1
|
Berchtenbreiter L, Mumcu AE, Rackevei AS, Cock JM, Kawai H, Wolf M. 18S and ITS2 rRNA gene sequence-structure phylogeny of the Phaeophyceae (SAR, Stramenopiles) with special reference to Laminariales. Eur J Protistol 2024; 95:126107. [PMID: 39024684 DOI: 10.1016/j.ejop.2024.126107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 07/11/2024] [Accepted: 07/11/2024] [Indexed: 07/20/2024]
Abstract
The phylogeny of brown algae (Phaeophyceae) has undergone extensive changes in the recent past due to regular new scientific insights. We used nuclear 18S rDNA with an extensive dataset, aiming to increase the accuracy and robustness of the reconstructed phylogenetic trees using a simultaneous sequence-structure approach. Individual secondary structures were generated for all 18S rDNA sequences. The sequence-structure information was encoded and used for an automated simultaneous sequence-structure alignment. Neighbor-joining and profile neighbor-joining trees were calculated based on 186 phaeophycean sequence-structure pairs. Additionally, sequence-structure neighbor-joining, maximum parsimony and maximum likelihood trees were reconstructed on a representative subset. Using a similar approach, ITS2 rDNA sequence-structure information was used to reconstruct a neighbor-joining tree including 604 sequence-structure pairs of the Laminariales. Our study results are in significant agreement with previous single marker 18S and ITS2 rDNA analyses. Moreover, the 18S results are in wide agreement with recent multi-marker analyses. The bootstrap support was significantly higher for our sequence-structure analysis in comparison to sequence-only analyses in this study and the available literature. This study supports the simultaneous inclusion of sequence-structure data at least for 18S to obtain more accurate and robust phylogenetic trees compared to sequence-only analyses.
Collapse
Affiliation(s)
- Leon Berchtenbreiter
- Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Abdullah Emir Mumcu
- Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | | | - J Mark Cock
- Department UMR 8227, CNRS-UPMC, Station Biologique, Place Georges Teissier, CS 90074, 29688 Roscoff, France
| | - Hiroshi Kawai
- Kobe University Research Center for Inland Seas, Rokkodai, Kobe 657-8501, Japan
| | - Matthias Wolf
- Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany.
| |
Collapse
|
2
|
Rapp E, Wolf M. 18S rDNA sequence-structure phylogeny of the eukaryotes simultaneously inferred from sequences and their individual secondary structures. BMC Res Notes 2024; 17:124. [PMID: 38693573 PMCID: PMC11064340 DOI: 10.1186/s13104-024-06786-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/23/2024] [Indexed: 05/03/2024] Open
Abstract
OBJECTIVE The eukaryotic tree of life has been subject of numerous studies ever since the nineteenth century, with more supergroups and their sister relations being decoded in the last years. In this study, we reconstructed the phylogeny of eukaryotes using complete 18S rDNA sequences and their individual secondary structures simultaneously. After the sequence-structure data was encoded, it was automatically aligned and analyzed using sequence-only as well as sequence-structure approaches. We present overall neighbor-joining trees of 211 eukaryotes as well as the respective profile neighbor-joining trees, which helped to resolve the basal branching pattern. A manually chosen subset was further inspected using neighbor-joining, maximum parsimony, and maximum likelihood analyses. Additionally, the 75 and 100 percent consensus structures of the subset were predicted. RESULTS All sequence-structure approaches show improvements compared to the respective sequence-only approaches: the average bootstrap support per node of the sequence-structure profile neighbor-joining analyses with 90.3, was higher than the average bootstrap support of the sequence-only profile neighbor-joining analysis with 73.9. Also, the subset analyses using sequence-structure data were better supported. Furthermore, more subgroups of the supergroups were recovered as monophyletic and sister group relations were much more comparable to results as obtained by multi-marker analyses.
Collapse
Affiliation(s)
- Eva Rapp
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Matthias Wolf
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.
| |
Collapse
|
3
|
Rackevei AS, Karnkowska A, Wolf M. 18S rDNA sequence-structure phylogeny of the Euglenophyceae (Euglenozoa, Euglenida). J Eukaryot Microbiol 2023; 70:e12959. [PMID: 36478494 DOI: 10.1111/jeu.12959] [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: 08/16/2022] [Revised: 11/14/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022]
Abstract
The phylogeny of Euglenophyceae (Euglenozoa, Euglenida) has been discussed for decades with new genera being described in the last few years. In this study, we reconstruct a phylogeny using 18S rDNA sequence and structural data simultaneously. Using homology modeling, individual secondary structures were predicted. Sequence-structure data are encoded and automatically aligned. Here, we present a sequence-structure neighbor-joining tree of more than 300 taxa classified as Euglenophyceae. Profile neighbor-joining was used to resolve the basal branching pattern. Neighbor-joining, maximum parsimony, and maximum likelihood analyses were performed using sequence-structure information for manually chosen subsets. All analyses supported the monophyly of Eutreptiella, Discoplastis, Lepocinclis, Strombomonas, Cryptoglena, Monomorphina, Euglenaria, and Colacium. Well-supported topologies were generally consistent with previous studies using a combined dataset of genetic markers. Our study supports the simultaneous use of sequence and structural data to reconstruct more accurate and robust trees. The average bootstrap value is significantly higher than the average bootstrap value obtained from sequence-only analyses, which is promising for resolving relationships between more closely related taxa.
Collapse
Affiliation(s)
- Antonia S Rackevei
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Anna Karnkowska
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Matthias Wolf
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| |
Collapse
|
4
|
Borges AR, Engstler M, Wolf M. 18S rRNA gene sequence-structure phylogeny of the Trypanosomatida (Kinetoplastea, Euglenozoa) with special reference to Trypanosoma. Eur J Protistol 2021; 81:125824. [PMID: 34352687 DOI: 10.1016/j.ejop.2021.125824] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 06/08/2021] [Accepted: 07/06/2021] [Indexed: 11/30/2022]
Abstract
Parasites of the order Trypanosomatida are known due to their medical relevance. Despite the progress made in the past decades on understanding the evolution of this group of organisms, there are still many open questions that require robust phylogenetic markers to increase the resolution of trees. Using two known 18S rRNA gene template structures (from Trypanosoma cruzi Chagas, 1909 and Trypanosoma brucei Plimmer and Bradford, 1899), individual 18S rRNA gene secondary structures were predicted by homology modeling. Sequences and their secondary structures, automatically encoded by a 12-letter alphabet (each nucleotide with its three structural states, paired left, paired right, unpaired), were simultaneously aligned. Sequence-structure trees were generated by neighbor joining and/or maximum likelihood. The reconstructed trees allowed us to discuss not only the big picture of trypanosomatid phylogeny but also a comprehensive sampling of trypanosomes evaluated in the context of trypanosomatid diversity. The robust support (bootstrap > 75) for well-known clades and critical branches suggests that the simultaneous use of 18S rRNA sequence and secondary structure data can reconstruct robust phylogenetic trees and can be used by the trypanosomatid research community for future analysis.
Collapse
Affiliation(s)
- Alyssa R Borges
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Markus Engstler
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Matthias Wolf
- Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany.
| |
Collapse
|
5
|
Heuristic Optimization of Culture Conditions for Stimulating Hyper-Accumulation of Biomass and Lipid in Golenkinia SDEC-16. ENERGIES 2020. [DOI: 10.3390/en13040964] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Overproduction of biomass and hyper-accumulation of lipids endow microalgae with promising characteristics to realize the cost-effective potential of advanced bioenergy. This study sought to heuristically optimize the culture conditions on a rarely reported Golenkinia sp. The results indicate that Golenkinia SDEC-16 can withstand the strong light intensity and grow in a modified BG11 medium. The optimal culture conditions for the favorable tradeoff between biomass and lipid accumulation were suggested as follows, 25,000 lux of light intensity, 9 mM of initial nitrogen concentration, and 20 mM of initial sodium chloride concentration. Under these conditions, the biomass concentration and productivity reached 6.65 g/L and 545 mg/L/d, and the synchronous lipid content and productivity reached 54.38% and 296.39 mg/L/d. Hypersalinity significantly promoted lipid contents at the cost of biomass and resulted in an increase of cell size but loss of spines of Golenkinia SDEC-16. The results shed new light on optimizing biomass and lipid productivity.
Collapse
|
6
|
Li M, Zhao H, Zhao F, Jiang L, Peng H, Zhang W, Simmons MP. Alternative analyses of compensatory base changes in an ITS2 phylogeny of Corydalis (Papaveraceae). ANNALS OF BOTANY 2019; 124:233-243. [PMID: 31152554 PMCID: PMC6758584 DOI: 10.1093/aob/mcz062] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 04/03/2019] [Indexed: 05/27/2023]
Abstract
BACKGROUND AND AIMS Compensatory base changes (CBCs) that occur in stems of ribosomal internal transcribed spacer 2 (ITS2) can have important phylogenetic implications because they are not expected to occur within a single species and also affect selection of appropriate DNA substitution models. These effects have been demonstrated when studying ancient lineages. Here we examine these effects to quantify their importance within a more recent lineage by using both DNA- and RNA-specific models. METHODS We examined the phylogenetic implications of the CBC process by using a comprehensive sampling of ITS2 from ten closely related species of Corydalis. We predicted ITS2 secondary structures by using homology modelling, which was then used for a structure-based alignment. Paired and unpaired regions were analysed separately and in combination by using both RNA-specific substitution models and conventional DNA models. We mapped all base-pair states of CBCs on the phylogenetic tree to infer their evolution and relative timing. KEY RESULTS Our results indicate that selection acted to increase the thermodynamic stability of the secondary structure. Thus, the unpaired and paired regions did not evolve under a common substitution model. Only two CBCs occurred within the lineage sampled and no striking differences in topology or support for the shared clades were found between trees constructed using DNA- or RNA-specific substitution models. CONCLUSIONS Although application of RNA-specific substitution models remains preferred over more conventional DNA models, we infer that application of conventional DNA models is unlikely to be problematic when conducting phylogenetic analyses of ITS2 within closely related lineages wherein few CBCs are observed. Each of the two CBCs was found within the same lineages but was not observed within a given species, which supports application of the CBC species concept.
Collapse
Affiliation(s)
- Meihui Li
- Marine College, Shandong University, Weihai, China
| | - Hong Zhao
- Marine College, Shandong University, Weihai, China
| | - Fengxi Zhao
- Marine College, Shandong University, Weihai, China
| | - Lu Jiang
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Huasheng Peng
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Wei Zhang
- Marine College, Shandong University, Weihai, China
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Mark P Simmons
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| |
Collapse
|
7
|
Dai X, Mak YL, Lu CK, Mei HH, Wu JJ, Lee WH, Chan LL, Lim PT, Mustapa NI, Lim HC, Wolf M, Li D, Luo Z, Gu H, Leaw CP, Lu D. Taxonomic assignment of the benthic toxigenic dinoflagellate Gambierdiscus sp. type 6 as Gambierdiscus balechii (Dinophyceae), including its distribution and ciguatoxicity. HARMFUL ALGAE 2017; 67:107-118. [PMID: 28755713 DOI: 10.1016/j.hal.2017.07.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 06/30/2017] [Accepted: 07/03/2017] [Indexed: 06/07/2023]
Abstract
Recent molecular phylogenetic studies of Gambierdiscus species flagged several new species and genotypes, thus leading to revitalizing its systematics. The inter-relationships of clades revealed by the primary sequence information of nuclear ribosomal genes (rDNA), however, can sometimes be equivocal, and therefore, in this study, the taxonomic status of a ribotype, Gambierdiscus sp. type 6, was evaluated using specimens collected from the original locality, Marakei Island, Republic of Kiribati; and specimens found in Rawa Island, Peninsular Malaysia, were further used for comparison. Morphologically, the ribotype cells resembled G. scabrosus, G. belizeanus, G. balechii, G. cheloniae and G. lapillus in thecal ornamentation, where the thecal surfaces are reticulate-foveated, but differed from G. scabrosus by its hatchet-shaped Plate 2', and G. belizeanus by the asymmetrical Plate 3'. To identify the phylogenetic relationship of this ribotype, a large dataset of the large subunit (LSU) and small subunit (SSU) rDNAs were compiled, and performed comprehensive analyses, using Bayesian-inference, maximum-parsimony, and maximum-likelihood, for the latter two incorporating the sequence-structure information of the SSU rDNA. Both the LSU and SSU rDNA phylogenetic trees displayed an identical topology and supported the hypothesis that the relationship between Gambierdiscus sp. type 6 and G. balechii was monophyletic. As a result, the taxonomic status of Gambierdiscus sp. type 6 was revised, and assigned as Gambierdiscus balechii. Toxicity analysis using neuroblastoma N2A assay confirmed that the Central Pacific strains were toxic, ranging from 1.1 to 19.9 fg P-CTX-1 eq cell-1, but no toxicity was detected in a Western Pacific strain. This suggested that the species might be one of the species contributing to the high incidence rate of ciguatera fish poisoning in Marakei Island.
Collapse
Affiliation(s)
- Xinfeng Dai
- Key Laboratory of Marine Ecosystem and Biogeochemistry, The Second Institute of Oceanography, SOA, Hangzhou 310012, China
| | - Yim Ling Mak
- State Key Laboratory in Marine Pollution, City University of Hong Kong, Hong Kong Special Administrative Region
| | - Chung-Kuang Lu
- National Research Institute of Chinese Medicine, Ministry of Health and Welfare, 155-1, Sec. 2, Linong St, Beitou District, Taipei 1121, Taiwan; Department of Bioscience and Institute of Genomics, National Yang Ming University, Taiwan
| | - Hua-Hsuan Mei
- Department of Bioscience and Institute of Genomics, National Yang Ming University, Taiwan
| | - Jia Jun Wu
- State Key Laboratory in Marine Pollution, City University of Hong Kong, Hong Kong Special Administrative Region; Shenzhen Key Laboratory in Sustainable Use of Marine Biodiversity, Research Centre for the Oceans and Human Health, City University of Hong Kong, Shenzhen, China
| | - Wai Hin Lee
- State Key Laboratory in Marine Pollution, City University of Hong Kong, Hong Kong Special Administrative Region
| | - Leo Lai Chan
- State Key Laboratory in Marine Pollution, City University of Hong Kong, Hong Kong Special Administrative Region; Department of Biomedical Science, City University of Hong Kong, Hong Kong Special Administrative Region
| | - Po Teen Lim
- Bachok Marine Research Station, Institute of Ocean and Earth Sciences, University of Malaya, 16310, Bachok, Kelantan, Malaysia
| | - Nurin Izzati Mustapa
- Bachok Marine Research Station, Institute of Ocean and Earth Sciences, University of Malaya, 16310, Bachok, Kelantan, Malaysia
| | - Hong Chang Lim
- Faculty of Applied Sciences, Tunku Abdul Rahman University College, Johor Branch Campus, 85000 Segamat, Johor, Malaysia
| | - Matthias Wolf
- Department of Bioinformatics, Biocenter, University of Wuerzburg, 97074 Wuerzburg, Germany
| | - Dongrong Li
- Key Laboratory of Marine Ecosystem and Biogeochemistry, The Second Institute of Oceanography, SOA, Hangzhou 310012, China
| | - Zhaohe Luo
- Third Institute of Oceanography, Xiamen, China
| | - Haifeng Gu
- Third Institute of Oceanography, Xiamen, China
| | - Chui Pin Leaw
- Bachok Marine Research Station, Institute of Ocean and Earth Sciences, University of Malaya, 16310, Bachok, Kelantan, Malaysia.
| | - Douding Lu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, The Second Institute of Oceanography, SOA, Hangzhou 310012, China; Shenzhen Key Laboratory in Sustainable Use of Marine Biodiversity, Research Centre for the Oceans and Human Health, City University of Hong Kong, Shenzhen, China.
| |
Collapse
|