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Isaychev A, Schepetov D, Zhou Y, Britayev TA, Ivanenko VN. New Myzostomids (Annelida) in Symbiosis with Feather Stars in the Shallow Waters of the South China Sea (Hainan Island). Animals (Basel) 2024; 14:2265. [PMID: 39123791 PMCID: PMC11310986 DOI: 10.3390/ani14152265] [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: 12/18/2023] [Revised: 07/22/2024] [Accepted: 07/29/2024] [Indexed: 08/12/2024] Open
Abstract
This research delves into the molecular and morphological characteristics of myzostomid worms associated with common shallow-water feather stars (Echinodermata: Crinoidea: Comatulidae) in the coastal waters near Sanya, Hainan Island. Through the examination of specimens collected at depths of up to 10 m using scuba diving techniques, we describe three new species (Myzostoma ordinatum sp. nov., M. scopus sp. nov., and M. solare sp. nov.) and report the first record of Myzostoma polycyclus Atkins, 1927 in the South China Sea. The absence of overlap with the seven previously documented Myzostomida species in the shallow waters of Hong Kong and Shenzhen reveals significant gaps in our understanding of marine biodiversity in the South China Sea. These findings, combined with an analysis of available molecular data, underscore the potential existence of unexplored and diverse symbiotic relationships among marine invertebrates within the region.
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Affiliation(s)
- Alexander Isaychev
- Biological Faculty, Shenzhen MSU-BIT University, Shenzhen 518172, China; (A.I.); (D.S.); (Y.Z.)
| | - Dimitry Schepetov
- Biological Faculty, Shenzhen MSU-BIT University, Shenzhen 518172, China; (A.I.); (D.S.); (Y.Z.)
- Department of Invertebrate Zoology, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Yutong Zhou
- Biological Faculty, Shenzhen MSU-BIT University, Shenzhen 518172, China; (A.I.); (D.S.); (Y.Z.)
| | - Temir A. Britayev
- A.N. Severtsov Institute of Ecology and Evolution Russian Academy of Sciences, Moscow 129164, Russia;
| | - Viatcheslav N. Ivanenko
- Biological Faculty, Shenzhen MSU-BIT University, Shenzhen 518172, China; (A.I.); (D.S.); (Y.Z.)
- Department of Invertebrate Zoology, Lomonosov Moscow State University, Moscow 119992, Russia
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2
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Melo BF, Conde-Saldaña CC, Villa-Navarro FA, McMahan CD, Oliveira C. Phylogeographic patterns of Cyphocharax from trans-Andean rivers and northward expansion to lower Central America (Teleostei, Curimatidae). JOURNAL OF FISH BIOLOGY 2024; 105:314-325. [PMID: 38757464 DOI: 10.1111/jfb.15777] [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: 08/31/2023] [Revised: 02/13/2024] [Accepted: 02/21/2024] [Indexed: 05/18/2024]
Abstract
Phylogenetic analyses of mitochondrial and nuclear data of 31 specimens of Cyphocharax from trans-Andean rivers support the presence of one lineage of Cyphocharax aspilos in Lago Maracaibo and three cryptic lineages of Cyphocharax magdalenae: (1) Cauca-Magdalena and Ranchería, (2) León and Atrato, and (3) Chucunaque-Tuira, Santa María, and Chiriquí basins of Central America. Results suggest that the Serranía del Perijá facilitated Late Miocene cladogenetic events, whereas post-Isthmian C. magdalenae expansion was enabled by gene flow across the lower Magdalena valley and Central American lowlands. Time-calibrated phylogenetics indicate that the C. magdalenae colonized lower Central America in the Pliocene (3.7 MYA; Ma), the divergence Atrato-Magdalena occurred in Late Pliocene (3.0 Ma) and the split Ranchería-Magdalena during the Middle Pleistocene (1.3 Ma). Updated geographic distribution data support the hypothesis that the Cordillera de Talamanca functions as a barrier to northward expansion of C. magdalenae in Central America.
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Affiliation(s)
- Bruno F Melo
- Department of Ichthyology, American Museum of Natural History, New York, New York, USA
| | | | | | | | - Claudio Oliveira
- Instituto de Biociências, Universidade Estadual Paulista, Botucatu, Brazil
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3
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Berman HL, Goltsman DSA, Anderson M, Relman DA, Callahan BJ. Gardnerella diversity and ecology in pregnancy and preterm birth. mSystems 2024; 9:e0133923. [PMID: 38752784 PMCID: PMC11338264 DOI: 10.1128/msystems.01339-23] [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: 12/18/2023] [Accepted: 04/08/2024] [Indexed: 06/19/2024] Open
Abstract
The vaginal microbiome has been linked to negative health outcomes including preterm birth. Specific taxa, including Gardnerella spp., have been identified as risk factors for these conditions. Historically, microbiome analysis methods have treated all Gardnerella spp. as one species, but the broad diversity of Gardnerella has become more apparent. We explore the diversity of Gardnerella clades and genomic species in the vaginal microbiome of pregnant women and their associations with microbiome composition and preterm birth. Relative abundance of Gardnerella clades and genomic species and other taxa was quantified in shotgun metagenomic sequencing data from three distinct cohorts of pregnant women. We also assessed the diversity and abundance of Gardnerella variants in 16S rRNA gene amplicon sequencing data from seven previously conducted studies in differing populations. Individual microbiomes often contained multiple Gardnerella variants, and the number of clades was associated with increased microbial load, or the ratio of non-human reads to human reads. Taxon co-occurrence patterns were largely consistent across Gardnerella clades and among cohorts. Some variants previously described as rare were prevalent in other cohorts, highlighting the importance of surveying a diverse set of populations to fully capture the diversity of Gardnerella. The diversity of Gardnerella both across populations and within individual vaginal microbiomes has long been unappreciated, as has been the intra-species diversity of many other members of the vaginal microbiome. The broad genomic diversity of Gardnerella has led to its reclassification as multiple species; here we demonstrate the diversity of Gardnerella found within and between vaginal microbiomes.IMPORTANCEThe present study shows that single microbiomes can contain all currently known species of Gardnerella and that multiple similar species can exist within the same environment. Furthermore, surveys of demographically distinct populations suggest that some species appear more commonly in certain populations. Further studies in broad and diverse populations will be necessary to fully understand the ecological roles of each Gardnerella sp., how they can co-exist, and their distinct impacts on microbial communities, preterm birth, and other health outcomes.
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Affiliation(s)
- Hanna L. Berman
- Department of
Population Health and Pathobiology, North Carolina State
University, Raleigh,
North Carolina, USA
| | - Daniela S. Aliaga Goltsman
- Department of
Microbiology and Immunology, Stanford University School of
Medicine, Stanford,
California, USA
- Department of
Medicine, Stanford University School of
Medicine, Stanford,
California, USA
| | - Megan Anderson
- Department of
Population Health and Pathobiology, North Carolina State
University, Raleigh,
North Carolina, USA
| | - David A. Relman
- Department of
Microbiology and Immunology, Stanford University School of
Medicine, Stanford,
California, USA
- Department of
Medicine, Stanford University School of
Medicine, Stanford,
California, USA
- Infectious Diseases
Section, Veterans Affairs Palo Alto Health Care
System, Palo Alto,
California, USA
| | - Benjamin J. Callahan
- Department of
Population Health and Pathobiology, North Carolina State
University, Raleigh,
North Carolina, USA
- Bioinformatics
Research Center, North Carolina State
University, Raleigh,
North Carolina, USA
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Perina G, Camacho A, Cooper SJ, Floeckner S, Blyth AJ, Saccò M. An integrated approach to explore the monophyletic status of the cosmopolitan genus Hexabathynella (Crustacea, Bathynellacea, Parabathynellidae): two new species from Rottnest Island (Wadjemup), Western Australia. SYST BIODIVERS 2023. [DOI: 10.1080/14772000.2022.2151662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Giulia Perina
- Western Australian Museum Collections and Research, 49 Kew Street, Welshpool, 6106, Western Australia, Australia
- Biologic Environmental Survey, 24-26 Wickham St, East Perth, 6004, Western Australia, Australia
- Subterranean Research and Groundwater Ecology (SuRGE) Group, Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, 6102, Western Australia, Australia
| | - Ana Camacho
- Museo Nacional de Ciencias Naturales (CSIC), Dpto. Biodiversidad y Biología Evolutiva, C/José Gutiérrez Abascal 2, Madrid, 28006, Spain
| | - Steven J.B. Cooper
- Environment Institute and Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of Adelaide, 5005, South Australia, Australia
- Evolutionary Genomics, South Australian Museum, North Terrace, Adelaide, 5000, South Australia, Australia
| | - Stephanie Floeckner
- Biologic Environmental Survey, 24-26 Wickham St, East Perth, 6004, Western Australia, Australia
| | - Alison J. Blyth
- The, Institute for Geoscience Research, School of Earth and Planetary Sciences, Curtin University, Perth, 6102, Western Australia, Australia
| | - Mattia Saccò
- Subterranean Research and Groundwater Ecology (SuRGE) Group, Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, 6102, Western Australia, Australia
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Swinnen K, Verstraete K, Baratto C, Hardy L, De Vos M, Topalovic M, Claessen G, Quarck R, Belge C, Vachiery JL, Janssens W, Delcroix M. Machine learning to differentiate pulmonary hypertension due to left heart disease from pulmonary arterial hypertension. ERJ Open Res 2023; 9:00229-2023. [PMID: 37727672 PMCID: PMC10505948 DOI: 10.1183/23120541.00229-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 07/04/2023] [Indexed: 09/21/2023] Open
Abstract
Background and aims Pulmonary hypertension due to left heart disease (PH-LHD) is the most frequent form of PH. As differential diagnosis with pulmonary arterial hypertension (PAH) has therapeutic implications, it is important to accurately and noninvasively differentiate PH-LHD from PAH before referral to PH centres. The aim was to develop and validate a machine learning (ML) model to improve prediction of PH-LHD in a population of PAH and PH-LHD patients. Methods Noninvasive PH-LHD predictors from 172 PAH and 172 PH-LHD patients from the PH centre database at the University Hospitals of Leuven (Leuven, Belgium) were used to develop an ML model. The Jacobs score was used as performance benchmark. The dataset was split into a training and test set (70:30) and the best model was selected after 10-fold cross-validation on the training dataset (n=240). The final model was externally validated using 165 patients (91 PAH, 74 PH-LHD) from Erasme Hospital (Brussels, Belgium). Results In the internal test dataset (n=104), a random forest-based model correctly diagnosed 70% of PH-LHD patients (sensitivity: n=35/50), with 100% positive predicted value, 78% negative predicted value and 100% specificity. The model outperformed the Jacobs score, which identified 18% (n=9/50) of the patients with PH-LHD without false positives. In external validation, the model had 64% sensitivity at 100% specificity, while the Jacobs score had a sensitivity of 3% for no false positives. Conclusions ML significantly improves the sensitivity of PH-LHD prediction at 100% specificity. Such a model may substantially reduce the number of patients referred for invasive diagnostics without missing PAH diagnoses.
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Affiliation(s)
- Katleen Swinnen
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism (CHROMETA), KU Leuven, Leuven, Belgium
- These authors contributed equally
| | - Kenneth Verstraete
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism (CHROMETA), KU Leuven, Leuven, Belgium
- STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics, Department of Electrical Engineering (ESAT), KU Leuven, Leuven, Belgium
- These authors contributed equally
| | - Claudia Baratto
- Department of Cardiology, Ospedale San Luca IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Laura Hardy
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism (CHROMETA), KU Leuven, Leuven, Belgium
| | - Maarten De Vos
- STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics, Department of Electrical Engineering (ESAT), KU Leuven, Leuven, Belgium
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | | | - Guido Claessen
- Department of Cardiology, University Hospitals of Leuven, Leuven, Belgium
| | - Rozenn Quarck
- Clinical Department of Respiratory Diseases, Centre of Pulmonary Vascular Diseases, University Hospitals of Leuven, BREATHE, CHROMETA, KU Leuven, Leuven, Belgium
| | - Catharina Belge
- Clinical Department of Respiratory Diseases, Centre of Pulmonary Vascular Diseases, University Hospitals of Leuven, BREATHE, CHROMETA, KU Leuven, Leuven, Belgium
| | - Jean-Luc Vachiery
- Department of Cardiology, Ospedale San Luca IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Wim Janssens
- Clinical Department of Respiratory Diseases, Centre of Pulmonary Vascular Diseases, University Hospitals of Leuven, BREATHE, CHROMETA, KU Leuven, Leuven, Belgium
| | - Marion Delcroix
- Clinical Department of Respiratory Diseases, Centre of Pulmonary Vascular Diseases, University Hospitals of Leuven, BREATHE, CHROMETA, KU Leuven, Leuven, Belgium
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Ao K, Rohmann PFW, Huang S, Li L, Lipka V, Chen S, Wiermer M, Li X. Puncta-localized TRAF domain protein TC1b contributes to the autoimmunity of snc1. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:591-612. [PMID: 36799433 DOI: 10.1111/tpj.16155] [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: 06/07/2022] [Accepted: 02/07/2023] [Indexed: 05/04/2023]
Abstract
Immune receptors play important roles in the perception of pathogens and initiation of immune responses in both plants and animals. Intracellular nucleotide-binding domain leucine-rich repeat (NLR)-type receptors constitute a major class of receptors in vascular plants. In the Arabidopsis thaliana mutant suppressor of npr1-1, constitutive 1 (snc1), a gain-of-function mutation in the NLR gene SNC1 leads to SNC1 overaccumulation and constitutive activation of defense responses. From a CRISPR/Cas9-based reverse genetics screen in the snc1 autoimmune background, we identified that mutations in TRAF CANDIDATE 1b (TC1b), a gene encoding a protein with four tumor necrosis factor receptor-associated factor (TRAF) domains, can suppress snc1 phenotypes. TC1b does not appear to be a general immune regulator as it is not required for defense mediated by other tested immune receptors. TC1b also does not physically associate with SNC1, affect SNC1 accumulation, or affect signaling of the downstream helper NLRs represented by ACTIVATED DISEASE RESISTANCE PROTEIN 1-L2 (ADR1-L2), suggesting that TC1b impacts snc1 autoimmunity in a unique way. TC1b can form oligomers and localizes to punctate structures of unknown function. The puncta localization of TC1b strictly requires its coiled-coil (CC) domain, whereas the functionality of TC1b requires the four TRAF domains in addition to the CC. Overall, we uncovered the TRAF domain protein TC1b as a novel positive contributor to plant immunity.
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Affiliation(s)
- Kevin Ao
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Philipp F W Rohmann
- Molecular Biology of Plant-Microbe Interactions Research Group, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, D-37077, Goettingen, Germany
- Biochemistry of Plant-Microbe Interactions, Dahlem Centre of Plant Sciences, Institute of Biology, Freie Universität Berlin, 14195, Berlin, Germany
| | - Shuai Huang
- Department of Molecular Genetics, College of Arts and Sciences, Ohio State University, Columbus, Ohio, 43210, USA
| | - Lin Li
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Volker Lipka
- Department of Plant Cell Biology, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, D-37077, Goettingen, Germany
- Central Microscopy Facility of the Faculty of Biology and Psychology, University of Goettingen, D-37077, Goettingen, Germany
| | - She Chen
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Marcel Wiermer
- Molecular Biology of Plant-Microbe Interactions Research Group, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, D-37077, Goettingen, Germany
- Biochemistry of Plant-Microbe Interactions, Dahlem Centre of Plant Sciences, Institute of Biology, Freie Universität Berlin, 14195, Berlin, Germany
| | - Xin Li
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
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Wang Y, Cai X, Zhang Y, Hörandl E, Zhang Z, He L. The male-heterogametic sex determination system on chromosome 15 of Salix triandra and Salix arbutifolia reveals ancestral male heterogamety and subsequent turnover events in the genus Salix. Heredity (Edinb) 2023; 130:122-134. [PMID: 36593355 PMCID: PMC9981616 DOI: 10.1038/s41437-022-00586-2] [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: 09/14/2022] [Revised: 12/08/2022] [Accepted: 12/09/2022] [Indexed: 01/03/2023] Open
Abstract
Dioecious Salix evolved more than 45 million years ago, but have homomorphic sex chromosomes, suggesting that turnover event(s) prevented major differentiation. Sex chromosome turnover events have been inferred in the sister genus Populus. The genus Salix includes two main clades, Salix and Vetrix, with several previously studied Vetrix clade species having female-heterogametic (ZW) or male-heterogametic (XY) sex-determining systems (SDSs) on chromosome 15, while three Salix clade species have XY SDSs on chromosome 7. We here studied two basal taxa of the Vetrix clade, S. arbutifolia and S. triandra using S. purpurea as the reference genome. Analyses of whole genome resequencing data for genome-wide associations (GWAS) with the sexes and genetic differentiation between the sexes (FST values) showed that both species have male heterogamety with a sex-determining locus on chromosome 15, suggesting an early turnover event within the Vetrix clade, perhaps promoted by sexually antagonistic or (and) sex-ratio selection. Changepoint analysis based on FST values identified small sex-linked regions of ~3.33 Mb and ~2.80 Mb in S. arbutifolia and S. triandra, respectively. The SDS of S. arbutifolia was consistent with recent results that used its own genome as reference. Ancestral state reconstruction of SDS suggests that at least two turnover events occurred in Salix.
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Affiliation(s)
- Yi Wang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Xinjie Cai
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yue Zhang
- Shenyang Arboretum, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, Göttingen, Germany
| | - Zhixiang Zhang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China.
| | - Li He
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China.
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Ancient proteins resolve controversy over the identity of Genyornis eggshell. Proc Natl Acad Sci U S A 2022; 119:e2109326119. [PMID: 35609205 PMCID: PMC9995833 DOI: 10.1073/pnas.2109326119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The realization that ancient biomolecules are preserved in "fossil" samples has revolutionized archaeological science. Protein sequences survive longer than DNA, but their phylogenetic resolution is inferior; therefore, careful assessment of the research questions is required. Here, we show the potential of ancient proteins preserved in Pleistocene eggshell in addressing a longstanding controversy in human and animal evolution: the identity of the extinct bird that laid large eggs which were exploited by Australia's indigenous people. The eggs had been originally attributed to the iconic extinct flightless bird Genyornis newtoni (†Dromornithidae, Galloanseres) and were subsequently dated to before 50 ± 5 ka by Miller et al. [Nat. Commun. 7, 10496 (2016)]. This was taken to represent the likely extinction date for this endemic megafaunal species and thus implied a role of humans in its demise. A contrasting hypothesis, according to which the eggs were laid by a large mound-builder megapode (Megapodiidae, Galliformes), would therefore acquit humans of their responsibility in the extinction of Genyornis. Ancient protein sequences were reconstructed and used to assess the evolutionary proximity of the undetermined eggshell to extant birds, rejecting the megapode hypothesis. Authentic ancient DNA could not be confirmed from these highly degraded samples, but morphometric data also support the attribution of the eggshell to Genyornis. When used in triangulation to address well-defined hypotheses, paleoproteomics is a powerful tool for reconstructing the evolutionary history in ancient samples. In addition to the clarification of phylogenetic placement, these data provide a more nuanced understanding of the modes of interactions between humans and their environment.
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Fleet J, Ansari M, Pittman JK. Phylogenetic analysis and structural prediction reveal the potential functional diversity between green algae SWEET transporters. FRONTIERS IN PLANT SCIENCE 2022; 13:960133. [PMID: 36186040 PMCID: PMC9520054 DOI: 10.3389/fpls.2022.960133] [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: 06/02/2022] [Accepted: 08/25/2022] [Indexed: 06/16/2023]
Abstract
Sugar-Will-Eventually-be-Exported-Transporters (SWEETs) are an important family of sugar transporters that appear to be ubiquitous in all organisms. Recent research has determined the structure of SWEETs in higher plants, identified specific residues required for monosaccharide or disaccharide transport, and begun to understand the specific functions of individual plant SWEET proteins. However, in green algae (Chlorophyta) these transporters are poorly characterised. This study identified SWEET proteins from across representative Chlorophyta with the aim to characterise their phylogenetic relationships and perform protein structure modelling in order to inform functional prediction. The algal genomes analysed encoded between one and six SWEET proteins, which is much less than a typical higher plant. Phylogenetic analysis identified distinct clusters of over 70 SWEET protein sequences, taken from almost 30 algal genomes. These clusters remain separate from representative higher or non-vascular plant SWEETs, but are close to fungi SWEETs. Subcellular localisation predictions and analysis of conserved amino acid residues revealed variation between SWEET proteins of different clusters, suggesting different functionality. These findings also showed conservation of key residues at the substrate-binding site, indicating a similar mechanism of substrate selectivity and transport to previously characterised higher plant monosaccharide-transporting SWEET proteins. Future work is now required to confirm the predicted sugar transport specificity and determine the functional role of these algal SWEET proteins.
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Affiliation(s)
- Jack Fleet
- Department of Earth and Environmental Sciences, Faculty of Science and Engineering, School of Natural Sciences, The University of Manchester, Manchester, United Kingdom
| | - Mujtaba Ansari
- School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Jon K. Pittman
- Department of Earth and Environmental Sciences, Faculty of Science and Engineering, School of Natural Sciences, The University of Manchester, Manchester, United Kingdom
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10
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Liu W, Yin X, Chen Y, Li M, Han D, Liu W. Quantitative determination of acacia honey adulteration by terahertz-frequency dielectric properties as an alternative technique. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 274:121106. [PMID: 35279002 DOI: 10.1016/j.saa.2022.121106] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 02/24/2022] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
The dielectric characteristics in the terahertz region contribute to a revealing insight into the material components and provide intermolecular information. The dielectric properties of adulterated honey, described as the real and imaginary parts of the complex dielectric constant (Re[ε] and Im[ε]), were obtained from 0.3 to 1.5 THz. The relationship between invert syrup proportions and complex dielectric constants at different frequencies implied the possibility of using the dielectric property as an indicator of honey authenticity. The selected effective dielectric variables of Re[ε] and Im[ε] and their combination were chosen by stability competitive adaptive reweighted sampling (SCARS) algorithm and then used to establish PLS models. The accuracy and uncertainty result revealed SCARS-PLS model based on the combination of Re[ε] and Im[ε] is the best model relatively. These findings indicated the potential utility of this rapid, non-destructive, and on-site method for authenticity verification.
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Affiliation(s)
- Wen Liu
- School of Chemical Engineering, Xiangtan University, Xiangtan 411105, PR China.
| | - Xurong Yin
- School of Chemical Engineering, Xiangtan University, Xiangtan 411105, PR China
| | - Yanjing Chen
- School of Chemical Engineering, Xiangtan University, Xiangtan 411105, PR China
| | - Ming Li
- Tianjin Key Laboratory of Food Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin 300134, PR China
| | - Donghai Han
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, PR China.
| | - Wenjie Liu
- School of Chemical Engineering, Xiangtan University, Xiangtan 411105, PR China
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11
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Świecimska M, Golińska P, Goodfellow M. Genome-based classification of Streptomyces pinistramenti sp. nov., a novel actinomycete isolated from a pine forest soil in Poland with a focus on its biotechnological and ecological properties. Antonie van Leeuwenhoek 2022; 115:783-800. [DOI: 10.1007/s10482-022-01734-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/19/2022] [Indexed: 10/18/2022]
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12
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Looney BP, Manz C, Matheny PB, Adamčík S. Systematic revision of the Roseinae clade of Russula, with a focus on eastern North American taxa. Mycologia 2022; 114:270-302. [PMID: 35394897 DOI: 10.1080/00275514.2021.2018881] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The Roseinae clade is a lineage of the genus Russula primarily composed of species of Russula subsect. Roseinae. Species in this morphologically distinct clade possess a white to pale cream spore print, mild taste, positive reaction to sulfovanillin, and primordial hyphae with acid-resistant crystals in the pileipellis. Here, we present a morphological and phylogenetic assessment that distinguishes seven eastern North American species of the core Roseinae lineage and a new subsection, Russula subsection Albidinae, to accommodate members of the Albida clade. We assign the previously described species R. peckii, R. rubellipes, and R. pseudopeckii to three species-level clades, and three other species, R. cardinalis, R. cordata, and R. rheubarbarina, are described as new. Comparative morphological analyses reveal differences in the conformation of terminal elements in the pileipellis, spore size, hymenial cystidia contents, and pigmentation on the stipe surface as key features to recognize species in the group. Based on the analysis of publicly available data, we recognize a potential total of nine temperate North American species within R. subsect. Roseinae, in addition to four from Central America, two from Europe, and 14 from Asia.
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Affiliation(s)
- Brian P Looney
- Department of Biology, Clark University, Worcester, Massachusetts 01610
| | - Cathrin Manz
- Mycology Research Group, Faculty of Biological Sciences, Goethe University, 60438 Frankfurt am Main, Germany
| | - P Brandon Matheny
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Slavomír Adamčík
- Laboratory of Molecular Ecology and Mycology, Institute of Botany, Plant Science and Biodiversity Center, Slovak Academy of Sciences, Bratislava, 84523 Slovakia
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13
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Cardoni S, Piredda R, Denk T, Grimm GW, Papageorgiou AC, Schulze E, Scoppola A, Salehi Shanjani P, Suyama Y, Tomaru N, Worth JRP, Cosimo Simeone M. 5S-IGS rDNA in wind-pollinated trees (Fagus L.) encapsulates 55 million years of reticulate evolution and hybrid origins of modern species. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:909-926. [PMID: 34808015 PMCID: PMC9299691 DOI: 10.1111/tpj.15601] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 11/02/2021] [Accepted: 11/18/2021] [Indexed: 05/31/2023]
Abstract
Standard models of plant speciation assume strictly dichotomous genealogies in which a species, the ancestor, is replaced by two offspring species. The reality in wind-pollinated trees with long evolutionary histories is more complex: species evolve from other species through isolation when genetic drift exceeds gene flow; lineage mixing can give rise to new species (hybrid taxa such as nothospecies and allopolyploids). The multi-copy, potentially multi-locus 5S rDNA is one of few gene regions conserving signal from dichotomous and reticulate evolutionary processes down to the level of intra-genomic recombination. Therefore, it can provide unique insights into the dynamic speciation processes of lineages that diversified tens of millions of years ago. Here, we provide the first high-throughput sequencing (HTS) of the 5S intergenic spacers (5S-IGS) for a lineage of wind-pollinated subtropical to temperate trees, the Fagus crenata - F. sylvatica s.l. lineage, and its distant relative F. japonica. The observed 4963 unique 5S-IGS variants reflect a complex history of hybrid origins, lineage sorting, mixing via secondary gene flow, and intra-genomic competition between two or more paralogous-homoeologous 5S rDNA lineages. We show that modern species are genetic mosaics and represent a striking case of ongoing reticulate evolution during the past 55 million years.
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Affiliation(s)
- Simone Cardoni
- Department of Agricultural and Forestry Science (DAFNE)Università degli studi della TusciaViterbo01100Italy
| | - Roberta Piredda
- Department of Veterinary MedicineUniversity of Bari ‘Aldo Moro’Valenzano70010Italy
| | - Thomas Denk
- Swedish Museum of Natural HistoryStockholm10405Sweden
| | | | | | | | - Anna Scoppola
- Department of Agricultural and Forestry Science (DAFNE)Università degli studi della TusciaViterbo01100Italy
| | - Parvin Salehi Shanjani
- Natural Resources Gene Bank, Research Institute of Forests and RangelandsAgricultural Research, Education and Extension OrganizationTehranIran
| | - Yoshihisa Suyama
- Graduate School of Agricultural ScienceTohoku UniversityOsakiMiyagi989‐6711Japan
| | - Nobuhiro Tomaru
- Graduate School of Bioagricultural SciencesNagoya UniversityNagoyaAichi464‐8601Japan
| | - James R. P. Worth
- Ecological Genetics LaboratoryForestry and Forest Products Research Institute (FFPRI)TsukubaIbaraki305‐8687Japan
| | - Marco Cosimo Simeone
- Department of Agricultural and Forestry Science (DAFNE)Università degli studi della TusciaViterbo01100Italy
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14
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Harper A, Baudouin Gonzalez L, Schönauer A, Janssen R, Seiter M, Holzem M, Arif S, McGregor AP, Sumner-Rooney L. Widespread retention of ohnologs in key developmental gene families following whole-genome duplication in arachnopulmonates. G3 (BETHESDA, MD.) 2021; 11:jkab299. [PMID: 34849767 PMCID: PMC8664421 DOI: 10.1093/g3journal/jkab299] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Revised: 07/19/2021] [Accepted: 08/03/2021] [Indexed: 01/12/2023]
Abstract
Whole-genome duplications (WGDs) have occurred multiple times during animal evolution, including in lineages leading to vertebrates, teleosts, horseshoe crabs, and arachnopulmonates. These dramatic events initially produce a wealth of new genetic material, generally followed by extensive gene loss. It appears, however, that developmental genes such as homeobox genes, signaling pathway components and microRNAs are frequently retained as duplicates (so-called ohnologs) following WGD. These not only provide the best evidence for WGD, but an opportunity to study its evolutionary consequences. Although these genes are well studied in the context of vertebrate WGD, similar comparisons across the extant arachnopulmonate orders are patchy. We sequenced embryonic transcriptomes from two spider species and two amblypygid species and surveyed three important gene families, Hox, Wnt, and frizzled, across these and 12 existing transcriptomic and genomic resources for chelicerates. We report extensive retention of putative ohnologs, further supporting the ancestral arachnopulmonate WGD. We also found evidence of consistent evolutionary trajectories in Hox and Wnt gene repertoires across three of the six arachnopulmonate orders, with interorder variation in the retention of specific paralogs. We identified variation between major clades in spiders and are better able to reconstruct the chronology of gene duplications and losses in spiders, amblypygids, and scorpions. These insights shed light on the evolution of the developmental toolkit in arachnopulmonates, highlight the importance of the comparative approach within lineages, and provide substantial new transcriptomic data for future study.
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Affiliation(s)
- Amber Harper
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Luis Baudouin Gonzalez
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Anna Schönauer
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Ralf Janssen
- Department of Earth Sciences, Uppsala University, Geocentrum, 752 36 Uppsala, Sweden
| | - Michael Seiter
- Department of Evolutionary Biology, Unit Integrative Zoology, University of Vienna, 1090 Vienna, Austria
| | - Michaela Holzem
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
- Division of Signalling and Functional Genomics, German Cancer Research Centre (DKFZ), Heidelberg, Germany and Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, 69120 Heidelberg, Germany
| | - Saad Arif
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
- Centre for Functional Genomics, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Alistair P McGregor
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
- Centre for Functional Genomics, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Lauren Sumner-Rooney
- Oxford University Museum of Natural History, University of Oxford, Oxford OX1 3PW, UK
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15
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Colgan DJ, Ahyong ST, Mardon K, Brereton IM. Rare specimen identification in an un-integrated taxonomy: implications of DNA sequences from a Taiwanese Philine (Mollusca, Philinidae). Zookeys 2021; 1060:93-110. [PMID: 34616205 PMCID: PMC8463522 DOI: 10.3897/zookeys.1060.28809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 08/24/2021] [Indexed: 11/12/2022] Open
Abstract
Many species of the gastropod genus Philine have been named from northeastern Asia but scanty descriptions based predominantly on shells make it difficult to determine which are valid. This, plus the sporadic anatomical and genetic information available for many of these species has led to what may be described as an un-integrated taxonomy. In this situation, it is generally preferable to postpone dissection of rare and unusual specimens until relevant diagnostic characters can be established in broader studies. Micro-CT scanning and DNA sequencing were used to examine such a specimen collected recently from deep waters off northeastern Taiwan. Micro-CT examination of the morphology of the internal shell and gizzard plates suggested that, among named species, the sequenced specimen is most similar to P.otukai. It cannot, however, be definitively referred to P.otukai as that species lacks adequate anatomical description or known DNA sequences. Phylogenetic analyses of newly collected DNA sequences show the specimen to be most closely related to, but distinct from the northern Atlantic Ocean and Mediterranean species, Philinequadripartita. The sequences also confirm genetically that five or more species of Philine occur in northeast Asia, including at least three subject to considerable taxonomic uncertainty.
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Affiliation(s)
- Donald J Colgan
- Australian Museum Research Institute, 1 William St., Sydney 2010 Australia Australian Museum Research Institute Sydney Australia
| | - Shane T Ahyong
- Australian Museum Research Institute, 1 William St., Sydney 2010 Australia Australian Museum Research Institute Sydney Australia.,School of Biological, Earth & Environmental Sciences, University of New South Wales, Kensington, NSW 2052, Australia University of New South Wales Kensington Australia
| | - Karine Mardon
- Centre for Advanced Imaging/National Imaging Facility, University of Queensland, Brisbane 4072, Australia University of Queensland Brisbane Australia
| | - Ian M Brereton
- Centre for Advanced Imaging/National Imaging Facility, University of Queensland, Brisbane 4072, Australia University of Queensland Brisbane Australia
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16
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Ghobad-Nejhad M, Langer E, Nakasone K, Diederich P, Nilsson RH, Rajchenberg M, Ginns J. Digging Up the Roots: Taxonomic and Phylogenetic Disentanglements in Corticiaceae s.s. (Corticiales, Basidiomycota) and Evolution of Nutritional Modes. Front Microbiol 2021; 12:704802. [PMID: 34512580 PMCID: PMC8425454 DOI: 10.3389/fmicb.2021.704802] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 07/23/2021] [Indexed: 11/25/2022] Open
Abstract
Corticiaceae is one of the traditional families of the Agaricomycetes and served for a long time as a convenient placement for basidiomycetes with a resupinate, corticioid form of fruiting body. Molecular studies have helped to assign many corticioid fungi to diverse families and orders; however, Corticiaceae still lacks a phylogenetic characterization and modern circumscription. Here, we provide the first comprehensive phylogenetic and taxonomic revision of the family Corticiaceae based on extensive type studies and sequences of nLSU, ITS, IGS, nSSU, and mtSSU regions. Our analyses support the recognition of ten monophyletic genera in the Corticiaceae, and show that nutritional mode is not a robust basis for generic delimitations in the family. The genus Mycobernardia and the species Corticium thailandicum, Erythricium vernum, and Marchandiomyces allantosporus are described as new to science, and five new combinations are proposed. Moreover, ancestral character state reconstruction revealed that saprotrophy is the plesiomorphic nutritional mode in the Corticiaceae, while several transitions have occurred to diverse nutritional modes in this family. Identification keys are provided to the genera in Corticiaceae s.s. as well as to the species in Corticium, Erythricium, Laetisaria, and Marchandiomyces.
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Affiliation(s)
- Masoomeh Ghobad-Nejhad
- Department of Biotechnology, Iranian Research Organization for Science and Technology, Tehran, Iran
| | - Ewald Langer
- Department of Ecology, FB 10 (Mathematics and Natural Sciences), University Kassel, Kassel, Germany
| | - Karen Nakasone
- Center for Forest Mycology Research, Northern Research Station, U.S. Forest Service, Madison, WI, United States
| | - Paul Diederich
- Musée national d'histoire naturelle, Luxembourg, Luxembourg
| | - R. Henrik Nilsson
- Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, Sweden
| | - Mario Rajchenberg
- Centro de Investigación y Extensión Forestal Andino Patagónico, National Research Council of Argentina (CONICET), Esquel, Argentina
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17
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Casalla R, Scheffrahn RH, Korb J. Rugitermesursulae (Isoptera, Kalotermitidae), a new drywood termite from the Caribbean coast of Colombia. Zookeys 2021; 1057:23-36. [PMID: 34539196 PMCID: PMC8410751 DOI: 10.3897/zookeys.1057.65877] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 07/12/2021] [Indexed: 11/23/2022] Open
Abstract
Rugitermesursulae sp. nov. is described from a sample collected inside a dead branch in a tropical dry forest of Colombia's Caribbean coast using molecular information and external morphological characters of the imago and soldier castes. Rugitermesursulae sp. nov. soldiers and imagoes are the smallest among all described Rugitermes species. The imago's head capsule coloration is dark castaneous, while the pronotum is contrastingly pale yellow. Our description includes soldier characters, such as subflangular elevation and shape of the antennal sockets, that can help in identification of samples lacking imagoes.
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Affiliation(s)
- Robin Casalla
- Universidad del Norte, Departamento de Química y Biología. Kilómetro 5 Antigua vía Puerto Colombia, Barranquilla ColombiaUniversidad del NorteBarranquillaColombia
| | - Rudolf H. Scheffrahn
- Fort Lauderdale Research and Education Center, University of Florida, 3205 College Avenue Davie, Florida 33314, USAUniversity of FloridaDavieUnited States of America
| | - Judith Korb
- Universität Freiburg, Evolutionary Biology & Ecology. Hauptstrasse 1, Freiburg 79104, GermanyUniversität FreiburgFreiburgGermany
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18
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Melo BF, Sidlauskas BL, Near TJ, Roxo FF, Ghezelayagh A, Ochoa LE, Stiassny MLJ, Arroyave J, Chang J, Faircloth BC, MacGuigan DJ, Harrington RC, Benine RC, Burns MD, Hoekzema K, Sanches NC, Maldonado-Ocampo JA, Castro RMC, Foresti F, Alfaro ME, Oliveira C. Accelerated Diversification Explains the Exceptional Species Richness of Tropical Characoid Fishes. Syst Biol 2021; 71:78-92. [PMID: 34097063 DOI: 10.1093/sysbio/syab040] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 06/01/2021] [Accepted: 06/04/2021] [Indexed: 11/12/2022] Open
Abstract
The Neotropics harbor the most species-rich freshwater fish fauna on the planet, but the timing of that exceptional diversification remains unclear. Did the Neotropics accumulate species steadily throughout their long history, or attain their remarkable diversity recently? Biologists have long debated the relative support for these museum and cradle hypotheses, but few phylogenies of megadiverse tropical clades have included sufficient taxa to distinguish between them. We used 1,288 ultraconserved element loci (UCE) spanning 293 species, 211 genera and 21 families of characoid fishes to reconstruct a new, fossil-calibrated phylogeny and infer the most likely diversification scenario for a clade that includes a third of Neotropical fish diversity. This phylogeny implies paraphyly of the traditional delimitation of Characiformes because it resolves the largely Neotropical Characoidei as the sister lineage of Siluriformes (catfishes), rather than the African Citharinodei. Time-calibrated phylogenies indicate an ancient origin of major characoid lineages and reveal a much more recent emergence of most characoid species. Diversification rate analyses infer increased speciation and decreased extinction rates during the Oligocene at around 30 million years ago (Ma) during a period of mega-wetland formation in the proto-Orinoco-Amazonas. Three species-rich and ecomorphologically diverse lineages (Anostomidae, Serrasalmidae, and Characidae) that originated more than 60 Ma in the Paleocene experienced particularly notable bursts of Oligocene diversification and now account collectively for 68% of the approximately 2,150 species of Characoidei. In addition to paleogeographic changes, we discuss potential accelerants of diversification in these three lineages. While the Neotropics accumulated a museum of ecomorphologically diverse characoid lineages long ago, this geologically dynamic region also cradled a much more recent birth of remarkable species-level diversity.
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Affiliation(s)
- Bruno F Melo
- Dept of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, SP, 16818-689, Brazil
| | - Brian L Sidlauskas
- Dept of Fisheries and Wildlife, Oregon State University, Corvallis, OR, 97331, USA
| | - Thomas J Near
- Dept of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Fabio F Roxo
- Sector of Zoology, Institute of Biosciences, São Paulo State University, Botucatu, SP, 18618-689, Brazil
| | - Ava Ghezelayagh
- Dept of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Luz E Ochoa
- Dept of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, SP, 16818-689, Brazil.,Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Palmira, Valle del Cauca, 763547, Colombia
| | - Melanie L J Stiassny
- Dept of Ichthyology, American Museum of Natural History, New York, NY, 10024, USA
| | - Jairo Arroyave
- Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México
| | - Jonathan Chang
- School of Biological Sciences, Monash University, Melbourne, VIC, 3800, Australia
| | - Brant C Faircloth
- Dept of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Daniel J MacGuigan
- Dept of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Richard C Harrington
- Dept of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Ricardo C Benine
- Sector of Zoology, Institute of Biosciences, São Paulo State University, Botucatu, SP, 18618-689, Brazil
| | - Michael D Burns
- Cornell Lab of Ornithology, Cornell University Museum of Vertebrates, Ithaca, NY, 14850, USA
| | - Kendra Hoekzema
- Dept of Fisheries and Wildlife, Oregon State University, Corvallis, OR, 97331, USA
| | - Natalia C Sanches
- Dept of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, SP, 16818-689, Brazil
| | - Javier A Maldonado-Ocampo
- Dept de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, DC, Colombia (in memoriam)
| | - Ricardo M C Castro
- Faculdade de Filosofia, Ciências e Letras, Universidade de São Paulo, Ribeirão Preto, SP, 14040-901, Brazil
| | - Fausto Foresti
- Dept of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, SP, 16818-689, Brazil
| | - Michael E Alfaro
- Dept of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA
| | - Claudio Oliveira
- Dept of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, SP, 16818-689, Brazil
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19
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Matsunaga KK, Smith SY. Fossil palm reading: using fruits to reveal the deep roots of palm diversity. AMERICAN JOURNAL OF BOTANY 2021; 108:472-494. [PMID: 33624301 PMCID: PMC8048450 DOI: 10.1002/ajb2.1616] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/22/2020] [Indexed: 05/11/2023]
Abstract
PREMISE Fossils are essential for understanding evolutionary history because they provide direct evidence of past diversity and geographic distributions. However, resolving systematic relationships between fossils and extant taxa, an essential step for many macroevolutionary studies, requires extensive comparative work on morphology and anatomy. While palms (Arecaceae) have an excellent fossil record that includes numerous fossil fruits, many are difficult to identify due in part to limited comparative data on modern fruit structure. METHODS We studied fruits of 207 palm species, representing nearly every modern genus, using X-ray microcomputed tomography. We then developed a morphological data set to test whether the fossil record of fruits can improve our understanding of palm diversity in the deep past. To evaluate the accuracy with which this data set recovers systematic relationships, we performed phylogenetic pseudofossilization analyses. We then used the data set to investigate the phylogenetic relationships of five previously published fossil palm fruits. RESULTS Phylogenetic analyses of fossils and pseudofossilization of extant taxa show that fossils can be placed accurately to the tribe and subtribe level with this data set, but node support must be considered. The phylogenetic relationships of the fossils suggest origins of many modern lineages in the Cretaceous and early Paleogene. Three of these fossils are suitable as new node calibrations for palms. CONCLUSIONS This work improves our knowledge of fruit structure in palms, lays a foundation for applying fossil fruits to macroevolutionary studies, and provides new insights into the evolutionary history and early diversification of Arecaceae.
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Affiliation(s)
- Kelly K.S. Matsunaga
- Department of Earth and Environmental Sciences & Museum of PaleontologyUniversity of MichiganAnn ArborMI48109USA
- Present address:
Department of Ecology and Evolutionary Biology & Biodiversity InstituteUniversity of KansasLawrenceKS66045USA
| | - Selena Y. Smith
- Department of Earth and Environmental Sciences & Museum of PaleontologyUniversity of MichiganAnn ArborMI48109USA
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20
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Phylogenomics of the Neotropical fish family Serrasalmidae with a novel intrafamilial classification (Teleostei: Characiformes). Mol Phylogenet Evol 2020; 153:106945. [DOI: 10.1016/j.ympev.2020.106945] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 08/14/2020] [Accepted: 08/21/2020] [Indexed: 01/04/2023]
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21
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Kontopoulos D, Smith TP, Barraclough TG, Pawar S. Adaptive evolution shapes the present-day distribution of the thermal sensitivity of population growth rate. PLoS Biol 2020; 18:e3000894. [PMID: 33064736 PMCID: PMC7592915 DOI: 10.1371/journal.pbio.3000894] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 10/28/2020] [Accepted: 09/14/2020] [Indexed: 12/23/2022] Open
Abstract
Developing a thorough understanding of how ectotherm physiology adapts to different thermal environments is of crucial importance, especially in the face of global climate change. A key aspect of an organism's thermal performance curve (TPC)-the relationship between fitness-related trait performance and temperature-is its thermal sensitivity, i.e., the rate at which trait values increase with temperature within its typically experienced thermal range. For a given trait, the distribution of thermal sensitivities across species, often quantified as "activation energy" values, is typically right-skewed. Currently, the mechanisms that generate this distribution are unclear, with considerable debate about the role of thermodynamic constraints versus adaptive evolution. Here, using a phylogenetic comparative approach, we study the evolution of the thermal sensitivity of population growth rate across phytoplankton (Cyanobacteria and eukaryotic microalgae) and prokaryotes (bacteria and archaea), 2 microbial groups that play a major role in the global carbon cycle. We find that thermal sensitivity across these groups is moderately phylogenetically heritable, and that its distribution is shaped by repeated evolutionary convergence throughout its parameter space. More precisely, we detect bursts of adaptive evolution in thermal sensitivity, increasing the amount of overlap among its distributions in different clades. We obtain qualitatively similar results from evolutionary analyses of the thermal sensitivities of 2 physiological rates underlying growth rate: net photosynthesis and respiration of plants. Furthermore, we find that these episodes of evolutionary convergence are consistent with 2 opposing forces: decrease in thermal sensitivity due to environmental fluctuations and increase due to adaptation to stable environments. Overall, our results indicate that adaptation can lead to large and relatively rapid shifts in thermal sensitivity, especially in microbes for which rapid evolution can occur at short timescales. Thus, more attention needs to be paid to elucidating the implications of rapid evolution in organismal thermal sensitivity for ecosystem functioning.
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Affiliation(s)
- Dimitrios—Georgios Kontopoulos
- Science and Solutions for a Changing Planet DTP, Imperial College London, London, United Kingdom
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, Berkshire, United Kingdom
| | - Thomas P. Smith
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, Berkshire, United Kingdom
| | - Timothy G. Barraclough
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, Berkshire, United Kingdom
- Department of Zoology, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Samraat Pawar
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, Berkshire, United Kingdom
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22
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Alves-Silva G, Reck MA, da Silveira RMB, Bittencourt F, Robledo GL, Góes-Neto A, Drechsler-Santos ER. The Neotropical Fomitiporia (Hymenochaetales, Basidiomycota): the redefinition of F. apiahyna s.s. allows revealing a high hidden species diversity. Mycol Prog 2020. [DOI: 10.1007/s11557-020-01593-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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23
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Erséus C, Williams BW, Horn KM, Halanych KM, Santos SR, James SW, Creuzé des Châtelliers M, Anderson FE. Phylogenomic analyses reveal a Palaeozoic radiation and support a freshwater origin for clitellate annelids. ZOOL SCR 2020. [DOI: 10.1111/zsc.12426] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Christer Erséus
- Department of Biological and Environmental Sciences University of Gothenburg Göteborg Sweden
| | - Bronwyn W. Williams
- School of Biological Sciences Southern Illinois University Carbondale IL USA
- Research Laboratory North Carolina Museum of Natural Sciences Raleigh NC USA
| | - Kevin M. Horn
- School of Biological Sciences Southern Illinois University Carbondale IL USA
- Division of Natural Sciences and Mathematics Kentucky Wesleyan College Owensboro Kentucky USA
| | - Kenneth M. Halanych
- Molette Biology Laboratory for Environmental and Climate Change Studies Department of Biological Sciences Auburn University Auburn AL USA
| | - Scott R. Santos
- Molette Biology Laboratory for Environmental and Climate Change Studies Department of Biological Sciences Auburn University Auburn AL USA
| | - Samuel W. James
- Sustainable Living Department Maharishi University of Management Fairfield IA USA
| | | | - Frank E. Anderson
- School of Biological Sciences Southern Illinois University Carbondale IL USA
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Cardoen B, Yedder HB, Sharma A, Chou KC, Nabi IR, Hamarneh G. ERGO: Efficient Recurrent Graph Optimized Emitter Density Estimation in Single Molecule Localization Microscopy. IEEE TRANSACTIONS ON MEDICAL IMAGING 2020; 39:1942-1956. [PMID: 31880546 DOI: 10.1109/tmi.2019.2962361] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Single molecule localization microscopy (SMLM) allows unprecedented insight into the three-dimensional organization of proteins at the nanometer scale. The combination of minimal invasive cell imaging with high resolution positions SMLM at the forefront of scientific discovery in cancer, infectious, and degenerative diseases. By stochastic temporal and spatial separation of light emissions from fluorescent labelled proteins, SMLM is capable of nanometer scale reconstruction of cellular structures. Precise localization of proteins in 3D astigmatic SMLM is dependent on parameter sensitive preprocessing steps to select regions of interest. With SMLM acquisition highly variable over time, it is non-trivial to find an optimal static parameter configuration. The high emitter density required for reconstruction of complex protein structures can compromise accuracy and introduce artifacts. To address these problems, we introduce two modular auto-tuning pre-processing methods: adaptive signal detection and learned recurrent signal density estimation that can leverage the information stored in the sequence of frames that compose the SMLM acquisition process. We show empirically that our contributions improve accuracy, precision and recall with respect to the state of the art. Both modules auto-tune their hyper-parameters to reduce the parameter space for practitioners, improve robustness and reproducibility, and are validated on a reference in silico dataset. Adaptive signal detection and density prediction can offer a practitioner, in addition to informed localization, a tool to tune acquisition parameters ensuring improved reconstruction of the underlying protein complex. We illustrate the challenges faced by practitioners in applying SMLM algorithms on real world data markedly different from the data used in development and show how ERGO can be run on new datasets without retraining while motivating the need for robust transfer learning in SMLM.
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Phylogenomic analysis of trichomycterid catfishes (Teleostei: Siluriformes) inferred from ultraconserved elements. Sci Rep 2020; 10:2697. [PMID: 32060350 PMCID: PMC7021825 DOI: 10.1038/s41598-020-59519-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 01/28/2020] [Indexed: 11/22/2022] Open
Abstract
The family Trichomycteridae is one of the most diverse groups of freshwater catfishes in South and Central America with eight subfamilies, 41 genera and more than 300 valid species. Its members are widely distributed throughout South America, reaching Costa Rica in Central America and are recognized by extraordinary anatomical specializations and trophic diversity. In order to assess the phylogenetic relationships of Trichomycteridae, we collected sequence data from ultraconserved elements (UCEs) of the genome from 141 specimens of Trichomycteridae and 12 outgroup species. We used a concatenated matrix to assess the phylogenetic relationships by Bayesian inference (BI) and maximum likelihood (ML) searches and a coalescent analysis of species trees. The results show a highly resolved phylogeny with broad agreement among the three distinct analyses, providing overwhelming support for the monophyletic status of subfamily Trichomycterinae including Ituglanis and Scleronema. Previous relationship hypotheses among subfamilies are strongly corroborated, such as the sister relationship between Copionodontinae and Trichogeninae forming a sister clade to the remaining trichomycterids and the intrafamilial clade TSVSG (Tridentinae-Stegophilinae-Vandelliinae-Sarcoglanidinae-Glanapteryginae). Monophyly of Glanapteryginae and Sarcoglanidinae was not supported and the enigmatic Potamoglanis is placed outside Tridentinae.
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Marx HE, Richards M, Johnson GM, Tank DC. Increasing phylogenetic stochasticity at high elevations on summits across a remote North American wilderness. AMERICAN JOURNAL OF BOTANY 2019; 106:958-970. [PMID: 31291472 DOI: 10.1002/ajb2.1328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 04/24/2019] [Indexed: 06/09/2023]
Abstract
PREMISE At the intersection of ecology and evolutionary biology, community phylogenetics can provide insights into overarching biodiversity patterns, particularly in remote and understudied ecosystems. To understand community assembly of the high alpine flora in the Sawtooth National Forest, USA, we analyzed phylogenetic structure within and between nine summit communities. METHODS We used high-throughput sequencing to supplement existing data and infer a nearly completely sampled community phylogeny of the alpine vascular flora. We calculated mean nearest taxon distance (MNTD) and mean pairwise distance (MPD) to quantify phylogenetic divergence within summits, and assessed whether maximum elevation explains phylogenetic structure. To evaluate similarities between summits, we quantified phylogenetic turnover, taking into consideration microhabitats (talus vs. meadows). RESULTS We found different patterns of community phylogenetic structure within the six most species-rich orders, but across all vascular plants phylogenetic structure was largely not different from random. There was a significant negative correlation between elevation and tree-wide phylogenetic diversity (MPD) within summits: overdispersion degraded as elevation increased. Between summits, we found high phylogenetic turnover driven by greater niche heterogeneity on summits with alpine meadows. CONCLUSIONS Our results provide further evidence that stochastic processes may also play an important role in the assembly of vascular plant communities in high alpine habitats at regional scales. However, order-specific patterns suggest that adaptations are still important for assembly of specific sectors of the plant tree of life. Further studies quantifying functional diversity will be important in disentangling the interplay of eco-evolutionary processes that likely shape broad community phylogenetic patterns in extreme environments.
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Affiliation(s)
- Hannah E Marx
- Department of Biological Sciences, University of Idaho, 875 Perimeter Dr. MS 3051, Moscow, Idaho, 83844-3051, USA
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, 875 Perimeter Dr. MS 3051, Moscow, Idaho, 83844-3051, USA
| | - Melissa Richards
- Department of Biological Sciences, University of Idaho, 875 Perimeter Dr. MS 3051, Moscow, Idaho, 83844-3051, USA
| | - Grahm M Johnson
- Department of Biological Sciences, University of Idaho, 875 Perimeter Dr. MS 3051, Moscow, Idaho, 83844-3051, USA
- Stillinger Herbarium, University of Idaho, 875 Perimeter Dr. MS 3026, Moscow, Idaho, 83844-3026, USA
| | - David C Tank
- Department of Biological Sciences, University of Idaho, 875 Perimeter Dr. MS 3051, Moscow, Idaho, 83844-3051, USA
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, 875 Perimeter Dr. MS 3051, Moscow, Idaho, 83844-3051, USA
- Stillinger Herbarium, University of Idaho, 875 Perimeter Dr. MS 3026, Moscow, Idaho, 83844-3026, USA
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27
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Auxier B, Dee J, Berbee ML, Momany M. Diversity of opisthokont septin proteins reveals structural constraints and conserved motifs. BMC Evol Biol 2019; 19:4. [PMID: 30616529 PMCID: PMC6323724 DOI: 10.1186/s12862-018-1297-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 11/19/2018] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Septins are cytoskeletal proteins important in cell division and in establishing and maintaining cell polarity. Although septins are found in various eukaryotes, septin genes had the richest history of duplication and diversification in the animals, fungi and protists that comprise opisthokonts. Opisthokont septin paralogs encode modular proteins that assemble into heteropolymeric higher order structures. The heteropolymers can create physical barriers to diffusion or serve as scaffolds organizing other morphogenetic proteins. How the paralogous septin modules interact to form heteropolymers is still unclear. Through comparative analyses, we hoped to clarify the evolutionary origin of septin diversity and to suggest which amino acid residues were responsible for subunit binding specificity. RESULTS Here we take advantage of newly sequenced genomes to reconcile septin gene trees with a species phylogeny from 22 animals, fungi and protists. Our phylogenetic analysis divided 120 septins representing the 22 taxa into seven clades (Groups) of paralogs. Suggesting that septin genes duplicated early in opisthokont evolution, animal and fungal lineages share septin Groups 1A, 4 and possibly also 1B and 2. Group 5 septins were present in fungi but not in animals and whether they were present in the opisthokont ancestor was unclear. Protein homology folding showed that previously identified conserved septin motifs were all located near interface regions between the adjacent septin monomers. We found specific interface residues associated with each septin Group that are candidates for providing subunit binding specificity. CONCLUSIONS This work reveals that duplication of septin genes began in an ancestral opisthokont more than a billion years ago and continued through the diversification of animals and fungi. Evidence for evolutionary conservation of ~ 49 interface residues will inform mutagenesis experiments and lead to improved understanding of the rules guiding septin heteropolymer formation and from there, to improved understanding of development of form in animals and fungi.
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Affiliation(s)
- Benjamin Auxier
- Department of Botany, University of British Columbia, Vancouver, Canada
- current address: Laboratory of Genetics, Wageningen University and Research, P.O. Box 16, 6700AA, Wageningen, The Netherlands
| | - Jaclyn Dee
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Mary L. Berbee
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Michelle Momany
- Fungal Biology Group and Plant Biology Department, University of Georgia, Athens, USA
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28
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Kruis AJ, Gallone B, Jonker T, Mars AE, van Rijswijck IMH, Wolkers-Rooijackers JCM, Smid EJ, Steensels J, Verstrepen KJ, Kengen SWM, van der Oost J, Weusthuis RA. Contribution of Eat1 and Other Alcohol Acyltransferases to Ester Production in Saccharomyces cerevisiae. Front Microbiol 2018; 9:3202. [PMID: 30622529 PMCID: PMC6308380 DOI: 10.3389/fmicb.2018.03202] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 12/10/2018] [Indexed: 12/16/2022] Open
Abstract
Esters are essential for the flavor and aroma of fermented products, and are mainly produced by alcohol acyl transferases (AATs). A recently discovered AAT family named Eat (Ethanol acetyltransferase) contributes to ethyl acetate synthesis in yeast. However, its effect on the synthesis of other esters is unknown. In this study, the role of the Eat family in ester synthesis was compared to that of other Saccharomyces cerevisiae AATs (Atf1p, Atf2p, Eht1p, and Eeb1p) in silico and in vivo. A genomic study in a collection of industrial S. cerevisiae strains showed that variation of the primary sequence of the AATs did not correlate with ester production. Fifteen members of the EAT family from nine yeast species were overexpressed in S. cerevisiae CEN.PK2-1D and were able to increase the production of acetate and propanoate esters. The role of Eat1p was then studied in more detail in S. cerevisiae CEN.PK2-1D by deleting EAT1 in various combinations with other known S. cerevisiae AATs. Between 6 and 11 esters were produced under three cultivation conditions. Contrary to our expectations, a strain where all known AATs were disrupted could still produce, e.g., ethyl acetate and isoamyl acetate. This study has expanded our understanding of ester synthesis in yeast but also showed that some unknown ester-producing mechanisms still exist.
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Affiliation(s)
- Aleksander J Kruis
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands.,Bioprocess Engineering, Wageningen University and Research, Wageningen, Netherlands
| | - Brigida Gallone
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB-UGent Center for Plant Systems Biology, Ghent, Belgium.,VIB-KU Leuven Center for Microbiology, Leuven, Belgium.,Laboratory of Genetics and Genomics, Centre of Microbial and Plant Genetics, Department of M2S, KU Leuven, Leuven, Belgium.,Leuven Institute for Beer Research (LIBR), Leuven, Belgium
| | - Timo Jonker
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Astrid E Mars
- Biobased Products, Wageningen University and Research, Wageningen, Netherlands
| | - Irma M H van Rijswijck
- Laboratory of Food Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | | | - Eddy J Smid
- Laboratory of Food Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Jan Steensels
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium.,Laboratory of Genetics and Genomics, Centre of Microbial and Plant Genetics, Department of M2S, KU Leuven, Leuven, Belgium.,Leuven Institute for Beer Research (LIBR), Leuven, Belgium
| | - Kevin J Verstrepen
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium.,Laboratory of Genetics and Genomics, Centre of Microbial and Plant Genetics, Department of M2S, KU Leuven, Leuven, Belgium.,Leuven Institute for Beer Research (LIBR), Leuven, Belgium
| | - Servé W M Kengen
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Ruud A Weusthuis
- Bioprocess Engineering, Wageningen University and Research, Wageningen, Netherlands
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Salgado MG, van Velzen R, Nguyen TV, Battenberg K, Berry AM, Lundin D, Pawlowski K. Comparative Analysis of the Nodule Transcriptomes of Ceanothus thyrsiflorus (Rhamnaceae, Rosales) and Datisca glomerata (Datiscaceae, Cucurbitales). FRONTIERS IN PLANT SCIENCE 2018; 9:1629. [PMID: 30487804 PMCID: PMC6246699 DOI: 10.3389/fpls.2018.01629] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/19/2018] [Indexed: 05/09/2023]
Abstract
Two types of nitrogen-fixing root nodule symbioses are known, rhizobial and actinorhizal symbioses. The latter involve plants of three orders, Fagales, Rosales, and Cucurbitales. To understand the diversity of plant symbiotic adaptation, we compared the nodule transcriptomes of Datisca glomerata (Datiscaceae, Cucurbitales) and Ceanothus thyrsiflorus (Rhamnaceae, Rosales); both species are nodulated by members of the uncultured Frankia clade, cluster II. The analysis focused on various features. In both species, the expression of orthologs of legume Nod factor receptor genes was elevated in nodules compared to roots. Since arginine has been postulated as export form of fixed nitrogen from symbiotic Frankia in nodules of D. glomerata, the question was whether the nitrogen metabolism was similar in nodules of C. thyrsiflorus. Analysis of the expression levels of key genes encoding enzymes involved in arginine metabolism revealed up-regulation of arginine catabolism, but no up-regulation of arginine biosynthesis, in nodules compared to roots of D. glomerata, while arginine degradation was not upregulated in nodules of C. thyrsiflorus. This new information corroborated an arginine-based metabolic exchange between host and microsymbiont for D. glomerata, but not for C. thyrsiflorus. Oxygen protection systems for nitrogenase differ dramatically between both species. Analysis of the antioxidant system suggested that the system in the nodules of D. glomerata leads to greater oxidative stress than the one in the nodules of C. thyrsiflorus, while no differences were found for the defense against nitrosative stress. However, induction of nitrite reductase in nodules of C. thyrsiflorus indicated that here, nitrite produced from nitric oxide had to be detoxified. Additional shared features were identified: genes encoding enzymes involved in thiamine biosynthesis were found to be upregulated in the nodules of both species. Orthologous nodule-specific subtilisin-like proteases that have been linked to the infection process in actinorhizal Fagales, were also upregulated in the nodules of D. glomerata and C. thyrsiflorus. Nodule-specific defensin genes known from actinorhizal Fagales and Cucurbitales, were also found in C. thyrsiflorus. In summary, the results underline the variability of nodule metabolism in different groups of symbiotic plants while pointing at conserved features involved in the infection process.
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Affiliation(s)
- Marco G. Salgado
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Robin van Velzen
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, Wageningen, Netherlands
| | - Thanh Van Nguyen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Kai Battenberg
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Alison M. Berry
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Daniel Lundin
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Katharina Pawlowski
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
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30
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Serrano ÉA, Melo BF, Freitas‐Souza D, Oliveira MLM, Utsunomia R, Oliveira C, Foresti F. Species delimitation in Neotropical fishes of the genus
Characidium
(Teleostei, Characiformes). ZOOL SCR 2018. [DOI: 10.1111/zsc.12318] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Érica A. Serrano
- Laboratório de Biologia e Genética de Peixes, Departamento de Morfologia, Instituto de Biociências Universidade Estadual Paulista Botucatu Brazil
| | - Bruno F. Melo
- Laboratório de Biologia e Genética de Peixes, Departamento de Morfologia, Instituto de Biociências Universidade Estadual Paulista Botucatu Brazil
- Department of Vertebrate Zoology National Museum of Natural History, Smithsonian Institution Washington District of Columbia
| | - Diogo Freitas‐Souza
- Laboratório de Biologia e Genética de Peixes, Departamento de Morfologia, Instituto de Biociências Universidade Estadual Paulista Botucatu Brazil
| | - Maria L. M. Oliveira
- Laboratório de Biologia e Genética de Peixes, Departamento de Morfologia, Instituto de Biociências Universidade Estadual Paulista Botucatu Brazil
| | - Ricardo Utsunomia
- Laboratório de Biologia e Genética de Peixes, Departamento de Morfologia, Instituto de Biociências Universidade Estadual Paulista Botucatu Brazil
| | - Claudio Oliveira
- Laboratório de Biologia e Genética de Peixes, Departamento de Morfologia, Instituto de Biociências Universidade Estadual Paulista Botucatu Brazil
| | - Fausto Foresti
- Laboratório de Biologia e Genética de Peixes, Departamento de Morfologia, Instituto de Biociências Universidade Estadual Paulista Botucatu Brazil
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31
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Woods HA, Kingsolver JG, Fey SB, Vasseur DA. Uncertainty in geographical estimates of performance and fitness. Methods Ecol Evol 2018. [DOI: 10.1111/2041-210x.13035] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- H. Arthur Woods
- Division of Biological Sciences University of Montana Missoula Montana
| | - Joel G. Kingsolver
- Department of Biology University of North Carolina Chapel Hill North Carolina
| | | | - David A. Vasseur
- Department of Ecology and Evolutionary Biology Yale University New Haven Connecticut
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32
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Melo BF, Dorini BF, Foresti F, Oliveira C. Little Divergence Among Mitochondrial Lineages of Prochilodus (Teleostei, Characiformes). Front Genet 2018; 9:107. [PMID: 29670644 PMCID: PMC5893770 DOI: 10.3389/fgene.2018.00107] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 03/19/2018] [Indexed: 11/13/2022] Open
Abstract
Evidence that migration prevents population structure among Neotropical characiform fishes has been reported recently but the effects upon species diversification remain unclear. Migratory species of Prochilodus have complex species boundaries and intrincate taxonomy representing a good model to address such questions. Here, we analyzed 147 specimens through barcode sequences covering all species of Prochilodus across a broad geographic area of South America. Species delimitation and population genetic methods revealed very little genetic divergence among mitochondrial lineages suggesting that extensive gene flow resulted likely from the highly migratory behavior, natural hybridization or recent radiation prevent accumulation of genetic disparity among lineages. Our results clearly delimit eight genetic lineages in which four of them contain a single species and four contain more than one morphologically problematic taxon including a trans-Andean species pair and species of the P. nigricans group. Information about biogeographic distribution of haplotypes presented here might contribute to further research on the population genetics and taxonomy of Prochilodus.
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Affiliation(s)
- Bruno F. Melo
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, Brazil
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Beatriz F. Dorini
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, Brazil
| | - Fausto Foresti
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, Brazil
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, Brazil
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33
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Wagner P, Greenbaum E, Bauer AM, Kusamba C, Leaché AD. Lifting the blue-headed veil – integrative taxonomy of the Acanthocercus atricollis species complex (Squamata: Agamidae). J NAT HIST 2018. [DOI: 10.1080/00222933.2018.1435833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Philipp Wagner
- Department of Research & Conservation, Allwetterzoo, Münster, Germany
- Department of Biology, Villanova University, Villanova, PA, USA
| | - Eli Greenbaum
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA
| | - Aaron M. Bauer
- Department of Biology, Villanova University, Villanova, PA, USA
| | - Chifundera Kusamba
- Laboratoire d’Herpétologie, Département de Biologie, Centre de Recherche en Sciences Naturelles, Lwiro, République Démocratique du Congo
| | - Adam D. Leaché
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, USA
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An AlgU-Regulated Antisense Transcript Encoded within the Pseudomonas syringae fleQ Gene Has a Positive Effect on Motility. J Bacteriol 2018; 200:JB.00576-17. [PMID: 29311280 DOI: 10.1128/jb.00576-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 01/04/2018] [Indexed: 12/29/2022] Open
Abstract
Production of bacterial flagella is controlled by a multitiered regulatory system that coordinates the expression of 40 to 50 subunits and ordered assembly of these elaborate structures. Flagellar expression is environmentally controlled, presumably to optimize the benefits and liabilities of having these organelles on cell growth and survival. We recently reported a global survey of AlgU-dependent regulation and binding in Pseudomonas syringae pv. tomato DC3000 that included evidence for strong downregulation of many flagellar and chemotaxis motility genes. Here, we returned to those data to look for other AlgU-dependent influences on the flagellar regulatory network. We identified an AlgU-dependent antisense transcript expressed from within the fleQ gene, the master regulator of flagellar biosynthesis in Pseudomonas We tested whether expression of this antisense RNA influenced bacterial behavior and found that it reduces AlgU-dependent downregulation of motility. Importantly, this antisense expression influenced motility only under conditions in which AlgU was expressed. Comparative sequence analysis of the locus containing the antisense transcript's AlgU-dependent promoter in over 300 Pseudomonas genomes revealed sequence conservation in most strains that encode AlgU. This suggests that the antisense transcript plays an important role that is conserved across most of the genus Pseudomonas IMPORTANCE Pseudomonas syringae is a globally distributed host-specific bacterial pathogen that causes disease in a wide-range of plants. An elaborate gene expression regulation network controls flagellum production, which is important for proper flagellum assembly and a key aspect of certain lifestyle transitions. P. syringae pv. tomato DC3000 uses flagellum-powered motility in the early stages of host colonization and adopts a sessile lifestyle after entering plant tissues, but the regulation of this transition is not understood. Our work demonstrates a link between regulation of motility and global transcriptional control that facilitates bacterial growth and disease in plants. Additionally, sequence comparisons suggest that this regulation mechanism is conserved in most members of the genus Pseudomonas.
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35
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Platt RN, Faircloth BC, Sullivan KAM, Kieran TJ, Glenn TC, Vandewege MW, Lee TE, Baker RJ, Stevens RD, Ray DA. Conflicting Evolutionary Histories of the Mitochondrial and Nuclear Genomes in New World Myotis Bats. Syst Biol 2018; 67:236-249. [PMID: 28945862 PMCID: PMC5837689 DOI: 10.1093/sysbio/syx070] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 07/31/2017] [Accepted: 08/15/2017] [Indexed: 01/05/2023] Open
Abstract
The rapid diversification of Myotis bats into more than 100 species is one of the most extensive mammalian radiations available for study. Efforts to understand relationships within Myotis have primarily utilized mitochondrial markers and trees inferred from nuclear markers lacked resolution. Our current understanding of relationships within Myotis is therefore biased towards a set of phylogenetic markers that may not reflect the history of the nuclear genome. To resolve this, we sequenced the full mitochondrial genomes of 37 representative Myotis, primarily from the New World, in conjunction with targeted sequencing of 3648 ultraconserved elements (UCEs). We inferred the phylogeny and explored the effects of concatenation and summary phylogenetic methods, as well as combinations of markers based on informativeness or levels of missing data, on our results. Of the 294 phylogenies generated from the nuclear UCE data, all are significantly different from phylogenies inferred using mitochondrial genomes. Even within the nuclear data, quartet frequencies indicate that around half of all UCE loci conflict with the estimated species tree. Several factors can drive such conflict, including incomplete lineage sorting, introgressive hybridization, or even phylogenetic error. Despite the degree of discordance between nuclear UCE loci and the mitochondrial genome and among UCE loci themselves, the most common nuclear topology is recovered in one quarter of all analyses with strong nodal support. Based on these results, we re-examine the evolutionary history of Myotis to better understand the phenomena driving their unique nuclear, mitochondrial, and biogeographic histories.
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Affiliation(s)
- Roy N Platt
- Department of Biological Sciences, Texas Tech University, 2901 Main St, Lubbock, TX, USA
| | - Brant C Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, 202 Life Science Building, Baton Rouge, LA, USA
| | - Kevin A M Sullivan
- Department of Biological Sciences, Texas Tech University, 2901 Main St, Lubbock, TX, USA
| | - Troy J Kieran
- Department of Environmental Health Science, University of Georgia, 206 Environmental Health Sciences Building, Athens, GA, USA
| | - Travis C Glenn
- Department of Environmental Health Science, University of Georgia, 206 Environmental Health Sciences Building, Athens, GA, USA
| | - Michael W Vandewege
- Department of Biological Sciences, Texas Tech University, 2901 Main St, Lubbock, TX, USA
| | - Thomas E Lee
- Department of Biology, Abilene Christian University, 1600 Campus Ct. Abilene, TX, USA
| | - Robert J Baker
- Department of Biological Sciences, Texas Tech University, 2901 Main St, Lubbock, TX, USA
| | - Richard D Stevens
- Natural Resource Management, Texas Tech University, 2901 Main St, Lubbock, TX, USA
| | - David A Ray
- Department of Biological Sciences, Texas Tech University, 2901 Main St, Lubbock, TX, USA
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36
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Guevara-Guerrero G, Bonito G, Smith ME, Healy R, Grupe AC, Cázares E, Castellano MA, Trappe JM. Tuber aztecorum sp. nov., a truffle species from Mexico belonging to the Maculatum clade (Tuberaceae, Pezizales). MycoKeys 2018:61-72. [PMID: 29681733 PMCID: PMC5904530 DOI: 10.3897/mycokeys.30.22887] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 02/16/2018] [Indexed: 11/12/2022] Open
Abstract
A new species of truffle, T. aztecorum, is described from central Mexico. Tuber aztecorum can be distinguished from other related Tuber species synoptically by a combination of morphological features including ascospore size, pellis cells with irregular thickness, cystidia, ascoma colour and associated host (Abies religiosa an endemic Abies species from central Mexico); sequence variation on the ITS rDNA also distinguishes T. aztecorum from related species. A phylogenetic analysis of the ITS rDNA demonstrates that T. aztecorum belongs to the Maculatum clade and is unique from other similar small, white-cream coloured Tuber species distributed in north-eastern Mexico such as T. castilloi and T. guevarai.
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Affiliation(s)
- Gonzalo Guevara-Guerrero
- Instituto Tecnológico de Cd. Victoria, Av. Portes Gil 1301 Pte. C.P. 87010, Cd. Victoria Tam. México
| | - Gregory Bonito
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, 48825, USA
| | - Matthew E Smith
- Department of Plant Pathology, University of Florida, Gainesville, Florida 32611, USA
| | - Rosanne Healy
- Department of Plant Pathology, University of Florida, Gainesville, Florida 32611, USA
| | - Arthur C Grupe
- Department of Plant Pathology, University of Florida, Gainesville, Florida 32611, USA
| | - Efrén Cázares
- US Department of Agriculture, Forest Service, Northern Research Station, 3200 Jefferson Way, Corvallis, Oregon, 97331, USA
| | - Michael A Castellano
- US Department of Agriculture, Forest Service, Northern Research Station, 3200 Jefferson Way, Corvallis, Oregon, 97331, USA
| | - James M Trappe
- US Department of Agriculture, Forest Service, Northern Research Station, 3200 Jefferson Way, Corvallis, Oregon, 97331, USA
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Morse P, Kjeldsen SR, Meekan MG, Mccormick MI, Finn JK, Huffard CL, Zenger KR. Genome-wide comparisons reveal a clinal species pattern within a holobenthic octopod-the Australian Southern blue-ringed octopus, Hapalochlaena maculosa (Cephalopoda: Octopodidae). Ecol Evol 2018; 8:2253-2267. [PMID: 29468041 PMCID: PMC5817145 DOI: 10.1002/ece3.3845] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 12/05/2017] [Accepted: 12/28/2017] [Indexed: 12/12/2022] Open
Abstract
The southern blue-ringed octopus, Hapalochlaena maculosa (Hoyle, 1883) lacks a planktonic dispersal phase, yet ranges across Australia's southern coastline. This species' brief and holobenthic life history suggests gene flow might be limited, leaving distant populations prone to strong genetic divergence. This study used 17,523 genome-wide SNP loci to investigate genetic structuring and local adaptation patterns of H. maculosa among eight sampling sites along its reported range. Within sites, interrelatedness was very high, consistent with the limited dispersal of this taxon. However, inbreeding coefficients were proportionally lower among sites where substructuring was not detected, suggesting H. maculosa might possess a mechanism for inbreeding avoidance. Genetic divergence was extremely high among all sites, with the greatest divergence observed between both ends of the distribution, Fremantle, WA, and Stanley, TAS. Genetic distances closely followed an isolation by geographic distance pattern. Outlier analyses revealed distinct selection signatures at all sites, with the strongest divergence reported between Fremantle and the other Western Australian sites. Phylogenetic reconstructions using the described sister taxon H. fasciata (Hoyle, 1886) further supported that the genetic divergence between distal H. maculosa sites in this study was equivalent to that of between established heterospecifics within this genus. However, it is advocated that taxonomic delineations within this species should be made with caution. These data indicate that H. maculosa forms a clinal species pattern across its geographic range, with gene flow present through allele sharing between adjacent populations. Morphological investigations are recommended for a robust resolution of the taxonomic identity and ecotype boundaries of this species.
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Affiliation(s)
- Peter Morse
- Australian Institute of Marine ScienceUWA Oceans InstituteCrawleyWAAustralia
- College of Science and EngineeringJames Cook UniversityTownsvilleQldAustralia
| | - Shannon R. Kjeldsen
- College of Science and EngineeringJames Cook UniversityTownsvilleQldAustralia
| | - Mark G. Meekan
- Australian Institute of Marine ScienceUWA Oceans InstituteCrawleyWAAustralia
| | - Mark I. Mccormick
- College of Science and EngineeringJames Cook UniversityTownsvilleQldAustralia
| | | | - Christine L. Huffard
- Monterey Bay Aquarium Research InstituteMoss LandingCAUSA
- California Academy of SciencesSan FranciscoCAUSA
| | - Kyall R. Zenger
- College of Science and EngineeringJames Cook UniversityTownsvilleQldAustralia
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38
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Hongsanan S, Maharachchikumbura SSN, Hyde KD, Samarakoon MC, Jeewon R, Zhao Q, Al-Sadi AM, Bahkali AH. An updated phylogeny of Sordariomycetes based on phylogenetic and molecular clock evidence. FUNGAL DIVERS 2017. [DOI: 10.1007/s13225-017-0384-2] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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39
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Li H, Liu J, Xiong L, Zhang H, Zhou H, Yin H, Jing W, Li J, Shi Q, Wang Y, Liu J, Nie L. Phylogenetic relationships and divergence dates of softshell turtles (Testudines: Trionychidae) inferred from complete mitochondrial genomes. J Evol Biol 2017; 30:1011-1023. [PMID: 28294452 DOI: 10.1111/jeb.13070] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 02/22/2017] [Accepted: 03/10/2017] [Indexed: 11/30/2022]
Abstract
The softshell turtles (Trionychidae) are one of the most widely distributed reptile groups in the world, and fossils have been found on all continents except Antarctica. The phylogenetic relationships among members of this group have been previously studied; however, disagreements regarding its taxonomy, its phylogeography and divergence times are still poorly understood as well. Here, we present a comprehensive mitogenomic study of softshell turtles. We sequenced the complete mitochondrial genomes of 10 softshell turtles, in addition to the GenBank sequence of Dogania subplana, Lissemys punctata, Trionyx triunguis, which cover all extant genera within Trionychidae except for Cyclanorbis and Cycloderma. These data were combined with other mitogenomes of turtles for phylogenetic analyses. Divergence time calibration and ancestral reconstruction were calculated using BEAST and RASP software, respectively. Our phylogenetic analyses indicate that Trionychidae is the sister taxon of Carettochelyidae, and support the monophyly of Trionychinae and Cyclanorbinae, which is consistent with morphological data and molecular analysis. Our phylogenetic analyses have established a sister taxon relationship between the Asian Rafetus and the Asian Palea + Pelodiscus + Dogania + Nilssonia + Amyda, whereas a previous study grouped the Asian Rafetus with the American Apalone. The results of divergence time estimates and area ancestral reconstruction show that extant Trionychidae originated in Asia at around 108 million years ago (MA), and radiations mainly occurred during two warm periods, namely Late Cretaceous-Early Eocene and Oligocene. By combining the estimated divergence time and the reconstructed ancestral area of softshell turtles, we determined that the dispersal of softshell turtles out of Asia may have taken three routes. Furthermore, the times of dispersal seem to be in agreement with the time of the India-Asia collision and opening of the Bering Strait, which provide evidence for the accuracy of our estimation of divergence time. Overall, the mitogenomes of this group were used to explore the origin and dispersal route of Trionychidae and have provided new insights on the evolution of this group.
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Affiliation(s)
- H Li
- Life Science College, The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, China
| | - J Liu
- The College of Life Sciences, Beijing Normal University, Beijing, China
| | - L Xiong
- Wannan medical college, Wuhu, Anhui, China
| | - H Zhang
- Life Science College, The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, China
| | - H Zhou
- Life Science College, The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, China
| | - H Yin
- Life Science College, The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, China
| | - W Jing
- Life Science College, The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, China
| | - J Li
- Life Science College, The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, China
| | - Q Shi
- Life Science College, The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, China
| | - Y Wang
- Life Science College, The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, China
| | - J Liu
- Life Science College, The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, China
| | - L Nie
- Life Science College, The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, Anhui, China
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40
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Grímsson F, Grimm GW, Zetter R. Evolution of pollen morphology in Loranthaceae. GRANA 2017; 57:16-116. [PMID: 29386990 PMCID: PMC5771552 DOI: 10.1080/00173134.2016.1261939] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 10/04/2016] [Indexed: 05/30/2023]
Abstract
Earlier studies indicate a strong correlation of pollen morphology and ultrastructure with taxonomy in Loranthaceae. Using high-resolution light microscopy and scanning electron microscopy imaging of the same pollen grains, we document pollen types of 35 genera including 15 studied for the first time. Using a molecular phylogenetic framework based on currently available sequence data with good genus-coverage, we reconstruct trends in the evolution of Loranthaceae pollen and pinpoint traits of high diagnostic value, partly confirming earlier intuitive hypotheses based on morphological observations. We find that pollen morphology in Loranthaceae is strongly linked to phylogenetic relationships. Some pollen types are diagnostic for discrete genera or evolutionary lineages, opening the avenue to recruit dispersed fossil pollen as age constraints for dated phylogenies and as independent data for testing biogeographic scenarios; so far based exclusively on modern-day data. Correspondences and discrepancies between palynological and molecular data and current taxonomic/systematic concepts are identified and suggestions made for future palynological and molecular investigations of Loranthaceae.
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Affiliation(s)
| | - Guido W. Grimm
- Department of Palaeontology, University of Vienna, Vienna, Austria
| | - Reinhard Zetter
- Department of Palaeontology, University of Vienna, Vienna, Austria
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41
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Tian Q, Doilom M, Luo ZL, Chomnunti P, Bhat JD, Xu JC, Hyde KD. IntroducingMelanoctona tectonaegen. et sp. nov. andMinimelanolocus yunnanensissp. nov. (Herpotrichiellaceae, Chaetothyriales). CRYPTOGAMIE MYCOL 2016. [DOI: 10.7872/crym/v37.iss4.2016.477] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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42
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Petzoldt D, Breves G, Rautenschlein S, Taras D. Harryflintia acetispora gen. nov., sp. nov., isolated from chicken caecum. Int J Syst Evol Microbiol 2016; 66:4099-4104. [DOI: 10.1099/ijsem.0.001317] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Diana Petzoldt
- Lohmann Animal Health GmbH, Heinz-Lohmann-Straße 4, D-27472 Cuxhaven, Germany
- Clinic for Poultry, University of Veterinary Medicine Hannover, Bünteweg 17, D-30559 Hannover, Germany
| | - Gerhard Breves
- Institute for Physiology, University of Veterinary Medicine Hannover, Bischofsholer Damm 15, D-30173 Hannover, Germany
| | - Silke Rautenschlein
- Clinic for Poultry, University of Veterinary Medicine Hannover, Bünteweg 17, D-30559 Hannover, Germany
| | - David Taras
- Lohmann Animal Health GmbH, Heinz-Lohmann-Straße 4, D-27472 Cuxhaven, Germany
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43
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Simões BF, Sampaio FL, Douglas RH, Kodandaramaiah U, Casewell NR, Harrison RA, Hart NS, Partridge JC, Hunt DM, Gower DJ. Visual Pigments, Ocular Filters and the Evolution of Snake Vision. Mol Biol Evol 2016; 33:2483-95. [DOI: 10.1093/molbev/msw148] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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44
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From a lost world: an integrative phylogenetic analysis of Ansonia Stoliczka, 1870 (Lissamphibia: Anura: Bufonidae), with the description of a new species. ORG DIVERS EVOL 2016. [DOI: 10.1007/s13127-016-0294-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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45
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Battelle BA, Ryan JF, Kempler KE, Saraf SR, Marten CE, Warren WC, Minx PJ, Montague MJ, Green PJ, Schmidt SA, Fulton L, Patel NH, Protas ME, Wilson RK, Porter ML. Opsin Repertoire and Expression Patterns in Horseshoe Crabs: Evidence from the Genome of Limulus polyphemus (Arthropoda: Chelicerata). Genome Biol Evol 2016; 8:1571-89. [PMID: 27189985 PMCID: PMC4898813 DOI: 10.1093/gbe/evw100] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2016] [Indexed: 12/19/2022] Open
Abstract
Horseshoe crabs are xiphosuran chelicerates, the sister group to arachnids. As such, they are important for understanding the most recent common ancestor of Euchelicerata and the evolution and diversification of Arthropoda. Limulus polyphemus is the most investigated of the four extant species of horseshoe crabs, and the structure and function of its visual system have long been a major focus of studies critical for understanding the evolution of visual systems in arthropods. Likewise, studies of genes encoding Limulus opsins, the protein component of the visual pigments, are critical for understanding opsin evolution and diversification among chelicerates, where knowledge of opsins is limited, and more broadly among arthropods. In the present study, we sequenced and assembled a high quality nuclear genomic sequence of L. polyphemus and used these data to annotate the full repertoire of Limulus opsins. We conducted a detailed phylogenetic analysis of Limulus opsins, including using gene structure and synteny information to identify relationships among different opsin classes. We used our phylogeny to identify significant genomic events that shaped opsin evolution and therefore the visual system of Limulus We also describe the tissue expression patterns of the 18 opsins identified and show that transcripts encoding a number, including a peropsin, are present throughout the central nervous system. In addition to significantly extending our understanding of photosensitivity in Limulus and providing critical insight into the genomic evolution of horseshoe crab opsins, this work provides a valuable genomic resource for addressing myriad questions related to xiphosuran physiology and arthropod evolution.
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Affiliation(s)
- Barbara-Anne Battelle
- Whitney Laboratory for Marine Bioscience, Departments of Neuroscience and Biology, University of Florida
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, Department of Biology, University of Florida
| | - Karen E Kempler
- Whitney Laboratory for Marine Bioscience, Departments of Neuroscience and Biology, University of Florida
| | - Spencer R Saraf
- Whitney Laboratory for Marine Bioscience, Departments of Neuroscience and Biology, University of Florida Present address: School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY
| | - Catherine E Marten
- Whitney Laboratory for Marine Bioscience, Departments of Neuroscience and Biology, University of Florida Present address: Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL
| | - Wesley C Warren
- McDonnell Genome Institute, Washington University School of Medicine in St. Louis
| | - Patrick J Minx
- McDonnell Genome Institute, Washington University School of Medicine in St. Louis
| | - Michael J Montague
- McDonnell Genome Institute, Washington University School of Medicine in St. Louis
| | - Pamela J Green
- Department of Plant and Soil Sciences, School of Marine Science and Policy, Delaware Biotechnology Institute, University of Delaware
| | - Skye A Schmidt
- Department of Plant and Soil Sciences, School of Marine Science and Policy, Delaware Biotechnology Institute, University of Delaware
| | - Lucinda Fulton
- McDonnell Genome Institute, Washington University School of Medicine in St. Louis
| | - Nipam H Patel
- Department of Molecular Cell Biology, Center for Integrative Genomics, University of California, Berkley
| | - Meredith E Protas
- Department of Molecular Cell Biology, Center for Integrative Genomics, University of California, Berkley Present address: Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, CA
| | - Richard K Wilson
- McDonnell Genome Institute, Washington University School of Medicine in St. Louis
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46
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Dejaco T, Gassner M, Arthofer W, Schlick-Steiner BC, Steiner FM. Taxonomist's Nightmare … Evolutionist's Delight : An Integrative Approach Resolves Species Limits in Jumping Bristletails Despite Widespread Hybridization and Parthenogenesis. Syst Biol 2016; 65:947-974. [PMID: 26869489 PMCID: PMC5066060 DOI: 10.1093/sysbio/syw003] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 10/26/2015] [Accepted: 01/14/2016] [Indexed: 11/13/2022] Open
Abstract
Accurate species delimitation is fundamental to biology. Traditionally, species were delimited based on morphological characters, sometimes leading to taxonomic uncertainty in morphologically conserved taxa. Recently, multiple taxonomically challenging cases have benefited from integrative taxonomy-an approach that highlights congruence among different disciplines and invokes evolutionary explanations for incongruence, acknowledging that different methods can mirror different stages of the speciation continuum. Here, we used a cohesive protocol for integrative taxonomy to revise species limits in 20 nominal species and 4 morphospecies of an ancestrally wingless insect group, the jumping bristletail genus Machilis from the European Eastern Alps. Even though morphologically conserved, several small-scale endemic species have been described from the Eastern Alps based on variation in hypodermal pigmentation patterns-a highly questionable character. As valuable as these endemics are for conservation, they have never been verified by alternative methods. Using traditional morphometrics, mitochondrial DNA, ribosomal DNA, and amplified fragment-length polymorphism markers, we identify six nominal species as taxonomic junior synonyms (Machilis alpicola Janetschek, 1953 syn. n. under M. vagans Wygodzinsky, 1941; M. ladensis Janetschek, 1950 syn. n., M. robusta Wygodzinsky, 1941 syn. n., and M. vicina Wygodzinsky, 1941 syn. n. under M. inermis Wygodzinsky, 1941; M. aleamaculata Wygodzinsky, 1941 syn. n. under M. montana Wygodzinsky, 1941; M. pulchra Janetschek, 1950 syn. n. under M. helleri Verhoeff, 1910) and describe two new species (Machilis cryptoglacialis sp. n. and Machilis albida sp. n.), one uncovered from morphological crypsis and one never sampled before. Building on numerous cases of incongruence among data sources, we further shed light on complex evolutionary histories including hybrid speciation, historical and recent hybridization, and ongoing speciation. We hypothesize that an inherent affinity to hybridization, combined with parallel switches to parthenogenesis and repeated postglacial colonization events may have boosted endemicity in Eastern Alpine Machilis We thus emphasize the importance of integrative taxonomy for rigorous species delimitation and its implication for evolutionary research and conservation in taxonomically challenging taxa.
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Affiliation(s)
- Thomas Dejaco
- Molecular Ecology Group, Institute of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria .,Museum of Nature South Tyrol, Bindergasse 1, 39100 Bozen/Bolzano, Italy
| | - Melitta Gassner
- Molecular Ecology Group, Institute of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Wolfgang Arthofer
- Molecular Ecology Group, Institute of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Birgit C Schlick-Steiner
- Molecular Ecology Group, Institute of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Florian M Steiner
- Molecular Ecology Group, Institute of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
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47
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Mwirichia R, Alam I, Rashid M, Vinu M, Ba-Alawi W, Anthony Kamau A, Kamanda Ngugi D, Göker M, Klenk HP, Bajic V, Stingl U. Metabolic traits of an uncultured archaeal lineage--MSBL1--from brine pools of the Red Sea. Sci Rep 2016; 6:19181. [PMID: 26758088 PMCID: PMC4725937 DOI: 10.1038/srep19181] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 12/04/2015] [Indexed: 11/24/2022] Open
Abstract
The candidate Division MSBL1 (Mediterranean Sea Brine Lakes 1) comprises a monophyletic group of uncultured archaea found in different hypersaline environments. Previous studies propose methanogenesis as the main metabolism. Here, we describe a metabolic reconstruction of MSBL1 based on 32 single-cell amplified genomes from Brine Pools of the Red Sea (Atlantis II, Discovery, Nereus, Erba and Kebrit). Phylogeny based on rRNA genes as well as conserved single copy genes delineates the group as a putative novel lineage of archaea. Our analysis shows that MSBL1 may ferment glucose via the Embden-Meyerhof-Parnas pathway. However, in the absence of organic carbon, carbon dioxide may be fixed via the ribulose bisphosphate carboxylase, Wood-Ljungdahl pathway or reductive TCA cycle. Therefore, based on the occurrence of genes for glycolysis, absence of the core genes found in genomes of all sequenced methanogens and the phylogenetic position, we hypothesize that the MSBL1 are not methanogens, but probably sugar-fermenting organisms capable of autotrophic growth. Such a mixotrophic lifestyle would confer survival advantage (or possibly provide a unique narrow niche) when glucose and other fermentable sugars are not available.
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Affiliation(s)
- Romano Mwirichia
- Red Sea Research Center, King Abdullah University of Science and
Technology (KAUST), Thuwal, Saudi Arabia
| | - Intikhab Alam
- Computational Bioscience Research Center, King Abdullah
University of Science and Technology (KAUST), Thuwal,
Saudi Arabia
| | - Mamoon Rashid
- Red Sea Research Center, King Abdullah University of Science and
Technology (KAUST), Thuwal, Saudi Arabia
| | - Manikandan Vinu
- Red Sea Research Center, King Abdullah University of Science and
Technology (KAUST), Thuwal, Saudi Arabia
| | - Wail Ba-Alawi
- Computational Bioscience Research Center, King Abdullah
University of Science and Technology (KAUST), Thuwal,
Saudi Arabia
| | - Allan Anthony Kamau
- Computational Bioscience Research Center, King Abdullah
University of Science and Technology (KAUST), Thuwal,
Saudi Arabia
| | - David Kamanda Ngugi
- Red Sea Research Center, King Abdullah University of Science and
Technology (KAUST), Thuwal, Saudi Arabia
| | - Markus Göker
- German Collection for Microorganisms and Cell Cultures GmbH
(DSMZ), Inhoffenstraße 7b, 38124
Braunschweig, Germany
| | - Hans-Peter Klenk
- School of Biology, Newcastle University, Newcastle
upon Tyne, United Kingdom
| | - Vladimir Bajic
- Computational Bioscience Research Center, King Abdullah
University of Science and Technology (KAUST), Thuwal,
Saudi Arabia
| | - Ulrich Stingl
- Red Sea Research Center, King Abdullah University of Science and
Technology (KAUST), Thuwal, Saudi Arabia
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48
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Wang QM, Yurkov A, Göker M, Lumbsch H, Leavitt S, Groenewald M, Theelen B, Liu XZ, Boekhout T, Bai FY. Phylogenetic classification of yeasts and related taxa within Pucciniomycotina. Stud Mycol 2016; 81:149-89. [PMID: 26951631 PMCID: PMC4777780 DOI: 10.1016/j.simyco.2015.12.002] [Citation(s) in RCA: 165] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Most small genera containing yeast species in the Pucciniomycotina (Basidiomycota, Fungi) are monophyletic, whereas larger genera including Bensingtonia, Rhodosporidium, Rhodotorula, Sporidiobolus and Sporobolomyces are polyphyletic. With the implementation of the “One Fungus = One Name” nomenclatural principle these polyphyletic genera were revised. Nine genera, namely Bannoa, Cystobasidiopsis, Colacogloea, Kondoa, Erythrobasidium, Rhodotorula, Sporobolomyces, Sakaguchia and Sterigmatomyces, were emended to include anamorphic and teleomorphic species based on the results obtained by a multi-gene phylogenetic analysis, phylogenetic network analyses, branch length-based methods, as well as morphological, physiological and biochemical comparisons. A new class Spiculogloeomycetes is proposed to accommodate the order Spiculogloeales. The new families Buckleyzymaceae with Buckleyzyma gen. nov., Chrysozymaceae with Chrysozyma gen. nov., Microsporomycetaceae with Microsporomyces gen. nov., Ruineniaceae with Ruinenia gen. nov., Symmetrosporaceae with Symmetrospora gen. nov., Colacogloeaceae and Sakaguchiaceae are proposed. The new genera Bannozyma, Buckleyzyma, Fellozyma, Hamamotoa, Hasegawazyma, Jianyunia, Rhodosporidiobolus, Oberwinklerozyma, Phenoliferia, Pseudobensingtonia, Pseudohyphozyma, Sampaiozyma, Slooffia, Spencerozyma, Trigonosporomyces, Udeniozyma, Vonarxula, Yamadamyces and Yunzhangia are proposed to accommodate species segregated from the genera Bensingtonia, Rhodosporidium, Rhodotorula, Sporidiobolus and Sporobolomyces. Ballistosporomyces is emended and reintroduced to include three Sporobolomyces species of the sasicola clade. A total of 111 new combinations are proposed in this study.
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Key Words
- B. aurantiaca (Saito) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- B. kluyveri-nielii (van der Walt) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- B. ogasawarensis (Hamam., Thanh & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- B. phyllomatis (van der Walt & Y. Yamada) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- B. salicina (B.N. Johri & Bandoni) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- B. syzygii (Hamam., Thanh & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- B. taupoensis (Hamam. & Nakase) F.Y. Bai, Q.M. Wang, M. Groenew. & Boekhout
- B. yamatoana (Nakase, M. Suzuki & M. Itoh) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Ballistosporomycessasicola (Nakase & M. Suzuki) F.Y. Bai, Q.M. Wang, M. Groenew. & Boekhout
- Bannoabischofiae (Hamam., Thanh & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Bannozyma Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Bannozymaarctica (Vishniac & M. Takash.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Buckleyzyma Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Buckleyzymaarmeniaca (R.G. Shivas & Rodr. Mir.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Buckleyzymaceae Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- C. diffluens (Ruinen) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- C. eucalyptica (C.H. Pohl, M.S. Smit & Albertyn) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- C. falcata (Nakase, M. Itoh & M. Suzuki) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- C. foliorum (Ruinen) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- C. griseoflava (Nakase & M. Suzuki) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- C. lophatheri (Nakase, Tsuzuki, F.L. Lee, Jindam. & M. Takash.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- C. philyla (van der Walt, Klift & D.B. Scott) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- C. retinophila (Thanh, M.S. Smit, Moleleki & Fell) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- C. terpenoidalis (Thanh, M.S. Smit, Moleleki & Fell) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Chrysozyma Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Chrysozymaceae Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Chrysozymafushanensis (Nakase, F.L. Lee & M. Takash.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Colacogloeaceae Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Colacogloeacycloclastica (Thanh, M.S. Smit, Moleleki & Fell) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Cystobasidiopsislactophilus (Nakase, M. Itoh, M. Suzuki & Bandoni) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Cystobasidiumportillonense (F. Laich, I. Vaca & R. Chávez) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- E. yunnanense (F.Y. Bai, M. Takash., Hamam. & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Erythrobasidiumelongatum (R.G. Shivas & Rodr. Mir.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Fellozyma Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Fellozymainositophila (Nakase & M. Suzuki) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Fungi
- GMYC approach
- H. singularis (Phaff & do Carmo-Sousa) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Hamamotoa Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Hamamotoalignophila (Dill, C. Ramírez & González) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Hasegawazyma Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Hasegawazymalactosa (Hasegawa) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Jianyunia Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Jianyuniasakaguchii (Sugita, M. Takash., Hamam. & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- K. miscanthi (Nakase & M. Suzuki) Q.M. Wang, M. Groenew., F.Y. Bai & Boekhout
- K. phyllada (van der Walt & Y. Yamada) Q.M. Wang, M. Groenew., F.Y. Bai & Boekhout
- K. sorbi (F.Y. Bai & Q.M. Wang) Q.M. Wang, M. Groenew., F.Y. Bai & Boekhout
- K. subrosea (Nakase & M. Suzuki) Q.M. Wang, M. Groenew., F.Y. Bai & Boekhout
- K. thailandica (Fungsin, Hamam. & Nakase ) Q.M. Wang, M. Groenew., F.Y. Bai & Boekhout
- K. yuccicola (Nakase & M. Suzuki) Q.M. Wang, M. Groenew., F.Y. Bai & Boekhout
- Kondoachangbaiensis (F.Y. Bai & Q.M. Wang) Q.M. Wang, M. Groenew., F.Y. Bai & Boekhout
- M. magnisporus (Nakase, Tsuzuki, F.L. Lee, Sugita, Jindam. & M. Takash.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- M. orientis (Pohl, M.S. Smit & Albertyn) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- M. pini (Pohl, M.S. Smit & Albertyn) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Microsporomyces Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Microsporomycesbloemfonteinensis (Pohl, M.S. Smit & Albertyn) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Microsporomycetaceae Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Molecular phylogeny
- O. straminea (Golubev & Scorzetti) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- O. yarrowii (Á. Fonseca & van Uden) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Oberwinklerozyma Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Oberwinklerozymasilvestris (Golubev & Scorzetti) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- P. buffonii (C. Ramírez) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- P. corallina (N. Furuya & M. Takash.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- P. dimennae (Hamam. & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- P. glacialis (Margesin & J.P. Samp.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- P. himalayensis (Shivaji, Bhadra & Rao) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- P. linderae (Nakase, M. Takash. & Hamam.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- P. musae (M. Takash., S.O. Suh & Nakase) F.Y. Bai, Q.M. Wang, M. Groenew. & Boekhout
- P. novozealandica (Hamam. & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- P. producta (N. Furuya & M. Takash.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- P. psychrophila (Margesin & J.P. Samp.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- P. pustula (Buhagiar) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- P. subbrunnea (Nakase & M. Suzuki) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Phenoliferia Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Phenoliferiapsychrophenolica (Margesin & J.P. Samp.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Phyllozyma Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Phyllozymacoprosmicola (Hamam. & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Phylogenetic rank boundary optimisation
- Pseudobensingtonia F.Y. Bai, Q.M. Wang, M. Groenew. & Boekhout
- Pseudobensingtoniaingoldii (Nakase & Itoh.) F.Y. Bai, Q.M. Wang, M. Groenew. & Boekhout
- Pseudohyphozyma Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Pseudohyphozymabogoriensis (Deinema) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Pucciniomycotina
- R. azoricus (J.P. Samp. & Gadanho) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. babjevae (Golubev) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. colostri (T. Castelli) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. diobovata (S.Y. Newell & I.L. Hunter) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. diospyroris (Nakase, Tsuzuki, F.L. Lee, Jindam. & M. Takash.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. dracophylli (Hamam. & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. kratochvilovae (Hamam., Sugiy. & Komag.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. lusitaniae (Á. Fonseca & J.P. Samp.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. microsporus (Higham ex Fell, Blatt & Statzell) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. nylandii (M. Takash. & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. odoratus (J.P. Samp., Á. Fonseca & Valério) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. paludigena (Fell & Tallman) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. poonsookiae (M. Takash. & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. pyrrosiae (Nakase, Tsuzuki, F.L. Lee, Jindam. & M. Takash.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. rubra (Nakase, Oakada & Sugiy.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. ruineniae (Holzschu, Tredick & Phaff) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. sphaerocarpa (S.Y. Newell & Fell) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- R. toruloides (I. Banno) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Rhodosporidiobolus Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Rhodosporidiobolus fluvialis (Fell, Kurtzman, Tallman & J.D. Buck) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Rhodotorulaalborubescens (Derx) Q.M. Wang, F.Y. Bai, Groenew. & Boekhout
- Ruinenia Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Ruineniaceae Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Ruineniaclavata (F.Y. Bai & Q.M. Wang) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- S. oryzae (F.Y. Bai & Y.M. Cai) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- S. foliicola (R.G. Shivas & Rodr. Mir.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- S. gracilis (Derx) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- S. johnsonii (Nyland) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- S. lamellibrachiae (Nagah., Hamam., Nakase & Horikoshi) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- S. marina (Phaff, Mrak & Williams) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- S. meli (Libkind, van Broock & J.P. Samp.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- S. novozelandica (W.B. Kendr. & X.D. Gong) F.Y. Bai, Q.M. Wang, Groenewald & Boekhout
- S. pilati (F.H. Jacob, Faure-Raynaud & Berton) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- S. pulcherrima (J.E. Wright) F.Y. Bai, Q.M. Wang, Groenewald & Boekhout
- S. symmetrica (F.Y. Bai & Q.M. Wang) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- S. tsugae (Phaff & do Carmo-Sousa) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- S. vanillica (J.P. Samp.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- S. vermiculata (M. Takash. & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Sakaguchiaceae Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Sakaguchiacladiensis (Fell, Statzell & Scorzetti) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Sampaiozyma Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Sampaiozymaingeniosa (Di Menna) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Slooffia Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Slooffia cresolica (Middelhoven & Spaaij) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Spencerozyma Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Spencerozymacrocea (Shifrine & Phaff) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Spiculogloeomycetes Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Sporobolomyceslongiusculus (Libkind, van Broock & J.P. Samp.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Sterigmatomyceshyphaenes (Har. & Pat.) F.Y. Bai, Q.M. Wang, Groenewald & Boekhout
- Symmetrospora Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Symmetrosporaceae Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Symmetrosporacoprosmae (Hamam. & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Taxonomy
- Trigonosporomyces Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Trigonosporomyceshylophilus (van der Walt, van der Klift & D.B. Scott) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Udeniozyma Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Udeniozymaferulica (J.P. Samp. & van Uden) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Ustilentylomagraminis (Rodr. Mir. & Diem) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Vonarxula Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Vonarxulajavanica (Ruinen) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Y. sonckii (Hopsu-Havu, Tunnela & Yarrow) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Yamadamyces Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Yamadamycesrosulatus (Golubev & Scorzetti) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Yeasts
- Yunzhangia Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
- Yunzhangiaauriculariae (Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout
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Affiliation(s)
- Q.-M. Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - A.M. Yurkov
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - M. Göker
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - H.T. Lumbsch
- Science & Education, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA
| | - S.D. Leavitt
- Science & Education, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA
| | - M. Groenewald
- CBS Fungal Biodiversity Centre (CBS–KNAW), Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - B. Theelen
- CBS Fungal Biodiversity Centre (CBS–KNAW), Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - X.-Z. Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - T. Boekhout
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- CBS Fungal Biodiversity Centre (CBS–KNAW), Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Shanghai Key Laboratory of Molecular Medical Mycology, Changzheng Hospital, Second Military Medical University, Shanghai, China
- Correspondence: T. Boekhout; F.-Y. Bai
| | - F.-Y. Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- CBS Fungal Biodiversity Centre (CBS–KNAW), Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Correspondence: T. Boekhout; F.-Y. Bai
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Austin CM, Tan MH, Croft LJ, Hammer MP, Gan HM. Whole Genome Sequencing of the Asian Arowana (Scleropages formosus) Provides Insights into the Evolution of Ray-Finned Fishes. Genome Biol Evol 2015; 7:2885-95. [PMID: 26446539 PMCID: PMC4684697 DOI: 10.1093/gbe/evv186] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The Asian arowana (Scleropages formosus) is of commercial importance, conservation concern, and is a representative of one of the oldest lineages of ray-finned fish, the Osteoglossomorpha. To add to genomic knowledge of this species and the evolution of teleosts, the genome of a Malaysian specimen of arowana was sequenced. A draft genome is presented consisting of 42,110 scaffolds with a total size of 708 Mb (2.85% gaps) representing 93.95% of core eukaryotic genes. Using a k-mer-based method, a genome size of 900 Mb was also estimated. We present an update on the phylogenomics of fishes based on a total of 27 species (23 fish species and 4 tetrapods) using 177 orthologous proteins (71,360 amino acid sites), which supports established relationships except that arowana is placed as the sister lineage to all teleost clades (Bayesian posterior probability 1.00, bootstrap replicate 93%), that evolved after the teleost genome duplication event rather than the eels (Elopomorpha). Evolutionary rates are highly heterogeneous across the tree with fishes represented by both slowly and rapidly evolving lineages. A total of 94 putative pigment genes were identified, providing the impetus for development of molecular markers associated with the spectacular colored phenotypes found within this species.
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Affiliation(s)
- Christopher M Austin
- School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia Monash University Malaysia Genomics Facility, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia
| | - Mun Hua Tan
- School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia Monash University Malaysia Genomics Facility, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia
| | - Larry J Croft
- School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia Monash University Malaysia Genomics Facility, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia Malaysian Genomics Resource Centre Berhad, Boulevard Signature Office, Kuala Lumpur, Malaysia
| | - Michael P Hammer
- Museum and Art Gallery of the Northern Territory, Darwin, NT, Australia
| | - Han Ming Gan
- School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia Monash University Malaysia Genomics Facility, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia
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50
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Collections on Lonicera in Northwest Iran represent an undescribed species in the Inonotus linteus complex (Hymenochaetales). Mycol Prog 2015. [DOI: 10.1007/s11557-015-1100-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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