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Macko P, Derka T, Čiamporová-Zaťovičová Z, Grabowski M, Čiampor F. Detailed DNA barcoding of mayflies in a small European country proved how far we are from having comprehensive barcode reference libraries. Mol Ecol Resour 2024; 24:e13954. [PMID: 38520175 DOI: 10.1111/1755-0998.13954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 02/28/2024] [Accepted: 03/07/2024] [Indexed: 03/25/2024]
Abstract
Mayflies (Ephemeroptera) are among the crucial water and habitat quality bioindicators. However, despite their intensive long-term use in various studies, more reliable mayfly DNA barcode data have been produced in a negligible number of countries, and only ~40% of European species had been barcoded with less than 50% of families covered. Despite being carried out in a small area, our study presents the second-most species-rich DNA reference library of mayflies from Europe and the first comprehensive view from an important biodiversity hotspot such as the Western Carpathians. Within 1153 sequences, 76 morphologically determined species were recorded and added to the Barcode of Life Data System (BOLD) database. All obtained sequences were assigned to 97 BINs, 11 of which were unique and three represented species never barcoded before. Sequences of 16 species with high intraspecific variability were divided into 40 BINs, confirming the presence of cryptic lineages. Due to the low interspecific divergence and the non-existing barcoding gap, sequences of six species were assigned to three shared BINs. Delimitation analyses resulted in 79 and 107 putative species respectively. Bayesian and maximum-likelihood phylogenies confirmed the monophyly of almost all species and complexes of cryptic taxa and proved that DNA barcoding distinguishes almost all studied mayfly species. We have shown that it is still sufficient to thoroughly investigate the fauna of a small but geographically important area to enrich global databases greatly. In particular, the insights gained here transcend the local context and may have broader implications for advancing barcoding efforts.
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Affiliation(s)
- Patrik Macko
- Department of Ecology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovak Republic
| | - Tomáš Derka
- Department of Ecology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovak Republic
| | - Zuzana Čiamporová-Zaťovičová
- Department of Ecology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovak Republic
- ZooLab, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Michal Grabowski
- Department of Invertebrate Zoology and Hydrobiology, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
| | - Fedor Čiampor
- ZooLab, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, Slovak Republic
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Zhang MZ, Xu JP, Callac P, Chen MY, Wu Q, Wach M, Mata G, Zhao RL. Insight into the evolutionary and domesticated history of the most widely cultivated mushroom Agaricus bisporus via mitogenome sequences of 361 global strains. BMC Genomics 2023; 24:182. [PMID: 37020265 PMCID: PMC10077685 DOI: 10.1186/s12864-023-09257-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 03/20/2023] [Indexed: 04/07/2023] Open
Abstract
Agaricus bisporus is the most widely cultivated edible mushroom in the world with a only around three hundred years known history of cultivation. Therefore, it represents an ideal organism not only to investigate the natural evolutionary history but also the understanding on the evolution going back to the early era of domestication. In this study, we generated the mitochondrial genome sequences of 352 A. bisporus strains and 9 strains from 4 closely related species around the world. The population mitogenomic study revealed all A. bisporus strains can be divided into seven clades, and all domesticated cultivars present only in two of those clades. The molecular dating analysis showed this species origin in Europe on 4.6 Ma and we proposed the main dispersal routes. The detailed mitogenome structure studies showed that the insertion of the plasmid-derived dpo gene caused a long fragment (MIR) inversion, and the distributions of the fragments of dpo gene were strictly in correspondence with these seven clades. Our studies also showed A. bisporus population contains 30 intron distribution patterns (IDPs), while all cultivars contain only two IDPs, which clearly exhibit intron loss compared to the others. Either the loss occurred before or after domestication, that could suggest that the change facilitates their adaptation to the cultivated environment.
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Affiliation(s)
- Ming-Zhe Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No3 1St Beichen West Road, Beijing, 100101, Chaoyang District, China
- College of Life Sciences, University of Chinese Academy of Sciences, Huairou District, Beijing, 101408, China
| | - Jian-Ping Xu
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | | | - Mei-Yuan Chen
- Edible Fungi Institute of Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China
| | - Qi Wu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No3 1St Beichen West Road, Beijing, 100101, Chaoyang District, China
- College of Life Sciences, University of Chinese Academy of Sciences, Huairou District, Beijing, 101408, China
| | - Mark Wach
- Sylvan BioSciences, Kittanning, PA, 16201, USA
| | - Gerardo Mata
- Instituto de Ecología A.C. Carretera Antigua a Coatepec, 351, El Haya, 91073, Veracruz, CPXalapa, Mexico
| | - Rui-Lin Zhao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No3 1St Beichen West Road, Beijing, 100101, Chaoyang District, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Huairou District, Beijing, 101408, China.
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Reviewing Introduction Histories, Pathways, Invasiveness, and Impact of Non-Indigenous Species in Danish Marine Waters. DIVERSITY 2023. [DOI: 10.3390/d15030434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Non-indigenous species (NIS) are of concern for biodiversity conservation and ecosystem functioning. We present an updated list of NIS, including cryptogenic species, from Danish marine waters containing 123 species. Benthic invertebrates (36%) and phytoplankton (28%) dominate the list, but fish (15%) and macroalgae (13%) are also important. The Limfjord in Northern Jutland emerges as a hotspot for the introduction of NIS. Data from multiple sources were included, i.e., the National Monitoring Program (NOVANA), the National Fish Atlas project, the citizen science project Arter.dk, research articles, and annual national reports of the ICES working group ITMO. Forty-six NIS species were subject to expert judging using a modified Harmonia protocol; 19 were found to fulfil the four selected criteria identifying a species as being ‘invasive’. Additionally, 38 species, not yet recorded in Danish waters, were evaluated using the same method, and 31 were found to fulfil the ‘invasive’ criteria. For nine selected species, introduction history, distribution maps, and time-series diagrams are presented. Our data document that the national monitoring efforts should be expanded to record macrozooplankton, coastal fish, and mobile epibenthic species. Furthermore, the national data repository, Arter.dk, should be expanded to enable more detailed documentation of new NIS records.
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Höpel CG, Yeo D, Grams M, Meier R, Richter S. Mitogenomics supports the monophyly of Mysidacea and Peracarida (Malacostraca). ZOOL SCR 2022. [DOI: 10.1111/zsc.12554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Christoph G. Höpel
- Allgemeine & Spezielle Zoologie, Institut für Biowissenschaften Universität Rostock Rostock Germany
| | - Darren Yeo
- Centre for Wildlife Forensics Animal and Plant Health Centre, National Parks Board Singapore Singapore
| | - Markus Grams
- Allgemeine & Spezielle Zoologie, Institut für Biowissenschaften Universität Rostock Rostock Germany
| | - Rudolf Meier
- Museum für Naturkunde Leibniz‐Institut für Evolutions‐ und Biodiversitätsforschung Berlin Germany
| | - Stefan Richter
- Allgemeine & Spezielle Zoologie, Institut für Biowissenschaften Universität Rostock Rostock Germany
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Yi MR, Hsu KC, Gu S, He XB, Luo ZS, Lin HD, Yan YR. Complete mitogenomes of four Trichiurus species: A taxonomic review of the T.lepturus species complex. Zookeys 2022; 1084:1-26. [PMID: 35173516 PMCID: PMC8810657 DOI: 10.3897/zookeys.1084.71576] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 12/31/2021] [Indexed: 02/06/2023] Open
Abstract
Four Trichiurus species, T.japonicus, T.lepturus, T.nanhaiensis, and T.brevis, from the coasts of the China Seas, have been identified and their entire mitochondrial genomes (mitogenomes) have been sequenced by next-generation sequencing technology. A comparative analysis of five mitogenomes was conducted, including the mitogenome of T.gangeticus. The mitogenomes contained 16.568-16.840 bp and encoded 36 typical mitochondrial genes (13 protein-coding, 2 ribosomal RNA-coding, and 21 transfer RNA-coding genes) and two typical noncoding control regions. Although tRNAPro is absent from Trichiurus mitogenomes, when compared with the 22 tRNAs reported in other vertebrates, the gene arrangements in the mitogenomes of the studied species are consistent with those in most teleost mitogenomes. The full-length sequences and protein-coding genes (PCGs) in the mitogenomes of the five species had obvious AT biases and negative GC skew values. Our study indicate that the specimens in the Indian Ocean are neither T.lepturus nor T.nanhaiensis but they are T.gangeticus; the Trichiurus species composition in the Indian Ocean is totally different from that in Pacific and Atlantic oceans; there are at least two Trichiurus species in Indian Ocean; and the worldwide systematics and diversity of the genus Trichiurus need to be reviewed.
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Affiliation(s)
- Mu-Rong Yi
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
- Marine Resources Big Data Center of South China Sea, Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang 524088, China
| | - Kui-Ching Hsu
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Sui Gu
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Xiong-Bo He
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Zhi-Sen Luo
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Hung-Du Lin
- The Affiliated School of National Tainan First Senior High School, Tainan 701, Taiwan
| | - Yun-Rong Yan
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
- Marine Resources Big Data Center of South China Sea, Southern Marine Science and Engineering Guangdong Laboratory, Zhanjiang 524088, China
- Guangdong Provincial Engineering and Technology Research Center of Far Sea Fisheries Management and Fishing of South China Sea, Guangdong Ocean University, Zhanjiang 524088, China
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Cucini C, Leo C, Iannotti N, Boschi S, Brunetti C, Pons J, Fanciulli PP, Frati F, Carapelli A, Nardi F. EZmito: a simple and fast tool for multiple mitogenome analyses. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:1101-1109. [PMID: 33796755 PMCID: PMC7995877 DOI: 10.1080/23802359.2021.1899865] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Complete mitochondrial genome data are frequently applied to address phylogenetic/phylogeographic issues at different taxonomic levels in ecology and evolution. While sample preparation/sequencing is becoming more and more straightforward thanks to dropping costs for next-generation sequencing (NGS), data preparation and visualization remains a manually intensive step that may lead to errors if improperly conducted. We have elaborated, and here introduce, EZmito, a simple and intuitive, freely accessible Web Server aimed at automating some of these tasks. EZmito is divided into three main tools: EZpipe that assembles DNA matrices for phylo-mitogenomic analyses; EZskew that calculates genome, strand, and codon nucleotide compositional skews and EZcodon which computes Relative Synonymous Codon Usage statistics as well as amino acid usage frequency over multiple mitogenomes. Output is produced in tabular format as well as publication-quality graphics.
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Affiliation(s)
- Claudio Cucini
- Department of Life Sciences, University of Siena, Siena, Italy
| | - Chiara Leo
- Department of Life Sciences, Imperial College London, London, UK
| | - Nicola Iannotti
- Department of Life Sciences, University of Siena, Siena, Italy
| | - Sara Boschi
- Department of Life Sciences, University of Siena, Siena, Italy
| | | | - Joan Pons
- Department de Biodiversitat Animal i Microbiana, Institut Mediterrani d'Estudis Avancats, Esporles, Spain
| | | | - Francesco Frati
- Department of Life Sciences, University of Siena, Siena, Italy
| | | | - Francesco Nardi
- Department of Life Sciences, University of Siena, Siena, Italy
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