | - Carlos DoNascimiento
- Grupo de Ictiología, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
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83
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Varsani A, Kraberger S, Opriessnig T, Maggi F, Celer V, Okamoto H, Biagini P. Anelloviridae taxonomy update 2023. Arch Virol 2023; 168:277. [PMID: 37864606 DOI: 10.1007/s00705-023-05903-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2023]
Abstract
The family Anelloviridae comprises negative single-stranded circular DNA viruses. Within this family, there are 30 established genera. Anelloviruses in the genus Gyrovirus have been identified infecting various avian species, whereas those in the remaining 29 genera have been found primarily infecting various mammal species. We renamed the 146 anellovirus species with binomial species names, as required by the International Committee on Taxonomy of Viruses (ICTV) using a "genus + freeform epithet" format.
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Affiliation(s)
- Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ, 85287-5001, USA.
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, 7925, South Africa.
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ, 85287-5001, USA
| | - Tanja Opriessnig
- Moredun Research Institute, Pentland Science Park, Bush Loan, Penicuik, Midlothian, EH26 0PZ, United Kingdom
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Fabrizio Maggi
- National Institute for Infectious Diseases Lazzaro Spallanzani-IRCCS, Rome, Italy
| | - Vladimir Celer
- Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Palackeho 1946, 612 42, Brno, Czech Republic
| | - Hiroaki Okamoto
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, 3311-1 Yakushiji, Shimotsuke-shi, Tochigi, 329-0498, Japan
| | - Philippe Biagini
- Equipe Biologie des Groupes Sanguins, UMR 7268 ADES, Aix-Marseille Université, CNRS, EFS, 27 Bd. Jean Moulin, 13005, Marseille, France
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84
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Cerri A, Bolatti EM, Zorec TM, Montani ME, Rimondi A, Hosnjak L, Casal PE, Di Domenica V, Barquez RM, Poljak M, Giri AA. Identification and characterization of novel alphacoronaviruses in Tadarida brasiliensis (Chiroptera, Molossidae) from Argentina: insights into recombination as a mechanism favoring bat coronavirus cross-species transmission. Microbiol Spectr 2023; 11:e0204723. [PMID: 37695063 PMCID: PMC10581097 DOI: 10.1128/spectrum.02047-23] [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: 05/16/2023] [Accepted: 07/14/2023] [Indexed: 09/12/2023] Open
Abstract
Bats are reservoirs of various coronaviruses that can jump between bat species or other mammalian hosts, including humans. This article explores coronavirus infection in three bat species (Tadarida brasiliensis, Eumops bonariensis, and Molossus molossus) of the family Molossidae from Argentina using whole viral metagenome analysis. Fecal samples of 47 bats from three semiurban or highly urbanized areas of the province of Santa Fe were investigated. After viral particle enrichment, total RNA was sequenced using the Illumina NextSeq 550 instrument; the reads were assembled into contigs and taxonomically and phylogenetically analyzed. Three novel complete Alphacoronavirus (AlphaCoV) genomes (Tb1-3) and two partial sequences were identified in T. brasiliensis (Tb4-5), and an additional four partial sequences were identified in M. molossus (Mm1-4). Phylogenomic analysis showed that the novel AlphaCoV clustered in two different lineages distinct from the 15 officially recognized AlphaCoV subgenera. Tb2 and Tb3 isolates appeared to be variants of the same virus, probably involved in a persistent infectious cycle within the T. brasiliensis colony. Using recombination analysis, we detected a statistically significant event in Spike gene, which was reinforced by phylogenetic tree incongruence analysis, involving novel Tb1 and AlphaCoVs identified in Eptesicus fuscus (family Vespertilionidae) from the U.S. The putative recombinant region is in the S1 subdomain of the Spike gene, encompassing the potential receptor-binding domain of AlphaCoVs. This study reports the first AlphaCoV genomes in molossids from the Americas and provides new insights into recombination as an important mode of evolution of coronaviruses involved in cross-species transmission. IMPORTANCE This study generated three novel complete AlphaCoV genomes (Tb1, Tb2, and Tb3 isolates) identified in individuals of Tadarida brasiliensis from Argentina, which showed two different evolutionary patterns and are the first to be reported in the family Molossidae in the Americas. The novel Tb1 isolate was found to be involved in a putative recombination event with alphacoronaviruses identified in bats of the genus Eptesicus from the U.S., whereas isolates Tb2 and Tb3 were found in different collection seasons and might be involved in persistent viral infections in the bat colony. These findings contribute to our knowledge of the global diversity of bat coronaviruses in poorly studied species and highlight the different evolutionary aspects of AlphaCoVs circulating in bat populations in Argentina.
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Affiliation(s)
- Agustina Cerri
- Human Virology Group, Rosario Institute of Molecular and Cellular Biology (IBR-CONICET), Rosario, Argentina
| | - Elisa M. Bolatti
- Human Virology Group, Rosario Institute of Molecular and Cellular Biology (IBR-CONICET), Rosario, Argentina
- Virology Area, Faculty of Biochemical and Pharmaceutical Sciences, National University of Rosario, Rosario, Argentina
- Bat Conservation Program of Argentina, San Miguel de Tucumán, Argentina
| | - Tomaz M. Zorec
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Maria E. Montani
- Bat Conservation Program of Argentina, San Miguel de Tucumán, Argentina
- Dr. Ángel Gallardo Provincial Museum of Natural Sciences, Rosario, Argentina
- Argentine Biodiversity Research Institute (PIDBA), Faculty of Natural Sciences, National University of Tucumán, San Miguel de Tucumán, Argentina
| | - Agustina Rimondi
- Institute of Virology and Technological Innovations (INTA/CONICET), Castelar, Argentina
- Robert Koch Institute, Berlin, Germany
| | - Lea Hosnjak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Pablo E. Casal
- DETx MOL S.A. La Segunda Núcleo Corporate Building, Alvear, Argentina
| | - Violeta Di Domenica
- Human Virology Group, Rosario Institute of Molecular and Cellular Biology (IBR-CONICET), Rosario, Argentina
- Bat Conservation Program of Argentina, San Miguel de Tucumán, Argentina
| | - Ruben M. Barquez
- Bat Conservation Program of Argentina, San Miguel de Tucumán, Argentina
- Argentine Biodiversity Research Institute (PIDBA), Faculty of Natural Sciences, National University of Tucumán, San Miguel de Tucumán, Argentina
| | - Mario Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Adriana A. Giri
- Human Virology Group, Rosario Institute of Molecular and Cellular Biology (IBR-CONICET), Rosario, Argentina
- Virology Area, Faculty of Biochemical and Pharmaceutical Sciences, National University of Rosario, Rosario, Argentina
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85
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Deng PT, Yan J, Liu XF, He ZM, Lin Y, Lu MX, Zhang P. Three coralloid species of the genus Trechispora (Trechisporales, Basidiomycota) in China: two newly discovered taxa and one reported for the first time. MycoKeys 2023; 99:153-170. [PMID: 37719303 PMCID: PMC10502705 DOI: 10.3897/mycokeys.99.109375] [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: 07/11/2023] [Accepted: 08/23/2023] [Indexed: 09/19/2023] Open
Abstract
Two new species of Trechispora indigenous to southern China, T.laxa and T.tongdaoensis, are described and illustrated, and the first record of T.khokpasiensis in China is reported. Molecular phylogenetic analyses of the concatenated nuclear rDNA ITS1-5.8S-ITS2 and nuclear large subunit sequences supported the inclusion of the three species within the Trechispora clade, together with species formerly classified in Scytinopogon. The new species are similar in micromorphology to species of Trechispora (as traditionally circumscribed) but are distinguished by having coralloid basidiomata. A key to the known coralloid Trechispora species in China is provided.
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Affiliation(s)
- Peng-Tao Deng
- College of Life Science, Hunan Normal University, Changsha 410081, ChinaHunan Normal UniversityChangshaChina
| | - Jun Yan
- College of Life Science, Hunan Normal University, Changsha 410081, ChinaHunan Normal UniversityChangshaChina
| | - Xiang-Fen Liu
- College of Life Science, Hunan Normal University, Changsha 410081, ChinaHunan Normal UniversityChangshaChina
| | - Zheng-Mi He
- College of Life Science, Hunan Normal University, Changsha 410081, ChinaHunan Normal UniversityChangshaChina
| | - Yuan Lin
- Bureau of Forestry, Tongdao Dong Autonomous County, Huaihua, Hunan 418500, ChinaBureau of Forestry,Tongdao Dong AutonomousHuaihuaChina
| | - Ming-Xin Lu
- Bureau of Forestry, Tongdao Dong Autonomous County, Huaihua, Hunan 418500, ChinaBureau of Forestry,Tongdao Dong AutonomousHuaihuaChina
| | - Ping Zhang
- College of Life Science, Hunan Normal University, Changsha 410081, ChinaHunan Normal UniversityChangshaChina
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86
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Dudka D, Akins RB, Lampson MA. FREEDA: An automated computational pipeline guides experimental testing of protein innovation. J Cell Biol 2023; 222:e202212084. [PMID: 37358475 PMCID: PMC10292211 DOI: 10.1083/jcb.202212084] [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: 12/17/2022] [Revised: 04/22/2023] [Accepted: 06/07/2023] [Indexed: 06/27/2023] Open
Abstract
Cell biologists typically focus on conserved regions of a protein, overlooking innovations that can shape its function over evolutionary time. Computational analyses can reveal potential innovations by detecting statistical signatures of positive selection that lead to rapid accumulation of beneficial mutations. However, these approaches are not easily accessible to non-specialists, limiting their use in cell biology. Here, we present an automated computational pipeline FREEDA that provides a simple graphical user interface requiring only a gene name; integrates widely used molecular evolution tools to detect positive selection in rodents, primates, carnivores, birds, and flies; and maps results onto protein structures predicted by AlphaFold. Applying FREEDA to >100 centromere proteins, we find statistical evidence of positive selection within loops and turns of ancient domains, suggesting innovation of essential functions. As a proof-of-principle experiment, we show innovation in centromere binding of mouse CENP-O. Overall, we provide an accessible computational tool to guide cell biology research and apply it to experimentally demonstrate functional innovation.
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Affiliation(s)
- Damian Dudka
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - R. Brian Akins
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael A. Lampson
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
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87
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Torkashvand N, Kamyab H, Shahverdi AR, Khoshayand MR, Sepehrizadeh Z. Isolation, characterization, and genome analysis of a broad host range Salmonella phage vB_SenS_TUMS_E4: a candidate bacteriophage for biocontrol. Vet Res Commun 2023; 47:1493-1503. [PMID: 37097546 DOI: 10.1007/s11259-023-10105-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 03/14/2023] [Indexed: 04/26/2023]
Abstract
Salmonella enteritidis is one of the most important foodborne pathogens that cause numerous outbreaks worldwide. Some strains of Salmonella have become progressively resistant to antibiotics, so they could represent a critical threat to public health and have led to the use of alternative therapeutic approaches like phage therapy. In this study, a lytic phage, vB_SenS_TUMS_E4 (E4), was isolated from poultry effluent and characterized to evaluate its potential and efficacy for bio-controlling S. enteritidis in foods. Transmission electron microscopy revealed that E4 has a siphovirus morphotype, with an isometric head and non-contractile tail. Determining the host range showed that this phage can effectively infect different motile as well as non-motile Salmonella enterica serovars. The biological characteristics of E4 showed that it has a short latent period of about 15 min and a large burst size of 287 PFU/cell, and is also significantly stable in a broad range of pHs and temperatures. The E4 whole genome contains 43,018 bp and encodes 60 coding sequences (CDSs) but no tRNA genes. Bioinformatics analysis revealed that the genome of E4 lacks any genes related to lysogeny behavior, antibiotic resistance, toxins, or virulence factors. The efficacy of phage E4 as a bio-control agent was assessed in various foodstuffs inoculated with S. enteritidis at 4°C and 25°C, and the resulting data indicated that it could eradicate S. enteritidis after a very short time of 15 min. The findings of the present study showed that E4 is a hopeful candidate as a bio-control agent against S. enteritidis and has the potential to be used in various foodstuffs.
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Affiliation(s)
- Narges Torkashvand
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy & Biotechnology Research Center, Tehran University of Medical Sciences, Tehran, PO Box 14155-6451, Iran
| | - Haniyeh Kamyab
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy & Biotechnology Research Center, Tehran University of Medical Sciences, Tehran, PO Box 14155-6451, Iran
| | - Ahmad Reza Shahverdi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy & Biotechnology Research Center, Tehran University of Medical Sciences, Tehran, PO Box 14155-6451, Iran
| | - Mohammad Reza Khoshayand
- Department of Food and Drug Control, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Zargham Sepehrizadeh
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy & Biotechnology Research Center, Tehran University of Medical Sciences, Tehran, PO Box 14155-6451, Iran.
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88
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He ZM, Yang ZL. A contribution to the knowledge of the genus Infundibulicybe (Tricholomatineae, Agaricales) in China: Two new species and five redescribed taxa. Mycologia 2023; 115:693-713. [PMID: 37478019 DOI: 10.1080/00275514.2023.2226893] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 06/14/2023] [Indexed: 07/23/2023]
Abstract
In China, species of the genus Infundibulicybe are often confused with other taxa and misdetermined. Here we describe two newly discovered species, I. bispora and I. ellipsospora, and redescribe five known taxa of this genus present in China. These identifications are supported by both morphological and DNA-based phylogenetic evidence. Additionally, a key to all known species of Infundibulicybe is provided.
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Affiliation(s)
- Zheng-Mi He
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- College of Life Sciences, Hunan Normal University, Changsha, Hunan, 410081, China
| | - Zhu L Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
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89
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Durut N, Kornienko AE, Schmidt HA, Lettner N, Donà M, Nordborg M, Mittelsten Scheid O. Long noncoding RNAs contribute to DNA damage resistance in Arabidopsis thaliana. Genetics 2023; 225:iyad135. [PMID: 37467473 PMCID: PMC10471225 DOI: 10.1093/genetics/iyad135] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/14/2023] [Accepted: 07/16/2023] [Indexed: 07/21/2023] Open
Abstract
Efficient repair of DNA lesions is essential for the faithful transmission of genetic information between somatic cells and for genome integrity across generations. Plants have multiple, partially redundant, and overlapping DNA repair pathways, probably due to the less constricted germline and the inevitable exposure to light including higher energy wavelengths. Many proteins involved in DNA repair and their mode of actions are well described. In contrast, a role for DNA damage-associated RNA components, evident from many other organisms, is less well understood. Here, we have challenged young Arabidopsis thaliana plants with two different types of genotoxic stress and performed de novo assembly and transcriptome analysis. We identified three long noncoding RNAs (lncRNAs) that are lowly or not expressed under regular conditions but up-regulated or induced by DNA damage. We generated CRISPR/Cas deletion mutants and found that the absence of the lncRNAs impairs the recovery capacity of the plants from genotoxic stress. The genetic loci are highly conserved among world-wide distributed Arabidopsis accessions and within related species in the Brassicaceae group. Together, these results suggest that the lncRNAs have a conserved function in connection with DNA damage and provide a basis for mechanistic analysis of their role.
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Affiliation(s)
- Nathalie Durut
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - Aleksandra E Kornienko
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - Heiko A Schmidt
- Center for Integrative Bioinformatics Vienna (CIBIV), Max Perutz Labs, University of Vienna and Medical University of Vienna, Vienna BioCenter (VBC), Dr. Bohr Gasse 9, 1030 Vienna, Austria
| | - Nicole Lettner
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - Mattia Donà
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr Gasse 3, 1030 Vienna, Austria
| | - Ortrun Mittelsten Scheid
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr Gasse 3, 1030 Vienna, Austria
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90
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Zhao P, Gu L, Gao Y, Pan Z, Liu L, Li X, Zhou H, Yu D, Han X, Qian L, Liu GE, Fang L, Wang Z. Young SINEs in pig genomes impact gene regulation, genetic diversity, and complex traits. Commun Biol 2023; 6:894. [PMID: 37652983 PMCID: PMC10471783 DOI: 10.1038/s42003-023-05234-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 08/09/2023] [Indexed: 09/02/2023] Open
Abstract
Transposable elements (TEs) are a major source of genetic polymorphisms and play a role in chromatin architecture, gene regulatory networks, and genomic evolution. However, their functional role in pigs and contributions to complex traits are largely unknown. We created a catalog of TEs (n = 3,087,929) in pigs and found that young SINEs were predominantly silenced by histone modifications, DNA methylation, and decreased accessibility. However, some transcripts from active young SINEs showed high tissue-specificity, as confirmed by analyzing 3570 RNA-seq samples. We also detected 211,067 dimorphic SINEs in 374 individuals, including 340 population-specific ones associated with local adaptation. Mapping these dimorphic SINEs to genome-wide associations of 97 complex traits in pigs, we found 54 candidate genes (e.g., ANK2 and VRTN) that might be mediated by TEs. Our findings highlight the important roles of young SINEs and provide a supplement for genotype-to-phenotype associations and modern breeding in pigs.
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Affiliation(s)
- Pengju Zhao
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Lihong Gu
- Institute of Animal Science & Veterinary Medicine, Hainan Academy of Agricultural Sciences, No. 14 Xingdan Road, Haikou, 571100, China
| | - Yahui Gao
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA
| | - Zhangyuan Pan
- Department of Animal Science, University of California, Davis, CA, 95616, USA
| | - Lei Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Xingzheng Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Huaijun Zhou
- Department of Animal Science, University of California, Davis, CA, 95616, USA
| | - Dongyou Yu
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Xinyan Han
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Lichun Qian
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.
| | - Lingzhao Fang
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, 8000, Denmark.
| | - Zhengguang Wang
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China.
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
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91
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Fu YT, Shao R, Suleman, Wang W, Wang HM, Liu GH. The fragmented mitochondrial genomes of two Linognathus lice reveal active minichromosomal recombination and recombination hotspots. iScience 2023; 26:107351. [PMID: 37520725 PMCID: PMC10382929 DOI: 10.1016/j.isci.2023.107351] [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: 04/18/2023] [Revised: 06/04/2023] [Accepted: 07/06/2023] [Indexed: 08/01/2023] Open
Abstract
Evidence for recombination between mitochondrial (mt) minichromosomes has been reported in sucking lice, but it is still not clear how frequent mt minichromosomal recombination occurs. We sequenced the mt genomes of the cattle louse Linognathus vituli and the goat louse L. africanus. Both Linognathus species have 10 mt minichromosomes, and seven of them have the same gene content and gene arrangement. Comparison of mt karyotypes revealed numerous inter-minichromosomal recombination events in the evolution of Linognathus species. Minichromosome merger, gene duplication and gene translocation occurred in the lineage leading to Linognathus lice. After the divergence of L. vituli and L. africanus, duplication, degeneration, deletion and translocation of genes also occurred independently in each species. Most of the recombination events in the Linognathus species occurred upstream of either cox3 or nad2, indicating these two locations were hotspots for inter-minichromosomal recombination. Our results provide an important perspective on mt genome evolution in metazoans.
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Affiliation(s)
- Yi-Tian Fu
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China
| | - Renfu Shao
- Centre for Bioinnovation, School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD 4556, Australia
| | - Suleman
- Department of Zoology, University of Swabi, Khyber Pakhtunkhwa 23430, Pakistan
| | - Wei Wang
- Centre for Bioinnovation, School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD 4556, Australia
| | - Hui-Mei Wang
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China
| | - Guo-Hua Liu
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China
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92
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Yu RM, Zhang N, Zhang BW, Liang Y, Pang XX, Cao L, Chen YD, Zhang WP, Yang Y, Zhang DY, Pang EL, Bai WN. Genomic insights into biased allele loss and increased gene numbers after genome duplication in autotetraploid Cyclocarya paliurus. BMC Biol 2023; 21:168. [PMID: 37553642 PMCID: PMC10408227 DOI: 10.1186/s12915-023-01668-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 07/25/2023] [Indexed: 08/10/2023] Open
Abstract
BACKGROUND Autopolyploidy is a valuable model for studying whole-genome duplication (WGD) without hybridization, yet little is known about the genomic structural and functional changes that occur in autopolyploids after WGD. Cyclocarya paliurus (Juglandaceae) is a natural diploid-autotetraploid species. We generated an allele-aware autotetraploid genome, a chimeric chromosome-level diploid genome, and whole-genome resequencing data for 106 autotetraploid individuals at an average depth of 60 × per individual, along with 12 diploid individuals at an average depth of 90 × per individual. RESULTS Autotetraploid C. paliurus had 64 chromosomes clustered into 16 homologous groups, and the majority of homologous chromosomes demonstrated similar chromosome length, gene numbers, and expression. The regions of synteny, structural variation and nonalignment to the diploid genome accounted for 81.3%, 8.8% and 9.9% of the autotetraploid genome, respectively. Our analyses identified 20,626 genes (69.18%) with four alleles and 9191 genes (30.82%) with one, two, or three alleles, suggesting post-polyploid allelic loss. Genes with allelic loss were found to occur more often in proximity to or within structural variations and exhibited a marked overlap with transposable elements. Additionally, such genes showed a reduced tendency to interact with other genes. We also found 102 genes with more than four copies in the autotetraploid genome, and their expression levels were significantly higher than their diploid counterparts. These genes were enriched in enzymes involved in stress response and plant defense, potentially contributing to the evolutionary success of autotetraploids. Our population genomic analyses suggested a single origin of autotetraploids and recent divergence (~ 0.57 Mya) from diploids, with minimal interploidy admixture. CONCLUSIONS Our results indicate the potential for genomic and functional reorganization, which may contribute to evolutionary success in autotetraploid C. paliurus.
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Affiliation(s)
- Rui-Min Yu
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Ning Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Bo-Wen Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Yu Liang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Xiao-Xu Pang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Lei Cao
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Yi-Dan Chen
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Wei-Ping Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Yang Yang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Da-Yong Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
| | - Er-Li Pang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
| | - Wei-Ning Bai
- State Key Laboratory of Earth Surface Processes and Resource Ecology, and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
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93
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Pas C, Latka A, Fieseler L, Briers Y. Phage tailspike modularity and horizontal gene transfer reveals specificity towards E. coli O-antigen serogroups. Virol J 2023; 20:174. [PMID: 37550759 PMCID: PMC10408124 DOI: 10.1186/s12985-023-02138-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/23/2023] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND The interaction between bacteriophages and their hosts is intricate and highly specific. Receptor-binding proteins (RBPs) of phages such as tail fibers and tailspikes initiate the infection process. These RBPs bind to diverse outer membrane structures, including the O-antigen, which is a serogroup-specific sugar-based component of the outer lipopolysaccharide layer of Gram-negative bacteria. Among the most virulent Escherichia coli strains is the Shiga toxin-producing E. coli (STEC) pathotype dominated by a subset of O-antigen serogroups. METHODS Extensive phylogenetic and structural analyses were used to identify and validate specificity correlations between phage RBP subtypes and STEC O-antigen serogroups, relying on the principle of horizontal gene transfer as main driver for RBP evolution. RESULTS We identified O-antigen specific RBP subtypes for seven out of nine most prevalent STEC serogroups (O26, O45, O103, O104, O111, O145 and O157) and seven additional E. coli serogroups (O2, O8, O16, O18, 4s/O22, O77 and O78). Eight phage genera (Gamaleya-, Justusliebig-, Kaguna-, Kayfuna-, Kutter-, Lederberg-, Nouzilly- and Uetakeviruses) emerged for their high proportion of serogroup-specific RBPs. Additionally, we reveal sequence motifs in the RBP region, potentially serving as recombination hotspots between lytic phages. CONCLUSION The results contribute to a better understanding of mosaicism of phage RBPs, but also demonstrate a method to identify and validate new RBP subtypes for current and future emerging serogroups.
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Affiliation(s)
- Célia Pas
- Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, 9000, Ghent, Belgium
| | - Agnieszka Latka
- Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, 9000, Ghent, Belgium
- Department of Pathogen Biology and Immunology, University of Wroclaw, Przybyszewskiego 63, 51-148, Wrocław, Poland
| | - Lars Fieseler
- Centre for Food Safety and Quality Management, ZHAW School of Life Sciences and Facility Management, Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland
| | - Yves Briers
- Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, 9000, Ghent, Belgium.
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94
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Murakami M, Tokiwa T, Sugiyama H, Shiroyama M, Morishima Y, Watanabe S, Sasamori T, Kondo M, Mano T, Tsuruga H. Trichinella T9 in wild bears in Japan: Prevalence, species/genotype identification, and public health implications. Int J Parasitol Parasites Wildl 2023; 21:264-268. [PMID: 37520899 PMCID: PMC10372044 DOI: 10.1016/j.ijppaw.2023.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/03/2023] [Accepted: 07/03/2023] [Indexed: 08/01/2023]
Abstract
In Japan, the recent series of sporadic outbreaks of human trichinellosis caused by Trichinella (Nematoda: Trichocephalida) has occurred owing to the consumption of raw or insufficiently cooked meat from wild bears. However, the infection status and molecular characteristics of Trichinella larvae in Japanese wild bears remain poorly understood. This study investigated the prevalence of Trichinella spp. in brown bears (Ursus arctos) from Hokkaido, and Japanese black bears (Ursus thibetanus japonicus) from three prefectures (Aomori, Akita, and Iwate) in northern Japan, between April 2019 and August 2022. Trichinella larvae were detected in 2.5% (6/236) of the brown bears and 0.9% (1/117) of the Japanese black bears. Sequence analysis using two genetic loci, the internal transcribed spacer region of nuclear ribosomal DNA and the mitochondrial cytochrome c oxidase subunit I gene, revealed that the larvae collected from the seven infected bears were identical to one of the two haplotypes of Trichinella T9. The prevalence of Trichinella T9 is low but is maintained in bears in the Hokkaido and Iwate prefectures suggesting that undercooked meat from these animals could cause human infection. Thus, continued health education campaigns are needed to raise awareness of the potential risk of trichinellosis among hunters, meat suppliers, consumers, and local governmental health agencies.
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Affiliation(s)
- Masaki Murakami
- Laboratory of Veterinary Parasitology, Nippon Veterinary and Life Science University, Musashino, Tokyo, 180-8602, Japan
- Laboratory of Helminthology, Department of Parasitology, National Institute of Infectious Diseases, Shinjuku, Tokyo, 162-8640, Japan
| | - Toshihiro Tokiwa
- Laboratory of Veterinary Parasitology, Nippon Veterinary and Life Science University, Musashino, Tokyo, 180-8602, Japan
| | - Hiromu Sugiyama
- Laboratory of Helminthology, Department of Parasitology, National Institute of Infectious Diseases, Shinjuku, Tokyo, 162-8640, Japan
- School of Life and Environmental Science, Azabu University, Sagamihara, Kanagawa, 252-5201, Japan
| | - Mitsuko Shiroyama
- School of Life and Environmental Science, Azabu University, Sagamihara, Kanagawa, 252-5201, Japan
| | - Yasuyuki Morishima
- Laboratory of Helminthology, Department of Parasitology, National Institute of Infectious Diseases, Shinjuku, Tokyo, 162-8640, Japan
| | - Sota Watanabe
- Graduate School of Arts and Science, Iwate University, Morioka, Iwate, 020-8550, Japan
| | - Takato Sasamori
- Agriculture, Forestry and Fisheries Division, Fukaura Town Office, Fukaura, Aomori, 038-2324, Japan
| | - Mami Kondo
- Nature Conservation Division, Department of Living and Environment, Akita Prefectural Office, Akita, Akita, 010-8570, Japan
| | - Tsutomu Mano
- Research Institute of Energy, Environment and Geology, Industrial Technology and Environment Research Department, Hokkaido Research Organization, Sapporo, Hokkaido, 060-0819, Japan
| | - Hifumi Tsuruga
- Research Institute of Energy, Environment and Geology, Industrial Technology and Environment Research Department, Hokkaido Research Organization, Sapporo, Hokkaido, 060-0819, Japan
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95
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Zhang X, Park WD, Thijssen M, Xu Y, Tse LPV, Pourkarim MR, Aurora R, Fan X. Expansion of Betatorquevirus and/or Gammatorquevirus in Patients with Severe Clinical Outcomes of the Liver Diseases. Viruses 2023; 15:1635. [PMID: 37631978 PMCID: PMC10457780 DOI: 10.3390/v15081635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Anellovirus (AV) is a ubiquitous virus in the human population. Individuals can be infected with multiple AV genera and species to form a heterogeneous repertoire, termed the anellome. Using advanced methods, we examined the anellomes from 12 paired serum and liver samples, as well as 2701 subjects with different clinical diagnoses. Overall, anellomes are remarkably individualized, with significant among-group differences (Kruskal-Wallis test p = 6.6 × 10-162 for richness and p = 7.48 × 10-162 for Shannon entropy). High dissimilarity scores (beta diversity) were observed between patient groups, except for paired serum and liver samples. At the population level, the relative abundance of combinational AV genus Betatorquevirus (torque teno mini viruses, TTMV), and Gammatorquevirus (torque teno midi viruses, TTMDV) exhibited an exponential distribution with a low bound point at 32%. Defined by this value, the AV TTMV/TTMDV-expanded anellome was significantly enriched among patients with acute liver failure (31.7%) and liver transplantation (40.7%), compared with other patient groups (χ2 test: p = 4.1 × 10-8-3.2 × 10-3). Therefore, anellome heterogeneity may be predictive of clinical outcomes in certain diseases, such as liver disease. The consistency of anellome between paired serum and liver samples indicates that a liquid biopsy approach would be suitable for longitudinal studies to clarify the causality of the AV TTMV/TTMDV-expanded anellome in the outcomes of liver disease.
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Affiliation(s)
- Xiaoan Zhang
- Division of Gastroenterology & Hepatology, Department of Internal Medicine, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
- School of Clinical Medicine, Henan University of Science and Technology, Luoyang 471000, China
| | - William D. Park
- Department of Molecular Microbiology & Immunology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Marijn Thijssen
- Laboratory for Clinical and Epidemiological Virology, Rega Institute, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Yanjuan Xu
- Division of Gastroenterology & Hepatology, Department of Internal Medicine, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Long Ping Victor Tse
- Department of Molecular Microbiology & Immunology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Mahmoud Reza Pourkarim
- Laboratory for Clinical and Epidemiological Virology, Rega Institute, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Rajeev Aurora
- Department of Molecular Microbiology & Immunology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Xiaofeng Fan
- Division of Gastroenterology & Hepatology, Department of Internal Medicine, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
- Saint Louis University Liver Center, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
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96
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Wu Z, Chu T, Sheng Y, Yu Y, Wang Y. Diversity, Relationship, and Distribution of Virophages and Large Algal Viruses in Global Ocean Viromes. Viruses 2023; 15:1582. [PMID: 37515268 PMCID: PMC10385804 DOI: 10.3390/v15071582] [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: 06/06/2023] [Revised: 07/10/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
Virophages are a group of small double-stranded DNA viruses that replicate and proliferate with the help of the viral factory of large host viruses. They are widely distributed in aquatic environments but are more abundant in freshwater ecosystems. Here, we mined the Global Ocean Viromes 2.0 (GOV 2.0) dataset for the diversity, distribution, and association of virophages and their potential host large viruses in marine environments. We identified 94 virophage sequences (>5 kbp in length), of which eight were complete genomes. The MCP phylogenetic tree showed that the GOV virophages were widely distributed on the global virophage tree but relatively clustered on three major branches. The gene-sharing network divided GOV virophages into 21 outliers, 2 overlaps, and 14 viral clusters, of which 4 consisted of only the GOV virophages. We also identified 45 large virus sequences, 8 of which were >100 kbp in length and possibly involved in cell-virus-virophage (C-V-v) trisome relationships. The potential eukaryotic hosts of these eight large viruses and the eight virophages with their complete genomes identified are likely to be algae, based on comparative genomic analysis. Both homologous gene and codon usage analyses support a possible interaction between a virophage (GOVv18) and a large algal virus (GOVLV1). These results indicate that diverse and novel virophages and large viruses are widespread in global marine environments, suggesting their important roles and the presence of complicated unknown C-V-v relationships in marine ecosystems.
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Affiliation(s)
- Zhenqi Wu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201304, China; (Z.W.); (T.C.); (Y.S.); (Y.Y.)
| | - Ting Chu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201304, China; (Z.W.); (T.C.); (Y.S.); (Y.Y.)
| | - Yijian Sheng
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201304, China; (Z.W.); (T.C.); (Y.S.); (Y.Y.)
| | - Yongxin Yu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201304, China; (Z.W.); (T.C.); (Y.S.); (Y.Y.)
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs, Shanghai 201304, China
| | - Yongjie Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201304, China; (Z.W.); (T.C.); (Y.S.); (Y.Y.)
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs, Shanghai 201304, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China
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97
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Marcionetti A, Salamin N. Insights into the Genomics of Clownfish Adaptive Radiation: The Genomic Substrate of the Diversification. Genome Biol Evol 2023; 15:evad088. [PMID: 37226990 PMCID: PMC10349533 DOI: 10.1093/gbe/evad088] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 05/01/2023] [Accepted: 05/17/2023] [Indexed: 05/26/2023] Open
Abstract
Clownfishes are an iconic group of coral reef fishes that evolved a mutualistic interaction with sea anemones, which triggered the rapid diversification of the group. Following the emergence of this mutualism, clownfishes diversified into different ecological niches and developed convergent phenotypes associated with their host use. The genetic basis of the initial acquisition of the mutualism with host anemones has been described, but the genomic architecture underlying clownfish diversification once the mutualism was established and the extent to which clownfish phenotypic convergence originated through shared genetic mechanisms are still unknown. Here, we investigated these questions by performing comparative genomic analyses on the available genomic data of five pairs of closely related but ecologically divergent clownfish species. We found that clownfish diversification was characterized by bursts of transposable elements, an overall accelerated coding evolution, incomplete lineage sorting, and ancestral hybridization events. Additionally, we detected a signature of positive selection in 5.4% of the clownfish genes. Among them, five presented functions associated with social behavior and ecology, and they represent candidate genes involved in the evolution of the size-based hierarchical social structure so particular to clownfishes. Finally, we found genes with patterns of either relaxation or intensification of purifying selection and signals of positive selection linked with clownfish ecological divergence, suggesting some level of parallel evolution during the diversification of the group. Altogether, this work provides the first insights into the genomic substrate of clownfish adaptive radiation and integrates the growing collection of studies investigating the genomic mechanisms governing species diversification.
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Affiliation(s)
- Anna Marcionetti
- Department of Computational Biology, Genopode, University of Lausanne, 1015 Lausanne, Switzerland
| | - Nicolas Salamin
- Department of Computational Biology, Genopode, University of Lausanne, 1015 Lausanne, Switzerland
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98
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Kämpfer P, Lipski A, Lamothe L, Clermont D, Criscuolo A, McInroy JA, Glaeser SP. Paenibacillus plantiphilus sp. nov. from the plant environment of Zea mays. Antonie Van Leeuwenhoek 2023:10.1007/s10482-023-01852-x. [PMID: 37338631 PMCID: PMC10371898 DOI: 10.1007/s10482-023-01852-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 06/01/2023] [Indexed: 06/21/2023]
Abstract
A Gram-strain positive, aerobic, endospore-forming bacterial strain (JJ-246T) was isolated from the rhizosphere of Zea mays. The 16S rRNA gene sequence similarity comparisons showed a most closely relationship to Paenibacillus oenotherae DT7-4T (98.4%) and Paenibacillus xanthinolyticus 11N27T (98.0%). The pairwise average nucleotide identity and digital DNA-DNA hybridisation values of the JJ-246T genome assembly against publicly available Paenibacillus type strain genomes were below 82% and 33%, respectively. The draft genome of JJ-246T shared many putative plant-beneficial functions contributing (PBFC) genes, related to plant root colonisation, oxidative stress protection, degradation of aromatic compounds, plant growth-promoting traits, disease resistance, drug and heavy metal resistance, and nutrient acquisition. The quinone system of strain JJ-246T, the polar lipid profile and the major fatty acids were congruent with those reported for members of the genus Paenibacillus. JJ-246T was shown to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus plantiphilus sp. nov. is proposed, with JJ-246T (= LMG 32093T = CCM 9089T = CIP 111893T) as the type strain.
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Affiliation(s)
- Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
| | - André Lipski
- Institut für Ernährungs- und Lebensmittelwissenschaften, Lebensmittelmikrobiologie und -hygiene, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Lucie Lamothe
- CNRS, IFB-Core, UMS 3601, Institut Français de Bioinformatique, Evry, France
- Institut Pasteur, Bioinformatics and Biostatistics Hub, Université de Paris, 75015, Paris, France
| | - Dominique Clermont
- Institut Pasteur, CIP - Collection of Institut Pasteur, Université de Paris, 75015, Paris, France
| | - Alexis Criscuolo
- Institut Pasteur, Bioinformatics and Biostatistics Hub, Université de Paris, 75015, Paris, France
| | - John A McInroy
- Department of Entomology and Plant Pathology, Auburn University, Alabama, USA
| | - Stefanie P Glaeser
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
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99
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Huang Y, Yang Y, Qi L, Hu H, Rasplus JY, Wang X. Novel Gene Rearrangement Pattern in Pachycrepoideus vindemmiae Mitochondrial Genome: New Gene Order in Pteromalidae (Hymenoptera: Chalcidoidea). Animals (Basel) 2023; 13:1985. [PMID: 37370495 DOI: 10.3390/ani13121985] [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: 04/18/2023] [Revised: 06/05/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
The mitochondrial genomes of Muscidifurax similadanacus, M. sinesensilla, Nasonia vitripennis, and Pachycrepoideus vindemmiae were sequenced to better understand the structural evolution of Pteromalidae mitogenomes. These newly sequenced mitogenomes all contained 37 genes. Nucleotide composition was AT-biased and the majority of the protein-coding genes exhibited a negative AT skew. All 13 protein-coding genes (PCGs) initiated with the standard start codon of ATN, excepted for nad1 of N. vitripennis, which started with TTG, and terminated with a typical stop codon TAA/TAG or an incomplete stop codon T. All transfer RNA (tRNA) genes were predicted to fold into the typical clover-leaf secondary structures, except for trnS1, which lacks the DHU arm in all species. In P. vindemmiae, trnR and trnQ lack the DHU arm and TΨC arm, respectively. Although most genes evolved under a strong purifying selection, the Ka/Ks value of the atp8 gene of P. vindemmiae was greater than 1, indicating putative positive selection. A novel transposition of trnR in P. vindemmiae was revealed, which was the first of this kind to be reported in Pteromalidae. Two kinds of datasets (PCG12 and AA) and two inference methods (maximum likelihood and Bayesian inference) were used to reconstruct a phylogenetic hypothesis for the newly sequenced mitogenomes of Pteromalidae and those deposited in GenBank. The topologies obtained recovered the monophyly of the three subfamilies included. Pachyneurinae and Pteromalinae were recovered as sister families, and both appeared sister to Sycophaginae. The pairwise breakpoint distances of mitogenome rearrangements were estimated to infer phylogeny among pteromalid species. The topology obtained was not totally congruent with those reconstructed using the ML and BI methods.
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Affiliation(s)
- Yixin Huang
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu 241000, China
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China
| | - Yuanhan Yang
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu 241000, China
| | - Liqing Qi
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu 241000, China
| | - Haoyuan Hu
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu 241000, China
| | - Jean-Yves Rasplus
- Centre de Biologie pour la Gestion des Populations (CBGP), INRAE, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, 34398 Montpellier, France
| | - Xu Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
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100
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Yan J, Wen J, Li GW, Wu SW, Zhang P. Taxonomy and Phylogenetic Relationships of Clavulinopsis (Clavariaceae, Agaricales): Description of Six New Species and One Newly Recorded Species from China. J Fungi (Basel) 2023; 9:656. [PMID: 37367591 DOI: 10.3390/jof9060656] [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: 04/15/2023] [Revised: 05/25/2023] [Accepted: 06/08/2023] [Indexed: 06/28/2023] Open
Abstract
Specimens of Clavulinopsis (Clavariaceae, Agaricales) collected in China were studied using morphological and molecular methods. Six species-C. aspersa, C. bicolor, C. bispora, C. erubescens, C. incarnata, and C. tropicalis-are described as new to science, and C. trigonospora is a newly recorded species in China. Phylogenetic analysis was conducted based on a combined dataset of internal transcribed spacer and nuclear ribosomal RNA large subunit sequences. The phylogenetic reconstruction revealed that the six new species each formed an independent lineage, and the samples of C. trigonospora from China were nested with accessions of C. trigonospora collected from Italy. The morphology of the seven Chinese species is described in detail, and is illustrated with line drawings and photographs. A key to the known Clavulinopsis species in China is provided.
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Affiliation(s)
- Jun Yan
- College of Life Sciences, Hunan Normal University, Changsha 410006, China
| | - Jing Wen
- College of Life Sciences, Hunan Normal University, Changsha 410006, China
| | - Gui-Wu Li
- College of Life Sciences, Hunan Normal University, Changsha 410006, China
| | - Shao-Wu Wu
- Bureau of Forestry, Tongdao Dong Autonomous County, Huaihua 418500, China
| | - Ping Zhang
- College of Life Sciences, Hunan Normal University, Changsha 410006, China
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