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Gutiérrez-Larruscain D, Vargas P, Fernández-Mazuecos M, Pausas JG. Phylogenomic analysis reveals the evolutionary history of Paleartic needle-leaved junipers. Mol Phylogenet Evol 2024; 199:108162. [PMID: 39067655 DOI: 10.1016/j.ympev.2024.108162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 07/10/2024] [Accepted: 07/24/2024] [Indexed: 07/30/2024]
Abstract
Needle-leaved junipers (Juniperus sect. Juniperus, Cupressaceae) are coniferous trees and shrubs with red or blue fleshy cones. They are distributed across Asia, Macaronesia and the Mediterranean Basin, with one species (J. communis) having a circumboreal distribution. Here we aim to resolve the phylogeny of this clade to infer its intricate evolutionary history. To do so, we built a comprehensive, time-calibrated phylogeny using genotyping-by-sequencing (GBS) and combine it with species occurrence using phylogeographic tools. Our results provide solid phylogenetic resolution to propose a new taxonomic classification and a biogeographical history of the section. Specifically, we confirm the monophyly of two groups within J. sect. Juniperus: the Asian (blue-cone) species including the circumboreal J. communis, and the Mediterranean-Macaronesian (red-cone) species. In addition, we provide strong phylogenetic evidence for three distinct species (J. badia, J. conferta, J. lutchuensis) previously considered subspecies or varieties, as well as for the differentiation between the eastern and western Mediterranean lineages of J. macrocarpa. Our findings suggest that the Mediterranean basin was the primary center of diversification for Juniperus sect. Juniperus, followed by an East Asian-Tethyan disjunction resulting from uplifts of the Qinghai-Tibetan Plateau and climatic shifts. The colonization history of Macaronesia by red-cone junipers from the western Mediterranean appears to have taken place independently in two different geological periods: the Miocene (Azores) and the Pliocene (Madeira-Canary Islands). Overall, genomic data and phylogenetic analysis are key to consider a new taxonomic proposal and reconstruct the biogeographical history of the iconic needle-leaved junipers across the Paleartic.
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Affiliation(s)
- David Gutiérrez-Larruscain
- Department of Ecology and Global Change, Desertification Research Centre (CIDE: CSIC-UV-GVA), Valencia, Spain.
| | - Pablo Vargas
- Department of Biodiversity and Conservation, Real Jardín Botánico (RJB: CSIC), Madrid, Spain
| | - Mario Fernández-Mazuecos
- Department of Biology (Botany), Faculty of Sciences, Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Juli G Pausas
- Department of Ecology and Global Change, Desertification Research Centre (CIDE: CSIC-UV-GVA), Valencia, Spain
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Qi L, Zhang N, Xu B, Xu Q, Han X, Kong L, Li Q. Increased microgastropoda sampling give new insights into the phylogenetic relationships of Littorinoidea (Littorinimorpha). Mol Phylogenet Evol 2024; 199:108139. [PMID: 38986757 DOI: 10.1016/j.ympev.2024.108139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 06/14/2024] [Accepted: 06/30/2024] [Indexed: 07/12/2024]
Abstract
Littorinoidea is one of the most diverse radiations and the most successful group that evolutionary transitions from marine to terrestrial within Littorinimorpha. With such an unmatched diversity, few phylogenetic investigations have attempted to understand their evolutionary relationships, and existing research has primarily focused on typical intertidal species. To address this gap, we conducted the first phylogenomic analysis of the Littorinoidea, leveraging 35 transcriptomes to investigate their internal relationships. Our analyses revealed significant revisions necessary within the Littorinoidea: 1) Pomatias appears distantly related to Littorinidae, suggesting a potential ancestral origin outside of Littorinoidea, challenging traditional classification. The homology of penial innervation within Littorinoidea warrants reevaluation. 2) Lacuna's placement indicates a close relationship with Naticidae, prompting consideration for its removal from Littorinidae. 3) Based on the current phylogenetic research, Peasiella may belong to a distinct family separate from Littorinidae. 4) Our findings support revising the placement of Pteropods within the Littorinimorpha, which is situated phylogenetically between the families Littorinoidea and Naticoidea. Additionally, we highlight the impact of site heterogeneity and evolutionary rate variation on phylogenetic inference. Our study provides a robust phylogenomic framework for the Littorinoidea, emphasizing the importance of including microgastropoda taxa in molecular phylogenetic reconstructions of gastropod subgroups.
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Affiliation(s)
- Lu Qi
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Ning Zhang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Biyang Xu
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Qinzeng Xu
- Key Laboratory of Science and Engineering for Marine Ecology and Environment, The First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
| | - Xiao Han
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao 266237, China; Sanya Oceanographic Institution, Ocean University of China, Sanya,572000, China.
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao 266237, China; Sanya Oceanographic Institution, Ocean University of China, Sanya,572000, China
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Wei ZR, Jiao D, Wehenkel CA, Wei XX, Wang XQ. Phylotranscriptomic and ecological analyses reveal the evolution and morphological adaptation of Abies. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024. [PMID: 39152659 DOI: 10.1111/jipb.13760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 07/18/2024] [Accepted: 07/19/2024] [Indexed: 08/19/2024]
Abstract
Coniferous forests are under severe threat of the rapid anthropogenic climate warming. Abies (firs), the fourth-largest conifer genus, is a keystone component of the boreal and temperate dark-coniferous forests and harbors a remarkably large number of relict taxa. However, the uncertainty of the phylogenetic and biogeographic history of Abies significantly impedes our prediction of future dynamics and efficient conservation of firs. In this study, using 1,533 nuclear genes generated from transcriptome sequencing and a complete sampling of all widely recognized species, we have successfully reconstructed a robust phylogeny of global firs, in which four clades are strongly supported and all intersectional relationships are resolved, although phylogenetic discordance caused mainly by incomplete lineage sorting and hybridization was detected. Molecular dating and ancestral area reconstruction suggest a Northern Hemisphere high-latitude origin of Abies during the Late Cretaceous, but all extant firs diversified during the Miocene to the Pleistocene, and multiple continental and intercontinental dispersals took place in response to the late Neogene climate cooling and orogenic movements. Notably, four critically endangered firs endemic to subtropical mountains of China, including A. beshanzuensis, A. ziyuanensis, A. fanjingshanensis and A. yuanbaoshanensis from east to west, have different origins and evolutionary histories. Moreover, three hotspots of species richness, including western North America, central Japan, and the Hengduan Mountains, were identified in Abies. Elevation and precipitation, particularly precipitation of the coldest quarter, are the most significant environmental factors driving the global distribution pattern of fir species diversity. Some morphological traits are evolutionarily constrained, and those linked to elevational variation (e.g., purple cone) and cold resistance (e.g., pubescent branch and resinous bud) may have contributed to the diversification of global firs. Our study sheds new light on the spatiotemporal evolution of global firs, which will be of great help to forest management and species conservation in a warming world.
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Affiliation(s)
- Zhou-Rui Wei
- State Key Laboratory of Plant Diversity and Specialty Crops and Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dan Jiao
- State Key Laboratory of Plant Diversity and Specialty Crops and Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
| | - Christian Anton Wehenkel
- Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, Durango, 34000, Mexico
| | - Xiao-Xin Wei
- State Key Laboratory of Plant Diversity and Specialty Crops and Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Xiao-Quan Wang
- State Key Laboratory of Plant Diversity and Specialty Crops and Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
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Gallone B, Kuyper TW, Nuytinck J. The genus Cortinarius should not (yet) be split. IMA Fungus 2024; 15:24. [PMID: 39138570 PMCID: PMC11321212 DOI: 10.1186/s43008-024-00159-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 07/25/2024] [Indexed: 08/15/2024] Open
Abstract
The genus Cortinarius (Agaricales, Basidiomycota) is one of the most species-rich fungal genera, with thousands of species reported. Cortinarius species are important ectomycorrhizal fungi and form associations with many vascular plants globally. Until recently Cortinarius was the single genus of the family Cortinariaceae, despite several attempts to provide a workable, lower-rank hierarchical structure based on subgenera and sections. The first phylogenomic study for this group elevated the old genus Cortinarius to family level and the family was split into ten genera, of which seven were described as new. Here, by careful re-examination of the recently published phylogenomic dataset, we detected extensive gene-tree/species-tree conflicts using both concatenation and multispecies coalescent approaches. Our analyses demonstrate that the Cortinarius phylogeny remains unresolved and the resulting phylogenomic hypotheses suffer from very short and unsupported branches in the backbone. We can confirm monophyly of only four out of ten suggested new genera, leaving uncertain the relationships between each other and the general branching order. Thorough exploration of the tree space demonstrated that the topology on which Cortinarius revised classification relies on does not represent the best phylogenetic hypothesis and should not be used as constrained topology to include additional species. For this reason, we argue that based on available evidence the genus Cortinarius should not (yet) be split. Moreover, considering that phylogenetic uncertainty translates to taxonomic uncertainty, we advise for careful evaluation of phylogenomic datasets before proposing radical taxonomic and nomenclatural changes.
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Affiliation(s)
- Brigida Gallone
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands.
| | - Thomas W Kuyper
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands
- Soil Biology Group, Wageningen University, 6700 AA, Wageningen, The Netherlands
| | - Jorinde Nuytinck
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands
- Research Group Mycology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium
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Zhan M, Xue L, Zhou JJ, Zhang Q, Qin XM, Liao XW, Wu L, Monro AK, Fu LF. Polyphyly of Boehmeria (Urticaceae) congruent with plastome structural variation. FRONTIERS IN PLANT SCIENCE 2024; 15:1297499. [PMID: 39139721 PMCID: PMC11319286 DOI: 10.3389/fpls.2024.1297499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 07/08/2024] [Indexed: 08/15/2024]
Abstract
Boehmeria is a taxonomically challenging group within the nettle family (Urticaceae). The polyphyly of the genus has been proposed by previous studies with respect to five genera (Debregeasia, Cypholophus, Sarcochlamys, Archiboehmeria, and Astrothalamus). Extensive homoplasy of morphological characters has made generic delimitation problematic. Previous studies in other plant groups suggest that plastome structural variations have the potential to provide characters useful in reconstructing evolutionary relationships. We aimed to test this across Boehmeria and its allied genera by mapping plastome structural variations onto a resolved strongly supported phylogeny. In doing so, we expanded the sampling of the plastome to include Cypholophus, Sarcochlamys, Archiboehmeria, and Astrothalamus for the first time. The results of our phylogenomic analyses provide strong support for Sarcochlamys as being more closely related to Leucosyke puya than to Boehmeria and for the clustering of Boehmeria s.l. into four subclades. The sizes of the plastomes in Boehmeria s.l. ranged from 142,627 bp to 170,958 bp. The plastomes recovered a typical quadripartite structure comprising 127~146 genes. We observe several obvious structural variations across the taxa such as gene loss and multiple gene duplication, inverted repeat (IR) contraction and wide expansions, and inversions. Moreover, we recover a trend for these variations that the early clades were relatively conserved in evolution, whereas the later diverging clades were variable. We propose that the structural variations documented may be linked to the adaptation of Boehmeria s.l. to a wide range of habitats, from moist broadleaf forests in Asia to xeric shrublands and deserts in Africa. This study confirms that variation in plastome gene loss/duplication, IR contraction/expansion, and inversions can provide evidence useful for the reconstruction of evolutionary relationships.
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Affiliation(s)
- Min Zhan
- College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Ling Xue
- College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Jian-Jun Zhou
- Hunan Monitoring Center of Forest Resources and Ecological Environment, Hunan Prospecting Designing and Research General Institute for Agriculture Forestry and Industry, Changsha, China
| | - Qiang Zhang
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
| | - Xin-Mei Qin
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
| | - Xiao-Wen Liao
- College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Lei Wu
- College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | | | - Long-Fei Fu
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, China
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Rose JP, Kriebel R, Sytsma KJ, Drew BT. Phylogenomic perspectives on speciation and reproductive isolation in a North American biodiversity hotspot: an example using California sages (Salvia subgenus Audibertia: Lamiaceae). ANNALS OF BOTANY 2024; 134:295-310. [PMID: 38733329 PMCID: PMC11232522 DOI: 10.1093/aob/mcae073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 05/07/2024] [Indexed: 05/13/2024]
Abstract
BACKGROUND AND AIMS The California Floristic Province (CA-FP) is the most species-rich region of North America north of Mexico. One of several proposed hypotheses explaining the exceptional diversity of the region is that the CA-FP harbours myriad recently diverged lineages with nascent reproductive barriers. Salvia subgenus Audibertia is a conspicuous element of the CA-FP, with multiple sympatric and compatible species. METHODS Using 305 nuclear loci and both organellar genomes, we reconstruct species trees, examine genomic discordance, conduct divergence-time estimation, and analyse contemporaneous patterns of gene flow and mechanical reproductive isolation. KEY RESULTS Despite strong genomic discordance, an underlying bifurcating tree is supported. Organellar genomes capture additional introgression events not detected in the nuclear genome. Most interfertility is found within clades, indicating that reproductive barriers arise with increasing genetic divergence. Species are generally not mechanically isolated, suggesting that it is unlikely to be the primary factor leading to reproductive isolation. CONCLUSIONS Rapid, recent speciation with some interspecific gene flow in conjunction with the onset of a Mediterranean-like climate is the underlying cause of extant diversity in Salvia subgenus Audibertia. Speciation has largely not been facilitated by gene flow. Its signal in the nuclear genome seems to mostly be erased by backcrossing, but organellar genomes each capture different instances of historical gene flow, probably characteristic of many CA-FP lineages. Mechanical reproductive isolation appears to be only part of a mosaic of factors limiting gene flow.
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Affiliation(s)
- Jeffrey P Rose
- Department of Biology, University of Nebraska at Kearney, Kearney, NE 68849, USA
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA
| | - Ricardo Kriebel
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA
- California Academy of Sciences, San Francisco, CA 94118, USA
| | - Kenneth J Sytsma
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA
| | - Bryan T Drew
- Department of Biology, University of Nebraska at Kearney, Kearney, NE 68849, USA
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Sharma S, Kumar S. Discovering Fragile Clades and Causal Sequences in Phylogenomics by Evolutionary Sparse Learning. Mol Biol Evol 2024; 41:msae131. [PMID: 38916040 PMCID: PMC11247346 DOI: 10.1093/molbev/msae131] [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: 01/02/2024] [Revised: 05/30/2024] [Accepted: 06/20/2024] [Indexed: 06/26/2024] Open
Abstract
Phylogenomic analyses of long sequences, consisting of many genes and genomic segments, reconstruct organismal relationships with high statistical confidence. But, inferred relationships can be sensitive to excluding just a few sequences. Currently, there is no direct way to identify fragile relationships and the associated individual gene sequences in species. Here, we introduce novel metrics for gene-species sequence concordance and clade probability derived from evolutionary sparse learning models. We validated these metrics using fungi, plant, and animal phylogenomic datasets, highlighting the ability of the new metrics to pinpoint fragile clades and the sequences responsible. The new approach does not necessitate the investigation of alternative phylogenetic hypotheses, substitution models, or repeated data subset analyses. Our methodology offers a streamlined approach to evaluating major inferred clades and identifying sequences that may distort reconstructed phylogenies using large datasets.
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Affiliation(s)
- Sudip Sharma
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122, USA
- Department of Biology, Temple University, Philadelphia, PA 19122, USA
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122, USA
- Department of Biology, Temple University, Philadelphia, PA 19122, USA
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Saha D, Gregor JB, Hoda S, Eastman KE, Navarrete M, Wisecaver JH, Briggs SD. Candida glabrata maintains two Hap1 homologs, Zcf27 and Zcf4, for distinct roles in ergosterol gene regulation to mediate sterol homeostasis under azole and hypoxic conditions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.20.599910. [PMID: 38979343 PMCID: PMC11230168 DOI: 10.1101/2024.06.20.599910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Candida glabrata exhibits innate resistance to azole antifungal drugs but also has the propensity to rapidly develop clinical drug resistance. Azole drugs, which target Erg11, is one of the three major classes of antifungals used to treat Candida infections. Despite their widespread use, the mechanism controlling azole-induced ERG gene expression and drug resistance in C. glabrata has primarily revolved around Upc2 and/or Pdr1. In this study, we determined the function of two zinc cluster transcription factors, Zcf27 and Zcf4, as direct but distinct regulators of ERG genes. Our phylogenetic analysis revealed C. glabrata Zcf27 and Zcf4 as the closest homologs to Saccharomyces cerevisiae Hap1. Hap1 is a known zinc cluster transcription factor in S. cerevisiae in controlling ERG gene expression under aerobic and hypoxic conditions. Interestingly, when we deleted HAP1 or ZCF27 in either S. cerevisiae or C. glabrata, respectively, both deletion strains showed altered susceptibility to azole drugs, whereas the strain deleted for ZCF4 did not exhibit azole susceptibility. We also determined that the increased azole susceptibility in a zcf27Δ strain is attributed to decreased azole-induced expression of ERG genes, resulting in decreased levels of total ergosterol. Surprisingly, Zcf4 protein expression is barely detected under aerobic conditions but is specifically induced under hypoxic conditions. However, under hypoxic conditions, Zcf4 but not Zcf27 was directly required for the repression of ERG genes. This study provides the first demonstration that Zcf27 and Zcf4 have evolved to serve distinct roles allowing C. glabrata to adapt to specific host and environmental conditions.
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Affiliation(s)
| | | | | | | | | | | | - Scott D. Briggs
- Department of Biochemistry
- Purdue University Institute for Cancer Research
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9
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Pokorny L, Pellicer J, Woudstra Y, Christenhusz MJM, Garnatje T, Palazzesi L, Johnson MG, Maurin O, Françoso E, Roy S, Leitch IJ, Forest F, Baker WJ, Hidalgo O. Genomic incongruence accompanies the evolution of flower symmetry in Eudicots: a case study in the poppy family (Papaveraceae, Ranunculales). FRONTIERS IN PLANT SCIENCE 2024; 15:1340056. [PMID: 38947944 PMCID: PMC11212465 DOI: 10.3389/fpls.2024.1340056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 04/18/2024] [Indexed: 07/02/2024]
Abstract
Reconstructing evolutionary trajectories and transitions that have shaped floral diversity relies heavily on the phylogenetic framework on which traits are modelled. In this study, we focus on the angiosperm order Ranunculales, sister to all other eudicots, to unravel higher-level relationships, especially those tied to evolutionary transitions in flower symmetry within the family Papaveraceae. This family presents an astonishing array of floral diversity, with actinomorphic, disymmetric (two perpendicular symmetry axes), and zygomorphic flowers. We generated nuclear and plastid datasets using the Angiosperms353 universal probe set for target capture sequencing (of 353 single-copy nuclear ortholog genes), together with publicly available transcriptome and plastome data mined from open-access online repositories. We relied on the fossil record of the order Ranunculales to date our phylogenies and to establish a timeline of events. Our phylogenomic workflow shows that nuclear-plastid incongruence accompanies topological uncertainties in Ranunculales. A cocktail of incomplete lineage sorting, post-hybridization introgression, and extinction following rapid speciation most likely explain the observed knots in the topology. These knots coincide with major floral symmetry transitions and thus obscure the order of evolutionary events.
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Affiliation(s)
- Lisa Pokorny
- Real Jardín Botánico (RJB-CSIC), Madrid, Spain
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Jaume Pellicer
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Institut Botànic de Barcelona (IBB), CSIC-CMCNB, Barcelona, Spain
| | - Yannick Woudstra
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Maarten J. M. Christenhusz
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Department of Environment and Agriculture, Curtin University, Perth, WA, Australia
| | - Teresa Garnatje
- Institut Botànic de Barcelona (IBB), CSIC-CMCNB, Barcelona, Spain
- Jardí Botànic Marimurtra, Fundació Carl Faust, Blanes, Spain
| | - Luis Palazzesi
- División Paleobotánica, Museo Argentino de Ciencias Naturales, CONICET, Buenos Aires, Argentina
| | - Matthew G. Johnson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
| | | | | | - Shyamali Roy
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | | | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | | | - Oriane Hidalgo
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Institut Botànic de Barcelona (IBB), CSIC-CMCNB, Barcelona, Spain
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Ma Y, Zhang L, Yang M, Qi Q, Yang Q, López-Pujol J, Wang L, Zhao D. Complete Organelle Genome of the Desiccation-Tolerant (DT) Moss Tortula atrovirens and Comparative Analysis of the Pottiaceae Family. Genes (Basel) 2024; 15:782. [PMID: 38927718 PMCID: PMC11202921 DOI: 10.3390/genes15060782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 06/06/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
Tortula atrovirens (Sm.) Lindb. is an important component of biological soil crusts and possesses an extraordinary tolerance against desiccation in dryland habitats. However, knowledge of the organelle genome of this desiccation-tolerant (DT) moss is still lacking. Here, we assembled the first reported Tortula organelle genome and conducted a comprehensive analysis within the Pottiaceae family. T. atrovirens exhibited the second largest chloroplast genome (129,646 bp) within the Pottiaceae, whereas its mitogenome (105,877 bp) and those of other mosses were smaller in size compared to other land plants. The chloroplast and mitochondrial genomes of T. atrovirens were characterized by the expansion of IR boundaries and the absence of homologous recombination-mediated by large repeats. A total of 57 RNA editing sites were detected through mapping RNA-seq data. Moreover, the gene content and order were highly conserved among the Pottiaceae organelle genomes. Phylogenetic analysis showed that bryophytes are paraphyletic, with their three lineages (hornworts, mosses, and liverworts) and vascular plants forming successive sister clades. Timmiella anomala is clearly separated from the monophyletic Pottiaceae, and T. atrovirens is closely related to Syntrichia filaris within the Pottioideae. In addition, we detected four hypervariable regions for candidate-molecular markers. Our findings provide valuable insights into the organelle genomes of T. atrovirens and the evolutionary relationships within the Pottiaceae family, facilitating future discovery of DT genetic resources from bryophytes.
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Affiliation(s)
- Yang Ma
- School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (Y.M.)
- School of Ecology and Environment, Inner Mongolia University, Hohhot 010020, China
| | - Lifang Zhang
- School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (Y.M.)
| | - Min Yang
- School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (Y.M.)
| | - Qin Qi
- School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (Y.M.)
| | - Qian Yang
- School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (Y.M.)
| | - Jordi López-Pujol
- Botanic Institute of Barcelona (IBB), CSIC-CMCNB, 08038 Barcelona, Spain;
- Escuela de Ciencias Ambientales, Universidad Espíritu Santo (UEES), Samborondón 091650, Ecuador
| | - Lihong Wang
- School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (Y.M.)
| | - Dongping Zhao
- School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (Y.M.)
- Key Laboratory of Herbage & Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
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Gupta A, Mirarab S, Turakhia Y. Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.27.596098. [PMID: 38854139 PMCID: PMC11160643 DOI: 10.1101/2024.05.27.596098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Inference of species trees plays a crucial role in advancing our understanding of evolutionary relationships and has immense significance for diverse biological and medical applications. Extensive genome sequencing efforts are currently in progress across a broad spectrum of life forms, holding the potential to unravel the intricate branching patterns within the tree of life. However, estimating species trees starting from raw genome sequences is quite challenging, and the current cutting-edge methodologies require a series of error-prone steps that are neither entirely automated nor standardized. In this paper, we present ROADIES, a novel pipeline for species tree inference from raw genome assemblies that is fully automated, easy to use, scalable, free from reference bias, and provides flexibility to adjust the tradeoff between accuracy and runtime. The ROADIES pipeline eliminates the need to align whole genomes, choose a single reference species, or pre-select loci such as functional genes found using cumbersome annotation steps. Moreover, it leverages recent advances in phylogenetic inference to allow multi-copy genes, eliminating the need to detect orthology. Using the genomic datasets released from large-scale sequencing consortia across three diverse life forms (placental mammals, pomace flies, and birds), we show that ROADIES infers species trees that are comparable in quality with the state-of-the-art approaches but in a fraction of the time. By incorporating optimal approaches and automating all steps from assembled genomes to species and gene trees, ROADIES is poised to improve the accuracy, scalability, and reproducibility of phylogenomic analyses.
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Affiliation(s)
- Anshu Gupta
- Department of Computer Science and Engineering, University of California, San Diego; San Diego, CA 92093, USA
| | - Siavash Mirarab
- Department of Electrical and Computer Engineering, University of California, San Diego; San Diego, CA 92093, USA
| | - Yatish Turakhia
- Department of Electrical and Computer Engineering, University of California, San Diego; San Diego, CA 92093, USA
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12
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Liu J, Lindstrom AJ, Gong Y, Dong S, Liu YC, Zhang S, Gong X. Eco-evolutionary evidence for the global diversity pattern of Cycas (Cycadaceae). JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:1170-1191. [PMID: 38477647 DOI: 10.1111/jipb.13638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 02/04/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024]
Abstract
The evolution of the latitudinal diversity gradient (LDG), characterized by a peak in diversity toward the tropics, has captured significant attention in evolutionary biology and ecology. However, the inverse LDG (i-LDG) mechanism, wherein species richness increases toward the poles, remains inadequately explored. Cycads are among one of the oldest lineages of extant seed plants and have undergone extensive diversification in the tropics. Intriguingly, the extant cycad abundance exhibits an i-LDG pattern, and the underlying causes for this phenomenon remain largely elusive. Here, using 1,843 nuclear genes from a nearly complete sampling, we conducted comprehensive phylogenomic analyses to establish a robust species-level phylogeny for Cycas, the largest genus within cycads. We then reconstructed the spatial-temporal dynamics and integrated global environmental data to evaluate the roles of species ages, diversification rates, contemporary environment, and conservatism to ancestral niches in shaping the i-LDG pattern. We found Cycas experienced decreased diversification rates, coupled with the cooling temperature since its origin in the Eocene from continental Asia. Different regions have distinctively contributed to the formation of i-LDG for Cycas, with the northern hemisphere acting as evolutionary museums and the southern hemisphere serving as cradles. Moreover, water-related climate variables, specifically precipitation seasonality and potential evapotranspiration, were identified as paramount factors constraining Cycas species richness in the rainforest biome near the equator. Notably, the adherence to ancestral monsoonal climates emerges as a critical factor in sustaining the diversity pattern. This study underscores the imperative of integrating both evolutionary and ecological approaches to comprehensively unravel the mechanisms underpinning global biodiversity patterns.
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Affiliation(s)
- Jian Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Anders J Lindstrom
- Global Biodiversity Conservancy, 144/124 Moo3, Soi Bua Thong, Bangsalae, Sattahip, Chonburi, 20250, Thailand
| | - Yiqing Gong
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, 518004, China
| | - Shanshan Dong
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, 518004, China
| | - Yusheng Chris Liu
- Department of Earth and Environmental Sciences, Indiana University-Indianapolis, Indianapolis, 46202, IN, USA
| | - Shouzhou Zhang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, 518004, China
| | - Xun Gong
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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13
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Zou Y, Zhang Z, Zeng Y, Hu H, Hao Y, Huang S, Li B. Common Methods for Phylogenetic Tree Construction and Their Implementation in R. Bioengineering (Basel) 2024; 11:480. [PMID: 38790347 PMCID: PMC11117635 DOI: 10.3390/bioengineering11050480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/04/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
A phylogenetic tree can reflect the evolutionary relationships between species or gene families, and they play a critical role in modern biological research. In this review, we summarize common methods for constructing phylogenetic trees, including distance methods, maximum parsimony, maximum likelihood, Bayesian inference, and tree-integration methods (supermatrix and supertree). Here we discuss the advantages, shortcomings, and applications of each method and offer relevant codes to construct phylogenetic trees from molecular data using packages and algorithms in R. This review aims to provide comprehensive guidance and reference for researchers seeking to construct phylogenetic trees while also promoting further development and innovation in this field. By offering a clear and concise overview of the different methods available, we hope to enable researchers to select the most appropriate approach for their specific research questions and datasets.
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Affiliation(s)
- Yue Zou
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; (Y.Z.); (Z.Z.); (Y.Z.); (H.H.); (Y.H.)
| | - Zixuan Zhang
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; (Y.Z.); (Z.Z.); (Y.Z.); (H.H.); (Y.H.)
| | - Yujie Zeng
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; (Y.Z.); (Z.Z.); (Y.Z.); (H.H.); (Y.H.)
| | - Hanyue Hu
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; (Y.Z.); (Z.Z.); (Y.Z.); (H.H.); (Y.H.)
| | - Youjin Hao
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; (Y.Z.); (Z.Z.); (Y.Z.); (H.H.); (Y.H.)
| | - Sheng Huang
- Animal Nutrition Institute, Chongqing Academy of Animal Science, Chongqing 402460, China
| | - Bo Li
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China; (Y.Z.); (Z.Z.); (Y.Z.); (H.H.); (Y.H.)
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Wang L, Zhang S, Li H, Wang S. The complete plastome and phylogenetic analysis of Commelina benghalensis L.1753 (Commelinaceae). Mitochondrial DNA B Resour 2024; 9:610-615. [PMID: 38737392 PMCID: PMC11086016 DOI: 10.1080/23802359.2024.2347508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 04/19/2024] [Indexed: 05/14/2024] Open
Abstract
Commelina benghalensis L. 1753, a member of the Commelinaceae family, holds significant medicinal and culinary value. This study represents the first documentation of the sequencing and assembly of the entire plastome of C. benghalensis. The genome spans a total length of 160,663 bp, exhibiting a conventional quadripartite architecture that comprises a large single-copy (LSC) region (87,750 bp), a small single-copy (SSC) region (18,417 bp), and two inverted repeats (IR) regions (both 27,248 bp). In its entirety, the C. benghalensis plastome encompasses 129 genes (with 108 being unique), incorporating 77 individual protein-coding genes, 37 unique tRNA genes, and four unique rRNA genes. Phylogenetic analysis revealed a close resemblance between C. benghalensis and C. communis. The sequencing of this plastome stands to expedite the development of molecular markers and significantly contribute to genetic assays involving this distinctive plant.
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Affiliation(s)
- Liqiang Wang
- College of Pharmacy, Heze University, Heze, Shandong Province, P. R. China
| | - Shuming Zhang
- College of Pharmacy, Heze University, Heze, Shandong Province, P. R. China
| | - Hongqin Li
- College of Pharmacy, Heze University, Heze, Shandong Province, P. R. China
| | - Shu Wang
- College of Pharmacy, Heze University, Heze, Shandong Province, P. R. China
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15
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Balamurugan C, Steenwyk JL, Goldman GH, Rokas A. The evolution of the gliotoxin biosynthetic gene cluster in Penicillium fungi. G3 (BETHESDA, MD.) 2024; 14:jkae063. [PMID: 38507596 PMCID: PMC11075534 DOI: 10.1093/g3journal/jkae063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 12/27/2023] [Accepted: 03/11/2024] [Indexed: 03/22/2024]
Abstract
Fungi biosynthesize diverse secondary metabolites, small organic bioactive molecules with key roles in fungal ecology. Fungal secondary metabolites are often encoded by physically clustered genes known as biosynthetic gene clusters (BGCs). Fungi in the genus Penicillium produce a cadre of secondary metabolites, some of which are useful (e.g. the antibiotic penicillin and the cholesterol-lowering drug mevastatin) and others harmful (e.g. the mycotoxin patulin and the immunosuppressant gliotoxin) to human affairs. Fungal genomes often also encode resistance genes that confer protection against toxic secondary metabolites. Some Penicillium species, such as Penicillium decumbens, are known to produce gliotoxin, a secondary metabolite with known immunosuppressant activity. To investigate the evolutionary conservation of homologs of the gliotoxin BGC and of genes involved in gliotoxin resistance in Penicillium, we analyzed 35 Penicillium genomes from 23 species. Homologous, lesser fragmented gliotoxin BGCs were found in 12 genomes, mostly fragmented remnants of the gliotoxin BGC were found in 21 genomes, whereas the remaining 2 Penicillium genomes lacked the gliotoxin BGC altogether. In contrast, broad conservation of homologs of resistance genes that reside outside the BGC across Penicillium genomes was observed. Evolutionary rate analysis revealed that BGCs with higher numbers of genes evolve slower than BGCs with few genes, suggestive of constraint and potential functional significance or more recent decay. Gene tree-species tree reconciliation analyses suggested that the history of homologs in the gliotoxin BGC across the genus Penicillium likely involved multiple duplications, losses, and horizontal gene transfers. Our analyses suggest that genes encoded in BGCs can have complex evolutionary histories and be retained in genomes long after the loss of secondary metabolite biosynthesis.
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Affiliation(s)
- Charu Balamurugan
- Department of Biological Sciences, Vanderbilt University, VU Station B #35-1634, Nashville, TN 37235, USA
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Jacob L Steenwyk
- Department of Biological Sciences, Vanderbilt University, VU Station B #35-1634, Nashville, TN 37235, USA
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
- Howards Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Gustavo H Goldman
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo CEP 14040-903, Brazil
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, VU Station B #35-1634, Nashville, TN 37235, USA
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
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16
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Mussig AJ, Chaumeil PA, Chuvochina M, Rinke C, Parks DH, Hugenholtz P. Putative genome contamination has minimal impact on the GTDB taxonomy. Microb Genom 2024; 10:001256. [PMID: 38809778 PMCID: PMC11261887 DOI: 10.1099/mgen.0.001256] [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: 01/15/2024] [Accepted: 05/10/2024] [Indexed: 05/31/2024] Open
Abstract
The Genome Taxonomy Database (GTDB) provides a species to domain classification of publicly available genomes based on average nucleotide identity (ANI) (for species) and a concatenated gene phylogeny normalized by evolutionary rates (for genus to phylum), which has been widely adopted by the scientific community. Here, we use the Genome UNClutterer (GUNC) software to identify putatively contaminated genomes in GTDB release 07-RS207. We found that GUNC reported 35,723 genomes as putatively contaminated, comprising 11.25 % of the 317,542 genomes in GTDB release 07-RS207. To assess the impact of this high level of inferred contamination on the delineation of taxa, we created 'clean' versions of the 34,846 putatively contaminated bacterial genomes by removing the most contaminated half. For each clean half, we re-calculated the ANI and concatenated gene phylogeny and found that only 77 (0.22 %) of the genomes were not consistent with their original classification. We conclude that the delineation of taxa in GTDB is robust to the putative contamination detected by GUNC.
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Affiliation(s)
- Aaron J. Mussig
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St Lucia, QLD, Australia
| | - Pierre-Alain Chaumeil
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St Lucia, QLD, Australia
| | - Maria Chuvochina
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St Lucia, QLD, Australia
| | - Christian Rinke
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St Lucia, QLD, Australia
| | - Donovan H. Parks
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St Lucia, QLD, Australia
| | - Philip Hugenholtz
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St Lucia, QLD, Australia
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17
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van der Gulik PTS, Hoff WD, Speijer D. The contours of evolution: In defence of Darwin's tree of life paradigm. Bioessays 2024; 46:e2400012. [PMID: 38436469 DOI: 10.1002/bies.202400012] [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: 01/15/2024] [Revised: 02/12/2024] [Accepted: 02/15/2024] [Indexed: 03/05/2024]
Abstract
Both the concept of a Darwinian tree of life (TOL) and the possibility of its accurate reconstruction have been much criticized. Criticisms mostly revolve around the extensive occurrence of lateral gene transfer (LGT), instances of uptake of complete organisms to become organelles (with the associated subsequent gene transfer to the nucleus), as well as the implications of more subtle aspects of the biological species concept. Here we argue that none of these criticisms are sufficient to abandon the valuable TOL concept and the biological realities it captures. Especially important is the need to conceptually distinguish between organismal trees and gene trees, which necessitates incorporating insights of widely occurring LGT into modern evolutionary theory. We demonstrate that all criticisms, while based on important new findings, do not invalidate the TOL. After considering the implications of these new insights, we find that the contours of evolution are best represented by a TOL.
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Affiliation(s)
| | - Wouter D Hoff
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Dave Speijer
- Department of Medical Biochemistry, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
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18
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Merondun J, Marques CI, Andrade P, Meshcheryagina S, Galván I, Afonso S, Alves JM, Araújo PM, Bachurin G, Balacco J, Bán M, Fedrigo O, Formenti G, Fossøy F, Fülöp A, Golovatin M, Granja S, Hewson C, Honza M, Howe K, Larson G, Marton A, Moskát C, Mountcastle J, Procházka P, Red’kin Y, Sims Y, Šulc M, Tracey A, Wood JMD, Jarvis ED, Hauber ME, Carneiro M, Wolf JBW. Evolution and genetic architecture of sex-limited polymorphism in cuckoos. SCIENCE ADVANCES 2024; 10:eadl5255. [PMID: 38657058 PMCID: PMC11042743 DOI: 10.1126/sciadv.adl5255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 03/20/2024] [Indexed: 04/26/2024]
Abstract
Sex-limited polymorphism has evolved in many species including our own. Yet, we lack a detailed understanding of the underlying genetic variation and evolutionary processes at work. The brood parasitic common cuckoo (Cuculus canorus) is a prime example of female-limited color polymorphism, where adult males are monochromatic gray and females exhibit either gray or rufous plumage. This polymorphism has been hypothesized to be governed by negative frequency-dependent selection whereby the rarer female morph is protected against harassment by males or from mobbing by parasitized host species. Here, we show that female plumage dichromatism maps to the female-restricted genome. We further demonstrate that, consistent with balancing selection, ancestry of the rufous phenotype is shared with the likewise female dichromatic sister species, the oriental cuckoo (Cuculus optatus). This study shows that sex-specific polymorphism in trait variation can be resolved by genetic variation residing on a sex-limited chromosome and be maintained across species boundaries.
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Affiliation(s)
- Justin Merondun
- Division of Evolutionary Biology, LMU Munich, Planegg-Martinsried, Germany
- Department of Ornithology, Max Planck Institute for Biological Intelligence, Seewiesen, Germany
| | - Cristiana I. Marques
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Pedro Andrade
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Swetlana Meshcheryagina
- Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences, Yekaterinburg, Russia
| | - Ismael Galván
- Departamento de Ecología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
| | - Sandra Afonso
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Joel M. Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
- Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, Oxford, OX1 3QY, UK
| | - Pedro M. Araújo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- Department of Life Sciences, MARE–Marine and Environmental Sciences Centre/ARNET–Aquatic Research Network, University of Coimbra, Coimbra, Portugal
| | | | - Jennifer Balacco
- The Vertebrate Genome Lab, Rockefeller University, New York, NY 10065, USA
| | - Miklós Bán
- HUN-REN-UD Behavioral Ecology Research Group, Department of Evolutionary Zoology and Human Biology, University of Debrecen, Debrecen, Hungary
| | - Olivier Fedrigo
- The Vertebrate Genome Lab, Rockefeller University, New York, NY 10065, USA
| | - Giulio Formenti
- The Vertebrate Genome Lab, Rockefeller University, New York, NY 10065, USA
| | - Frode Fossøy
- Centre for Biodiversity Genetics, Norwegian Institute for Nature Research, Trondheim, Norway
| | - Attila Fülöp
- HUN-REN-UD Behavioral Ecology Research Group, Department of Evolutionary Zoology and Human Biology, University of Debrecen, Debrecen, Hungary
- Evolutionary Ecology Group, Hungarian Department of Biology and Ecology, Babeş-Bolyai University, Cluj-Napoca, Romania
- STAR-UBB Institute of Advanced Studies in Science and Technology, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Mikhail Golovatin
- Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences, Yekaterinburg, Russia
| | - Sofia Granja
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, Oxford, OX1 3QY, UK
| | | | - Marcel Honza
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Kerstin Howe
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Greger Larson
- Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, Oxford, OX1 3QY, UK
| | - Attila Marton
- Evolutionary Ecology Group, Faculty of Biology and Geology, Babeș-Bolyai University, Cluj-Napoca, Romania
- Department of Evolutionary Zoology and Human Biology, University of Debrecen, Debrecen, Hungary
| | - Csaba Moskát
- Hungarian Natural History Museum, Budapest, Hungary
| | | | - Petr Procházka
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | | | - Ying Sims
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Michal Šulc
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Alan Tracey
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Erich D. Jarvis
- The Vertebrate Genome Lab, Rockefeller University, New York, NY 10065, USA
| | - Mark E. Hauber
- Advanced Science Research Center and Program in Psychology, Graduate Center of the City University of New York, New York, NY 10031, USA
| | - Miguel Carneiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Jochen B. W. Wolf
- Division of Evolutionary Biology, LMU Munich, Planegg-Martinsried, Germany
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Steenwyk JL, Balamurugan C, Raja HA, Gonçalves C, Li N, Martin F, Berman J, Oberlies NH, Gibbons JG, Goldman GH, Geiser DM, Houbraken J, Hibbett DS, Rokas A. Phylogenomics reveals extensive misidentification of fungal strains from the genus Aspergillus. Microbiol Spectr 2024; 12:e0398023. [PMID: 38445873 PMCID: PMC10986620 DOI: 10.1128/spectrum.03980-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/18/2024] [Indexed: 03/07/2024] Open
Abstract
Modern taxonomic classification is often based on phylogenetic analyses of a few molecular markers, although single-gene studies are still common. Here, we leverage genome-scale molecular phylogenetics (phylogenomics) of species and populations to reconstruct evolutionary relationships in a dense data set of 710 fungal genomes from the biomedically and technologically important genus Aspergillus. To do so, we generated a novel set of 1,362 high-quality molecular markers specific for Aspergillus and provided profile Hidden Markov Models for each, facilitating their use by others. Examining the resulting phylogeny helped resolve ongoing taxonomic controversies, identified new ones, and revealed extensive strain misidentification (7.59% of strains were previously misidentified), underscoring the importance of population-level sampling in species classification. These findings were corroborated using the current standard, taxonomically informative loci. These findings suggest that phylogenomics of species and populations can facilitate accurate taxonomic classifications and reconstructions of the Tree of Life.IMPORTANCEIdentification of fungal species relies on the use of molecular markers. Advances in genomic technologies have made it possible to sequence the genome of any fungal strain, making it possible to use genomic data for the accurate assignment of strains to fungal species (and for the discovery of new ones). We examined the usefulness and current limitations of genomic data using a large data set of 710 publicly available genomes from multiple strains and species of the biomedically, agriculturally, and industrially important genus Aspergillus. Our evolutionary genomic analyses revealed that nearly 8% of publicly available Aspergillus genomes are misidentified. Our work highlights the usefulness of genomic data for fungal systematic biology and suggests that systematic genome sequencing of multiple strains, including reference strains (e.g., type strains), of fungal species will be required to reduce misidentification errors in public databases.
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Affiliation(s)
- Jacob L. Steenwyk
- Howards Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, USA
| | - Charu Balamurugan
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, USA
| | - Huzefa A. Raja
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina, USA
| | - Carla Gonçalves
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, USA
| | - Ningxiao Li
- Department of Plant Pathology, University of California, Davis, California, USA
- USDA-ARS, Salinas, California, USA
| | | | - Judith Berman
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
| | - Nicholas H. Oberlies
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina, USA
| | - John G. Gibbons
- Department of Food Science, University of Massachusetts, Amherst, Massachusetts, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts, USA
- Organismic and Evolutionary Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts, USA
| | - Gustavo H. Goldman
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - David M. Geiser
- Department of Plant Pathology and Environmental Microbiology, Penn State University, University Park, Pennsylvania, USA
| | - Jos Houbraken
- Food and Indoor Mycology, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - David S. Hibbett
- Biology Department, Clark University, Worcester, Massachusetts, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, USA
- Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg, Heidelberg, Germany
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20
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Eme L, Tamarit D. Microbial Diversity and Open Questions about the Deep Tree of Life. Genome Biol Evol 2024; 16:evae053. [PMID: 38620144 PMCID: PMC11018274 DOI: 10.1093/gbe/evae053] [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] [Accepted: 03/11/2024] [Indexed: 04/17/2024] Open
Abstract
In this perspective, we explore the transformative impact and inherent limitations of metagenomics and single-cell genomics on our understanding of microbial diversity and their integration into the Tree of Life. We delve into the key challenges associated with incorporating new microbial lineages into the Tree of Life through advanced phylogenomic approaches. Additionally, we shed light on enduring debates surrounding various aspects of the microbial Tree of Life, focusing on recent advances in some of its deepest nodes, such as the roots of bacteria, archaea, and eukaryotes. We also bring forth current limitations in genome recovery and phylogenomic methodology, as well as new avenues of research to uncover additional key microbial lineages and resolve the shape of the Tree of Life.
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Affiliation(s)
- Laura Eme
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif sur-Yvette, France
| | - Daniel Tamarit
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht 3584CH, The Netherlands
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21
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Bou Dagher L, Madern D, Malbos P, Brochier-Armanet C. Persistent homology reveals strong phylogenetic signal in 3D protein structures. PNAS NEXUS 2024; 3:pgae158. [PMID: 38689707 PMCID: PMC11058471 DOI: 10.1093/pnasnexus/pgae158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 04/01/2024] [Indexed: 05/02/2024]
Abstract
Changes that occur in proteins over time provide a phylogenetic signal that can be used to decipher their evolutionary history and the relationships between organisms. Sequence comparison is the most common way to access this phylogenetic signal, while those based on 3D structure comparisons are still in their infancy. In this study, we propose an effective approach based on Persistent Homology Theory (PH) to extract the phylogenetic information contained in protein structures. PH provides efficient and robust algorithms for extracting and comparing geometric features from noisy datasets at different spatial resolutions. PH has a growing number of applications in the life sciences, including the study of proteins (e.g. classification, folding). However, it has never been used to study the phylogenetic signal they may contain. Here, using 518 protein families, representing 22,940 protein sequences and structures, from 10 major taxonomic groups, we show that distances calculated with PH from protein structures correlate strongly with phylogenetic distances calculated from protein sequences, at both small and large evolutionary scales. We test several methods for calculating PH distances and propose some refinements to improve their relevance for addressing evolutionary questions. This work opens up new perspectives in evolutionary biology by proposing an efficient way to access the phylogenetic signal contained in protein structures, as well as future developments of topological analysis in the life sciences.
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Affiliation(s)
- Léa Bou Dagher
- Université Claude Bernard Lyon 1, CNRS, VetAgro Sup, Laboratoire de Biométrie et BiologieÉvolutive, UMR5558, F-69622 Villeurbanne, France
- Université Claude Bernard Lyon 1, CNRS, Institut Camille Jordan, UMR5208, F-69622 Villeurbanne, France
- Université Libanaise, Laboratoire de Mathématiques, École Doctorale en Science et Technologie, PO BOX 5 Hadath, Liban
| | - Dominique Madern
- University Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | - Philippe Malbos
- Université Claude Bernard Lyon 1, CNRS, Institut Camille Jordan, UMR5208, F-69622 Villeurbanne, France
| | - Céline Brochier-Armanet
- Université Claude Bernard Lyon 1, CNRS, VetAgro Sup, Laboratoire de Biométrie et BiologieÉvolutive, UMR5558, F-69622 Villeurbanne, France
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22
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Tellini N, De Chiara M, Mozzachiodi S, Tattini L, Vischioni C, Naumova ES, Warringer J, Bergström A, Liti G. Ancient and recent origins of shared polymorphisms in yeast. Nat Ecol Evol 2024; 8:761-776. [PMID: 38472432 DOI: 10.1038/s41559-024-02352-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 01/30/2024] [Indexed: 03/14/2024]
Abstract
Shared genetic polymorphisms between populations and species can be ascribed to ancestral variation or to more recent gene flow. Here, we mapped shared polymorphisms in Saccharomyces cerevisiae and its sister species Saccharomyces paradoxus, which diverged 4-6 million years ago. We used a dense map of single-nucleotide diagnostic markers (mean distance 15.6 base pairs) in 1,673 sequenced S. cerevisiae isolates to catalogue 3,852 sequence blocks (≥5 consecutive markers) introgressed from S. paradoxus, with most being recent and clade-specific. The highly diverged wild Chinese S. cerevisiae lineages were depleted of introgressed blocks but retained an excess of individual ancestral polymorphisms derived from incomplete lineage sorting, perhaps due to less dramatic population bottlenecks. In the non-Chinese S. cerevisiae lineages, we inferred major hybridization events and detected cases of overlapping introgressed blocks across distinct clades due to either shared histories or convergent evolution. We experimentally engineered, in otherwise isogenic backgrounds, the introgressed PAD1-FDC1 gene pair that independently arose in two S. cerevisiae clades and revealed that it increases resistance against diverse antifungal drugs. Overall, our study retraces the histories of divergence and secondary contacts across S. cerevisiae and S. paradoxus populations and unveils a functional outcome.
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Affiliation(s)
- Nicolò Tellini
- CNRS, INSERM, IRCAN, Côte d'Azur University, Nice, France
| | | | | | | | | | - Elena S Naumova
- Kurchatov Complex for Genetic Research (GosNIIgenetika), National Research Center 'Kurchatov Institute', Moscow, Russia
| | - Jonas Warringer
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Anders Bergström
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Gianni Liti
- CNRS, INSERM, IRCAN, Côte d'Azur University, Nice, France.
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23
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Ye R, Biango-Daniels M, Steenwyk JL, Rokas A, Louw NL, Nardella R, Wolfe BE. Genomic, transcriptomic, and ecological diversity of Penicillium species in cheese rind microbiomes. Fungal Genet Biol 2024; 171:103862. [PMID: 38218228 DOI: 10.1016/j.fgb.2023.103862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/06/2023] [Accepted: 12/23/2023] [Indexed: 01/15/2024]
Abstract
Although Penicillium molds can have significant impacts on agricultural, industrial, and biomedical systems, the ecological roles of Penicillium species in many microbiomes are not well characterized. Here we utilized a collection of 35 Penicillium strains isolated from cheese rinds to broadly investigate the genomic potential for secondary metabolism in cheese-associated Penicillium species, the impact of Penicillium on bacterial community assembly, and mechanisms of Penicillium-bacteria interactions. Using antiSMASH, we identified 1558 biosynthetic gene clusters, 406 of which were mapped to known pathways, including several mycotoxins and antimicrobial compounds. By measuring bacterial abundance and fungal mRNA expression when culturing representative Penicillium strains with a cheese rind bacterial community, we observed divergent impacts of different Penicillium strains, from strong inhibitors of bacterial growth to those with no impact on bacterial growth or community composition. Through differential mRNA expression analyses, Penicillium strains demonstrated limited differential gene expression in response to the bacterial community. We identified a few shared responses between the eight tested Penicillium strains, primarily upregulation of nutrient metabolic pathways, but we did not identify a conserved fungal response to growth in a multispecies community. These results in tandem suggest high variation among cheese-associated Penicillium species in their ability to shape bacterial community development and highlight important ecological diversity within this iconic genus.
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Affiliation(s)
- Ruby Ye
- Department of Biology, Tufts University, Medford, MA, USA
| | | | - Jacob L Steenwyk
- Department of Molecular and Cellular Biology, University of California-Berkeley, Berkeley, CA, USA
| | - Antonis Rokas
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Nicolas L Louw
- Department of Biology, Tufts University, Medford, MA, USA
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24
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Nguyen NH. Genetics and Genomics of Infectious Diseases in Key Aquaculture Species. BIOLOGY 2024; 13:29. [PMID: 38248460 PMCID: PMC10813283 DOI: 10.3390/biology13010029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/02/2024] [Accepted: 01/02/2024] [Indexed: 01/23/2024]
Abstract
Diseases pose a significant and pressing concern for the sustainable development of the aquaculture sector, particularly as their impact continues to grow due to climatic shifts such as rising water temperatures. While various approaches, ranging from biosecurity measures to vaccines, have been devised to combat infectious diseases, their efficacy is disease and species specific and contingent upon a multitude of factors. The fields of genetics and genomics offer effective tools to control and prevent disease outbreaks in aquatic animal species. In this study, we present the key findings from our recent research, focusing on the genetic resistance to three specific diseases: White Spot Syndrome Virus (WSSV) in white shrimp, Bacterial Necrotic Pancreatitis (BNP) in striped catfish, and skin fluke (a parasitic ailment) in yellowtail kingfish. Our investigations reveal that all three species possess substantial heritable genetic components for disease-resistant traits, indicating their potential responsiveness to artificial selection in genetic improvement programs tailored to combat these diseases. Also, we observed a high genetic association between disease traits and survival rates. Through selective breeding aimed at enhancing resistance to these pathogens, we achieved substantial genetic gains, averaging 10% per generation. These selection programs also contributed positively to the overall production performance and productivity of these species. Although the effects of selection on immunological traits or immune responses were not significant in white shrimp, they yielded favorable results in striped catfish. Furthermore, our genomic analyses, including shallow genome sequencing of pedigreed populations, enriched our understanding of the genomic architecture underlying disease resistance traits. These traits are primarily governed by a polygenic nature, with numerous genes or genetic variants, each with small effects. Leveraging a range of advanced statistical methods, from mixed models to machine and deep learning, we developed prediction models that demonstrated moderate-to-high levels of accuracy in forecasting these disease-related traits. In addition to genomics, our RNA-seq experiments identified several genes that undergo upregulation in response to infection or viral loads within the populations. Preliminary microbiome data, while offering limited predictive accuracy for disease traits in one of our studied species, underscore the potential for combining such data with genome sequence information to enhance predictive power for disease traits in our populations. Lastly, this paper briefly discusses the roles of precision agriculture systems and AI algorithms and outlines the path for future research to expedite the development of disease-resistant genetic lines tailored to our target species. In conclusion, our study underscores the critical role of genetics and genomics in fortifying the aquaculture sector against the threats posed by diseases, paving the way for more sustainable and resilient aquaculture development.
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Affiliation(s)
- Nguyen Hong Nguyen
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
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25
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Hu H, Wang Q, Hao G, Zhou R, Luo D, Cao K, Yan Z, Wang X. Insights into the phylogenetic relationships and species boundaries of the Myricaria squamosa complex (Tamaricaceae) based on the complete chloroplast genome. PeerJ 2023; 11:e16642. [PMID: 38099308 PMCID: PMC10720482 DOI: 10.7717/peerj.16642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 11/19/2023] [Indexed: 12/17/2023] Open
Abstract
Myricaria plants are widely distributed in Eurasia and are helpful for windbreak and embankment protection. Current molecular evidence has led to controversy regarding species boundaries within the Myricaria genus and interspecific phylogenetic relationships between three specific species-M. bracteata, M. paniculata and M. squamosa-which have remained unresolved. This study treated these three unresolved taxa as a species complex, named the M. squamosa complex. The genome skimming approach was used to determine 35 complete plastome sequences and nuclear ribosomal DNA sequences for the said complex and other closely related species, followed by de novo assembly. Comparative analyses were conducted across Myricaria to identify the genome size, gene content, repeat type and number, SSR (simple sequence repeat) abundance, and codon usage bias of chloroplast genomes. Tree-based species delimitation results indicated that M. bracteata, M. paniculata and M. squamosa could not be distinguished and formed two monophyletic lineages (P1 and P2) that were clustered together. Compared to plastome-based species delimitation, the standard nuclear DNA barcode had the lowest species resolution, and the standard chloroplast DNA barcode and group-specific barcodes delimitated a maximum of four out of the five species. Plastid phylogenomics analyses indicated that the monophyletic M. squamosa complex is comprised of two evolutionarily significant units: one in the western Tarim Basin and the other in the eastern Qinghai-Tibet Plateau. This finding contradicts previous species discrimination and promotes the urgent need for taxonomic revision of the threatened genus Myricaria. Dense sampling and plastid genomes will be essential in this effort. The super-barcodes and specific barcode candidates outlined in this study will aid in further studies of evolutionary history.
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Affiliation(s)
- Huan Hu
- Microbial Resources and Drug Development Key Laboratory of Guizhou Tertiary Institution, Zunyi Medical University, Zunyi, China
| | - Qian Wang
- Microbial Resources and Drug Development Key Laboratory of Guizhou Tertiary Institution, Zunyi Medical University, Zunyi, China
| | - Guoqian Hao
- School of Life Science and Food Engineering, Yibin University, Yibin, China
| | - Ruitao Zhou
- School of Preclinical Medicine, Zunyi Medical University, Zunyi, China
| | - Dousheng Luo
- School of Preclinical Medicine, Zunyi Medical University, Zunyi, China
| | - Kejun Cao
- School of Preclinical Medicine, Zunyi Medical University, Zunyi, China
| | - Zhimeng Yan
- School of Medical Information Engineering, Zunyi Medical University, Zunyi, China
| | - Xinyu Wang
- Key Laboratory of Medical Electrophysiology, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, China
- Department of Cardiology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
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26
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Thalén F, Köhne CG, Bleidorn C. Patchwork: Alignment-Based Retrieval and Concatenation of Phylogenetic Markers from Genomic Data. Genome Biol Evol 2023; 15:evad227. [PMID: 38085033 PMCID: PMC10735302 DOI: 10.1093/gbe/evad227] [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] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
Low-coverage whole-genome sequencing (also known as "genome skimming") is becoming an increasingly affordable approach to large-scale phylogenetic analyses. While already routinely used to recover organellar genomes, genome skimming is rather rarely utilized for recovering single-copy nuclear markers. One reason might be that only few tools exist to work with this data type within a phylogenomic context, especially to deal with fragmented genome assemblies. We here present a new software tool called Patchwork for mining phylogenetic markers from highly fragmented short-read assemblies as well as directly from sequence reads. Patchwork is an alignment-based tool that utilizes the sequence aligner DIAMOND and is written in the programming language Julia. Homologous regions are obtained via a sequence similarity search, followed by a "hit stitching" phase, in which adjacent or overlapping regions are merged into a single unit. The novel sliding window algorithm trims away any noncoding regions from the resulting sequence. We demonstrate the utility of Patchwork by recovering near-universal single-copy orthologs within a benchmarking study, and we additionally assess the performance of Patchwork in comparison with other programs. We find that Patchwork allows for accurate retrieval of (putatively) single-copy genes from genome skimming data sets at different sequencing depths with high computational speed, outperforming existing software targeting similar tasks. Patchwork is released under the GNU General Public License version 3. Installation instructions, additional documentation, and the source code itself are all available via GitHub at https://github.com/fethalen/Patchwork.
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Affiliation(s)
- Felix Thalén
- Department for Animal Evolution and Biodiversity, Georg-August-Universität Göttingen, Göttingen 37073, Germany
- Cardio-CARE AG, Medizincampus Davos, Davos Wolfgang 7265, Switzerland
| | - Clara G Köhne
- Department for Animal Evolution and Biodiversity, Georg-August-Universität Göttingen, Göttingen 37073, Germany
| | - Christoph Bleidorn
- Department for Animal Evolution and Biodiversity, Georg-August-Universität Göttingen, Göttingen 37073, Germany
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27
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Steenwyk JL, Knowles S, Bastos RW, Balamurugan C, Rinker D, Mead ME, Roberts CD, Raja HA, Li Y, Colabardini AC, de Castro PA, dos Reis TF, Canóvas D, Sanchez RL, Lagrou K, Torrado E, Rodrigues F, Oberlies NH, Zhou X, Goldman GH, Rokas A. Evolutionary origin, population diversity, and diagnostics for a cryptic hybrid pathogen. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.03.547508. [PMID: 37461539 PMCID: PMC10350022 DOI: 10.1101/2023.07.03.547508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Cryptic fungal pathogens pose significant identification and disease management challenges due to their morphological resemblance to known pathogenic species while harboring genetic and (often) infectionrelevant trait differences. The cryptic fungal pathogen Aspergillus latus, an allodiploid hybrid originating from Aspergillus spinulosporus and an unknown close relative of Aspergillus quadrilineatus within section Nidulantes, remains poorly understood. The absence of accurate diagnostics for A. latus has led to misidentifications, hindering epidemiological studies and the design of effective treatment plans. We conducted an in-depth investigation of the genomes and phenotypes of 44 globally distributed isolates (41 clinical isolates and three type strains) from Aspergillus section Nidulantes. We found that 21 clinical isolates were A. latus; notably, standard methods of pathogen identification misidentified all A. latus isolates. The remaining isolates were identified as A. spinulosporus (8), A. quadrilineatus (1), or A. nidulans (11). Phylogenomic analyses shed light on the origin of A. latus, indicating one or two hybridization events gave rise to the species during the Miocene, approximately 15.4 to 8.8 million years ago. Characterizing the A. latus pangenome uncovered substantial genetic diversity within gene families and biosynthetic gene clusters. Transcriptomic analysis revealed that both parental genomes are actively expressed in nearly equal proportions and respond to environmental stimuli. Further investigation into infection-relevant chemical and physiological traits, including drug resistance profiles, growth under oxidative stress conditions, and secondary metabolite biosynthesis, highlight distinct phenotypic profiles of the hybrid A. latus compared to its parental and closely related species. Leveraging our comprehensive genomic and phenotypic analyses, we propose five genomic and phenotypic markers as diagnostics for A. latus species identification. These findings provide valuable insights into the evolutionary origin, genomic outcome, and phenotypic implications of hybridization in a cryptic fungal pathogen, thus enhancing our understanding of the underlying processes contributing to fungal pathogenesis. Furthermore, our study underscores the effectiveness of extensive genomic and phenotypic analyses as a promising approach for developing diagnostics applicable to future investigations of cryptic and emerging pathogens.
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Affiliation(s)
- Jacob L. Steenwyk
- Howards Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Vanderbilt University, Department of Biological Sciences, VU Station B #35–1634, Nashville, TN 37235, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Sonja Knowles
- Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Rafael W. Bastos
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
- Department of Microbiology and Parasitology, Bioscience Center, Federal University of Rio Grande do Norte, Natal-RN, Brazil
| | - Charu Balamurugan
- Vanderbilt University, Department of Biological Sciences, VU Station B #35–1634, Nashville, TN 37235, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - David Rinker
- Vanderbilt University, Department of Biological Sciences, VU Station B #35–1634, Nashville, TN 37235, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Matthew E. Mead
- Vanderbilt University, Department of Biological Sciences, VU Station B #35–1634, Nashville, TN 37235, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Christopher D. Roberts
- Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Huzefa A. Raja
- Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Yuanning Li
- Institute of Marine Science and Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China
| | - Ana Cristina Colabardini
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Patrícia Alves de Castro
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Thaila Fernanda dos Reis
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - David Canóvas
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Rafael Luperini Sanchez
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Katrien Lagrou
- Department of Microbiology, Immunology and Transplantation, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
- Department of Laboratory Medicine and National Reference Centre for Mycosis, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Egídio Torrado
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4715-495 Braga, Portugal; ICVS/3B’s-PT Government Associate Laboratory, 4715-495 Braga, Portugal
| | - Fernando Rodrigues
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4715-495 Braga, Portugal; ICVS/3B’s-PT Government Associate Laboratory, 4715-495 Braga, Portugal
| | - Nicholas H. Oberlies
- Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Xiaofan Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Gustavo H. Goldman
- Faculdade de Ciencias Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Antonis Rokas
- Vanderbilt University, Department of Biological Sciences, VU Station B #35–1634, Nashville, TN 37235, United States of America
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
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