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Hu S, Li K, Zhang Y, Wang Y, Fu L, Xiao Y, Tang X, Gao J. New Insights Into the Threshold Values of Multi-Locus Sequence Analysis, Average Nucleotide Identity and Digital DNA-DNA Hybridization in Delineating Streptomyces Species. Front Microbiol 2022; 13:910277. [PMID: 35711787 PMCID: PMC9195134 DOI: 10.3389/fmicb.2022.910277] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/03/2022] [Indexed: 11/15/2022] Open
Abstract
Multi-locus sequence analysis (MLSA) has been proved to be a useful method for Streptomyces identification and MLSA distance of 0.007 is considered as the boundary value. However, we found that MLSA distance of 0.007 might be insufficient to act as a threshold according to the correlations among average nucleotide identity based on MuMmer ultra-rapid aligning tool (ANIm), digital DNA-DNA hybridization (dDDH) and MLSA from the 80 pairs of Streptomyces species; in addition, a 70% dDDH value did not correspond to a 95∼96% ANIm value but approximately to 96.7% in the genus Streptomyces. Based on our analysis, it was proposed that when the MLSA distance value between a novel Streptomyces and a reference strain was < 0.008, the novel strain could be considered as a heterotypic synonym of the reference strain; when the MLSA distance value was ≥ 0.014, the novel strain could be regarded as a new Streptomyces species; when the MLSA distance value was between 0.008 and 0.014 (not included), the dDDH or ANIm value between a new strain and a reference strain must be calculated in order to determine the taxonomic status of a novel strain. In this context, a 70% dDDH or 96.7% ANIm value could act as the threshold value in delineating Streptomyces species, but if the dDDH or ANIm value was less than but close to 70 or 96.7% cut-off point, the taxonomic status of a novel strain could only be determined by a combination of phenotypic characteristics, chemotaxonomic characteristics and phylogenomic analysis.
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Affiliation(s)
- Siren Hu
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan, China
| | - Kaiqin Li
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan, China
| | - Yifei Zhang
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan, China
| | - Yinfeng Wang
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan, China
| | - Li Fu
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan, China
| | - Yan Xiao
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan, China
| | - Xinke Tang
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan, China
| | - Jian Gao
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan, China
- Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-Polluted Soils, College of Hunan Province, Xiangtan, China
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Tihelka E, Cai C, Giacomelli M, Lozano-Fernandez J, Rota-Stabelli O, Huang D, Engel MS, Donoghue PCJ, Pisani D. The evolution of insect biodiversity. Curr Biol 2021; 31:R1299-R1311. [PMID: 34637741 DOI: 10.1016/j.cub.2021.08.057] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Insects comprise over half of all described animal species. Together with the Protura (coneheads), Collembola (springtails) and Diplura (two-pronged bristletails), insects form the Hexapoda, a terrestrial arthropod lineage characterised by possessing six legs. Exponential growth of genome-scale data for the hexapods has substantially altered our understanding of the origin and evolution of insect biodiversity. Phylogenomics has provided a new framework for reconstructing insect evolutionary history, resolving their position among the arthropods and some long-standing internal controversies such as the placement of the termites, twisted-winged insects, lice and fleas. However, despite the greatly increased size of phylogenomic datasets, contentious relationships among key insect clades remain unresolved. Further advances in insect phylogeny cannot rely on increased depth and breadth of genome and taxon sequencing. Improved modelling of the substitution process is fundamental to countering tree-reconstruction artefacts, while gene content, modelling of duplications and deletions, and comparative morphology all provide complementary lines of evidence to test hypotheses emerging from the analysis of sequence data. Finally, the integration of molecular and morphological data is key to the incorporation of fossil species within insect phylogeny. The emerging integrated framework of insect evolution will help explain the origins of insect megadiversity in terms of the evolution of their body plan, species diversity and ecology. Future studies of insect phylogeny should build upon an experimental, hypothesis-driven approach where the robustness of hypotheses generated is tested against increasingly realistic evolutionary models as well as complementary sources of phylogenetic evidence.
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Affiliation(s)
- Erik Tihelka
- School of Earth Sciences, University of Bristol, Bristol, UK; State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Centre for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing, China.
| | - Chenyang Cai
- School of Earth Sciences, University of Bristol, Bristol, UK; State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Centre for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing, China.
| | | | - Jesus Lozano-Fernandez
- School of Biological Sciences, University of Bristol, Bristol, UK; Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
| | - Omar Rota-Stabelli
- Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all Adige, Italy; Center Agriculture Food Environment, University of Trento, 38010 San Michele all Adige, Italy
| | - Diying Huang
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Centre for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing, China
| | - Michael S Engel
- Division of Entomology, Natural History Museum, University of Kansas, Lawrence, KS, USA; Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
| | | | - Davide Pisani
- School of Earth Sciences, University of Bristol, Bristol, UK; School of Biological Sciences, University of Bristol, Bristol, UK.
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