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Nathans JF, Ayers JL, Shendure J, Simpson CL. Genetic Tools for Cell Lineage Tracing and Profiling Developmental Trajectories in the Skin. J Invest Dermatol 2024; 144:936-949. [PMID: 38643988 PMCID: PMC11034889 DOI: 10.1016/j.jid.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/28/2024] [Accepted: 02/08/2024] [Indexed: 04/23/2024]
Abstract
The epidermis is the body's first line of protection against dehydration and pathogens, continually regenerating the outermost protective skin layers throughout life. During both embryonic development and wound healing, epidermal stem and progenitor cells must respond to external stimuli and insults to build, maintain, and repair the cutaneous barrier. Recent advances in CRISPR-based methods for cell lineage tracing have remarkably expanded the potential for experiments that track stem and progenitor cell proliferation and differentiation over the course of tissue and even organismal development. Additional tools for DNA-based recording of cellular signaling cues promise to deepen our understanding of the mechanisms driving normal skin morphogenesis and response to stressors as well as the dysregulation of cell proliferation and differentiation in skin diseases and cancer. In this review, we highlight cutting-edge methods for cell lineage tracing, including in organoids and model organisms, and explore how cutaneous biology researchers might leverage these techniques to elucidate the developmental programs that support the regenerative capacity and plasticity of the skin.
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Affiliation(s)
- Jenny F Nathans
- Medical Scientist Training Program, University of Washington, Seattle, Washington, USA; Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Jessica L Ayers
- Molecular Medicine and Mechanisms of Disease PhD Program, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA; Department of Dermatology, University of Washington, Seattle, Washington, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA; Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, Washington, USA
| | - Cory L Simpson
- Department of Dermatology, University of Washington, Seattle, Washington, USA; Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, Washington, USA.
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Al-Sarar AS, Abobakr Y, Alzabib AA, Saleh AA. First Report on Banana Weevil, Cosmopolites sordidus (Germar 1823) (Coleoptera: Curculionidae), an Exotic Economically Important Pest from Saudi Arabia. Neotrop Entomol 2024:10.1007/s13744-024-01141-w. [PMID: 38656593 DOI: 10.1007/s13744-024-01141-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 02/23/2024] [Indexed: 04/26/2024]
Abstract
We report the first record of the occurrence of the banana weevil, Cosmopolites sordidus (Germar, 1823) (Coleoptera: Curculionidae), an economically important pest of bananas (Musa spp.), from Fifa Mountains in Saudi Arabia. Moreover, we recorded the first observation of damage caused to bananas by C. sordidus in a banana farm in Jazan Province, southwestern Saudi Arabia, in March 2022. Molecular characterization using DNA sequences of the mitochondrial COI gene confirmed the morphological identification of C. sordidus. This discovery is considered a warning notice to prevent the potential establishment and spread of this dangerous pest in the banana cultivation regions in Saudi Arabia. Therefore, it is recommended that detection and monitoring of banana weevil should be undertaken in Saudi banana farms in order to restrict the dissemination of this weevil to other banana cultivation areas.
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Affiliation(s)
- Ali S Al-Sarar
- Department of Plant Protection, College of Food and Agriculture Sciences, King Saud Univ, Riyadh, Saudi Arabia.
| | - Yasser Abobakr
- Department of Plant Protection, College of Food and Agriculture Sciences, King Saud Univ, Riyadh, Saudi Arabia
- Department of Animal Pests, Plant Protection Research Institute (PPRI), Agricultural Research Center (ARC), Alexandria, Egypt
| | - Ali A Alzabib
- Department of Plant Protection, College of Food and Agriculture Sciences, King Saud Univ, Riyadh, Saudi Arabia
| | - Amgad A Saleh
- Department of Plant Protection, College of Food and Agriculture Sciences, King Saud Univ, Riyadh, Saudi Arabia
- Agriculture Research Center (ARC), Agricultural Genetic Engineering Research Institute (AGERI), Giza, Egypt
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3
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Patil GS, Pinto N, Nath R, Goswami M. Decoding the molecular phylogenetics of ornamental catfishes (siluriformes) of North East India using DNA barcoding approach. Mol Biol Rep 2024; 51:528. [PMID: 38637345 DOI: 10.1007/s11033-024-09487-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 03/26/2024] [Indexed: 04/20/2024]
Abstract
BACKGROUND Catfishes (order Siluriformes) are among the most diverse and widely distributed fish groups in the world. They are not only used for human consumption but are also a major part of the ornamental fish trade. Being a Biodiversity Hotspot, the North Eastern Region of India is home to a diverse population of ornamental fishes. Catfishes contain a humongous number of species; in this study, the authors have tried to elucidate the phylogenetic relationship of some important ornamental catfishes found in North East India using DNA barcodes. METHODS AND RESULTS In this study, we have tried to explore the phylogenetic history of 13 species (41 specimens) of ornamental catfishes spanning 12 genera and 9 families of Siluriformes using DNA barcoding. Pairwise genetic distances using Kimura 2-Parameter (K2P) were calculated at intra-specific and inter-specific levels. A Neighbor-Joining tree was constructed to understand the phylogenetic relationship among the nine different catfish families. All the specimens under this study clustered with their respective species under the same family and formed three sub-clades. However, Olyra longicaudata, belonging to the Bagridae family, did not cluster with other species from the same family. In this study, the authors have suggested a revision of the classification of O. longicaudata back to its original family, Olyridae. CONCLUSIONS In this study, the maximum intraspecific genetic distance of 0.03 and the minimum interspecific genetic distance of 0.14 were observed among the species. Therefore, it is evident that there is a barcoding gap among the species, which helped in the correct identification of the species. Thus, DNA barcoding helped complement the phenetic approach and also revealed a different phylogenetic relationship among the catfishes belonging to the Bagridae family.
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Affiliation(s)
- Grishma S Patil
- ICAR-Central Institute of Fisheries Education, Mumbai, India
- Mangalore University, Mangaluru, Karnataka, India
| | - Nevil Pinto
- ICAR-Central Institute of Fisheries Education, Mumbai, India
| | - Rupak Nath
- St. Anthony's College, Shillong, Meghalaya, India
| | - Mukunda Goswami
- ICAR-Central Institute of Fisheries Education, Mumbai, India.
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Kim S, Čkrkić J, Tomanović Ž, Sohn JH, Lim J, Kim H. A new species of genus Monoctonus (Hymenoptera, Braconidae, Aphidiinae) from South Korea. Biodivers Data J 2024; 12:e119476. [PMID: 38655011 PMCID: PMC11035975 DOI: 10.3897/bdj.12.e119476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 03/30/2024] [Indexed: 04/26/2024] Open
Abstract
Background The genus Monoctonus Haliday, 1833 is a small group which consists of 24 species worldwide. In South Korea, Chang and Youn (1983) recorded one species, M.similis Starý & Schlinger, 1967, but the evidence for identification of this species is doubtful and further confirmation is required (personal communication with Prof. Jong-Cheol Paik). New information An additional Monoctonus species is recorded as new to science from South Korea. Descriptions and illustrations of the new species -Monoctonuskoreanus sp. nov. - are provided, together with its mitochondrial cytochrome c oxidase subunit I (COI) data and phylogenetic position. A key to the female of the two species present in Korea is provided.
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Affiliation(s)
- Sangjin Kim
- Kunsan National University, Gunsan, Republic of KoreaKunsan National UniversityGunsanRepublic of Korea
| | - Jelisaveta Čkrkić
- University of Belgrade, Belgrade, SerbiaUniversity of BelgradeBelgradeSerbia
- Centre for Biodiversity Genomics, University of Guelph, Guelph, CanadaCentre for Biodiversity Genomics, University of GuelphGuelphCanada
| | - Željko Tomanović
- University of Belgrade, Belgrade, SerbiaUniversity of BelgradeBelgradeSerbia
- Serbian Academy of Sciences and Arts, Belgrade, SerbiaSerbian Academy of Sciences and ArtsBelgradeSerbia
| | - Ju-Hyeong Sohn
- Kunsan National University, Gunsan, Republic of KoreaKunsan National UniversityGunsanRepublic of Korea
| | - Jongok Lim
- Wonkwang University, Iksan, Republic of KoreaWonkwang UniversityIksanRepublic of Korea
| | - Hyojoong Kim
- Kunsan National University, Gunsan, Republic of KoreaKunsan National UniversityGunsanRepublic of Korea
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Ståhls G. Pelecocera ( Pelecocera) tricincta and Pelecocera ( Chamaesyrphus) caledonica (Diptera, Syrphidae) reared from Rhizopogon fungal host in Finland. Biodivers Data J 2024; 12:e118563. [PMID: 38655012 PMCID: PMC11035976 DOI: 10.3897/bdj.12.e118563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 04/02/2024] [Indexed: 04/26/2024] Open
Abstract
MtDNA COI barcodes have frequently been used in identification to associate an unknown life stage in insects with a known species. This study reports the discovery of hoverfly larvae in the fungal fruit bodies of Rhizopogonluteolus Fr. & Nordholm, 1817 in Finland. The identity of the larvae was firstly resolved using mtDNA COI barcodes generated from the larvae and tree-based identification confirming the species Pelecocera (Pelecocera) tricincta Meigen, 1822 and Pelecocera (Chamaesyrphus) caledonica (Collin, 1940) (Diptera, Syrphidae). Obtained pupae were reared into adult flies and produced the same two species. The morphological features of these mycophagous larvae are compared with those of other fungus-feeding hoverfly species. This study confirms Rhizopogonluteolus as fungal host for these Pelecocera species in the Western Palaearctic Region.
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Affiliation(s)
- Gunilla Ståhls
- Finnish Museum of Natural History Luomus, Helsinki, FinlandFinnish Museum of Natural History LuomusHelsinkiFinland
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Afifi MAM, Azab AM, Ali E, Ghazy A, El-Tabakh MAM. DNA barcoding, phylogeography and evolutionary dynamics of Chrysichthys auratus. Gene 2024; 917:148448. [PMID: 38583817 DOI: 10.1016/j.gene.2024.148448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 04/01/2024] [Accepted: 04/04/2024] [Indexed: 04/09/2024]
Abstract
This study embarked on an exploration into the genetic structure and evolutionary history of the Chrysichthys auratus species, leveraging PCR amplification, phylogenetic trees, and haplotype networks. Specific DNA segments were successfully amplified and visualized through electrophoresis. Newly obtained sequences were Bank into GenBank and given accession numbers (OR730807-OR730808-OR730809). The Neighbor-Joining method provided insights into the evolutionary relationships among taxa, further augmented by bootstrap values and the Tamura 3-parameter method. A comprehensive geographical haplotype network showcased pronounced genetic differentiation, especially between remote populations. Nonetheless, shared haplotypes between proximate regions indicated either ancestral genetic connections or ongoing gene flow. Employing the COI-DNA barcodes, an in-depth understanding of intra- and inter-populational genetic diversity was achieved. The study's findings unravel the intricate genetic landscape and evolutionary dynamics of C. auratus, offering novel perspectives into its demographic history across its vast native habitat.
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Affiliation(s)
| | - Ahmad Mosad Azab
- Zoology Department Faculty of Science for Boys, Alazhar University, Cairo, Egypt.
| | | | - Ahmed Ghazy
- Zoology Department Faculty of Science for Boys, Alazhar University, Cairo, Egypt.
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Vella A, Vella N. The First Report of Pennella (Crustacea: Copepoda) Infesting Stenella coeruleoalba Stranded in Malta: Morphological and Genetic Analyses. Animals (Basel) 2024; 14:1107. [PMID: 38612346 PMCID: PMC11010884 DOI: 10.3390/ani14071107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/20/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
Here, we document the stranding of a striped dolphin Stenella coeruleoalba (Meyen, 1833) (Mammalia: Delphinidae), which was found dead in Maltese waters in July 2020. The stranded dolphin exhibited a severe infestation of the mesoparasitic copepod, Pennella balaenoptera Koren and Danielssen, 1877 (Copepoda: Pennelidae). Parasites of this genus represent the largest known mesoparasites to infest cetaceans. Under normal circumstances, cetaceans may have a few P. balaenoptera individuals attached to them, but cetaceans with compromised health are more prone to heavy infestations. The identification of the parasite was accomplished through morphological and genetic analyses. This incident highlights the significance of monitoring mesoparasitic infestations, offering valuable insights into the health of cetacean populations and emphasizing the potential implications for conservation efforts in the region.
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Affiliation(s)
- Adriana Vella
- Conservation Biology Research Group, Department of Biology, University of Malta, MSD 2080 Msida, Malta
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Li P, Zhao Z, Li Z, Zeng R, Li W. Distinguishing features of Prunus humilis, P. japonica, P. pedunculata seeds and their adulterant based on DNA barcoding, morphological characterization, and chemical profiles. Fitoterapia 2024; 175:105942. [PMID: 38575088 DOI: 10.1016/j.fitote.2024.105942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 03/28/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024]
Abstract
Pruni Semen, the dried ripe seed of Prunus humilis, P. japonica, or P. pedunculata as recorded in the Chinese Pharmacopoeia, has been widely used in pharmaceutical and food industries. The adulteration of the marketed product with morphologically similar plants of the same genus has led to variable product quality and clinical effectiveness. This study systematically investigated the phylogenetic relationships, morphological traits, and chemical profiles of 37 Pruni Semen samples from planting bases, markets, and fields. DNA barcoding could successfully distinguish the genuine and counterfeit Pruni Semen, and the results indicated that there was almost no authentic Pruni Semen available in the market. The samples were divided into "big seed" (P. pedunculata and P. salicina seeds) and "small seed" (P. humilis, P. japonica, P. tomentosa, and P. avium seeds) categories based on morphology results. The notable discrepancy in the chemical characteristics of "big seed" and "small seed" was that "small seeds" were rich in flavonoids and low in amygdalin, whereas "big seeds" were the opposite. Furthermore, principal component analysis and clustered heatmap analysis verified the distinguishing features of "big seed" and "small seed" based on morphological and chemical characteristics. This study suggested that a combination of DNA barcoding and morphological and chemical characteristics can aid in the identification and quality evaluation of authentic and adulterated Pruni Semen. These findings may help standardize Pruni Semen available in the market and protect the rights and interests of customers.
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Affiliation(s)
- Ping Li
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China; Engineering Research Center of Standardized production of traditional Chinese Medicine, Ministry of Education, Beijing 102488, China
| | - Zihan Zhao
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China; National Resource Center for Chinese Materia medica, China academy of Chinese medical sciences, Beijing 100700, China
| | - Zongshuo Li
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Rong Zeng
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing 100029, China
| | - Weidong Li
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 102488, China; Engineering Research Center of Standardized production of traditional Chinese Medicine, Ministry of Education, Beijing 102488, China.
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Yeo D, Chan AHJ, Hiong KC, Ong J, Ng JY, Lim JM, Zhang W, Lim SR, Fernandez CJ, Wong AMS, Lee BPYH, Khoo MDY, Cheng TXW, Lim BTM, Yeo HHT, Tan MMQ, Sng WBG, Adam SS, Ang WF, How CB, Xie R, Wasser SK, Finch KN, Loo AHB, Yap HH, Leong CC, Er KBH. Uncovering the magnitude of African pangolin poaching with extensive nanopore DNA genotyping of seized scales. Conserv Biol 2024; 38:e14162. [PMID: 37551767 DOI: 10.1111/cobi.14162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/31/2023] [Accepted: 07/19/2023] [Indexed: 08/09/2023]
Abstract
Trade in pangolins is illegal, and yet tons of their scales and products are seized at various ports. These large seizures are challenging to process and comprehensively genotype for upstream provenance tracing and species identification for prosecution. We implemented a scalable DNA barcoding pipeline in which rapid DNA extraction and MinION sequencing were used to genotype a substantial proportion of pangolin scales subsampled from 2 record shipments seized in Singapore in 2019 (37.5 t). We used reference sequences to match the scales to phylogeographical regions of origin. In total, we identified 2346 cytochrome b (cytb) barcodes of white-bellied (Phataginus tricuspis) (from 1091 scales), black-bellied (Phataginus tetradactyla) (227 scales), and giant (Smutsia gigantea) (1028 scales) pangolins. Haplotype diversity was higher for P. tricuspis scales (121 haplotypes, 66 novel) than that for P. tetradactyla (22 haplotypes, 15 novel) and S. gigantea (25 haplotypes, 21 novel) scales. Of the novel haplotypes, 74.2% were likely from western and west-central Africa, suggesting potential resurgence of poaching and newly exploited populations in these regions. Our results illustrate the utility of extensively subsampling large seizures and outline an efficient molecular approach for rapid genetic screening that should be accessible to most forensic laboratories and enforcement agencies.
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Affiliation(s)
- Darren Yeo
- Centre for Wildlife Forensics, National Parks Board, Singapore
| | - Amy H J Chan
- Centre for Wildlife Forensics, National Parks Board, Singapore
| | - Kum Chew Hiong
- Centre for Wildlife Forensics, National Parks Board, Singapore
| | - Jasmine Ong
- Centre for Wildlife Forensics, National Parks Board, Singapore
| | - Jun Yuan Ng
- Centre for Wildlife Forensics, National Parks Board, Singapore
| | - Jie Min Lim
- School of Life Sciences & Chemical Technology, Ngee Ann Polytechnic, Singapore, Singapore
| | - Wendy Zhang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Sara R Lim
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | | | - Anna M-S Wong
- Centre for Wildlife Forensics, National Parks Board, Singapore
| | | | - Max D Y Khoo
- Centre for Wildlife Forensics, National Parks Board, Singapore
| | | | - Bryan T M Lim
- Centre for Wildlife Forensics, National Parks Board, Singapore
| | | | - Maxine M Q Tan
- Centre for Wildlife Forensics, National Parks Board, Singapore
| | - Wendy B G Sng
- Centre for Wildlife Forensics, National Parks Board, Singapore
| | - Shaun S Adam
- Centre for Wildlife Forensics, National Parks Board, Singapore
| | - Wee Foong Ang
- Centre for Wildlife Forensics, National Parks Board, Singapore
| | - Choon Beng How
- Centre for Wildlife Forensics, National Parks Board, Singapore
| | - Renhui Xie
- Centre for Wildlife Forensics, National Parks Board, Singapore
| | - Samuel K Wasser
- Department of Biology, Center for Environmental Forensic Science, University of Washington, Seattle, Washington, USA
| | - Kristen N Finch
- Department of Biology, Center for Environmental Forensic Science, University of Washington, Seattle, Washington, USA
| | - Adrian H B Loo
- Centre for Wildlife Forensics, National Parks Board, Singapore
| | - Him Hoo Yap
- Centre for Wildlife Forensics, National Parks Board, Singapore
| | | | - Kenneth B H Er
- Centre for Wildlife Forensics, National Parks Board, Singapore
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Banerjee P, Dey G, Maity JP, Stewart KA, Sharma RK, Chan MWY, Lee K, Chen C. The unseen invaders: Tracking phylogeographic dynamics and genetic diversity of cryptic Pomacea canaliculata and P. maculata (Golden apple snails) across Taiwan. Ecol Evol 2024; 14:e11268. [PMID: 38646006 PMCID: PMC11027011 DOI: 10.1002/ece3.11268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 03/28/2024] [Accepted: 04/02/2024] [Indexed: 04/23/2024] Open
Abstract
The cryptic invasion of golden apple snails (Pomacea canaliculata and P. maculata) in Taiwan has caused significant ecological and economical damage over the last few decades, however, their management remains difficult due to inadequate taxonomic identification, complex phylogeny, and limited population genetic information. We aim to understand the current distribution, putative population of origin, genetic diversity, and potential path of cryptic invasion of Pomacea canaliculata and P. maculata across Taiwan to aid in improved mitigation approaches. The present investigation conducted a nationwide survey with 254 samples collected from 41 locations in 14 counties or cities across Taiwan. We identified P. canaliculata and P. maculata based on mitochondrial COI and compared their genetic diversity across Taiwan, as well as other introduced and native countries (based on publicly available COI data) to understand the possible paths of invasion to Taiwan. Based on mitochondrial COI barcoding, sympatric and heterogeneous distributions of invasive P. canaliculata and P. maculata were noted. Our haplotype analysis and mismatch distribution results suggested multiple introductions of P. canaliculata in Taiwan was likely originated directly from Argentina, whereas P. maculata was probably introduced from a single, or a few, introduction event(s) from Argentina and Brazil. Our population genetic data further demonstrated a higher haplotype and genetic diversity for P. canaliculata and P. maculata in Taiwan compared to other introduced regions. Based on our current understanding, the establishment of P. canaliculata and P. maculata is alarming and widespread beyond geopolitical borders, requiring a concerted and expedited national and international invasive species mitigation program.
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Affiliation(s)
- Pritam Banerjee
- Department of Environmental Science, Policy and ManagementUniversity of CaliforniaBerkeleyCaliforniaUSA
- Department of Biomedical SciencesGraduate Institute of Molecular Biology, National Chung Cheng UniversityMin‐HsiungChiayi CountyTaiwan
| | - Gobinda Dey
- Department of Biomedical SciencesGraduate Institute of Molecular Biology, National Chung Cheng UniversityMin‐HsiungChiayi CountyTaiwan
- Department of Agricultural ChemistryNational Taiwan UniversityTaipeiTaiwan
| | - Jyoti Prakash Maity
- Environmental Science Laboratory, Department of Chemistry, Biological Laboratory, School of Applied SciencesKIIT Deemed to be UniversityBhubaneswarOdishaIndia
| | - Kathryn A. Stewart
- Institute of Environmental Sciences, Leiden UniversityLeidenThe Netherlands
| | - Raju Kumar Sharma
- Doctoral Program in Science, Technology, Environment and Mathematics, Department of Earth and Environmental SciencesNational Chung Cheng UniversityMin‐HsiungChiayi CountyTaiwan
| | - Michael W. Y. Chan
- Department of Biomedical SciencesGraduate Institute of Molecular Biology, National Chung Cheng UniversityMin‐HsiungChiayi CountyTaiwan
| | - Kuanhsuen Lee
- Department of Emergency MedicineDitmanson Medical Foundation Chia‐Yi Christian HospitalChiayiTaiwan
| | - Chien‐Yen Chen
- Department of Earth and Environmental SciencesNational Chung Cheng UniversityMin‐HsiungChiayi CountyTaiwan
- Center for Nano Bio‐Detection, Center for Innovative Research on Aging SocietyAIM‐HI, National Chung Cheng UniversityChiayiTaiwan
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Cardinali I, Ceccarelli M. Molecular and cytogenetic analyses in Geranium macrorrhizum L. wild Italian plants. R Soc Open Sci 2024; 11:240035. [PMID: 38601032 PMCID: PMC11004676 DOI: 10.1098/rsos.240035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/07/2024] [Accepted: 03/08/2024] [Indexed: 04/12/2024]
Abstract
Geranium macrorrhizum L. is a herbaceous species native to southern Europe and was introduced in central Europe and North America. It is also widely distributed in Italy. In this study, molecular and cytogenetic analyses were carried out on 22 wild plants, collected in central and southern Italy, compared with five cultivated plants, with the main purpose to identify those living near the Marmore waterfalls in central Italy, recently described as the new species Geranium lucarinii. Four barcoding markers (rbcL, matK, trnH-psbA intergenic spacer and internal transcribed spacer region) were sequenced and their variability among the plants was evaluated. Chromosome numbers were determined and 45S rDNA was physically mapped by fluorescence in situ hybridization. Moreover, genomic affinity between wild and cultivated plants was evaluated by genomic in situ hybridization. The results of this study supported that all the plants belong to G. macrorrhizum, including the Marmore population. Barcoding analyses showed a close similarity among the wild plants, and a differentiation, although not significant, between the wild plants on one hand and the cultivated plants on the other. Integrated studies focusing on morphological, genetic and ecological characterization of a larger number of wild populations would allow us to know the extent of the variability within the species.
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Affiliation(s)
- Irene Cardinali
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia06123, Italy
| | - Marilena Ceccarelli
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia06123, Italy
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12
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Lan X, Wang J, Zhang M, Zhou Q, Xiang H, Jiang W. Molecular Identification of Acrossocheilus jishouensis (Teleostei: Cyprinidae) and Its Complete Mitochondrial Genome. Biochem Genet 2024; 62:1396-1412. [PMID: 37620638 DOI: 10.1007/s10528-023-10501-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 08/09/2023] [Indexed: 08/26/2023]
Abstract
Molecular identification, such as DNA barcoding, is a useful tool that is widely applied in distinguishing species. To identify the cyprinid Acrossocheilus jishouensis, which was previously known to be restricted to only its type locality, we conducted molecular identification of this species based on 23 samples in five localities. Molecular identification based on the mitochondrial COI gene sequence showed that the morphologically similar samples from the five populations were all A. jishouensis, as the mean genetic distances between populations were very small (0.1-1.6%); thus, the distribution of this species was substantially expanded. The whole mitochondrial genome of one sample was also assembled, which was 16,594 bp in length and consisted of 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes, and one control region. All PCGs began with ATG except the COI gene, which started with GTG; seven PCGs used the complete stop codon TAA, while four terminated in T(AA) and two ended with TAG. The overall base composition reflected a higher proportion of A+T than G+C and a positive AT-skew and negative GC-skew pattern except for the opposite in ND6. Phylogenetic relationships inferred using BI and ML methods revealed that both Acrossocheilus and Onychostoma were nonmonophyletic, which indicated that the traditional diagnoses between these two genera need to be assessed further. The results of this study not only expanded the known distribution ranges of A. jishouensis, but also provided a valuable data resource for future molecular and evolutionary studies of Acrossocheilus and other cyprinids in Barbinae.
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Affiliation(s)
- Xiangying Lan
- Hunan Engineering Laboratory for Chinese Giant Salamander's Resource Protection and Comprehensive Utilization, and Key Laboratory of Hunan Forest Products and Chemical Industry Engineering, National and Local United Engineering Laboratory of Integrative Utilization Technology of Eucommia Ulmoides, Jishou University, Zhangjiajie, China
- College of Biology and Environmental Sciences, Jishou University, Jishou, China
| | - Jinxiu Wang
- Hunan Engineering Laboratory for Chinese Giant Salamander's Resource Protection and Comprehensive Utilization, and Key Laboratory of Hunan Forest Products and Chemical Industry Engineering, National and Local United Engineering Laboratory of Integrative Utilization Technology of Eucommia Ulmoides, Jishou University, Zhangjiajie, China
- College of Biology and Environmental Sciences, Jishou University, Jishou, China
| | - Mingyao Zhang
- Hunan Engineering Laboratory for Chinese Giant Salamander's Resource Protection and Comprehensive Utilization, and Key Laboratory of Hunan Forest Products and Chemical Industry Engineering, National and Local United Engineering Laboratory of Integrative Utilization Technology of Eucommia Ulmoides, Jishou University, Zhangjiajie, China
- College of Biology and Environmental Sciences, Jishou University, Jishou, China
| | - Qiang Zhou
- Hunan Engineering Laboratory for Chinese Giant Salamander's Resource Protection and Comprehensive Utilization, and Key Laboratory of Hunan Forest Products and Chemical Industry Engineering, National and Local United Engineering Laboratory of Integrative Utilization Technology of Eucommia Ulmoides, Jishou University, Zhangjiajie, China
- College of Biology and Environmental Sciences, Jishou University, Jishou, China
| | - Hongmei Xiang
- Hunan Engineering Laboratory for Chinese Giant Salamander's Resource Protection and Comprehensive Utilization, and Key Laboratory of Hunan Forest Products and Chemical Industry Engineering, National and Local United Engineering Laboratory of Integrative Utilization Technology of Eucommia Ulmoides, Jishou University, Zhangjiajie, China
| | - Wansheng Jiang
- Hunan Engineering Laboratory for Chinese Giant Salamander's Resource Protection and Comprehensive Utilization, and Key Laboratory of Hunan Forest Products and Chemical Industry Engineering, National and Local United Engineering Laboratory of Integrative Utilization Technology of Eucommia Ulmoides, Jishou University, Zhangjiajie, China.
- College of Biology and Environmental Sciences, Jishou University, Jishou, China.
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Kim CJ, Tan JL, Kim JK, Choi MB. Confirmation of the valid specific status of Dolichovespulakuami Kim & Yoon, 1996 (Hymenoptera, Vespidae) based on molecular and morphological evidence. Zookeys 2024; 1196:111-119. [PMID: 38560091 PMCID: PMC10980876 DOI: 10.3897/zookeys.1196.110224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 02/15/2024] [Indexed: 04/04/2024] Open
Abstract
The taxonomic validity of Dolichovespulakuami, especially in relation to D.flora, has been the subject of a long-term debate. Herein, the valid specific status of the former was supported through an integrated analysis of morphological characters and DNA barcodes. The pronotal rugae and male genitalia of the two species are different, and partial mitochondrial genes (cytochrome oxidase subunit I, COI) indicate that they form significantly distinct lineages. The hitherto unknown male of D.kuami is described for the first time, and a brief discussion of the D.maculata species group is provided.
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Affiliation(s)
- Chang-Jun Kim
- Division of Gardens and Education, Korea National Arboretum, Pocheon, 11186, Republic of KoreaKorea National ArboretumPocheonRepublic of Korea
| | - Jiang-Li Tan
- Key Laboratory for Animal Conservation / Key Laboratory of Resource Biology and Biotechnology in Western China, College of Life Sciences, Northwest University, Xi’an, Shaanxi 710069, ChinaNorthwest UniversityXi'anChina
| | - Jeong Kyu Kim
- Department of Bio Environment Health, Dongnam Health University, Suwon, 16328, Republic of KoreaDongnam Health UniversitySuwonRepublic of Korea
| | - Moon Bo Choi
- Institute of Plant Medicine, Kyungpook National University, Daegu, 41566, Republic of KoreaKyungpook National UniversityDaeguRepublic of Korea
- Department of R&D, Wild Beei, Chilgok, 39864, Republic of KoreaDepartment of R&D, Wild BeeiChilgokRepublic of Korea
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Wojciechowska D, Salamon S, Wróblewska-Seniuk K. It's time to shed some light on the importance of fungi in neonatal intensive care units: what do we know about the neonatal mycobiome? Front Microbiol 2024; 15:1355418. [PMID: 38567073 PMCID: PMC10985264 DOI: 10.3389/fmicb.2024.1355418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 03/08/2024] [Indexed: 04/04/2024] Open
Abstract
The 21st century, thanks to the development of molecular methods, including DNA barcoding, using Sanger sequencing, and DNA metabarcoding, based on next-generation sequencing (NGS), is characterized by flourishing research on the human microbiome. Microbial dysbiosis is perceived as a new pathogenetic factor for neonatal diseases. Fungi are crucial, but neglected, components of the neonatal microbiome, which, despite their low abundance, significantly impact morbidity and mortality rates of premature infants hospitalized in Neonatal Intensive Care Units (NICUs). The neonatal mycobiome's composition and effect on health remain poorly studied research areas. Our knowledge about neonatal mycobiome, composed of limited genera, is mainly based on research on the bacterial microbiome. We presume it is influenced by clinical factors, including prematurity, antibiotic therapy, and type of delivery. Understanding these risk factors may be useful in prevention strategies against dysbiosis and invasive fungal infections. Despite the methodological challenges resulting from the biology of the fungal cell, this topic is an attractive area of research that may contribute to more effective treatment, especially of newborns from risk groups. In this mini review, we discuss the current state of knowledge, research gaps, study difficulties, and future research directions on the neonatal mycobiome, concerning potential future clinical applications.
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Affiliation(s)
- Dobrochna Wojciechowska
- II Department of Neonatology, Poznan University of Medical Sciences, Poznan, Poland
- Doctoral School, Poznan University of Medical Sciences, Poznan, Poland
| | - Sylwia Salamon
- Department of Plant Microbiomics, Institute of Plant Genetics, Academy of Sciences, Poznan, Poland
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Chan KT, Wu HY, Tin WY, But PPH, Cheung SCH, Shaw PC. Ethnopharmacology of five flowers herbal tea, a popular traditional beverage in Hong Kong and South China. J Ethnobiol Ethnomed 2024; 20:36. [PMID: 38491512 PMCID: PMC10943788 DOI: 10.1186/s13002-024-00674-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 03/06/2024] [Indexed: 03/18/2024]
Abstract
BACKGROUND It has been a long-standing tradition of using herbal tea for preventive and therapeutic healthcare in Hong Kong and South China and Five Flowers Tea is one of the most popular herbal teas. Based on the principle of traditional Chinese medicine, the pharmacological functions are to clear heat and dispel dampness in the body. Heat and dampness are thought to contribute to a range of health problems, especially during the hot and humid season in South China and Hong Kong. The most prevalent herbs in the formula contain bioactive compounds including flavonoids, alkaloids and terpenoids, which have a wide range of pharmacological properties including anti-inflammation, antivirus, antidiarrhoea, antibacteria, and antioxidation. However, with the composition varies widely, the ethnopharmacological benefits described may not be delivered uniformly. This study is to provide a comprehensive analysis on the composition of the Five Flowers Tea sold in Hong Kong and investigate the rationale behind the selection of herbs used in the formula. This study also provides information on the variation and quality of the Five Flowers Tea in the market. METHODS Thirty-three Five Flowers Tea samples were collected from various locations in Hong Kong. The size, texture, colour and organoleptic properties were documented. Macroscopic and molecular authentication methods were employed to identify the individual components. RESULTS Macroscopic identification revealed there were 23 herbs belonging to 18 plant families. The most prevalent herb was Bombax ceiba L., followed by Chrysanthemum morifolium. Ten adulterants and the existence of insect Lasioderma serricorne were confirmed by DNA barcoding techniques. CONCLUSION This study employed a comprehensive approach to authenticate the herbs in Five Flowers Tea samples collected from various locations in Hong Kong. Macroscopic and molecular methods were used to identify the herbs and adulterants. The findings revealed the varied composition in Five Flowers Tea and the occurrence of adulterants in some samples. This shows that quality assurance of Five Flowers Tea is essential for the effective use of this popular folk medicine.
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Affiliation(s)
- Kwun-Tin Chan
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Hoi-Yan Wu
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Wing-Yee Tin
- Institute of Future Cities, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Paul Pui-Hay But
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | | | - Pang-Chui Shaw
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
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Vargas HA. On Ypsolopha micromoths (Lepidoptera, Ypsolophidae) associated with Adesmia shrubs (Fabaceae) in the arid western slope of the central Andes. Zookeys 2024; 1195:131-138. [PMID: 38525354 PMCID: PMC10958161 DOI: 10.3897/zookeys.1195.116134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/21/2024] [Indexed: 03/26/2024] Open
Abstract
Ypsolopha Latreille, 1796 (Lepidoptera, Ypsolophidae) is a genus comprised mostly of Holarctic micromoth species with a fairly broad range of larval hosts (e.g. Aceraceae, Rosaceae, and Fagaceae). The only previous record of herbivory on a representative of the South American genus Adesmia DC. (Fabaceae) was based on the discovery of Ypsolophamoltenii Vargas, 2018 larvae feeding on Adesmiaverrucosa Meyen in the Andes of northern Chile. Further surveys revealed Adesmiaatacamensis Phil. as another host for Y.moltenii, and Adesmiaspinosissima Meyen as the single host of Ypsolopha sp. The genetic distance between DNA barcodes of the two micromoth species was 7.9-8.1% (K2P). These results suggest narrow host ranges for Adesmia-feeding Ypsolopha and highlight the need to further explore the taxonomic diversity of these micromoths in other South American environments.
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Affiliation(s)
- Héctor A. Vargas
- Departamento de Recursos Ambientales, Facultad de Ciencias Agronómicas, Universidad de Tarapacá, Arica, ChileUniversidad de TarapacáAricaChile
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Kim S, Sohn J, Kim H. Two new records of the genus Trioxys (Hymenoptera, Braconidae, Aphidiinae) parasitic on bamboo aphids from South Korea. Biodivers Data J 2024; 12:e118599. [PMID: 38524900 PMCID: PMC10958183 DOI: 10.3897/bdj.12.e118599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 02/29/2024] [Indexed: 03/26/2024] Open
Abstract
Background The genus Trioxys Haliday, 1833 consists of more than 80 species worldwide with three species being recorded in South Korea. In this study, we report the first observation of the two additional species, T.liui Chou & Chou, 1993 from Takecallisarundinariae (Essig, 1917) on Phyllostachysbambusoides Siebold & Zucc., 1843 and T.remaudierei Starý & Rakhshani, 2017 from T.taiwana (Takahashi, 1926) on Sasaborealis (Hack.) Makino & Shibata, 1901. New information Trioxysliui and T.remaudierei are described and reported with phototographs of the diagnostic morphological characters and the mitochondrial cytochrome c oxidase subunit I (COI) data (barcode region) and Bayesian tree of the phylogenetic analysis amongst the closely-related taxa are provided.
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Affiliation(s)
- Sangjin Kim
- Kunsan National University, Gunsan, Republic of KoreaKunsan National UniversityGunsanRepublic of Korea
| | - Juhyeong Sohn
- Kunsan National University, Gunsan, Republic of KoreaKunsan National UniversityGunsanRepublic of Korea
| | - Hyojoong Kim
- Kunsan National University, Gunsan, Republic of KoreaKunsan National UniversityGunsanRepublic of Korea
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Schols R, Smitz N, Vanderheyden A, Huyse T. Expanding the swimmer's itch pool of the Benelux: a first record of the neurotropic Trichobilharzia regenti and potential link to human infection. Parasit Vectors 2024; 17:126. [PMID: 38481352 PMCID: PMC10938770 DOI: 10.1186/s13071-024-06218-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 02/27/2024] [Indexed: 03/17/2024] Open
Abstract
BACKGROUND Swimmer's itch, an allergic contact dermatitis caused by avian and mammalian blood flukes, is a parasitic infection affecting people worldwide. In particular, avian blood flukes of the genus Trichobilharzia are infamous for their role in swimmer's itch cases. These parasites infect waterfowl as a final host, but incidental infections by cercariae in humans are frequently reported. Upon accidental infections of humans, parasite larvae will be recognized by the immune system and destroyed, leading to painful itchy skin lesions. However, one species, Trichobilharzia regenti, can escape this response in experimental animals and reach the spinal cord, causing neuroinflammation. In the last few decades, there has been an increase in case reports across Europe, making it an emerging zoonosis. METHODS Following a reported case of swimmer's itch in Kampenhout in 2022 (Belgium), the transmission site consisting of a private pond and an adjacent creek was investigated through a malacological and parasitological survey. RESULTS Six snail species were collected, including the widespread Ampullaceana balthica, a well-known intermediate host for Trichobilharzia parasites. Shedding experiments followed by DNA barcoding revealed a single snail specimen to be infected with T. regenti, a new species record for Belgium and by extension the Benelux. Moreover, it is the most compelling case to date of the link between this neurotropic parasite and cercarial dermatitis. Additionally, an Echinostomatidae sp. and Notocotylus sp. were isolated from two other specimens of A. balthica. However, the lack of reference DNA sequences for these groups in the online repositories prevented genus- and species-level identification, respectively. CONCLUSIONS The presence of T. regenti in Belgium might have severe clinical implications and its finding highlights the need for increased vigilance and diagnostic awareness among medical professionals. The lack of species-level identification of the other two parasite species showcases the barcoding void for trematodes. Overall, these findings demonstrate the need for a Belgian framework to rapidly detect and monitor zoonotic outbreaks of trematode parasites within the One Health context.
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Affiliation(s)
- Ruben Schols
- Department of Biology & BopCo, Royal Museum for Central Africa, Tervuren, Belgium.
- Laboratory of Aquatic Biology, KU Leuven, Campus Kortrijk, Kortrijk, Belgium.
| | - Nathalie Smitz
- Department of Biology & BopCo, Royal Museum for Central Africa, Tervuren, Belgium
| | - Ann Vanderheyden
- BopCo, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Tine Huyse
- Department of Biology & BopCo, Royal Museum for Central Africa, Tervuren, Belgium
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Hou JW, Xu Y, Hu TH, Zhang ZH, Wu SY, Gong P, He ZQ. A new species of Svistella Gorochov, 1987 from Xizang, China (Orthoptera, Trigonidiidae, Trigonidiinae). Zookeys 2024; 1193:145-160. [PMID: 38487668 PMCID: PMC10938059 DOI: 10.3897/zookeys.1193.117612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 02/01/2024] [Indexed: 03/17/2024] Open
Abstract
The genus Svistella Gorochov, 1987 includes 10 species from Asia, with nine documented in China. In this study, a new species, Svistellayayun He, sp. nov., is described from Xizang, China. Morphologically, it resembles S.rufonotata (Chopard, 1932) but can be distinguished by a smaller inner tympanum, dark-brown setae on the 5th segment of the maxillary palp, and a rounded apex on the ectoparamere. To validate our morphological inferences and support the description of S.yayunsp. nov. as a new species, we performed a PCA based on bioacoustics parameters and molecular analysis. All Svistella species documented in China are distinguished by integrating their songs and DNA barcoding.
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Affiliation(s)
- Jing-Wen Hou
- School of Life Science, East China Normal University, Shanghai 200241, ChinaEast China Normal UniversityShanghaiChina
| | - Yue Xu
- School of Life Science, East China Normal University, Shanghai 200241, ChinaEast China Normal UniversityShanghaiChina
| | - Tian-Hao Hu
- School of Life Science, East China Normal University, Shanghai 200241, ChinaEast China Normal UniversityShanghaiChina
| | - Zi-Heng Zhang
- School of Life Science, East China Normal University, Shanghai 200241, ChinaEast China Normal UniversityShanghaiChina
| | - Shi-Yang Wu
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, USAUniversity of CaliforniaBerkeleyUnited States of America
| | - Pu Gong
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang, 310051, ChinaZhejiang Provincial Center for Disease Control and PreventionHangzhouChina
| | - Zhu-Qing He
- School of Life Science, East China Normal University, Shanghai 200241, ChinaEast China Normal UniversityShanghaiChina
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Lonare N, Patil G, Waghmare S, Bhor R, Hardikar H, Tembe S. DNA Barcoding of Invasive Terrestrial Plant Species in India. Mol Biotechnol 2024:10.1007/s12033-024-01102-z. [PMID: 38430432 DOI: 10.1007/s12033-024-01102-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 01/31/2024] [Indexed: 03/03/2024]
Abstract
Invasive plants are known to cause biodiversity loss and pose a major risk to human health and environment. Identification of invasive plants and distinguishing them from native species has been relied on morphological examination. Stringent requirement of floral characters and decreasing number of expert taxonomists are making conventional morphology-based identification system tedious and resource-intensive. DNA barcoding may help in quick identification of invasive species if distinct sequence divergence pattern at various taxonomic levels is observed. The present work evaluates the utility of four molecular markers; rbcL, matK, their combination (rbcL + matK), and psbA-trnH for identification of 37 invasive plant species from India and also in distinguishing them from 97 native species. A psbA-trnH locus was found to be of restricted utility in this work as it was represented by the members of a single family. A hierarchical increase in K2P mean divergence across different taxonomic levels was found to be the maximum for matK alone followed by rbcL + matK and rbcL alone, respectively. NJ clustering analysis, however, confirmed the suitability of combined locus (rbcL + matK) over individual rbcL and matK as the DNA barcode. RbcL showed the lowest resolution power among the three markers studied. MatK exhibited much better performance compared to rbcL alone in identifying most of the species accurately although it failed to show monophyly of genus Dinebra. Two families; Asteraceae and Poaceae, remained polyphyletic in the trees constructed by all three markers. Combined locus (rbcL + matK) was found to be the most suitable marker as it raised the resolution power of both the markers and could identify more than 90% of genera correctly. Phylogenetic tree constructed by Maximum-Parsimony method using combined locus as a molecular marker exhibited the best resolution, thus, supporting the significance of two-locus combination of rbcL + matK for barcoding invasive plant species from India. Present study contributes to the global barcode data of invasive plant species by adding fifty-one new sequences to it. Effective barcoding of additional number of native as well as invasive plant species from India is possible using this dual locus if it is combined with one or more new molecular plastid markers. Expansion of barcode database with a focus on barcode performance optimisation to improve discrimination ability at species level can be undertaken in future.
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Affiliation(s)
- Nayan Lonare
- Department of Biotechnology, Fergusson College (Autonomous), Shivajinagar, Pune, Maharashtra, 411004, India
| | - Gayatri Patil
- Department of Biotechnology, Fergusson College (Autonomous), Shivajinagar, Pune, Maharashtra, 411004, India
| | - Suprriya Waghmare
- IMT Technologies Pvt. Ltd, Kondhwa Khurd, Pune, Maharashtra, 411048, India
| | - Reshma Bhor
- IMT Technologies Pvt. Ltd, Kondhwa Khurd, Pune, Maharashtra, 411048, India
| | - Hrishikesh Hardikar
- Department of Biotechnology, Fergusson College (Autonomous), Shivajinagar, Pune, Maharashtra, 411004, India
| | - Sanket Tembe
- Department of Biotechnology, Fergusson College (Autonomous), Shivajinagar, Pune, Maharashtra, 411004, India.
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Minami M, Tanaka R, Mori T, Fujii T, Tsuchida T. Identification of Angelica acutiloba, A. sinensis, and other Chinese medicinal Apiaceae plants by DNA barcoding. J Nat Med 2024:10.1007/s11418-024-01796-0. [PMID: 38427209 DOI: 10.1007/s11418-024-01796-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 02/25/2024] [Indexed: 03/02/2024]
Abstract
Crude drug Angelicae acutilobae radix is one of the most important crude drugs in Japanese traditional medicine and is used mainly for the treatment of gynecological disorders. In the listing in the Japanese Pharmacopoeia XVIII, Angelicae acutilobae radix is defined as the root of Angelica acutiloba (Apiaceae), which has long been produced on an industrial scale in Japan. With the aging of farmers and depopulation of production areas, the domestic supply has recently declined and the majority of the supply is now imported from China. Due to having only slightly different morphological and chemical characteristics for the Apiaceae roots used to produce dried roots for Chinese medicines, the plant species originating the crude drug Apiaceae roots may be incorrectly identified. In particular, Angelicae sinensis radix, which is widely used in China, and Angelicae acutilobae radix are difficult to accurately identify by morphology and chemical profiles. Thus, in order to differentiate among Angelicae acutilobae radix and other radixes originated from Chinese medicinal Apiaceae plants, we established DNA markers. Using DNA sequences for the chloroplast psbA-trnH intergenic spacer and nuclear internal transcribed spacer regions, Angelicae acutilobae radix and other Chinese Apiaceae roots, including Angelicae sinensis radix, can be definitively identified.
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Affiliation(s)
- Motoyasu Minami
- College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501, Japan.
| | - Ryusaku Tanaka
- College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501, Japan
| | - Takako Mori
- College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501, Japan
| | - Taichi Fujii
- College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501, Japan
| | - Takashi Tsuchida
- Central R&D Laboratory, Kobayashi Pharmaceutical Co., Ltd, 1-30-3 Toyokawa, Ibaraki, Osaka, 567-0057, Japan
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Dufresnes C, Monod-Broca B, Bellati A, Canestrelli D, Ambu J, Wielstra B, Dubey S, Crochet PA, Denoël M, Jablonski D. Piecing the barcoding puzzle of Palearctic water frogs (Pelophylax) sheds light on amphibian biogeography and global invasions. Glob Chang Biol 2024; 30:e17180. [PMID: 38465701 DOI: 10.1111/gcb.17180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/04/2024] [Accepted: 01/11/2024] [Indexed: 03/12/2024]
Abstract
Palearctic water frogs (genus Pelophylax) are an outstanding model in ecology and evolution, being widespread, speciose, either threatened or threatening to other species through biological invasions, and capable of siring hybrid offspring that escape the rules of sexual reproduction. Despite half a century of genetic research and hundreds of publications, the diversity, systematics and biogeography of Pelophylax still remain highly confusing, in no small part due to a lack of correspondence between studies. To provide a comprehensive overview, we gathered >13,000 sequences of barcoding genes from >1700 native and introduced localities and built multigene mitochondrial (~17 kb) and nuclear (~10 kb) phylogenies. We mapped all currently recognized taxa and their phylogeographic lineages (>40) to get a grasp on taxonomic issues, cyto-nuclear discordances, the genetic makeup of hybridogenetic hybrids, and the origins of introduced populations. Competing hypotheses for the molecular calibration were evaluated through plausibility tests, implementing a new approach relying on predictions from the anuran speciation continuum. Based on our timetree, we propose a new biogeographic paradigm for the Palearctic since the Paleogene, notably by attributing a prominent role to the dynamics of the Paratethys, a vast paleo-sea that extended over most of Europe. Furthermore, our results show that distinct marsh frog lineages from Eastern Europe, the Balkans, the Near East, and Central Asia (P. ridibundus ssp.) are naturally capable of inducing hybridogenesis with pool frogs (P. lessonae). We identified 14 alien lineages (mostly of P. ridibundus) over ~20 areas of invasions, especially in Western Europe, with genetic signatures disproportionally pointing to the Balkans and Anatolia as the regions of origins, in line with exporting records of the frog leg industry and the stocks of pet sellers. Pelophylax thus emerges as one of the most invasive amphibians worldwide, and deserves much higher conservation concern than currently given by the authorities fighting biological invasions.
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Affiliation(s)
- Christophe Dufresnes
- Laboratory of Amphibian Systematics and Evolutionary Research (LASER), College of Biology and the Environment, Nanjing Forestry University, Nanjing, People's Republic of China
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Benjamin Monod-Broca
- Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, Villeurbanne, France
| | - Adriana Bellati
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Daniele Canestrelli
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Johanna Ambu
- Laboratory of Amphibian Systematics and Evolutionary Research (LASER), College of Biology and the Environment, Nanjing Forestry University, Nanjing, People's Republic of China
| | - Ben Wielstra
- Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Sylvain Dubey
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | | | - Mathieu Denoël
- Laboratory of Ecology and Conservation of Amphibians (LECA), FOCUS, University of Liège, Liège, Belgium
| | - Daniel Jablonski
- Department of Zoology, Comenius University in Bratislava, Bratislava, Slovakia
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23
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Gajski D, Wolff JO, Melcher A, Weber S, Prost S, Krehenwinkel H, Kennedy SR. Facilitating taxonomy and phylogenetics: An informative and cost-effective protocol integrating long amplicon PCRs and third-generation sequencing. Mol Phylogenet Evol 2024; 192:107988. [PMID: 38072140 DOI: 10.1016/j.ympev.2023.107988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/22/2023] [Accepted: 12/07/2023] [Indexed: 12/31/2023]
Abstract
Phylogenetic inference has become a standard technique in integrative taxonomy and systematics, as well as in biogeography and ecology. DNA barcodes are often used for phylogenetic inference, despite being strongly limited due to their low number of informative sites. Also, because current DNA barcodes are based on a fraction of a single, fast-evolving gene, they are highly unsuitable for resolving deeper phylogenetic relationships due to saturation. In recent years, methods that analyse hundreds and thousands of loci at once have improved the resolution of the Tree of Life, but these methods require resources, experience and molecular laboratories that most taxonomists do not have. This paper introduces a PCR-based protocol that produces long amplicons of both slow- and fast-evolving unlinked mitochondrial and nuclear gene regions, which can be sequenced by the affordable and portable ONT MinION platform with low infrastructure or funding requirements. As a proof of concept, we inferred a phylogeny of a sample of 63 spider species from 20 families using our proposed protocol. The results were overall consistent with the results from approaches based on hundreds and thousands of loci, while requiring just a fraction of the cost and labour of such approaches, making our protocol accessible to taxonomists worldwide.
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Affiliation(s)
- Domagoj Gajski
- Department of Biogeography, Faculty of Spatial and Environmental Sciences, University of Trier, Universitätsring 15, Trier 54296, Germany; Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno 611 37, Czech Republic
| | - Jonas O Wolff
- Evolutionary Biomechanics, Zoological Institute and Museum, University of Greifswald, Loitzer Str. 26, Greifswald 17489, Germany; School of Natural Sciences, Macquarie University, NSW 2109, Sydney, Australia
| | - Anja Melcher
- Department of Biogeography, Faculty of Spatial and Environmental Sciences, University of Trier, Universitätsring 15, Trier 54296, Germany
| | - Sven Weber
- Department of Biogeography, Faculty of Spatial and Environmental Sciences, University of Trier, Universitätsring 15, Trier 54296, Germany
| | - Stefan Prost
- Ecology and Genetics Research Unit, University of Oulu, Pentti Kaiteran katu 1, Linnanmaa, Finland
| | - Henrik Krehenwinkel
- Department of Biogeography, Faculty of Spatial and Environmental Sciences, University of Trier, Universitätsring 15, Trier 54296, Germany
| | - Susan R Kennedy
- Department of Biogeography, Faculty of Spatial and Environmental Sciences, University of Trier, Universitätsring 15, Trier 54296, Germany.
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24
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Rodrigues BL, da Silva Costa G, Godoy RE, Pereira Júnior AM, Cella W, Ferreira GEM, de Medeiros JF, Shimabukuro PHF. Molecular and morphometric study of Brazilian populations of Psychodopygus davisi. Med Vet Entomol 2024; 38:83-98. [PMID: 37867259 DOI: 10.1111/mve.12701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/06/2023] [Indexed: 10/24/2023]
Abstract
In this study, we analysed the molecular and morphometric differences of several populations of the putative sand fly vector Psychodopygus davisi (Root, 1934) (Diptera, Psychodidae, Phlebotominae) in Brazil. We amplified the 658 base pair fragments of the DNA barcoding region-cytochrome c oxidase subunit 1 (COI) gene-for 57 specimens of P. davisi and three specimens of Psychodopygus claustrei (Abonnenc, Léger & Fauran, 1979). We merged our data with public sequences of the same species available from GenBank. Then, the combined dataset-87 sequences and 20 localities-was analysed using population structure analysis and different species delimitation approaches. Geometric morphometry of wings was performed for 155 specimens of P. davisi populations from the North, Midwest and Southeast Brazilian regions, analysing the differences in centroid sizes and canonical variates. Molecular analysis indicated high intraspecific genetic distance values for P. davisi (maximum p distance = 5.52%). All algorithms identified P. davisi and P. claustrei as distinct molecular taxonomic units, despite the low interspecific distance (p distance to the nearest neighbour = 4.79%). P. davisi sequences were split into four genetic clusters by population structure analysis and at least five genetic lineages using intermediate scenarios of the species delimitation algorithms. The species validation analysis of BPP strongly supported the five-species model in our dataset. We found high genetic diversity in this taxon, which is in agreement with its wide geographic distribution in Brazil. Furthermore, the wing analysis showed that specimens from the Southeast Region of Brazil are different from those in the North and the Midwest. The evolutionary patterns of P. davisi populations in Brazil suggest the presence of candidate species, which need to be validated in future studies using a more comprehensive approach with both genomic data and morphological characters.
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Affiliation(s)
- Bruno Leite Rodrigues
- Programa de Pós-Graduação em Saúde Pública, Faculdade de Saúde Pública da Universidade de São Paulo (FSP/USP), São Paulo, Brazil
| | - Glaucilene da Silva Costa
- Programa de Pós-Graduação em Biologia Experimental, Fundação Universidade Federal de Rondônia, Porto Velho, Brazil
- Laboratório Central de Saúde Pública do Estado de Rondônia, LACEN-RO, Porto Velho, Brazil
| | | | | | - Wilsandrei Cella
- Programa de Pós Graduação em Ciência Animal com Ênfase em Produtos Bioativos, Universidade Paranaense, Paraná, Brazil
- Universidade do Estado do Amazonas (UEA), Tefé, Brazil
| | - Gabriel Eduardo Melim Ferreira
- Programa de Pós-Graduação em Biologia Experimental, Fundação Universidade Federal de Rondônia, Porto Velho, Brazil
- Laboratório de Epidemiologia Genética, Fiocruz Rondônia, Porto Velho, Brazil
| | - Jansen Fernandes de Medeiros
- Programa de Pós-Graduação em Biologia Experimental, Fundação Universidade Federal de Rondônia, Porto Velho, Brazil
- Laboratório de Entomologia, Fiocruz Rondônia, Porto Velho, Brazil
| | - Paloma Helena Fernandes Shimabukuro
- Grupo de Estudos em Leishmanioses, Instituto René Rachou, Fiocruz Minas, Belo Horizonte, Brazil
- Coleção de Flebotomíneos (Fiocruz/COLFLEB), Instituto René Rachou, Fiocruz Minas, Belo Horizonte, Brazil
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25
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Victor BC, Frable BW, Ludt WB. Halichoeres sanchezi n. sp., a new wrasse from the Revillagigedo Archipelago of Mexico, tropical eastern Pacific Ocean (Teleostei: Labridae). PeerJ 2024; 12:e16828. [PMID: 38436023 PMCID: PMC10908266 DOI: 10.7717/peerj.16828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/04/2024] [Indexed: 03/05/2024] Open
Abstract
A new labrid fish species, Halichoeres sanchezi n. sp., is described from eight specimens collected in the Revillagigedo Archipelago in the tropical eastern Pacific Ocean, off the coast of Mexico. The new species belongs to the Halichoeres melanotis species complex that is found throughout the region, differing by 2.4% in the mtDNA cytochrome c oxidase I sequence from its nearest relative, H. melanotis from Panama, and 2.9% from Halichoeres salmofasciatus from Cocos Island, off Costa Rica. The complex is distinguished from others in the region by having a black spot on the opercular flap and a prominent black area on the caudal fin of males. The juveniles and initial phase of the new species closely resemble those of H. salmofasciatus and Halichoeres malpelo from Malpelo Island of Colombia, differing in having an oblong black spot with a yellow dorsal margin on the mid-dorsal fin of initial-phase adults as well as on juveniles. In contrast, the terminal-phase male color pattern is distinct from other relatives, being vermilion to orangish brown with dark scale outlines, a white patch on the upper abdomen, and a prominent black band covering the posterior caudal peduncle and base of the caudal fin. The new species adds to the list of endemic fish species for the isolated archipelago and is an interesting case of island endemism in the region. The discovery was made during the joint 2022 collecting expedition to the archipelago, which featured a pioneering collaborative approach to an inventory of an island ichthyofauna, specifically including expert underwater photographers systematically documenting specimens in situ, before hand-collection, and then photographed fresh, tissue-sampled, and subsequently vouchered in museum collections.
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Affiliation(s)
- Benjamin C. Victor
- Guy Harvey Research Institute, Nova Southeastern University, Dania Beach, Florida, United States
- Marine Biology, Ocean Science Foundation, Irvine, California, United States
| | - Benjamin W. Frable
- Marine Vertebrate Collection, Scripps Institution of Oceanography, La Jolla, California, United States
| | - William B. Ludt
- Ichthyology, Natural History Museum of Los Angeles County, Los Angeles, California, United States
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26
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Braglia L, Ceschin S, Iannelli MA, Bog M, Fabriani M, Frugis G, Gavazzi F, Gianì S, Mariani F, Muzzi M, Pelella E, Morello L. Characterization of the cryptic interspecific hybrid Lemna × mediterranea by an integrated approach provides new insights into duckweed diversity. J Exp Bot 2024:erae059. [PMID: 38387000 DOI: 10.1093/jxb/erae059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Indexed: 02/24/2024]
Abstract
Lemnaceae taxonomy is challenged by the particular morphology of these tiny free-floating angiosperms. Although molecular taxonomy has helped clarify the phylogenetic history of this family, some inconsistency with morphological data leads to frequent misclassifications in the genus Lemna. Recently, the finding that Lemna japonica is an interspecific hybrid between Lemna minor and Lemna turionifera, provided a clear explanation to one of such taxonomic questions. Here we demonstrated that L. minor is also capable to hybridize with Lemna gibba, generating a cryptic but widespread taxon in the Mediterranean area. The nothotaxon Lemna × mediterranea is described and compared with clones of the putative parental species L. minor and L. gibba. Genetic analysis by nuclear and plastid markers, as well as genome size measurement, revealed that two different cytotypes, diploid and triploid, originated by at least two independent hybridization events. Despite high overall similarity, morphometrical, physiological and biochemical analyses showed an intermediate position of L. × mediterranea between its parental species in most qualitative and quantitative characters, and also separation of the two hybrid cytotypes by some criteria. These data provide evidence that hybridization and polyploidization, driving forces of terrestrial plant evolution, contribute to the duckweed genetic diversity and may have shaped the phylogenetic history of these mainly asexual, aquatic plants.
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Affiliation(s)
- Luca Braglia
- Institute of Agricultural Biology and Biotechnology, National Research Council, Via Bassini 15, 20133 Milan, Italy
| | - Simona Ceschin
- Department of Sciences University of Roma Tre, Viale G. Marconi 446, 00146 Rome, Italy Università Roma Tre, Italy
- NBFC -National Biodiversity Future Center, 90133 Palermo, Italy
| | - M Adelaide Iannelli
- Institute of Agricultural Biology and Biotechnology, National Research Council, Via Salaria Km. 29,300, 00015 Monterotondo, Roma, Italy
| | - Manuela Bog
- Institute of Botany and Landscape Ecology, University Greifswald, Soldmannstr. 15, 17489 Greifswald, Germany
| | - Marco Fabriani
- Institute of Agricultural Biology and Biotechnology, National Research Council, Via Salaria Km. 29,300, 00015 Monterotondo, Roma, Italy
| | - Giovanna Frugis
- Institute of Agricultural Biology and Biotechnology, National Research Council, Via Salaria Km. 29,300, 00015 Monterotondo, Roma, Italy
| | - Floriana Gavazzi
- Institute of Agricultural Biology and Biotechnology, National Research Council, Via Bassini 15, 20133 Milan, Italy
| | - Silvia Gianì
- Institute of Agricultural Biology and Biotechnology, National Research Council, Via Bassini 15, 20133 Milan, Italy
| | - Flaminia Mariani
- Department of Sciences University of Roma Tre, Viale G. Marconi 446, 00146 Rome, Italy Università Roma Tre, Italy
| | - Maurizio Muzzi
- Department of Sciences University of Roma Tre, Viale G. Marconi 446, 00146 Rome, Italy Università Roma Tre, Italy
| | - Emanuele Pelella
- Department of Sciences University of Roma Tre, Viale G. Marconi 446, 00146 Rome, Italy Università Roma Tre, Italy
| | - Laura Morello
- Institute of Agricultural Biology and Biotechnology, National Research Council, Via Bassini 15, 20133 Milan, Italy
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27
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Kirichenko NI, Ageev AA, Astapenko SA, Golovina AN, Kasparyan DR, Kosheleva OV, Timokhov AV, Tselikh EV, Zakharov EV, Musolin DL, Belokobylskij SA. The Diversity of Parasitoids and Their Role in the Control of the Siberian Moth, Dendrolimus sibiricus (Lepidoptera: Lasiocampidae), a Major Coniferous Pest in Northern Asia. Life (Basel) 2024; 14:268. [PMID: 38398777 PMCID: PMC10890493 DOI: 10.3390/life14020268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
The Siberian moth, Dendrolimus sibiricus Tschetv., 1908 (Lepidoptera: Lasiocampidae) is a conifer pest that causes unprecedented forest mortality in Northern Asia, leading to enormous ecological and economic losses. This is the first study summarizing data on the parasitoid diversity and parasitism of this pest over the last 118 years (1905-2022). Based on 860 specimens of freshly reared and archival parasitoids, 16 species from two orders (Hymenoptera and Diptera) were identified morphologically and/or with the use of DNA barcoding. For all of them, data on distribution and hosts and images of parasitoid adults are provided. Among them, the braconid species, Meteorus versicolor (Wesmael, 1835), was documented as a parasitoid of D. sibiricus for the first time. The eastern Palaearctic form, Aleiodes esenbeckii (Hartig, 1838) dendrolimi (Matsumura, 1926), status nov., was resurrected from synonymy as a valid subspecies, and a key for its differentiation from the western Palaearctic subspecies Aleiodes esenbeckii ssp. esenbecki is provided. DNA barcodes of 11 parasitoid species from Siberia, i.e., nine hymenopterans and two dipterans, represented novel records and can be used for accurate molecular genetic identification of species. An exhaustive checklist of parasitoids accounting for 93 species associated with D. sibirisus in northern Asia was compiled. Finally, the literature and original data on parasitism in D. sibiricus populations for the last 83 years (1940-2022) were analysed taking into account the pest population dynamics (i.e., growth, outbreak, decline, and depression phases). A gradual time-lagged increase in egg and pupal parasitism in D. sibiricus populations was detected, with a peak in the pest decline phase. According to long-term observations, the following species are able to cause significant mortality of D. sibiricus in Northern Asia: the hymenopteran egg parasitoids Telenomus tetratomus and Ooencyrtus pinicolus; the larval parasitoids Aleiodes esenbeckii sp. dendrolimi, Cotesia spp., and Glyptapanteles liparidis; and the dipteran pupal parasitoids Masicera sphingivora, Tachina sp., and Blepharipa sp. Their potential should be further explored in order to develop biocontrol programs for this important forest pest.
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Affiliation(s)
- Natalia I. Kirichenko
- Federal Research Center, Sukachev Institute of Forest, Siberian Branch of the Russian Academy of Sciences, Akademgorodok 50/28, 660036 Krasnoyarsk, Russia
- Institute of Ecology and Geography, Siberian Federal University, Svobodny pr. 79, 660041 Krasnoyarsk, Russia
- All-Russian Plant Quarantine Center (FGBU VNIIKR), Krasnoyarsk Branch, Zhelyabova Str., 6/6, 660020 Krasnoyarsk, Russia
| | - Alexander A. Ageev
- All-Russian Research Institute of Forestry and Forestry Mechanization (VNIILM), “Forest Pyrology Center”, Krasnoyarsk Branch, Krupskoy St., 42, 660062 Krasnoyarsk, Russia; (A.A.A.); (S.A.A.); (A.N.G.)
| | - Sergey A. Astapenko
- All-Russian Research Institute of Forestry and Forestry Mechanization (VNIILM), “Forest Pyrology Center”, Krasnoyarsk Branch, Krupskoy St., 42, 660062 Krasnoyarsk, Russia; (A.A.A.); (S.A.A.); (A.N.G.)
- Federal Budgetary Institution “Russian Forest Protection Center”, Akademgorodok 50/2, 660036 Krasnoyarsk, Russia
| | - Anna N. Golovina
- All-Russian Research Institute of Forestry and Forestry Mechanization (VNIILM), “Forest Pyrology Center”, Krasnoyarsk Branch, Krupskoy St., 42, 660062 Krasnoyarsk, Russia; (A.A.A.); (S.A.A.); (A.N.G.)
| | - Dmitry R. Kasparyan
- Zoological Institute of the Russian Academy of Sciences, Universitetskaya nab. 1, 199034 Saint Petersburg, Russia; (D.R.K.); (E.V.T.)
| | - Oksana V. Kosheleva
- All-Russian Institute of Plant Protection (FSBSI VIZR), Podbelskogo 3, 196608 Saint Petersburg, Russia;
| | - Alexander V. Timokhov
- Department of Entomology, Lomonosov Moscow State University, Leninskie Gory, 119234 Moscow, Russia;
| | - Ekaterina V. Tselikh
- Zoological Institute of the Russian Academy of Sciences, Universitetskaya nab. 1, 199034 Saint Petersburg, Russia; (D.R.K.); (E.V.T.)
| | - Evgeny V. Zakharov
- Canadian Center for DNA Barcoding, Centre for Biodiversity Genomics, College of Biological Sciences, University of Guelph, 50 Stone Road, Guelph, ON N1G 2W1, Canada;
| | - Dmitrii L. Musolin
- European and Mediterranean Plant Protection Organization, 21 Boulevard Richard Lenoir, 75011 Paris, France;
| | - Sergey A. Belokobylskij
- Zoological Institute of the Russian Academy of Sciences, Universitetskaya nab. 1, 199034 Saint Petersburg, Russia; (D.R.K.); (E.V.T.)
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28
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Li QQ, Yao WW, Zhang K, Wang ZQ, Che YL. Six new species of Margattea Shelford, 1911 (Blaberoidea, Pseudophyllodromiidae, Neoblattellini) from China. Zookeys 2024; 1191:339-367. [PMID: 38405678 PMCID: PMC10892154 DOI: 10.3897/zookeys.1191.113147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 01/12/2024] [Indexed: 02/27/2024] Open
Abstract
Six Margattea species are established and described: three are cryptic species, namely, M.parabisignata Li & Che, sp. nov., M.semicircularis Li & Che, sp. nov., and M.forcipata Li & Che, sp. nov. They are distinguished from known species M.bisignata, M.spinifera, and M.paratransversa by their male genitalia with the aid of molecular species delimitation method (ABGD) using COI as the molecular marker. The other three new species are M.pedata Li & Che, sp. nov., M.undulata Li & Che, sp. nov., and M.bisphaerica Li & Che, sp. nov. Morphological and genitalia photographs of these new species of Margattea, as well as a key to the species of Margattea from China, are provided.
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Affiliation(s)
- Qian-Qian Li
- College of Plant Protection, Southwest University, Beibei, Chongqing 400715, ChinaSouthwest UniversityChongqingChina
| | - Wen-Wen Yao
- College of Plant Protection, Southwest University, Beibei, Chongqing 400715, ChinaSouthwest UniversityChongqingChina
| | - Ke Zhang
- College of Plant Protection, Southwest University, Beibei, Chongqing 400715, ChinaSouthwest UniversityChongqingChina
| | - Zong-Qing Wang
- College of Plant Protection, Southwest University, Beibei, Chongqing 400715, ChinaSouthwest UniversityChongqingChina
| | - Yan-Li Che
- College of Plant Protection, Southwest University, Beibei, Chongqing 400715, ChinaSouthwest UniversityChongqingChina
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29
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Cornalba M, Quaranta M, Selis M, Flaminio S, Gamba S, Mei M, Bonifacino M, Cappellari A, Catania R, Niolu P, Tempesti S, Biella P. Exploring the hidden riches: Recent remarkable faunistic records and range extensions in the bee fauna of Italy (Hymenoptera, Apoidea, Anthophila). Biodivers Data J 2024; 12:e116014. [PMID: 38405380 PMCID: PMC10892157 DOI: 10.3897/bdj.12.e116014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 12/29/2023] [Indexed: 02/27/2024] Open
Abstract
Background The area sourrounding the Mediterranean basin is recognised as a major biodiversity hotspot for bees, and Italy is amongst the European countries with the highest bee species richness. Detailed knowledge of bee distribution is crucial for understanding bee biology and designing tailored conservation strategies, but is still insufficient in southern European countries, especially in Italy. New information We report recent finds of 48 bee species that yield significant novelties for the Italian bee fauna. Eight species, namely Andrenaconfinis Stöckhert, Anthidiellumbreviusculum Pérez, Coelioxysalatus Foerster, Lasioglossumalgericolellum Strand, Megachilelapponica Thomson, Megachileopacifrons Pérez, Megachilesemicircularis auct. nec Zanden and Trachusaintegra Eversmann are reported as new for Italy. In addition, Andrenabinominata Smith, Andrenacompta Lepeletier, Colletesacutus Pérez, Lasioglossumstrictifrons Vachal, Rhodanthidiumsiculum Spinola and Rhodanthidiumsticticum Fabricius are newly recorded from mainland Italy, Osmiaheteracantha Pérez from Sardegna and Nomadaflavopicta Kirby from Sicilia. We also report significant range extensions for other bee species and recent records of species that had long gone unrecorded in Italy. The combination of morphology and DNA barcoding provided reliable identifications even for the most challenging specimens. As several of our records come from areas neglected by bee experts in the past, this study stands out as a key indicator of a bee faunistic richness still awaiting discovery and hopefully it will stimulate the interest of taxonomists and stakeholders in pursuing bee research in Italy in the near future.
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Affiliation(s)
- Maurizio Cornalba
- Department of Mathematics, University of Pavia, Pavia, ItalyDepartment of Mathematics, University of PaviaPaviaItaly
| | - Marino Quaranta
- Centro di Ricerca Agricoltura e Ambiente, (CREA) Consiglio per la Ricerca in Agricoltura e l’analisi dell’Economia Agraria, Bologna, ItalyCentro di Ricerca Agricoltura e Ambiente, (CREA) Consiglio per la Ricerca in Agricoltura e l’analisi dell’Economia AgrariaBolognaItaly
| | - Marco Selis
- Via dei Tarquini, Viterbo, ItalyVia dei TarquiniViterboItaly
| | - Simone Flaminio
- Centro di Ricerca Agricoltura e Ambiente, (CREA) Consiglio per la Ricerca in Agricoltura e l’analisi dell’Economia Agraria, Bologna, ItalyCentro di Ricerca Agricoltura e Ambiente, (CREA) Consiglio per la Ricerca in Agricoltura e l’analisi dell’Economia AgrariaBolognaItaly
- Laboratory of Zoology, Research Institute for Biosciences, University of Mons, Monsa, BelgiumLaboratory of Zoology, Research Institute for Biosciences, University of MonsMonsaBelgium
| | - Sirio Gamba
- Strada Sanferian, San Biagio della Cima (Imperia), ItalyStrada SanferianSan Biagio della Cima (Imperia)Italy
| | - Maurizio Mei
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Rome, ItalyDepartment of Biology and Biotechnology “Charles Darwin”, Sapienza University of RomeRomeItaly
| | - Marco Bonifacino
- Department of Biology, University of Florence, Sesto Fiorentino, ItalyDepartment of Biology, University of FlorenceSesto FiorentinoItaly
| | - Andree Cappellari
- Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova, Padova, ItalyDepartment of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE), University of PadovaPadovaItaly
| | - Roberto Catania
- Department of Agriculture, Food and Environment (Di3A), sec. Applied Entomology, Catania, ItalyDepartment of Agriculture, Food and Environment (Di3A), sec. Applied EntomologyCataniaItaly
| | - Pietro Niolu
- Via Sassari, Alghero, ItalyVia SassariAlgheroItaly
| | - Stefano Tempesti
- Via Vincenzo Bellini, Santa Sofia (Forlì-Cesena), ItalyVia Vincenzo BelliniSanta Sofia (Forlì-Cesena)Italy
| | - Paolo Biella
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, ItalyDepartment of Biotechnology and Biosciences, University of Milano-BicoccaMilanoItaly
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30
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Seniczak S, Seniczak A, Jordal BH. Morphological Ontogeny, Ecology, and Biogeography of Fuscozetes fuscipes (Acari, Oribatida, Ceratozetidae). Animals (Basel) 2024; 14:538. [PMID: 38396506 PMCID: PMC10885992 DOI: 10.3390/ani14040538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
The systematic status of Fuscozetes Sellnick, 1928, is not clear in the literature. Therefore, the morphological ontogeny of F. fuscipes (C.L. Koch, 1844), the type species of this genus, was investigated and compared with its congeners in this study, and a new diagnosis of Fuscozetes is given. The juveniles of F. fuscipes are light brown, with a brown prodorsum, sclerites, epimeres, and legs. In all juveniles, a humeral organ and a humeral macrosclerite are present. The gastronotum of the larva has 12 pairs of setae (h3 is present), whereas the nymphs have 15 pairs. In the larva, the gastronotal shield is weakly developed, and most gastronotal setae are short except for a slightly longer h2. Most of the gastronotal setae are inserted on the microsclerites except for h3, and several other macrosclerites and many microsclerites are present on the hysterosoma. In the nymphs, the gastronotal shield is well developed, with 10 pairs of setae (d-, l-, and h-series, and p1), and setae p2 and p3 are located on a large posteroventral macrosclerite. In all the instars, femora I and II are oval in cross-section, without a large ventral carina. Mitochondrial COI sequence data revealed a deep split between the Nearctic and Palearctic populations of F. fuscipes, and a less, but significant, divergence within each continent. These strong geographical barriers were contrasted with multiple cases of shared haplotypes over long distances in the Palearctic, indicating high migration rates in modern times.
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Affiliation(s)
- Stanisław Seniczak
- Department of Evolutionary Biology, Faculty of Biological Sciences, Kazimierz Wielki University, 85-093 Bydgoszcz, Poland;
| | - Anna Seniczak
- Faculty of Applied Ecology, Agricultural Sciences and Biotechnology, Inland Norway University of Applied Sciences, 2318 Elverum, Norway
| | - Bjarte H. Jordal
- University Museum of Bergen, University of Bergen, 5007 Bergen, Norway;
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Mück F, Scotti F, Mauvisseau Q, Thorbek BLG, Wangensteen H, de Boer HJ. Three-tiered authentication of herbal traditional Chinese medicine ingredients used in women's health provides progressive qualitative and quantitative insight. Front Pharmacol 2024; 15:1353434. [PMID: 38375033 PMCID: PMC10875096 DOI: 10.3389/fphar.2024.1353434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 01/16/2024] [Indexed: 02/21/2024] Open
Abstract
Traditional Chinese Medicine (TCM) herbal products are increasingly used in Europe, but prevalent authentication methods have significant gaps in detection. In this study, three authentication methods were tested in a tiered approach to improve accuracy on a collection of 51 TCM plant ingredients obtained on the European market. We show the relative performance of conventional barcoding, metabarcoding and standardized chromatographic profiling for TCM ingredients used in one of the most diagnosed disease patterns in women, endometriosis. DNA barcoding using marker ITS2 and chromatographic profiling are methods of choice reported by regulatory authorities and relevant national pharmacopeias. HPTLC was shown to be a valuable authentication tool, combined with metabarcoding, which gives an increased resolution on species diversity, despite dealing with highly processed herbal ingredients. Conventional DNA barcoding as a recommended method was shown to be an insufficient tool for authentication of these samples, while DNA metabarcoding yields an insight into biological contaminants. We conclude that a tiered identification strategy can provide progressive qualitative and quantitative insight in an integrative approach for quality control of processed herbal ingredients.
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Affiliation(s)
- Felicitas Mück
- Section for Pharmaceutical Chemistry, Department of Pharmacy, University of Oslo, Oslo, Norway
| | - Francesca Scotti
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College London, London, United Kingdom
| | | | | | - Helle Wangensteen
- Section for Pharmaceutical Chemistry, Department of Pharmacy, University of Oslo, Oslo, Norway
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Jamonneau T, Dahruddin H, Limmon G, Sukmono T, Busson F, Nurjirana, Gani A, Patikawa J, Wuniarto E, Sauri S, Nurhaman U, Wowor D, Steinke D, Keith P, Hubert N. Jump dispersal drives the relationship between micro- and macroevolutionary dynamics in the Sicydiinae (Gobiiformes: Oxudercidae) of Sundaland and Wallacea. J Evol Biol 2024:voae017. [PMID: 38306450 DOI: 10.1093/jeb/voae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Indexed: 02/04/2024]
Abstract
Insular biodiversity hotspots of Southeast Asia are remarkable for their biodiverse faunas. With a marine larval phase lasting up to several months, the freshwater fish subfamily Sicydiinae has colonized most islands of these hotspots. However, Sicydiinae diversity is still poorly understood in Southeast Asia. With the objective to estimate intraspecific genetic diversity and infer past demography, we conducted the molecular inventory of Sicydiinae species in Sundaland and Wallacea using 652 bp of the mitochondrial cytochrome oxidase I gene, species delimitation methods and Bayesian Skyline plot reconstructions. In total, 24 Molecular Operational Taxonomic Units are delimited among the 603 sequences belonging to 27 species and five genera. Two cases of discordance between morphology and mitochondrial sequence are observed suggesting ongoing speciation and/or introgression in two genera. Multiple new occurrences are reported, either for a single biodiversity hotspot or both, some of which corresponding to observations of a few individuals far from the range distribution of their conspecifics. Among the ten species or species group whose intraspecific diversity was examined, high levels of genetic diversity and past population expansion are revealed by Tajima's D tests and Bayesian Skyline Plot reconstructions. Together these results indicate that long-distance dispersal is common and suggest that most endemic species originated through founder events followed by population expansion. Patterns of sexual dimorphism and males' coloration among diverging species pair seem to point to sexual selection as an important mechanism contributing to speciation in the Sicydiinae of Sundaland and Wallacea.
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Affiliation(s)
- Tom Jamonneau
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier cedex 05, France
| | - Hadi Dahruddin
- Research Center for Biosystematics and Evolution, National Research and Innovation Agency, Cibinong Science Center, Jl. Raya Jakarta - Bogor Km 46, Cibinong, West Java, Indonesia
| | - Gino Limmon
- Universitas Pattimura, Maritime and Marine Science Center of Excellence, Jalan Wim Reawaru 9C, 678267 Ambon, Moluccas, Indonesia
| | - Tedjo Sukmono
- Universitas Jambi, Department of Biology, Jalan Lintas Jambi - Muara Bulian Km15, 36122 Jambi, Sumatra, Indonesia
| | - Frédéric Busson
- UMR 7208 BOREA (MNHN, CNRS, UPMC, IRD, UCBN), Muséum National d'Histoire Naturelle, 43 rue Cuvier, 75231 Paris cedex 05, France
| | - Nurjirana
- Research Center for Biosystematics and Evolution, National Research and Innovation Agency, Cibinong Science Center, Jl. Raya Jakarta - Bogor Km 46, Cibinong, West Java, Indonesia
| | - Abdul Gani
- Universitas Luwuk Muhammadiyah, Department of Biology, Jalan KH Ahmad Dahlan, 94712 Luwuk, Silawesi, Indonesia
| | - Jesaya Patikawa
- Universitas Pattimura, Maritime and Marine Science Center of Excellence, Jalan Wim Reawaru 9C, 678267 Ambon, Moluccas, Indonesia
| | - Erwin Wuniarto
- Universitas Luwuk Muhammadiyah, Department of Biology, Jalan KH Ahmad Dahlan, 94712 Luwuk, Silawesi, Indonesia
| | - Sopian Sauri
- Research Center for Biosystematics and Evolution, National Research and Innovation Agency, Cibinong Science Center, Jl. Raya Jakarta - Bogor Km 46, Cibinong, West Java, Indonesia
| | - Ujang Nurhaman
- Research Center for Biosystematics and Evolution, National Research and Innovation Agency, Cibinong Science Center, Jl. Raya Jakarta - Bogor Km 46, Cibinong, West Java, Indonesia
| | - Daisy Wowor
- Research Center for Biosystematics and Evolution, National Research and Innovation Agency, Cibinong Science Center, Jl. Raya Jakarta - Bogor Km 46, Cibinong, West Java, Indonesia
| | - Dirk Steinke
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Rd E, Guelph, ON N1G2W1, Canada
| | - Philippe Keith
- UMR 7208 BOREA (MNHN, CNRS, UPMC, IRD, UCBN), Muséum National d'Histoire Naturelle, 43 rue Cuvier, 75231 Paris cedex 05, France
| | - Nicolas Hubert
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier cedex 05, France
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Bhooma V, Vassou SL, Kaliappan I, Parani M. Identification of adulteration in the market samples of saffron using morphology, HPLC, HPTLC, and DNA barcoding methods. Genome 2024; 67:43-52. [PMID: 37922517 DOI: 10.1139/gen-2022-0059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2023]
Abstract
Saffron, the stigma of Crocus sativus L., is the most expensive spice used for culinary, medicinal, dye, and cosmetics purposes. It is highly adulterated because of its limited production and high commercial value. In this study, 104 saffron market samples collected from 16 countries were tested using morphology, high-performance liquid chromatography (HPLC), high-performance thin-layer chromatography (HPTLC), and deoxyribonucleic acid (DNA) barcoding. Overall, 45 samples (43%) were adulterated. DNA barcoding identified the highest number of adulterated saffron (44 samples), followed by HPTLC (39 samples), HPLC (38 samples), and morphology (32 samples). Only DNA barcoding identified the adulterated samples containing saffron and other plants' parts as bulking agents. In addition, DNA barcoding identified 20 adulterant plant species, which will help develop quality control methods and market surveillance. Some of the adulterant plants are unsafe for human consumption. The HPLC method helped identify the saffron samples adulterated with synthetic safranal. HPLC and HPTLC methods will help identify the samples adulterated with other parts of the saffron plant (auto-adulteration).
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Affiliation(s)
- Varadharajan Bhooma
- Center for DNA Barcoding, Department of Genetic Engineering, College of Engineering and Technology, Faculty of Engineering and Technology, , SRM Institute of Science and Technology, SRM Nagar, Kattankulathur 603203, Kanchipuram, Chennai, TN, India
| | - Sophie Lorraine Vassou
- Center for DNA Barcoding, Department of Genetic Engineering, College of Engineering and Technology, Faculty of Engineering and Technology, , SRM Institute of Science and Technology, SRM Nagar, Kattankulathur 603203, Kanchipuram, Chennai, TN, India
| | - Ilango Kaliappan
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur 603203, Kanchipuram, Chennai, TN, India
| | - Madasamy Parani
- Center for DNA Barcoding, Department of Genetic Engineering, College of Engineering and Technology, Faculty of Engineering and Technology, , SRM Institute of Science and Technology, SRM Nagar, Kattankulathur 603203, Kanchipuram, Chennai, TN, India
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Salam MR, Ezaouine A, Zekhnini H, El Messal M, El Mellouli F, Chegdani F, Bennis F. Morphological, molecular identification and evaluation of antioxidant activity of seahorses from the Moroccan coasts. Saudi J Biol Sci 2024; 31:103898. [PMID: 38188538 PMCID: PMC10770750 DOI: 10.1016/j.sjbs.2023.103898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 12/03/2023] [Accepted: 12/08/2023] [Indexed: 01/09/2024] Open
Abstract
Seahorses, part of the small marine teleost fish family Syngnathidae, are increasingly under threat due to habitat degradation and overfishing. Notably used in traditional Chinese medicine, these fish have demonstrated significant pharmacological and cosmetic properties. In Morocco, however, seahorses are minimally exploited. This study aims to explore the biodiversity of Moroccan seahorses, focusing on identifying species from the Atlantic and Mediterranean coasts both morphologically and molecularly, and evaluating their antioxidant activity. The research involved collecting 62 dried seahorses from local fishermen. These specimens were subjected to detailed morphological and molecular identification through the DNA barcoding method, concentrating on the mitochondrial marker Cytochrome Oxidase I (COI) gene. Following DNA extraction and amplification, the sequences were analyzed for species identification and phylogenetic relationships. Additionally, the antioxidant activities of the seahorses were quantified using assays such as ABTS, reducing power, phosphomolybdenum, and β-carotene-linoleic acid. The combined morphological and molecular analyses consistently identified all specimens as Hippocampus hippocampus, and phylogenetic trees suggested a close relation with European and Turkish counterparts. Furthermore, the antioxidant assays revealed significant activity, with the ABTS assay showing an IC50 of 14.571 mg/mL ± 0.334, and the β-carotene-linoleic acid assay showing an IC50 of 1.273 mg/mL ± 0.166. The reducing power and phosphomolybdenum assays recorded EC50 values of 1.868 mg/mL ± 0.033 and 1.156 mg/mL ± 0.112, respectively. These results confirm the high antioxidant potential of Moroccan seahorses, suggesting their therapeutic value and necessitating measures for their biodiversity preservation at a national level.
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Affiliation(s)
- Mohamed Rida Salam
- Laboratory of Immunology and Biodiversity, Faculty of Sciences Aïn Chock, University Hassan II of Casablanca, Morocco
| | - Abdelkarim Ezaouine
- Laboratory of Immunology and Biodiversity, Faculty of Sciences Aïn Chock, University Hassan II of Casablanca, Morocco
| | - Hasnae Zekhnini
- Laboratory of Immunology and Biodiversity, Faculty of Sciences Aïn Chock, University Hassan II of Casablanca, Morocco
- National Office for Food Safety (ONSSA), Regional Laboratory for Analysis and Research of Casablanca, Casablanca, Morocco
| | - Mariame El Messal
- Laboratory of Immunology and Biodiversity, Faculty of Sciences Aïn Chock, University Hassan II of Casablanca, Morocco
| | - Fatiha El Mellouli
- National Office for Food Safety (ONSSA), Regional Laboratory for Analysis and Research of Casablanca, Casablanca, Morocco
| | - Fatima Chegdani
- Laboratory of Immunology and Biodiversity, Faculty of Sciences Aïn Chock, University Hassan II of Casablanca, Morocco
| | - Faiza Bennis
- Laboratory of Immunology and Biodiversity, Faculty of Sciences Aïn Chock, University Hassan II of Casablanca, Morocco
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Li D, Jin XH, Li Y, Wang YC, He HY, Zhang HB. Fungal communities associated with early immature tubers of wild Gastrodia elata. Ecol Evol 2024; 14:e11004. [PMID: 38389997 PMCID: PMC10881901 DOI: 10.1002/ece3.11004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 01/19/2024] [Accepted: 01/24/2024] [Indexed: 02/24/2024] Open
Abstract
Full myco-heterotrophic orchid Gastrodia elata Bl. is widely distributed in Northeast Asia, and previous research has not fully investigated the symbiotic fungal community of its early immature tubers. This study utilized Illumina sequencing to compare symbiotic fungal communities in natural G. elata immature tubers and their habitats. LEfSe (Linear Discriminant Analysis Effect Size) was used to screen for Biomarkers that could explain variations among different fungal communities, and correlation analyses were performed among Biomarkers and other common orchid mycorrhizal fungi. Our results illustrate that the symbiotic fungal communities of immature G. elata tubers cannot be simply interpreted as subsets of the environmental fungal communities because some key members cannot be traced back to the environment. The early growth of G. elata was related to a small group of fungi, such as Sebacina, Thelephora, and Inocybe, which were also common mycorrhizal fungi from other orchids. In addition, Mycena, Auricularia, and Cryptococcus were unique fungal partners of G. elata, and many new species have yet to be discovered. Possible symbiotic Mycena should be M. plumipes and its sibling species in this case. Our results provide insight into the symbiotic partner switch and trophic pattern change during the development and maturation of G. elata.
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Affiliation(s)
- Dong Li
- State Key Laboratory Conservation and Utilization of Bio-Resources in Yunnan Kunming China
- School of Ecology and Environmental Science Yunnan University Kunming China
| | - Xiao-Han Jin
- State Key Laboratory Conservation and Utilization of Bio-Resources in Yunnan Kunming China
- School of Ecology and Environmental Science Yunnan University Kunming China
| | - Yu Li
- State Key Laboratory Conservation and Utilization of Bio-Resources in Yunnan Kunming China
| | - Yu-Chuan Wang
- Gastrodia Tuber Research Institute of Zhaotong Zhaotong China
| | - Hai-Yan He
- The Agriculture and Life Sciences College Zhaotong University Zhaotong China
- Yunnan Key Laboratory of Gastrodia elata and Fungus Symbiotic Biology Zhaotong China
| | - Han-Bo Zhang
- State Key Laboratory Conservation and Utilization of Bio-Resources in Yunnan Kunming China
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Wei Z, Ren G. Review of the genus Laena Dejean, 1821 (Coleoptera, Tenebrionidae) from Gansu Province, China, with the description of a new species. Zookeys 2024; 1190:121-130. [PMID: 38304893 PMCID: PMC10831857 DOI: 10.3897/zookeys.1190.114201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/08/2024] [Indexed: 02/03/2024] Open
Abstract
A new species of the genus Laena from Xiaolongshan in Gansu Province, China is described as Laenahuisp. nov. All Laena species known to occur in Gansu Province are reviewed, and an identification key is provided. The mitochondrial gene COI to confirm the identity of the new species, which is morphologically most similar and phylogenetically close to L.fengileana. The new species can be recognized by features of elytra and tibiae.
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Affiliation(s)
- Zhonghua Wei
- The Key Laboratory of Southwest China Wildlife Resources Conservation of the Ministry of Education, College of Life Sciences, China West Normal University, 637009, Nanchong, Sichuan Province, ChinaChina West Normal UniversityNanchongChina
| | - Guodong Ren
- College of Life Sciences, Hebei University, 071002, Baoding, Hebei Province, ChinaHebei UniversityBaodingChina
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Cheng R, Luo A, Orr M, Ge D, Hou Z, Qu Y, Guo B, Zhang F, Sha Z, Zhao Z, Wang M, Shi X, Han H, Zhou Q, Li Y, Liu X, Shao C, Zhang A, Zhou X, Zhu C. Cryptic diversity begets challenges and opportunities in biodiversity research. Integr Zool 2024. [PMID: 38263700 DOI: 10.1111/1749-4877.12809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
How many species of life are there on Earth? This is a question that we want to know but cannot yet answer. Some scholars speculate that the number of species may reach 2.2 billion when considering cryptic diversity and that each morphology-based insect species may contain an average of 3.1 cryptic species. With nearly two million described species, such high estimates of cryptic diversity would suggest that cryptic species are widespread. The development of molecular species delimitation has led to the discovery of a large number of cryptic species, and cryptic biodiversity has gradually entered our field of vision and attracted more attention. This paper introduces the concept of cryptic species, how they evolve, and methods by which they may be discovered and confirmed, and provides theoretical and methodological guidance for the study of hidden species. A workflow of how to confirm cryptic species is provided. In addition, the importance and reliability of multi-evidence-based integrated taxonomy are reaffirmed as a way to better standardize decision-making processes. Special focus on cryptic diversity and increased funding for taxonomy is needed to ensure that cryptic species in hyperdiverse groups are discoverable and described. An increased focus on cryptic species in the future will naturally arise as more difficult groups are studied, and thereby, we may finally better understand the rules governing the evolution and maintenance of cryptic biodiversity.
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Affiliation(s)
- Rui Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Arong Luo
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Michael Orr
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Entomologie, Staatliches Museum für Naturkunde Stuttgart, Stuttgart, Germany
| | - Deyan Ge
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zhong'e Hou
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Baocheng Guo
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Feng Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Zhongli Sha
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Zhe Zhao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Mingqiang Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Xiaoyu Shi
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Hongxiang Han
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qingsong Zhou
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yuanning Li
- Institute of Oceanography, Shandong University, Qingdao, China
| | - Xingyue Liu
- Department of Entomology, China Agricultural University, Beijing, China
| | - Chen Shao
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Aibing Zhang
- College of Life Science, Capital Normal University, Beijing, China
| | - Xin Zhou
- Department of Entomology, China Agricultural University, Beijing, China
| | - Chaodong Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Integrated Pest Management, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences/International College, University of Chinese Academy of Sciences, Beijing, China
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Vargas HA. Argyrotaeniasocoromaensis sp. nov. (Lepidoptera, Tortricidae), a sexually dimorphic micromoth with polyphagous larvae from the arid Andes of northern Chile. Zookeys 2024; 1189:327-336. [PMID: 38314115 PMCID: PMC10836216 DOI: 10.3897/zookeys.1189.113678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 12/21/2023] [Indexed: 02/06/2024] Open
Abstract
Argyrotaeniasocoromaensissp. nov. (Lepidoptera, Tortricidae, Tortricinae, Archipini) from the arid Andes of northern Chile is described and illustrated. Adults are sexually dimorphic, with differences in wing size, shape and pattern. The larvae feed on Steviaphilippiana Hieron. (Asteraceae) and Lupinusoreophilus Phil. (Fabaceae). Genetic distance between DNA barcodes of male and female adults reared from larvae collected on the two hosts was 0-0.2% (K2P). The discovery of A.socoromaensissp. nov. represents the first record of the genus Argyrotaenia Stephens, 1852 and the tribe Archipini for the Chilean fauna of Tortricidae.
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Affiliation(s)
- Héctor A Vargas
- Departamento de Recursos Ambientales, Facultad de Ciencias Agronómicas, Universidad de Tarapacá, Arica, Chile Universidad de Tarapacá Arica Chile
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Zograf JK, Semenchenko AA, Mordukhovich VV. New deep-sea species of Aborjinia (Nematoda, Leptosomatidae) from the North-Western Pacific: an integrative taxonomy and phylogeny. Zookeys 2024; 1189:231-256. [PMID: 38282715 PMCID: PMC10809327 DOI: 10.3897/zookeys.1189.111825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 11/15/2023] [Indexed: 01/30/2024] Open
Abstract
Marimermithid nematodes parasitising invertebrates are mainly found in the deep-sea environments. Several adult and juvenile specimens marimermithids of the genus Aborjinia have been found in bottom sediments and inside Polychaeta during recent cruises to the Kuril-Kamchatka trench and the Kuril Basin (the Sea of Okhotsk). New species are described based on integrative study. Aborjiniaprofundasp. nov. differs from A.eulagiscae by the location of the ventral gland cell bodies (posterior to the nerve ring vs posterior to the cardia), by the smaller body size (23-28 mm vs 103-132 mm) and shorter tail (193-263 µm vs 500-850 µm). BI and ML phylogenetic analyses based on 18S and 28S rDNA suggest that genus Aborjinia belongs to the family Leptosomatidae. Based on molecular and morphological characters the new genus Paraborjiniagen. nov. is proposed for A.corallicola. Within the family Leptosomatidae the new genus differs from all genera except Aborjinia by its endoparasitic lifestyle and hologonic ovaries. Paraborjiniagen. nov. differs from Aborjinia by the position of cephalic sensitive organs (outer labial and cephalic papillae in two separate circles vs outer labial and cephalic papillae in one circle) and by the parasitic adult (vs free-living in Aborjinia).
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Affiliation(s)
- Julia K. Zograf
- A.V. Zhirmunsky National Scientific Center of Marine Biology, FEB RAS, 690041, Vladivostok, RussiaA.V. Zhirmunsky National Scientific Center of Marine BiologyVladivostokRussia
| | - Alexander A. Semenchenko
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, FEB RAS, 690022, Vladivostok, RussiaFederal Scientific Center of the East Asia Terrestrial BiodiversityVladivostokRussia
| | - Vladimir V. Mordukhovich
- A.V. Zhirmunsky National Scientific Center of Marine Biology, FEB RAS, 690041, Vladivostok, RussiaA.V. Zhirmunsky National Scientific Center of Marine BiologyVladivostokRussia
- Far Eastern Federal University, 690922, Vladivostok, RussiaFar Eastern Federal UniversityVladivostokRussia
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Schmid-Egger C, Schmidt S, Bogusch P. DNA Barcoding of Central European Gasteruptiidae and the rarely-collected families Evaniidae, Stephanidae, Trigonalidae, and Aulacidae (Hymenoptera, Apocrita). Zookeys 2024; 1189:275-286. [PMID: 38282716 PMCID: PMC10809266 DOI: 10.3897/zookeys.1189.114478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 12/15/2023] [Indexed: 01/30/2024] Open
Abstract
The study presents DNA barcoding results of five families of Hymenoptera in Germany. DNA barcodes are provided for 24 of the 25 species of Gasteruption occurring in Central Europe, including 18 of the 19 species recorded from Germany. The genetic diversity was higher than expected, with five species exhibiting two or more Barcode Index Number (BINs), whereas BIN sharing occurred in four species. Gasteruptionfoveiceps Semenov, 1892, stat. nov. is removed from synonymy with G.nigrescens Schletterer, 1885 and treated as a distinct species.
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Affiliation(s)
| | - Stefan Schmidt
- SNSB-Zoologische Staatssammlung München, Munich, GermanySNSB-Zoologische Staatssammlung MünchenMunichGermany
| | - Petr Bogusch
- University of Hradec Králové, Faculty of Science, Department of Biology, Hradec Králové, Czech RepublicUniversity of Hradec KrálovéHradec KrálovéCzech Republic
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Harris CM, Kim DY, Jordan CR, Miranda MI, Hellberg RS. DNA barcoding of herbal supplements on the US commercial market associated with the purported treatment of COVID-19. Phytochem Anal 2024. [PMID: 38225696 DOI: 10.1002/pca.3320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 11/17/2023] [Accepted: 12/17/2023] [Indexed: 01/17/2024]
Abstract
INTRODUCTION The COVID-19 pandemic was associated with an increased global use of traditional medicines, including Ayurvedic herbal preparations. Due to their growing demand, their processed nature, and the complexity of the global supply chain, there is an increased risk of adulteration in these products. OBJECTIVES The objective of this study was to assess the use of DNA barcoding for species identification in herbal supplements on the US market associated with the Ayurvedic treatment of respiratory symptoms. METHODS A total of 54 commercial products containing Ayurvedic herbs were tested with four DNA barcoding regions (i.e., rbcL, matK, ITS2, and mini-ITS2) using two composite samples per product. Nine categories of herbs were targeted: amla, ashwagandha, cinnamon, ginger, guduchi, tribulus, tulsi, turmeric, and vacha. RESULTS At least one species was identified in 64.8% of products and the expected species was detected in 38.9% of products. Undeclared plant species, including other Ayurvedic herbs, rice, and pepper, were detected in 19 products, and fungal species were identified in 12 products. The presence of undeclared plant species may be a result of intentional substitution or contamination during harvest or processing, while fungal DNA was likely associated with the plant material or the growing environment. The greatest sequencing success (42.6-46.3%) was obtained with the matK and rbcL primers. CONCLUSION The results of this study indicate that a combination of genetic loci should be used for DNA barcoding of herbal supplements. Due to the limitations of DNA barcoding in identification of these products, future research should incorporate chemical characterization techniques.
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Affiliation(s)
- Calin M Harris
- Chapman University, Schmid College of Science and Technology, Food Science Program, One University Drive, Orange, California, USA
| | - Diane Y Kim
- Chapman University, Schmid College of Science and Technology, Food Science Program, One University Drive, Orange, California, USA
| | - Chevon R Jordan
- Chapman University, Schmid College of Science and Technology, Food Science Program, One University Drive, Orange, California, USA
| | - Miranda I Miranda
- Chapman University, Schmid College of Science and Technology, Food Science Program, One University Drive, Orange, California, USA
| | - Rosalee S Hellberg
- Chapman University, Schmid College of Science and Technology, Food Science Program, One University Drive, Orange, California, USA
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Höcherl A, Shaw MR, Boudreault C, Rabl D, Haszprunar G, Raupach MJ, Schmidt S, Baranov V, Fernández-Triana J. Scratching the tip of the iceberg: integrative taxonomy reveals 30 new species records of Microgastrinae (Braconidae) parasitoid wasps for Germany, including new Holarctic distributions. Zookeys 2024; 1188:305-386. [PMID: 38250474 PMCID: PMC10797786 DOI: 10.3897/zookeys.1188.112516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 10/24/2023] [Indexed: 01/23/2024] Open
Abstract
Substantial parts of the European and German insect fauna still remain largely unexplored, the so-called "dark taxa". In particular, midges (Diptera) and parasitoid wasps (Hymenoptera) are abundant and species-rich throughout Europe, yet are often neglected in biodiversity research. One such dark taxon is Microgastrinae wasps (Hymenoptera: Braconidae), a group of parasitoids of lepidopteran caterpillars with 252 species reported in Germany so far. As part of the German Barcode of Life Project GBOL III: Dark Taxa, reverse DNA barcoding and integrative taxonomic approaches were used to shed some light on the German Fauna of Microgastrinae wasps. In our workflow, DNA barcoding was used for molecular clustering of our specimens in a first step, morphological examination of the voucher specimens in a second step, and host data compared in a third step. Here, 30 species are reported for the first time in Germany, adding more than 10% to the known German fauna. Information for four species is provided in a new Holarctic context, reporting them for the Nearctic or, respectively, Palaearctic region, and 26 additional country records are added from sequenced material available in the collections accessible to us. Molecular clusters that show signs of discrepancies are discussed. Results show that we are just scratching the tip of the iceberg of the unexplored Microgastrinae diversity in Germany.
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Affiliation(s)
- Amelie Höcherl
- SNSB-Zoologische Staatssammlung München, Münchhausenstr. 21, 81247 München, GermanySNSB-Zoologische Staatssammlung MünchenMünchenGermany
| | - Mark R. Shaw
- National Museums of Scotland, Chambers Street, Edinburgh EH1 1JF, UKNational Museums of ScotlandEdinburghUnited Kingdom
| | - Caroline Boudreault
- Canadian National Collection of Insects, Arachnids and Nematodes, 960 Carling Ave., Ottawa, K1A0C6, CanadaCanadian National Collection of Insects, Arachnids and NematodesOttawaCanada
| | - Dominik Rabl
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Glashüttenstr. 5, Würzburg, 96181 Rauhenebrach, GermanyUniversity of WürzburgWürzburgGermany
| | - Gerhard Haszprunar
- Department Biology II, Ludwig-Maximilians-Universität München (LMU), Großhaderner Str. 2, Martinsried, 82152 Planegg, GermanyLudwig-Maximilians-Universität MünchenPlaneggGermany
| | - Michael J. Raupach
- SNSB-Zoologische Staatssammlung München, Münchhausenstr. 21, 81247 München, GermanySNSB-Zoologische Staatssammlung MünchenMünchenGermany
| | - Stefan Schmidt
- SNSB-Zoologische Staatssammlung München, Münchhausenstr. 21, 81247 München, GermanySNSB-Zoologische Staatssammlung MünchenMünchenGermany
| | - Viktor Baranov
- Estación Biológica de Doñana-CSIC/Doñana Biological Station-CSIC, Seville, SpainEstación Biológica de Doñana-CSICSevilleSpain
| | - José Fernández-Triana
- Canadian National Collection of Insects, Arachnids and Nematodes, 960 Carling Ave., Ottawa, K1A0C6, CanadaCanadian National Collection of Insects, Arachnids and NematodesOttawaCanada
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McFadden CS, Benayahu Y, Samimi-Namin K. A new genus of soft coral (Octocorallia, Malacalcyonacea, Cladiellidae) and three new species from Indo-Pacific coral reefs. Zookeys 2024; 1188:275-304. [PMID: 38239385 PMCID: PMC10795068 DOI: 10.3897/zookeys.1188.110617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 11/23/2023] [Indexed: 01/22/2024] Open
Abstract
Molecular systematic studies of the anthozoan class Octocorallia have revealed widespread incongruence between phylogenetic relationships and taxonomic classification at all levels of the Linnean hierarchy. Among the soft coral taxa in order Malacalcyonacea, the family Alcyoniidae and its type genus Alcyonium have both been recognised to be highly polyphyletic. A recent family-level revision of Octocorallia established a number of new families for genera formerly considered to belong to Alcyoniidae, but revision of Alcyonium is not yet complete. Previous molecular studies have supported the placement of Alcyoniumverseveldti (Benayahu, 1982) in family Cladiellidae rather than Alcyoniidae, phylogenetically distinct from the other three genera in that family. Here we describe a new genus, Ofwegenumgen. nov. to accommodate O.verseveldticomb. nov. and three new species of that genus, O.coronalucissp. nov., O.kloogisp. nov., and O.collisp. nov., bringing the total number of species in this genus to four. Ofwegenumgen. nov. is a rarely encountered genus so far known from only a few locations spanning the Indian and western Pacific Oceans. We present the morphological characters of each species and use molecular data from both DNA barcoding and target-enrichment of conserved elements to explore species boundaries and phylogenetic relationships within the genus.
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Affiliation(s)
- Catherine S. McFadden
- Department of Biology, Harvey Mudd College, Claremont, CA 91711, USAHarvey Mudd CollegeClaremontUnited States of America
| | - Yehuda Benayahu
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978, Tel Aviv, IsraelTel Aviv UniversityTel AvivIsrael
| | - Kaveh Samimi-Namin
- Marine Evolution and Ecology Group, Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, NetherlandsMarine Evolution and Ecology Group, Naturalis Biodiversity CenterLeidenNetherlands
- Department of Biology, University of Oxford, Oxfordshire, Oxford OX1 3SZ, UKUniversity of OxfordOxfordUnited Kingdom
- Natural History Museum, Cromwell Road, London SW7 5BD, UKNatural History MuseumLondonUnited Kingdom
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Choudhary A, Shekhawat D, Pathania J, Sita K, Sharma S, Chawla A, Jaiswal V. Exploring DNA barcode for accurate identification of threatened Aconitum L. species from Western Himalaya. Mol Biol Rep 2024; 51:75. [PMID: 38175298 DOI: 10.1007/s11033-023-08927-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND Aconitum species, belonging to Ranunculaceae, have high medicinal importance but due to their overexploitation come under IUCN (International Union for Conservation of Nature) red list. The precise identification of the Aconitum species is equally important because they are used in herbal formulations. The present study aimed to develop an efficient DNA barcode system for the authentic identification of Aconitum species. METHODS AND RESULTS A set of 92 barcode gene sequences (including 12 developed during the present study and 80 retrieved from NCBI) of 5 Aconitum species (A. heterophyllum, A. vialoceum, A. japonicum, A. napellus, and A. stapfianum) were analyzed using three methods (tree-based, distance-based, and similarity-based) for species discrimination. The PWG-distance method was found most effective for species discrimination. The discrimination rate of PWG- distance ranged from 33.3% (rbcL + trnH-psbA) to 100% (ITS, rbcL + ITS, ITS + trnH-psbA and rbcL + ITS + trnH-psbA). Among DNA barcodes and their combinations, the ITS marker had the highest degree of species discrimination (NJ-40%, PWG-100% and BLAST-40%), followed by trnH-psbA (NJ-20%, PWG-60% and BLAST-20%). ITS also had higher barcoding gap as compared to other individual barcodes and their combinations. Further, we also analyzed six Aconitum species (A. balfourii, A. ferox, A. heterophyllum, A. rotundifolium, A. soongaricum and A. violaceum) existing in Western Himalaya. These species were distinguished clearly through tree-based method using the ITS barcode gene with 100% species resolution. CONCLUSION ITS showed the best species discrimination power and was used to develop species-specific barcodes for Aconitum species. DNA barcodes developed during the present study can be used to identify Aconitum species.
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Affiliation(s)
- Anita Choudhary
- Biotechnology, Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Deepika Shekhawat
- Biotechnology, Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Jyotsna Pathania
- Biotechnology, Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Kumari Sita
- Environmental Technology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Shailika Sharma
- Environmental Technology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Amit Chawla
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- Environmental Technology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Vandana Jaiswal
- Biotechnology, Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Laojun S, Changbunjong T, Sumruayphol S, Pimsuka S, Chaiphongpachara T. Wing geometric morphometrics and DNA barcoding to distinguish three closely related species of Armigeres mosquitoes (Diptera: Culicidae) in Thailand. Vet Parasitol 2024; 325:110092. [PMID: 38070383 DOI: 10.1016/j.vetpar.2023.110092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 12/25/2023]
Abstract
Armigeres subalbatus, a mosquito species widely found in Thailand and other Asian countries, serves as a vector for filarial parasites, affecting both humans and animals. However, the surveillance of this vector is complicated because of its morphological similarity to two other species, Armigeres dohami and Armigeres kesseli. To differentiate these morphologically similar species, our study employed both wing geometric morphometrics (GM) and DNA barcoding, offering a comprehensive approach to accurately identify these closely related Armigeres species in Thailand. Our GM analyses based on shape demonstrated significant accuracy in differentiating Armigeres species. Specifically, the outline-based GM method focusing on the 3rd posterior cell exhibited an accuracy rate of 82.61%, closely followed by the landmark-based GM method with 81.54%. Both these GM techniques effectively distinguished Ar. subalbatus from Ar. dohami and Ar. kesseli. Regarding DNA barcoding, our investigation of pairwise intra- and interspecific divergences revealed a "barcoding gap". Furthermore, the results of species confirmation using both species delimitation methods including the automatic barcode gap discovery method (ABGD) and the Multi-rate Poisson tree process (mPTP) were consistent with those of morphological identification, sequence comparisons with the GenBank and Barcode of Life Data System (BOLD) databases, and the neighbor-joining tree construction. These consistent results emphasize the efficacy of DNA barcoding in the precise identification of Armigeres species.
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Affiliation(s)
- Sedthapong Laojun
- Department of Public Health and Health Promotion, College of Allied Health Sciences, Suan Sunandha Rajabhat University, Samut Songkhram 75000, Thailand
| | - Tanasak Changbunjong
- Department of Pre-Clinic and Applied Animal Science, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand; The Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals (MoZWE), Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand
| | - Suchada Sumruayphol
- Department of Medical Entomology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Siripong Pimsuka
- School of Public Health, Eastern Asia University, Pathumthani 12110, Thailand
| | - Tanawat Chaiphongpachara
- Department of Public Health and Health Promotion, College of Allied Health Sciences, Suan Sunandha Rajabhat University, Samut Songkhram 75000, Thailand.
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Swenie RA, Looney BP, Ke YH, Alejandro Rojas J, Cubeta MA, Langer GJ, Vilgalys R, Brandon Matheny P. PacBio high-throughput multi-locus sequencing reveals high genetic diversity in mushroom-forming fungi. Mol Ecol Resour 2024; 24:e13885. [PMID: 37902171 DOI: 10.1111/1755-0998.13885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 10/11/2023] [Accepted: 10/16/2023] [Indexed: 10/31/2023]
Abstract
Multi-locus sequence data are widely used in fungal systematic and taxonomic studies to delimit species and infer evolutionary relationships. We developed and assessed the efficacy of a multi-locus pooled sequencing method using PacBio long-read high-throughput sequencing. Samples included fresh and dried voucher specimens, cultures and archival DNA extracts of Agaricomycetes with an emphasis on the order Cantharellales. Of the 283 specimens sequenced, 93.6% successfully amplified at one or more loci with a mean of 3.3 loci amplified. Our method recovered multiple sequence variants representing alleles of rDNA loci and single copy protein-coding genes rpb1, rpb2 and tef1. Within-sample genetic variation differed by locus and taxonomic group, with the greatest genetic divergence observed among sequence variants of rpb2 and tef1 from corticioid Cantharellales. Our method is a cost-effective approach for generating accurate multi-locus sequence data coupled with recovery of alleles from polymorphic samples and multi-organism specimens. These results have important implications for understanding intra-individual genomic variation among genetic loci commonly used in species delimitation of fungi.
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Affiliation(s)
- Rachel A Swenie
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Brian P Looney
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - Yi-Hong Ke
- Department of Biology, Duke University, Durham, North Carolina, USA
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - J Alejandro Rojas
- Department of Biology, Duke University, Durham, North Carolina, USA
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
| | - Marc A Cubeta
- Department of Entomology and Plant Pathology, Center for Integrated Fungal Research, North Carolina State University, Raleigh, North Carolina, USA
| | - Gitta J Langer
- Department of Forest Protection, Northwest German Forest Research Institute, Göttingen, Germany
| | - Rytas Vilgalys
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - P Brandon Matheny
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee, USA
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Gahtori R, Tripathi AH, Chand G, Pande A, Joshi P, Rai RC, Upadhyay SK. Phytochemical Screening of Nyctanthes arbor-tristis Plant Extracts and Their Antioxidant and Antibacterial Activity Analysis. Appl Biochem Biotechnol 2024; 196:436-456. [PMID: 37140779 DOI: 10.1007/s12010-023-04552-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/18/2023] [Indexed: 05/05/2023]
Abstract
Nyctanthes arbor-tristis, alias "Vishnu Parijat," is a medicinal plant used to treat various inflammation-associated ailments and to combat innumerable infections in the traditional system of medicine. In the present study, we collected the samples of N. arbor-tristis from the lower Himalayan region of Uttarakhand, India, and carried out their molecular identification through DNA barcoding. To examine the antioxidant and antibacterial activities, we prepared the ethanolic and aqueous extracts (from flowers and leaves) and performed their phytochemical analysis by using different qualitative and quantitative approaches. The phytoextracts showed marked antioxidant potential, as revealed by a comprehensive set of assays. The ethanolic leaf extract showed marked antioxidant potential towards DPPH, ABTS, and NO scavenging (IC50 = 30.75 ± 0.006, 30.83 ± 0.002, and 51.23 ± 0.009 μg/mL, respectively). We used TLC-bioautography assay to characterize different antioxidant constituents (based on their Rf values) in the chromatograms ran under different mobile phases. For one of the prominent antioxidant spots in TLC bioautography, GC-MS analysis identified cis-9-hexadecenal and n-hexadecanoic acid as the major constituents. Furthermore, in antibacterial study, the ethanolic leaf extract showed marked activity against Aeromonas salmonicida (113.40 mg/mL of extract was equivalent to 100 μg/mL of kanamycin). In contrast, the ethanolic flower extract showed considerable antibacterial activity against Pseudomonas aeruginosa (125.85 mg/mL of extract ≡100 μg/mL of kanamycin). This study presents the phylogenetic account and unravels the antioxidant-related properties and antibacterial potential of N. arbor-tristis.
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Affiliation(s)
- Rekha Gahtori
- Department of Biotechnology, Kumaun University, Bhimtal Campus, Nainital, Uttarakhand, 263136, India
| | - Ankita H Tripathi
- Department of Biotechnology, Kumaun University, Bhimtal Campus, Nainital, Uttarakhand, 263136, India
| | - Garima Chand
- Department of Chemistry, Kumaun University, DSB Campus, Nainital, Uttarakhand, 263001, India
| | - Amit Pande
- ICAR-Directorate Coldwater Fisheries Research, Bhimtal, Uttarakhand, 263136, India
| | - Penny Joshi
- Department of Chemistry, Kumaun University, DSB Campus, Nainital, Uttarakhand, 263001, India
| | - Ramesh Chandra Rai
- Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, 121001, India.
| | - Santosh K Upadhyay
- Department of Biotechnology, Kumaun University, Bhimtal Campus, Nainital, Uttarakhand, 263136, India.
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Tnah LH, Lee SL, Lee CT, Ng KKS, Ng CH, Zawiah N. DNA barcode identification of cultivated and wild tropical fruit species. 3 Biotech 2024; 14:7. [PMID: 38074292 PMCID: PMC10703749 DOI: 10.1007/s13205-023-03848-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 11/08/2023] [Indexed: 01/19/2024] Open
Abstract
With the rapid growth of the fruit industry worldwide, it is important to assess adulteration to ensure the authenticity and the safety of fruit products. The DNA barcoding approach offers a quick and accurate way of identifying and authenticating species. In this study, we developed reference DNA barcodes (rbcL, ITS2, and trnH-psbA) for 70 cultivated and wild tropical fruit species, representing 43 genera and 26 families. In terms of species recoverability, rbcL has a greater recoverability (100%) than ITS2 (95.7%) and trnH-psbA (88.6%). We evaluated the performance of these barcodes in species discrimination using similarity BLAST, phylogenetic tree, and barcoding gap analyses. The efficiency of rbcL, ITS2, and trnH-psbA in discriminating species was 80%, 100%, and 93.6%, respectively. We employed a multigene-tiered approach for species identification, with the rbcL region used for primary differentiation and ITS2 or trnH-psbA used for secondary differentiation. The two-locus barcodes rbcL + ITS2 and rbcL + trnH-psbA demonstrated robustness, achieving species discrimination rates of 100% and 94.3% respectively. Beyond the conventional species identification method based on plant morphology, the developed reference barcodes will aid the fruit agroindustry and trade, by making fruit-based product authentication possible. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03848-w.
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Affiliation(s)
- Lee Hong Tnah
- Forest Research Institute Malaysia, 52109 Kepong, Selangor Darul Ehsan Malaysia
| | - Soon Leong Lee
- Forest Research Institute Malaysia, 52109 Kepong, Selangor Darul Ehsan Malaysia
| | - Chai Ting Lee
- Forest Research Institute Malaysia, 52109 Kepong, Selangor Darul Ehsan Malaysia
| | - Kevin Kit Siong Ng
- Forest Research Institute Malaysia, 52109 Kepong, Selangor Darul Ehsan Malaysia
| | - Chin Hong Ng
- Forest Research Institute Malaysia, 52109 Kepong, Selangor Darul Ehsan Malaysia
| | - Ngah Zawiah
- Forest Research Institute Malaysia, 52109 Kepong, Selangor Darul Ehsan Malaysia
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Graham K, Houston R. Evaluation of chloroplast DNA barcoding markers to individualize Papaver somniferum for forensic intelligence purposes. Int J Legal Med 2024; 138:267-275. [PMID: 35788906 DOI: 10.1007/s00414-022-02862-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 06/24/2022] [Indexed: 10/17/2022]
Abstract
The opium poppy, Papaver somniferum L., is a forensically important plant due to the medicinal and illegal uses for the milky latex stored in the pods. This latex contains the alkaloids morphine, codeine, and thebaine that are used for their analgesic properties and/or for synthesizing other opioids. However, these compounds are highly addictive and have caused a national opioid epidemic. Two other Papaver species, P. setigerum DC. and P. bracteatum Lindl., are also of forensic interest because they pose both forensic and legal issues. They are largely uncontrolled under the Controlled Substances Act, making these species a common defense strategy. Current morphological and chemical identification methods have been moderately successful but have drawbacks. There is also a lack of sequencing data available. Therefore, exploiting the genome using chloroplast DNA barcoding markers could help to accurately identify these species of interest when plant material is taken. This study screened and assessed the genetic variation both between species and within populations of P. somniferum in nine cpDNA barcode regions (ndhF-rpl32, petA-psbJ, rpl32-trnL, rps16-trnQ, trnE-trnT, trnH-psbA, trnL-trnF, rpl16 intron, and psbE-petL). Published reference genomes from the NCBI GenBank database were aligned and compared for an initial in silico screening. Additionally, ten P. somniferum seed samples from various vendors were sequenced and compared across samples and to published reference data at the various barcode regions of interest. This study showed that the regions trnH-psbA and petA-psbJ have promise for utility in individualization for both inter- and intra-species individualization of P. somniferum.
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Affiliation(s)
- Kari Graham
- Department of Forensic Science, Sam Houston State University, 1003 Bowers Blvd, Huntsville, TX, 77340, USA
| | - Rachel Houston
- Department of Forensic Science, Sam Houston State University, 1003 Bowers Blvd, Huntsville, TX, 77340, USA.
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Mshiywa FM, Edwards S, Bradley G. Rhodophyta DNA Barcoding: Ribulose-1, 5-Bisphosphate Carboxylase Gene and Novel Universal Primers. Int J Mol Sci 2023; 25:58. [PMID: 38203228 PMCID: PMC10871077 DOI: 10.3390/ijms25010058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 01/12/2024] Open
Abstract
Red algae (Rhodophyta) are a heterogeneous group of marine algal species that have served as a source of high-value molecules, including antioxidants and scaffolds, for novel drug development. However, it is challenging to identify Rhodophytes through morphological features alone, and in most instances, that has been the prevailing approach to identification. Consequently, this study undertook the identification of red algae species in Kenton-on-Sea, South Africa, as a baseline for future research on red algae biodiversity and conservation. The identification was achieved by designing, analysing, and using a set of universal primers through DNA barcoding of the rbcL gene. The PCR products of the rbcL gene were sequenced, and 96% of the amplicons were successfully sequenced from this set and matched with sequences on BOLD, which led to these species being molecularly described. Amongst these species are medicinally essential species, such as Laurencia natalensis and Hypnea spinella, and potential cryptic species. This calls for further investigation into the biodiversity of the studied region. Meanwhile, the availability of these primers will ease the identification process of red algae species from other coastal regions.
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Affiliation(s)
- Faith Masilive Mshiywa
- Department of Biochemistry and Microbiology, University of Fort Hare, Alice 5700, South Africa
| | - Shelley Edwards
- Department of Zoology & Entomology, Rhodes University, Makhanda 6139, South Africa;
| | - Graeme Bradley
- Department of Biochemistry and Microbiology, University of Fort Hare, Alice 5700, South Africa
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