1
|
Wang Y, Hu B, Peng J, Zhou Q. The complete chloroplast genome of Sinosenecio globigerus (C. C. Chang) B. Nordenstam (Asteraceae). Mitochondrial DNA B Resour 2024; 9:204-208. [PMID: 38288251 PMCID: PMC10823894 DOI: 10.1080/23802359.2024.2309262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 01/18/2024] [Indexed: 01/31/2024] Open
Abstract
The genus Sinosenecio B. Nordenstam is a group of perennial or sometimes annual or biennial herbs in the family Asteraceae. Here, we have successfully assembled and characterized the complete chloroplast (cp) genome of S. globigerus, which shows a typical quadratic structure with an overall GC content of 37.4%, comprising a pair of inverted repeat regions (IRs) of 24,848 bp, a large single-copy region (LSC) of 83,379 bp and a small single-copy region (SSC) of 18,180 bp. 133 genes were annotated, including 88 protein-coding genes, 37 tRNA genes and eight rRNA genes. Further nucleotide diversity analysis indicated that three genomic regions (accD-psaI, trnK-rps16, and ycf1) exhibited sufficient variability and thus could be recommended as valuable barcodes for the delimitation and identification of Sinosenecio species. Phylogenetic reconstruction presented clear interspecific relationships within Sinosenecio, which were supported to some extent by cytology, morphology and geographic distributions. Our study will provide valuable and high-quality genetic information to further elucidate the diversified mechanisms in Sinosenecio.
Collapse
Affiliation(s)
- Yi Wang
- College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, China
| | - Bin Hu
- College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, China
| | - Jingyi Peng
- College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, China
| | - Qiang Zhou
- College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan, China
| |
Collapse
|
2
|
Hyde JR, Armond T, Herring JA, Hope S, Grose JH, Breakwell DP, Pickett BE. Diversity and conservation of the genome architecture of phages infecting the Alphaproteobacteria. Microbiol Spectr 2024; 12:e0282723. [PMID: 37991376 PMCID: PMC10783043 DOI: 10.1128/spectrum.02827-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/24/2023] [Indexed: 11/23/2023] Open
Abstract
IMPORTANCE This study reports the results of the largest analysis of genome sequences from phages that infect the Alphaproteobacteria class of bacterial hosts. We analyzed over 100 whole genome sequences of phages to construct dotplots, categorize them into genetically distinct clusters, generate a bootstrapped phylogenetic tree, compute protein orthologs, and predict packaging strategies. We determined that the phage sequences primarily cluster by the bacterial host family, phage morphotype, and genome size. We expect that the findings reported in this seminal study will facilitate future analyses that will improve our knowledge of the phages that infect these hosts.
Collapse
Affiliation(s)
- Jonathan R. Hyde
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Thomas Armond
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Jacob A. Herring
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Sandra Hope
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Julianne H. Grose
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Donald P. Breakwell
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| | - Brett E. Pickett
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
| |
Collapse
|
3
|
Xu D, Wang Z, Zhuang W, Wang T, Xie Y. Family characteristics, phylogenetic reconstruction, and potential applications of the plant BAHD acyltransferase family. Front Plant Sci 2023; 14:1218914. [PMID: 37868312 PMCID: PMC10585174 DOI: 10.3389/fpls.2023.1218914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 09/14/2023] [Indexed: 10/24/2023]
Abstract
The BAHD acyltransferase family is a class of proteins in plants that can acylate a variety of primary and specialized secondary metabolites. The typically acylated products have greatly improved stability, lipid solubility, and bioavailability and thus show significant differences in their physicochemical properties and pharmacological activities. Here, we review the protein structure, catalytic mechanism, and phylogenetic reconstruction of plant BAHD acyltransferases to describe their family characteristics, acylation reactions, and the processes of potential functional differentiation. Moreover, the potential applications of the BAHD family in human activities are discussed from the perspectives of improving the quality of economic plants, enhancing the efficacy of medicinal plants, improving plant biomass for use in biofuel, and promoting stress resistance of land plants. This review provides a reference for the research and production of plant BAHD acyltransferases.
Collapse
Affiliation(s)
- Donghuan Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, China
| | - Zhong Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, China
| | - Weibing Zhuang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, China
| | - Tao Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, China
| | - Yinfeng Xie
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing, China
| |
Collapse
|
4
|
Pyziel AM, Laskowski Z, Klich D, Demiaszkiewicz AW, Kaczor S, Merta D, Kobielski J, Nowakowska J, Anusz K, Höglund J. Distribution of large lungworms (Nematoda: Dictyocaulidae) in free-roaming populations of red deer Cervus elaphus (L.) with the description of Dictyocaulus skrjabini n. sp. Parasitology 2023; 150:956-966. [PMID: 37694391 PMCID: PMC10577652 DOI: 10.1017/s003118202300080x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/29/2023] [Accepted: 08/22/2023] [Indexed: 09/12/2023]
Abstract
Lungworms of the genus Dictyocaulus are causative agents of parasitic bronchitis in domestic and wild ungulates. This study investigates the distribution, morphology and genetic diversity of D. cervi and a new lungworm species, Dictyocaulus skrjabini n. sp. infecting red deer Cervus elaphus, fallow deer Dama dama and moose Alces alces in Poland and Sweden. The study was conducted on 167 red deer from Poland and on the DNA of lungworms derived from 7 fallow deer, 4 red deer and 2 moose collected in Sweden. The prevalence of D. cervi and D. skrjabini n. sp. in dissected red deer in Poland was 31.1% and 7.2%, respectively. Moreover, D. skrjabini n. sp. was confirmed molecularly in 7 isolates of fallow deer lungworms and 1 isolate of red deer lungworms from Sweden. Dictyocaulus skrjabini n. sp. was established based on combination of their distinct molecular and morphological features; these included the length of cephalic vesicle, buccal capsule (BC), buccal capsule wall (BCW), distance from anterior extremity to the nerve ring, the width of head, oesophagus, cephalic vesicle, BC and BCW, as well as the dimensions of reproductive organs of male and female. Additionally, molecular analyses revealed 0.9% nucleotide sequence divergence for 1,605 bp SSU rDNA, and 16.5–17.3% nucleotide sequence divergence for 642 bp mitochondrial cytB between D. skrjabini n. sp. and D. cervi, respectively, and 18.7–19% between D. skrjabini n. sp. and D. eckerti, which translates into 18.2–18.7% amino acid sequence divergence between D. skrjabini n. sp. and both lungworms.
Collapse
Affiliation(s)
- Anna Maria Pyziel
- Department of Food Hygiene and Public Health Protection, Institute of Veterinary Medicine, Warsaw University of Life Sciences (WULS-SGGW), Warsaw, Poland
| | - Zdzisław Laskowski
- Polish Academy of Sciences, W. Stefański Institute of Parasitology, Warsaw, Poland
| | - Daniel Klich
- Department of Animal Genetics and Conservation, Institute of Animal Sciences, Warsaw University of Life Sciences (WULS-SGGW), Warsaw, Poland
| | | | | | - Dorota Merta
- Institute of Biology and Earth Sciences, Pedagogical University of Cracow, Kraków, Poland
| | | | - Julita Nowakowska
- Institute of Biology, University of Warsaw, Imaging Laboratory, Warsaw, Poland
| | - Krzysztof Anusz
- Department of Food Hygiene and Public Health Protection, Institute of Veterinary Medicine, Warsaw University of Life Sciences (WULS-SGGW), Warsaw, Poland
| | - Johan Höglund
- Department of Biomedical Sciences and Veterinary Public Health (BVF), Division of Parasitology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| |
Collapse
|
5
|
Gupta MK, Vadde R. Next-generation development and application of codon model in evolution. Front Genet 2023; 14:1091575. [PMID: 36777719 PMCID: PMC9911445 DOI: 10.3389/fgene.2023.1091575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/17/2023] [Indexed: 01/28/2023] Open
Abstract
To date, numerous nucleotide, amino acid, and codon substitution models have been developed to estimate the evolutionary history of any sequence/organism in a more comprehensive way. Out of these three, the codon substitution model is the most powerful. These models have been utilized extensively to detect selective pressure on a protein, codon usage bias, ancestral reconstruction and phylogenetic reconstruction. However, due to more computational demanding, in comparison to nucleotide and amino acid substitution models, only a few studies have employed the codon substitution model to understand the heterogeneity of the evolutionary process in a genome-scale analysis. Hence, there is always a question of how to develop more robust but less computationally demanding codon substitution models to get more accurate results. In this review article, the authors attempted to understand the basis of the development of different types of codon-substitution models and how this information can be utilized to develop more robust but less computationally demanding codon substitution models. The codon substitution model enables to detect selection regime under which any gene or gene region is evolving, codon usage bias in any organism or tissue-specific region and phylogenetic relationship between different lineages more accurately than nucleotide and amino acid substitution models. Thus, in the near future, these codon models can be utilized in the field of conservation, breeding and medicine.
Collapse
|
6
|
Del Amparo R, Arenas M. HIV Protease and Integrase Empirical Substitution Models of Evolution: Protein-Specific Models Outperform Generalist Models. Genes (Basel) 2021; 13:61. [PMID: 35052404 PMCID: PMC8774313 DOI: 10.3390/genes13010061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 12/22/2021] [Accepted: 12/22/2021] [Indexed: 12/24/2022] Open
Abstract
Diverse phylogenetic methods require a substitution model of evolution that should mimic, as accurately as possible, the real substitution process. At the protein level, empirical substitution models have traditionally been based on a large number of different proteins from particular taxonomic levels. However, these models assume that all of the proteins of a taxonomic level evolve under the same substitution patterns. We believe that this assumption is highly unrealistic and should be relaxed by considering protein-specific substitution models that account for protein-specific selection processes. In order to test this hypothesis, we inferred and evaluated four new empirical substitution models for the protease and integrase of HIV and other viruses. We found that these models more accurately fit, compared with any of the currently available empirical substitution models, the evolutionary process of these proteins. We conclude that evolutionary inferences from protein sequences are more accurate if they are based on protein-specific substitution models rather than taxonomic-specific (generalist) substitution models. We also present four new empirical substitution models of protein evolution that could be useful for phylogenetic inferences of viral protease and integrase.
Collapse
Affiliation(s)
- Roberto Del Amparo
- Centro de Investigacións Biomédicas (CINBIO), University of Vigo, 36310 Vigo, Spain;
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
| | - Miguel Arenas
- Centro de Investigacións Biomédicas (CINBIO), University of Vigo, 36310 Vigo, Spain;
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), 36310 Vigo, Spain
| |
Collapse
|
7
|
Jin Y, Zhou W, Zhan Q, Zheng B, Chen Y, Luo Q, Shen P, Xiao Y. Genomic Epidemiology and Characterization of Methicillin-Resistant Staphylococcus aureus from Bloodstream Infections in China. mSystems 2021;:e0083721. [PMID: 34726482 DOI: 10.1128/mSystems.00837-21] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Since 2010, methicillin-resistant Staphylococcus aureus (MRSA) ST59 began to increase in prevalence in China, gradually replacing ST239 and has become the dominant clone in most hospitals in China. Here, we investigated the changing epidemiology, phylogenetic reconstruction, and genomic characterization of MRSA clones in China to identify the genomic driving factors in the prevalence of ST59. Most MRSA isolates were identified as ST59 (36.98%; 277/749), which increased from 25.09% in 2014 to 35.53% in 2019. The phylogenetic analysis of the 749 MRSA isolates showed a high level of diversity and the copresence of hospital-associated, community-associated, livestock-associated, and hypervirulent clones. Furthermore, minimum spanning trees revealed that ST59 MRSA clones from different hospitals and regions were integrated, suggesting that frequent exchanges had occurred between regions and hospitals. ST59 clones displayed higher susceptibility to antimicrobials than did ST239 and ST5 MRSA clones, indicating that resistance to non-β-lactam and fluoroquinolone antibiotics may be not critical for the epidemic success of ST59 clones. Virulence factors detection showed that sak and chp genes enriched in MRSA ST59 may be associated with the enhanced spreading success of ST59, whereas qacA may have contributed to the predominance of ST5 in East China. Our refined analysis of different clones among ST239, ST5, ST59, and ST398 demonstrated the existence of potential driving factors for the evolution of nosocomial MRSA populations and diversity of the evolutionary events surrounding clonal replacement. IMPORTANCE As a developing country, China has an unbalanced health care system due to regional differences in economic development. However, China is also a country worthy of study with regard to the population dynamics of MRSA within the more resource-rich health care systems. In this study, we carried out genomic analysis to investigate the genomic epidemiology and characterization of MRSA isolated from bloodstream infections over a timespan of 6 years. Our refined analysis of different MRSA clones among ST59, ST5, ST239, and ST398 demonstrated the existence of driving factors for the evolution of nosocomial MRSA populations and diversity of the evolutionary events surrounding clonal replacement.
Collapse
|
8
|
Janzen T, Bokma F, Etienne RS. Nucleotide substitutions during speciation may explain substitution rate variation. Syst Biol 2021; 71:1244-1254. [PMID: 34672354 PMCID: PMC9366449 DOI: 10.1093/sysbio/syab085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/11/2021] [Accepted: 10/16/2021] [Indexed: 11/14/2022] Open
Abstract
Although molecular mechanisms associated with the generation of mutations are highly conserved across taxa, there is widespread variation in mutation rates between evolutionary lineages. When phylogenies are reconstructed based on nucleotide sequences, such variation is typically accounted for by the assumption of a relaxed molecular clock, which is a statistical distribution of mutation rates without much underlying biological mechanism. Here, we propose that variation in accumulated mutations may be partly explained by an elevated mutation rate during speciation. Using simulations, we show how shifting mutations from branches to speciation events impacts inference of branching times in phylogenetic reconstruction. Furthermore, the resulting nucleotide alignments are better described by a relaxed than by a strict molecular clock. Thus, elevated mutation rates during speciation potentially explain part of the variation in substitution rates that is observed across the tree of life. [Molecular clock; phylogenetic reconstruction; speciation; substitution rate variation.]
Collapse
Affiliation(s)
- Thijs Janzen
- Correspondence to be sent to: Groningen Institute for Evolutionary Life Sciences, University of Groningen, Box 11103, 9700 CC Groningen, The Netherlands; E-mail:
| | - Folmer Bokma
- Department of BioSciences, Center for Ecological and Evolutionary Synthesis (CEES), University of Oslo, PO Box 1066, Blindern, 0316 Oslo, Norway
| | - Rampal S Etienne
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Box 11103, 9700 CC Groningen, The Netherlands
| |
Collapse
|
9
|
Zhang Y, Kohrn BF, Yang M, Nachmanson D, Soong TR, Lee IH, Tao Y, Clevers H, Swisher EM, Brentnall TA, Loeb LA, Kennedy SR, Salk JJ, Naxerova K, Risques RA. PolyG-DS: An ultrasensitive polyguanine tract-profiling method to detect clonal expansions and trace cell lineage. Proc Natl Acad Sci U S A 2021; 118:e2023373118. [PMID: 34330826 DOI: 10.1073/pnas.2023373118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Polyguanine tracts (PolyGs) are short guanine homopolymer repeats that are prone to accumulating mutations when cells divide. This feature makes them especially suitable for cell lineage tracing, which has been exploited to detect and characterize precancerous and cancerous somatic evolution. PolyG genotyping, however, is challenging because of the inherent biochemical difficulties in amplifying and sequencing repetitive regions. To overcome this limitation, we developed PolyG-DS, a next-generation sequencing (NGS) method that combines the error-correction capabilities of duplex sequencing (DS) with enrichment of PolyG loci using CRISPR-Cas9-targeted genomic fragmentation. PolyG-DS markedly reduces technical artifacts by comparing the sequences derived from the complementary strands of each original DNA molecule. We demonstrate that PolyG-DS genotyping is accurate, reproducible, and highly sensitive, enabling the detection of low-frequency alleles (<0.01) in spike-in samples using a panel of only 19 PolyG markers. PolyG-DS replicated prior results based on PolyG fragment length analysis by capillary electrophoresis, and exhibited higher sensitivity for identifying clonal expansions in the nondysplastic colon of patients with ulcerative colitis. We illustrate the utility of this method for resolving the phylogenetic relationship among precancerous lesions in ulcerative colitis and for tracing the metastatic dissemination of ovarian cancer. PolyG-DS enables the study of tumor evolution without prior knowledge of tumor driver mutations and provides a tool to perform cost-effective and easily scalable ultra-accurate NGS-based PolyG genotyping for multiple applications in biology, genetics, and cancer research.
Collapse
|
10
|
Salehi S, Kabeer F, Ceglia N, Andronescu M, Williams MJ, Campbell KR, Masud T, Wang B, Biele J, Brimhall J, Gee D, Lee H, Ting J, Zhang AW, Tran H, O'Flanagan C, Dorri F, Rusk N, de Algara TR, Lee SR, Cheng BYC, Eirew P, Kono T, Pham J, Grewal D, Lai D, Moore R, Mungall AJ, Marra MA, McPherson A, Bouchard-Côté A, Aparicio S, Shah SP. Clonal fitness inferred from time-series modelling of single-cell cancer genomes. Nature 2021; 595:585-590. [PMID: 34163070 PMCID: PMC8396073 DOI: 10.1038/s41586-021-03648-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 05/17/2021] [Indexed: 02/02/2023]
Abstract
Progress in defining genomic fitness landscapes in cancer, especially those defined by copy number alterations (CNAs), has been impeded by lack of time-series single-cell sampling of polyclonal populations and temporal statistical models1-7. Here we generated 42,000 genomes from multi-year time-series single-cell whole-genome sequencing of breast epithelium and primary triple-negative breast cancer (TNBC) patient-derived xenografts (PDXs), revealing the nature of CNA-defined clonal fitness dynamics induced by TP53 mutation and cisplatin chemotherapy. Using a new Wright-Fisher population genetics model8,9 to infer clonal fitness, we found that TP53 mutation alters the fitness landscape, reproducibly distributing fitness over a larger number of clones associated with distinct CNAs. Furthermore, in TNBC PDX models with mutated TP53, inferred fitness coefficients from CNA-based genotypes accurately forecast experimentally enforced clonal competition dynamics. Drug treatment in three long-term serially passaged TNBC PDXs resulted in cisplatin-resistant clones emerging from low-fitness phylogenetic lineages in the untreated setting. Conversely, high-fitness clones from treatment-naive controls were eradicated, signalling an inversion of the fitness landscape. Finally, upon release of drug, selection pressure dynamics were reversed, indicating a fitness cost of treatment resistance. Together, our findings define clonal fitness linked to both CNA and therapeutic resistance in polyclonal tumours.
Collapse
Affiliation(s)
- Sohrab Salehi
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Farhia Kabeer
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nicholas Ceglia
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mirela Andronescu
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marc J Williams
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kieran R Campbell
- Lunenfeld-Tanenbaum Research Institute Mount Sinai Hospital Joseph & Wolf Lebovic Health Complex, Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Tehmina Masud
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Beixi Wang
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Justina Biele
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Jazmine Brimhall
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - David Gee
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Hakwoo Lee
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Jerome Ting
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Allen W Zhang
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Hoa Tran
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Ciara O'Flanagan
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Fatemeh Dorri
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
- Department of Computer Science, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nicole Rusk
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - So Ra Lee
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Brian Yu Chieh Cheng
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Peter Eirew
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Takako Kono
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Jenifer Pham
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Diljot Grewal
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel Lai
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Richard Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Andrew McPherson
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexandre Bouchard-Côté
- Department of Statistics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Samuel Aparicio
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada.
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Sohrab P Shah
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| |
Collapse
|
11
|
Vite-Garín T, Estrada-Bárcenas DA, Gernandt DS, Reyes-Montes MDR, Sahaza JH, Canteros CE, Ramírez JA, Rodríguez-Arellanes G, Serra-Damasceno L, Zancopé-Oliveira RM, Taylor JW, Taylor ML. Histoplasma capsulatum Isolated from Tadarida brasiliensis Bats Captured in Mexico Form a Sister Group to North American Class 2 Clade. J Fungi (Basel) 2021; 7:529. [PMID: 34209122 PMCID: PMC8305335 DOI: 10.3390/jof7070529] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/03/2021] [Accepted: 06/11/2021] [Indexed: 01/11/2023] Open
Abstract
Histoplasma capsulatum is a dimorphic fungus associated with respiratory and systemic infections in mammalian hosts that have inhaled infective mycelial propagules. A phylogenetic reconstruction of this pathogen, using partial sequences of arf, H-anti, ole1, and tub1 protein-coding genes, proposed that H. capsulatum has at least 11 phylogenetic species, highlighting a clade (BAC1) comprising three H. capsulatum isolates from infected bats captured in Mexico. Here, relationships for each individual locus and the concatenated coding regions of these genes were inferred using parsimony, maximum likelihood, and Bayesian inference methods. Coalescent-based analyses, a concatenated sequence-types (CSTs) network, and nucleotide diversities were also evaluated. The results suggest that six H. capsulatum isolates from the migratory bat Tadarida brasiliensis together with one isolate from a Mormoops megalophylla bat support a NAm 3 clade, replacing the formerly reported BAC1 clade. In addition, three H. capsulatum isolates from T. brasiliensis were classified as lineages. The concatenated sequence analyses and the CSTs network validate these findings, suggesting that NAm 3 is related to the North American class 2 clade and that both clades could share a recent common ancestor. Our results provide original information on the geographic distribution, genetic diversity, and host specificity of H. capsulatum.
Collapse
Affiliation(s)
- Tania Vite-Garín
- Unidad de Micología, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad de México 04510, Mexico; (T.V.-G.); (M.d.R.R.-M.); (J.H.S.); (J.A.R.); (G.R.-A.)
| | - Daniel A. Estrada-Bárcenas
- Colección Nacional de Cepas Microbianas y Cultivos Celulares, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional (CINVESTAV, IPN), Ciudad de México 07360, Mexico;
| | - David S. Gernandt
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México (UNAM), Ciudad de México 04510, Mexico;
| | - María del Rocío Reyes-Montes
- Unidad de Micología, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad de México 04510, Mexico; (T.V.-G.); (M.d.R.R.-M.); (J.H.S.); (J.A.R.); (G.R.-A.)
| | - Jorge H. Sahaza
- Unidad de Micología, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad de México 04510, Mexico; (T.V.-G.); (M.d.R.R.-M.); (J.H.S.); (J.A.R.); (G.R.-A.)
| | - Cristina E. Canteros
- Departamento de Micología, Instituto Nacional de Enfermedades Infecciosas (INEI), Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) “Dr. Carlos G. Malbrán”, Buenos Aires 1281, Argentina;
| | - José A. Ramírez
- Unidad de Micología, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad de México 04510, Mexico; (T.V.-G.); (M.d.R.R.-M.); (J.H.S.); (J.A.R.); (G.R.-A.)
| | - Gabriela Rodríguez-Arellanes
- Unidad de Micología, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad de México 04510, Mexico; (T.V.-G.); (M.d.R.R.-M.); (J.H.S.); (J.A.R.); (G.R.-A.)
| | - Lisandra Serra-Damasceno
- Centro de Ciências da Saúde, Departamento de Saúde Comunitária, Universidade Federal do Ceará, Fortaleza 60455-610, Brazil;
| | - Rosely M. Zancopé-Oliveira
- Laboratório de Micologia, Setor Imunodiagnóstico, Instituto Nacional de Infectología Evandro Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-360, Brazil;
| | - John W. Taylor
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA;
| | - Maria Lucia Taylor
- Unidad de Micología, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad de México 04510, Mexico; (T.V.-G.); (M.d.R.R.-M.); (J.H.S.); (J.A.R.); (G.R.-A.)
| |
Collapse
|
12
|
O'Toole KH, Imperiali B, Allen KN. Glycoconjugate pathway connections revealed by sequence similarity network analysis of the monotopic phosphoglycosyl transferases. Proc Natl Acad Sci U S A 2021; 118:e2018289118. [PMID: 33472976 DOI: 10.1073/pnas.2018289118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The monotopic phosphoglycosyl transferase (monoPGT) superfamily comprises over 38,000 nonredundant sequences represented in bacterial and archaeal domains of life. Members of the superfamily catalyze the first membrane-committed step in en bloc oligosaccharide biosynthetic pathways, transferring a phosphosugar from a soluble nucleoside diphosphosugar to a membrane-resident polyprenol phosphate. The singularity of the monoPGT fold and its employment in the pivotal first membrane-committed step allows confident assignment of both protein and corresponding pathway. The diversity of the family is revealed by the generation and analysis of a sequence similarity network for the superfamily, with fusion of monoPGTs with other pathway members being the most frequent and extensive elaboration. Three common fusions were identified: sugar-modifying enzymes, glycosyl transferases, and regulatory domains. Additionally, unexpected fusions of the monoPGT with members of the polytopic PGT superfamily were discovered, implying a possible evolutionary link through the shared polyprenol phosphate substrate. Notably, a phylogenetic reconstruction of the monoPGT superfamily shows a radial burst of functionalization, with a minority of members comprising only the minimal PGT catalytic domain. The commonality and identity of the fusion partners in the monoPGT superfamily is consistent with advantageous colocalization of pathway members at membrane interfaces.
Collapse
|
13
|
Escárraga ME, Lattke JE, Pie MR, Guerrero RJ. Morphological and genetic evidence supports the separation of two Tapinoma ants (Formicidae, Dolichoderinae) from the Atlantic Forest biome. Zookeys 2021; 1033:35-62. [PMID: 33958919 PMCID: PMC8084850 DOI: 10.3897/zookeys.1033.59880] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 03/19/2021] [Indexed: 11/12/2022] Open
Abstract
The taxonomic boundaries of many Neotropical ant species of the genus Tapinoma are still unclear. Tapinoma atriceps and T. atriceps breviscapum are two morphologically similar taxa which occur sympatrically in the southern Atlantic Forest of Brazil. Some characters such as the scape length and head shape suggest that these taxa may be different species. We used DNA analysis and morphological evidence, including scanning electron microscopy, to evaluate the taxonomic validity of these taxa. We found distinct morphological characteristics that allow separating them as two different species, Tapinoma atriceps and Tapinoma breviscapum status novo, and this decision is supported by the DNA results, where Tapinoma atriceps was recovered as a lineage independent of T. breviscapum.
Collapse
Affiliation(s)
- Mayron E Escárraga
- Facultad de Ciencias Básicas, Programa de Biología, Universidad del Magdalena, Carrera 32 # 22-08, Santa Marta, Magdalena, Colombia Universidad del Magdalena Santa Marta Colombia
| | - John E Lattke
- Departamento de Zoologia, Universidade Federal do Paraná, Curitiba, Brazil Universidade Federal do Paraná Curitiba Brazil
| | - Marcio R Pie
- Departamento de Zoologia, Universidade Federal do Paraná, Curitiba, Brazil Universidade Federal do Paraná Curitiba Brazil
| | - Roberto J Guerrero
- Facultad de Ciencias Básicas, Programa de Biología, Universidad del Magdalena, Carrera 32 # 22-08, Santa Marta, Magdalena, Colombia Universidad del Magdalena Santa Marta Colombia
| |
Collapse
|
14
|
Abadi S, Avram O, Rosset S, Pupko T, Mayrose I. ModelTeller: Model Selection for Optimal Phylogenetic Reconstruction Using Machine Learning. Mol Biol Evol 2021; 37:3338-3352. [PMID: 32585030 DOI: 10.1093/molbev/msaa154] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Statistical criteria have long been the standard for selecting the best model for phylogenetic reconstruction and downstream statistical inference. Although model selection is regarded as a fundamental step in phylogenetics, existing methods for this task consume computational resources for long processing time, they are not always feasible, and sometimes depend on preliminary assumptions which do not hold for sequence data. Moreover, although these methods are dedicated to revealing the processes that underlie the sequence data, they do not always produce the most accurate trees. Notably, phylogeny reconstruction consists of two related tasks, topology reconstruction and branch-length estimation. It was previously shown that in many cases the most complex model, GTR+I+G, leads to topologies that are as accurate as using existing model selection criteria, but overestimates branch lengths. Here, we present ModelTeller, a computational methodology for phylogenetic model selection, devised within the machine-learning framework, optimized to predict the most accurate nucleotide substitution model for branch-length estimation. We demonstrate that ModelTeller leads to more accurate branch-length inference than current model selection criteria on data sets simulated under realistic processes. ModelTeller relies on a readily implemented machine-learning model and thus the prediction according to features extracted from the sequence data results in a substantial decrease in running time compared with existing strategies. By harnessing the machine-learning framework, we distinguish between features that mostly contribute to branch-length optimization, concerning the extent of sequence divergence, and features that are related to estimates of the model parameters that are important for the selection made by current criteria.
Collapse
Affiliation(s)
- Shiran Abadi
- School of Plant Sciences and Food security, Tel-Aviv University, Tel-Aviv, Israel
| | - Oren Avram
- School of Molecular Cell Biology & Biotechnology, Tel-Aviv University, Tel-Aviv, Israel
| | - Saharon Rosset
- Department of Statistics and Operations Research, School of Mathematical Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Tal Pupko
- School of Molecular Cell Biology & Biotechnology, Tel-Aviv University, Tel-Aviv, Israel
| | - Itay Mayrose
- School of Plant Sciences and Food security, Tel-Aviv University, Tel-Aviv, Israel
| |
Collapse
|
15
|
Claverie JM. Fundamental Difficulties Prevent the Reconstruction of the Deep Phylogeny of Viruses. Viruses 2020; 12:E1130. [PMID: 33036160 PMCID: PMC7600955 DOI: 10.3390/v12101130] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/01/2020] [Accepted: 10/03/2020] [Indexed: 12/11/2022] Open
Abstract
The extension of virology beyond its traditional medical, veterinary, or agricultural applications, now called environmental virology, has shown that viruses are both the most numerous and diverse biological entities on Earth. In particular, virus isolations from unicellular eukaryotic hosts (heterotrophic and photosynthetic protozoans) revealed numerous viral types previously unexpected in terms of virion structure, gene content, or mode of replication. Complemented by large-scale metagenomic analyses, these discoveries have rekindled interest in the enigma of the origin of viruses, for which a description encompassing all their diversity remains not available. Several laboratories have repeatedly tackled the deep reconstruction of the evolutionary history of viruses, using various methods of molecular phylogeny applied to the few shared "core" genes detected in certain virus groups (e.g., the Nucleocytoviricota). Beyond the practical difficulties of establishing reliable homology relationships from extremely divergent sequences, I present here conceptual arguments highlighting several fundamental limitations plaguing the reconstruction of the deep evolutionary history of viruses, and even more the identification of their unique or multiple origin(s). These arguments also underline the risk of establishing premature high level viral taxonomic classifications. Those limitations are direct consequences of the random mechanisms governing the reductive/retrogressive evolution of all obligate intracellular parasites.
Collapse
Affiliation(s)
- Jean-Michel Claverie
- Structural & Genomic Information Laboratory (IGS, UMR 7256), Mediterranean Institute of Microbiology (FR3479), Aix-Marseille University and CNRS, 13288 Marseille, France
| |
Collapse
|
16
|
Abstract
In many mammals, breeding females are intolerant of each other and seldom associate closely but, in some, they aggregate in groups that vary in size, stability, and kinship structure. Aggregation frequently increases competition for food, and interspecific differences in female sociality among mammals are commonly attributed to contrasts in ecological parameters, including variation in activity timing, the distribution of resources, as well as the risk of predation. However, there is increasing indication that differences in female sociality are also associated with phylogenetic relationships and with contrasts in life-history parameters. We show here that evolutionary transitions from systems where breeding females usually occupy separate ranges ("singular breeding") to systems where breeding females usually aggregate ("plural breeding") have occurred more frequently in monotocous lineages where females produce single young than in polytocous ones where they produce litters. A likely explanation of this association is that competition between breeding females for resources is reduced where they produce single young and is more intense where they produce litters. Our findings reinforce evidence that variation in life-history parameters plays an important role in shaping the evolution of social behavior.
Collapse
Affiliation(s)
- Dieter Lukas
- Department of Zoology, University of Cambridge, Cambridge, UK
- Department of Human Behavior, Ecology and Culture, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | |
Collapse
|
17
|
Wang Y, Jin X, Zhang W, Cui W, Kong T, Chen C, Guo Y, Meng H, Zhu B. Comprehensive analyses for genetic diversities of 19 autosomal STRs in Chinese Kazak group and its phylogenetic relationships with other continental populations. Forensic Sci Res 2020; 7:163-171. [PMID: 35784425 PMCID: PMC9245996 DOI: 10.1080/20961790.2020.1751379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Short tandem repeats (STRs) play an essential role in forensic genetics due to their high degree of polymorphisms, wide distributions and easy detection method. In this study, allelic frequencies and forensic statistical parameters of the 19 autosomal STR loci in a Kazak ethnic group were calculated, and its genetic relationships with reference populations were assessed in order to understand population structure better and enrich population genetic data for forensic practice in Chinese Kazak ethnic group. There were 226 identified alleles with the corresponding allelic frequencies ranging from 0.0008 to 0.5295 in the 628 unrelated healthy Kazak individuals in Xinjiang Uygur Autonomous Region. All autosomal STRs were conformed to the Hardy-Weinberg equilibrium after Bonferroni’s correction. The cumulative power of discrimination and the combined probability of exclusion of all the 19 autosomal STRs were 0.999 999 999 999 999 999 999 997 162 and 0.999 999 994 484, respectively. Furthermore, the DA distances and Fixation index values of pairwise populations, principal component analysis, multidimensional scaling analysis, phylogenetic tree analysis and structure analysis were conducted to probe the genetic relationships between the Kazak group and other reference populations. The population genetic results showed that these 19 autosomal STR loci were characterised by high genetic diversities in the Kazak group. Furthermore, the studied Kazak group had close genetic relationships with the Uyghur group and the Uzbek group. The present results may facilitate understanding the genetic background of the Chinese Xinjiang Kazak group.
Collapse
Affiliation(s)
- Yijie Wang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
| | - Xiaoye Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Wenqing Zhang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
| | - Wei Cui
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Tingting Kong
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
| | - Chong Chen
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Yuxin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Haotian Meng
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Bofeng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
| |
Collapse
|
18
|
Zou X, He G, Wang M, Huo L, Chen X, Liu J, Wang S, Ye Z, Wang F, Wang Z, Hou Y. Genetic diversity and phylogenetic structure of four Tibeto-Burman-speaking populations in Tibetan-Yi corridor revealed by insertion/deletion polymorphisms. Mol Genet Genomic Med 2020; 8:e1140. [PMID: 32017463 PMCID: PMC7196475 DOI: 10.1002/mgg3.1140] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 01/01/2020] [Accepted: 01/03/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Insertion/deletion polymorphisms (InDels), combined with all the desirable features of both short tandem repeat and single nucleotide polymorphism, have been used in archaeological and anthropological research, population genetics and forensic application. METHODS Thirty InDels in 530 individuals residing in the Tibetan-Yi corridor (142 Dujiangyan Tibetans, 164 Muli Tibetans, 187 Xichang Yis, and 37 Yanyuan Mosuos) were genotyped using the Investigator DIPplex. Forensic parameters and allele frequency spectrum were calculated. Genetic relationships between the investigated populations and worldwide and nationwide populations were assessed based on both the allele frequency distribution and genotype data. RESULTS The combined powers of exclusion were 0.9807 (Dujiangyan Tibetan), 0.9880 (Muli Tibetan), 0.9852 (Xichang Yi) and 0.9892 (Yanyuan Mosuo). The combined powers of discrimination were 0.999999999983 (Dujiangyan Tibetan), 0.999999999942 (Muli Tibetan), 0.999999999982 (Xichang Yi) and 0.999999999962 (Yanyuan Mosuo), respectively. The comprehensive population comparisons among worldwide and nationwide populations uniformly illustrated that the investigated populations have a genetically closer relationship with Tibeto-Burman-speaking populations and geographically adjacent populations. CONCLUSION These 30 loci can be regarded as an efficient genetic tool in forensic individual identification and as a supplementary tool in paternity testing in Dujiangyan Tibetan, Muli Tibetan, Xichang Yi, and Yanyuan Mosuo. The genetic proximity between the four populations in the Tibetan-Yi corridor and other populations is strongly correlated with the linguistic origin and geographical distance.
Collapse
Affiliation(s)
- Xing Zou
- Institute of Forensic MedicineWest China School of Basic Science & Forensic MedicineSichuan UniversityChengduChina
| | - Guanglin He
- Institute of Forensic MedicineWest China School of Basic Science & Forensic MedicineSichuan UniversityChengduChina
| | - Mengge Wang
- Institute of Forensic MedicineWest China School of Basic Science & Forensic MedicineSichuan UniversityChengduChina
| | - Liwen Huo
- Chongqing Hechuan District Public Security BureauChongqingChina
| | - Xu Chen
- Department of Clinical LaboratoryThe First People’s Hospital of Liangshan Yi Autonomous PrefectureXichangChina
| | - Jing Liu
- Institute of Forensic MedicineWest China School of Basic Science & Forensic MedicineSichuan UniversityChengduChina
| | - Shouyu Wang
- Institute of Forensic MedicineWest China School of Basic Science & Forensic MedicineSichuan UniversityChengduChina
| | - Ziwei Ye
- Institute of Forensic MedicineWest China School of Basic Science & Forensic MedicineSichuan UniversityChengduChina
| | - Fei Wang
- Institute of Forensic MedicineWest China School of Basic Science & Forensic MedicineSichuan UniversityChengduChina
| | - Zheng Wang
- Institute of Forensic MedicineWest China School of Basic Science & Forensic MedicineSichuan UniversityChengduChina
| | - Yiping Hou
- Institute of Forensic MedicineWest China School of Basic Science & Forensic MedicineSichuan UniversityChengduChina
| |
Collapse
|
19
|
Ren L, Huang W, Cannon SB. Reconstruction of ancestral genome reveals chromosome evolution history for selected legume species. New Phytol 2019; 223:2090-2103. [PMID: 30834536 DOI: 10.1111/nph.15770] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 02/24/2019] [Indexed: 05/18/2023]
Abstract
Reconstruction of an ancestral genome for a set of plant species has been a challenging task because of complex histories that may include whole-genome duplications, segmental duplications, independent gene duplications or losses, diploidization and rearrangement events. Here, we describe the reconstruction a hypothetical ancestral genome for the papilionoid legumes (the largest subfamily within the third largest family in flowering plants), and evaluate the results relative to phylogenetic and chromosomal count data for this group of legumes, spanning 294 diverse papilionoid genera. To reconstruct the ancestral genomes for nine legume species with sequenced genomes, we used a maximum likelihood approach combined with a novel method for identifying informative markers for this purpose. Analyzing genomes from four species within the Phaseoleae, two in Dalbergieae, two in the 'inverted repeat loss' clade, and one in the Robinieae, we infer a common ancestral genome with nine chromosomes. The reconstructed genome structural histories are consistent with chromosomal and phylogenetic histories, but we also infer that a common ancestor with nine chromosomes was probably intermediate to an earlier state of 14 chromosomes following a whole-genome duplication that pre-dated the radiation of the papilionoid legumes, evidence for which is found in early-diverging papilionoid lineages.
Collapse
Affiliation(s)
- Longhui Ren
- Interdepartmental Genetics Graduate Program, 2014 Molecular Biology, Iowa State University, 2437 Pammel Drive, Ames, IA, 50011, USA
| | - Wei Huang
- Department of Agronomy, Iowa State University, 716 Farm House Ln, Ames, IA, 50011, USA
| | - Steven B Cannon
- Corn Insects and Crop Genetics Research Unit, US Department of Agriculture-Agricultural Research Service, 819 Wallace Rd, Ames, IA, 50011, USA
| |
Collapse
|
20
|
Napolitano S, Reber RJ, Rubini M, Glockshuber R. Functional analyses of ancestral thioredoxins provide insights into their evolutionary history. J Biol Chem 2019; 294:14105-14118. [PMID: 31366732 PMCID: PMC6755812 DOI: 10.1074/jbc.ra119.009718] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 07/29/2019] [Indexed: 12/24/2022] Open
Abstract
Thioredoxin (Trx) is a conserved, cytosolic reductase in all known organisms. The enzyme receives two electrons from NADPH via thioredoxin reductase (TrxR) and passes them on to multiple cellular reductases via disulfide exchange. Despite the ubiquity of thioredoxins in all taxa, little is known about the functions of resurrected ancestral thioredoxins in the context of a modern mesophilic organism. Here, we report on functional in vitro and in vivo analyses of seven resurrected Precambrian thioredoxins, dating back 1–4 billion years, in the Escherichia coli cytoplasm. Using synthetic gene constructs for recombinant expression of the ancestral enzymes, along with thermodynamic and kinetic assays, we show that all ancestral thioredoxins, as today's thioredoxins, exhibit strongly reducing redox potentials, suggesting that thioredoxins served as catalysts of cellular reduction reactions from the beginning of evolution, even before the oxygen catastrophe. A detailed, quantitative characterization of their interactions with the electron donor TrxR from Escherichia coli and the electron acceptor methionine sulfoxide reductase, also from E. coli, strongly hinted that thioredoxins and thioredoxin reductases co-evolved and that the promiscuity of thioredoxins toward downstream electron acceptors was maintained during evolution. In summary, our findings suggest that thioredoxins evolved high specificity for their sole electron donor TrxR while maintaining promiscuity to their multiple electron acceptors.
Collapse
Affiliation(s)
- Silvia Napolitano
- Institute of Molecular Biology and Biophysics, Department of Biology, Swiss Federal Institute of Technology Zurich, Otto-Stern-Weg 5, CH-8093 Zurich, Switzerland
| | - Robin J Reber
- Institute of Molecular Biology and Biophysics, Department of Biology, Swiss Federal Institute of Technology Zurich, Otto-Stern-Weg 5, CH-8093 Zurich, Switzerland
| | - Marina Rubini
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
| | - Rudi Glockshuber
- Institute of Molecular Biology and Biophysics, Department of Biology, Swiss Federal Institute of Technology Zurich, Otto-Stern-Weg 5, CH-8093 Zurich, Switzerland
| |
Collapse
|
21
|
Makarieva T, Shubina L, Kurilenko V, Isaeva M, Chernysheva N, Popov R, Bystritskaya E, Dmitrenok P, Stonik AV. Marine Bacterium V ibrio sp. CB1-14 Produces Guanidine Alkaloid 6- epi-Monanchorin, Previously Isolated from Marine Polychaete and Sponges. Mar Drugs 2019; 17:E213. [PMID: 30987405 DOI: 10.3390/md17040213] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 03/26/2019] [Accepted: 03/26/2019] [Indexed: 02/08/2023] Open
Abstract
Twenty-three bacterial strains were isolated from the secreted mucus trapping net of themarine polychaete Chaetopterus variopedatus (phylum Annelida) and twenty strains were identifiedusing 16S rRNA gene analysis. Strain CB1-14 was recognized as a new species of the genus Vibriousing the eight-gene multilocus sequence analysis (MLSA) and genome sequences of nineteen typeVibrio strains. This Vibrio sp. was cultured, and 6-epi-monanchorin (2), previously isolated from thepolychaete and two sponge species, was found in the cells and culture broth. The presence of the 6-epi-monanchorin was confirmed by its isolation followed by 1H NMR and HRESIMS analysis. Theseresults showed the microbial origin of the bicyclic guanidine alkaloid 2 in C. variopedatus.
Collapse
|
22
|
Wang Z, Lu B, Jin X, Yan J, Meng H, Zhu B. Genetic and structural characterization of 20 autosomal short tandem repeats in the Chinese Qinghai Han population and its genetic relationships and interpopulation differentiations with other reference populations. Forensic Sci Res 2018; 3:145-152. [PMID: 30483663 PMCID: PMC6197092 DOI: 10.1080/20961790.2018.1485199] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 06/03/2018] [Indexed: 11/18/2022] Open
Abstract
China is a multinational country composed of 56 ethnic groups of which the Han Chinese accounts for 91.60%. Qinghai Province is located in the northeastern part of the Qinghai–Tibet Plateau, has an area of 72.12 km2, and is the fourth largest province in China. In the present study, we investigated the genetic polymorphisms of 20 short tandem repeat (STR) loci in a Qinghai Han population, as well as its genetic relationships with other populations. A total of 273 alleles were identified in 2 000 individuals at 20 loci, and the allelic frequency ranged from 0.000 2 to 0.532 7. The 20 STR loci showed a relatively high polymorphic rate in the studied group. Observed and expected heterozygosities ranged 0.613 0–0.907 5 and 0.614 8–0.920 0, respectively. The combined power of discrimination, and the probability of exclusion in duo and trio cases were 0.999 999 999 999 999 999 999 999 34, 0.999 996 0 and 0.999 999 996 5, respectively. Analyses of interpopulation differentiation revealed that the most significant differences were found between the Qinghai Han and Malaysian, while no significant differences were found between the Qinghai Han and Han people from Shaanxi and Jiangsu. The results of principal component analysis, multidimensional scaling analysis and phylogenetic reconstructions also suggested the close relationships between the Qinghai Han and other two Han populations. The present results, therefore, indicated that these 20 STR loci could be used for paternity testing and individual identification in forensic applications, and may also provide information for the studies of genetic relationships between Qinghai Han and other groups.
Collapse
Affiliation(s)
- Zhanhai Wang
- The Public Security Bureau of Qinghai Province, Xining, China
| | - Bin Lu
- The Public Security Bureau of Qinghai Province, Xining, China
| | - Xiaoye Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Research Center of Stomatology, Stomatological Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Jiangwei Yan
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Haotian Meng
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Research Center of Stomatology, Stomatological Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Bofeng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Research Center of Stomatology, Stomatological Hospital, Xi'an Jiaotong University, Xi'an, China
| |
Collapse
|
23
|
Sehner S, Fichtel C, Kappeler PM. Primate tails: Ancestral state reconstruction and determinants of interspecific variation in primate tail length. Am J Phys Anthropol 2018; 167:750-759. [PMID: 30341951 DOI: 10.1002/ajpa.23703] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 07/30/2018] [Accepted: 08/04/2018] [Indexed: 12/21/2022]
Abstract
OBJECTIVE Living primates vary considerably in tail length-body size relation, ranging from tailless species to those where the tail is more than twice as long as the body. Because the general pattern and determinants of tail evolution remain incompletely known, we reconstructed evolutionary changes in relative tail length across all primates and sought to explain interspecific variation in this trait. METHODS We combined data on tail length, head-body length, intermembral index (IMI), habitat use, locomotion type, and range latitude for 340 species from published sources. We reconstructed the evolution of relative tail length to identify all independent cases of regime shifts on a primate phylogeny, using several methods based on Ornstein-Uhlenbeck (OU) models. Accounting for phylogeny, we also examined the effects of habitat, locomotion type, distance from the equator and IMI on interspecific variation in tail length-body size relation. RESULTS Primate tail length is not sexually dimorphic. A phylogenetic reconstruction allowing multiple optima explains the observed regime shifts best. During the evolutionary history of primates, relative tail length changed 50 times under an OU model. Specifically, relative tail length increased 26 and decreased 24 times. Most of these changes occurred among Old World primates. Among the variables tested here, interspecific variation in IMI and the difference between leaping and non-leaping locomotion explained interspecific variation in relative tail length: Evolutionary decreases in relative tail length are generally associated with an increase in IMI and an absence of leaping behavior. CONCLUSIONS Regime shifts for relative tail length in living primates occurred in concert with fundamental changes in IMI and a change from leaping to non-leaping locomotion, or vice versa. Exceptions from this general pattern are linked to the presence of a prehensile tail or specialized foraging strategies. Thus, the primate tail appears to have evolved in functional coordination with limb proportions, presumably to assist body balance.
Collapse
Affiliation(s)
- Sandro Sehner
- Department of Anthropology/Sociobiology, University of Göttingen, Göttingen, Germany
| | - Claudia Fichtel
- Behavioral Ecology and Sociobiology Unit, German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany
| | - Peter M Kappeler
- Department of Anthropology/Sociobiology, University of Göttingen, Göttingen, Germany
- Behavioral Ecology and Sociobiology Unit, German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany
| |
Collapse
|
24
|
Fuentes-Aragón D, Juárez-Vázquez SB, Vargas-Hernández M, Silva-Rojas HV. Colletotrichum fructicola, a Member of Colletotrichum gloeosporioides sensu lato, is the Causal Agent of Anthracnose and Soft Rot in Avocado Fruits cv. "Hass". Mycobiology 2018; 46:92-100. [PMID: 29963310 PMCID: PMC6023250 DOI: 10.1080/12298093.2018.1454010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 12/07/2017] [Accepted: 01/11/2018] [Indexed: 05/26/2023]
Abstract
The filamentous Ascomycota Colletotrichum gloeosporioides sensu lato is a fungus that has been reported worldwide as a causal agent of anthracnose disease in avocado and other crops. In Mexico, this species affects fruits from an early stage of development in the orchard until the post-harvest stage. Although fungicides are continuously applied to control Colletotrichum species, pericarp cankers and soft rot mesocarp in fruits are still frequently observed. Considering the lack of a precise description of the causative agent, the aim of the current study was to determine the pathogens involved in this symptomatology. Twenty-four isolates were consistently obtained from the pericarp of avocado fruits cv. "Hass" collected in the central avocado-producing area of Mexico. Morphological features such as colony growth, conidia size, and mycelial appressorium were assessed. Bayesian multilocus phylogenetic analyses were performed using amplified sequences of the internal transcribed spacer region of the nuclear ribosomal DNA; actin, chitin synthase, glyceraldehyde-3-phosphate dehydrogenase partial genes; and APn2-Mat1-2 intergenic spacer and mating type Mat1-2 partial gene from the nine selected isolates. In addition, fruits were inoculated with a conidial suspension and reproducible symptoms confirmed the presence of Colletotrichum fructicola in this area. This pathogenic species can now be added to those previously reported in the country, such as C. acutatum, C. boninense, C. godetiae, C. gloeosporioides, and C. karstii. Disease management programs to reduce the incidence of anthracnose should include C. fructicola to determine its response to fungicides that are routinely applied, considering that the appearance of new species is affecting the commercial quality of the fruits and shifting the original population structure.
Collapse
Affiliation(s)
- Dionicio Fuentes-Aragón
- Posgrado en Fitopatología, Campus Montecillo, Colegio de Postgraduados, Texcoco, Estado de México, México
| | | | - Mateo Vargas-Hernández
- Posgrado en Protección Vegetal Universidad Autónoma Chapingo Chapingo, Texcoco, Estado de México, México
| | - Hilda Victoria Silva-Rojas
- Posgrado en Recursos Genéticos y Productividad, Producción de Semillas, Campus Montecillo, Colegio de Postgraduados, Texcoco, Estado de México, México
| |
Collapse
|
25
|
Pereira TTP, dos Reis ACCC, Cardoso DC, Cristiano MP. Molecular phylogenetic reconstruction and localization of the (TTAGG)n telomeric repeats in the chromosomes of Acromyrmex striatus (Roger, 1863) suggests a lower ancestral karyotype for leafcutter ants (Hymenoptera). Comp Cytogenet 2018; 12:13-21. [PMID: 29362670 PMCID: PMC5770561 DOI: 10.3897/compcytogen.v12i1.21799] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 11/27/2017] [Indexed: 05/24/2023]
Abstract
Chromosome counts and karyotype characterization have proved to be important features of a genome. Chromosome changes during the diversification of ants might play an important role, given the diversity and success of Formicidae. Comparative karyotype analyses on ants have enriched and helped ant systematics. Among leafcutter ants, two major chromosome counts have been described, one frequent in Atta Fabricius, 1804 (2n = 22 in all Atta spp. whose karyotype is known) and the other frequent in Acromyrmex Mayr, 1865 (2n = 38 in the majority of species whose karyotype is known). The main exception is Acromyrmex striatus (Roger, 1863), which harbors a diploid chromosome set of 22. Here we describe the use of fluorescence in situ hybridization (FISH) with telomeric probes with (TTAGG)6 repeats to describe the telomere composition of A. striatus and to recover potential interstitial non-telomeric signals that may reflect fusion events during the evolution of leafcutter lineage from 38 to 22 chromosomes. Further, we reconstruct the ancestral chromosome numbers of the leafcutter clade based on a recently proposed molecular phylogenetic hypothesis and phylogenomic tree. Distinct signals have been observed in both extremities on the telomere chromosomes of A. striatus. Non-telomeric signals have not been retrieved in our analysis. It could be supposed that the low-numbered karyotype indeed represents the ancestral chromosome number of leafcutters. The phylogenetic reconstruction also recovered a low chromosome number from the diverse approaches implemented, suggesting that n = 11 is the most likely ancestral karyotype of the leafcutter ants and is a plesiomorphic feature shared between A. striatus and Atta spp.
Collapse
Affiliation(s)
- Tássia Tatiane Pontes Pereira
- Departamento de Biodiversidade, Evolução e Meio Ambiente, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
- Programa de Pós-graduação em Genética, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | | | - Danon Clemes Cardoso
- Departamento de Biodiversidade, Evolução e Meio Ambiente, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
- Programa de Pós-graduação em Genética, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Maykon Passos Cristiano
- Departamento de Biodiversidade, Evolução e Meio Ambiente, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
| |
Collapse
|
26
|
Moghe GD, Leong BJ, Hurney SM, Daniel Jones A, Last RL. Evolutionary routes to biochemical innovation revealed by integrative analysis of a plant-defense related specialized metabolic pathway. eLife 2017; 6:28468. [PMID: 28853706 PMCID: PMC5595436 DOI: 10.7554/elife.28468] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 07/25/2017] [Indexed: 12/22/2022] Open
Abstract
The diversity of life on Earth is a result of continual innovations in molecular networks influencing morphology and physiology. Plant specialized metabolism produces hundreds of thousands of compounds, offering striking examples of these innovations. To understand how this novelty is generated, we investigated the evolution of the Solanaceae family-specific, trichome-localized acylsugar biosynthetic pathway using a combination of mass spectrometry, RNA-seq, enzyme assays, RNAi and phylogenomics in different non-model species. Our results reveal hundreds of acylsugars produced across the Solanaceae family and even within a single plant, built on simple sugar cores. The relatively short biosynthetic pathway experienced repeated cycles of innovation over the last 100 million years that include gene duplication and divergence, gene loss, evolution of substrate preference and promiscuity. This study provides mechanistic insights into the emergence of plant chemical novelty, and offers a template for investigating the ~300,000 non-model plant species that remain underexplored. There are about 300,000 species of plant on Earth, which together produce over a million different small molecules called metabolites. Plants use many of these molecules to grow, to communicate with each other or to defend themselves against pests and disease. Humans have co-opted many of the same molecules as well; for example, some are important nutrients while others are active ingredients in medicines. Many plant metabolites are found in almost all plants, but hundreds of thousands of them are more specialized and only found in small groups of related plant species. These specialized metabolites have a wide variety of structures, and are made by different enzymes working together to carry out a series of biochemical reactions. Acylsugars are an example of a group of specialized metabolites with particularly diverse structures. These small molecules are restricted to plants in the Solanaceae family, which includes tomato and tobacco plants. Moghe et al. have now focused on acylsugars to better understand how plants produce the large diversity of chemical structures found in specialized metabolites, and how these processes have evolved over time. An analysis of over 35 plant species from across the Solanaceae family revealed hundreds of acylsugars, with some plants accumulating 300 or more different types of these specialized metabolites. Moghe et al. then looked at the enzymes that make acylsugars from a poorly studied flowering plant called Salpiglossis sinuata, partly because it produces a large diversity of these small molecules and partly because it sits in a unique position in the Solanaceae family tree. The activities of the enzymes were confirmed both in test tubes and in plants. This suggested that many of the enzymes were “promiscuous”, meaning that they could likely use a variety of molecules as starting points for their chemical reactions. This finding could help to explain how this plant species can make such a wide variety of acylsugars. Moghe et al. also discovered that many of the enzymes that make acylsugars are encoded by genes that were originally copies of other genes and that have subsequently evolved new activities. Plant scientists and plant breeders value tomato plants that produce acylsugars because these natural chemicals protect against pests like whiteflies and spider mites. A clearer understanding of the diversity of acylsugars in the Solanaceae family, as well as the enzymes that make these specialized metabolites, could help efforts to breed crops that are more resistant to pests. Some of the enzymes related to those involved in acylsugar production could also help to make chemicals with pharmaceutical value. These new findings might also eventually lead to innovative ways to produce these chemicals on a large scale.
Collapse
Affiliation(s)
- Gaurav D Moghe
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States
| | - Bryan J Leong
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States.,Department of Plant Biology, Michigan State University, East Lansing, United States
| | - Steven M Hurney
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States.,Department of Chemistry, Michigan State University, East Lansing, United States
| | - A Daniel Jones
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States.,Department of Chemistry, Michigan State University, East Lansing, United States
| | - Robert L Last
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States.,Department of Plant Biology, Michigan State University, East Lansing, United States
| |
Collapse
|
27
|
Hultqvist G, Åberg E, Camilloni C, Sundell GN, Andersson E, Dogan J, Chi CN, Vendruscolo M, Jemth P. Emergence and evolution of an interaction between intrinsically disordered proteins. eLife 2017; 6:e16059. [PMID: 28398197 PMCID: PMC5419745 DOI: 10.7554/elife.16059] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 03/28/2017] [Indexed: 12/25/2022] Open
Abstract
Protein-protein interactions involving intrinsically disordered proteins are important for cellular function and common in all organisms. However, it is not clear how such interactions emerge and evolve on a molecular level. We performed phylogenetic reconstruction, resurrection and biophysical characterization of two interacting disordered protein domains, CID and NCBD. CID appeared after the divergence of protostomes and deuterostomes 450-600 million years ago, while NCBD was present in the protostome/deuterostome ancestor. The most ancient CID/NCBD formed a relatively weak complex (Kd∼5 µM). At the time of the first vertebrate-specific whole genome duplication, the affinity had increased (Kd∼200 nM) and was maintained in further speciation. Experiments together with molecular modeling using NMR chemical shifts suggest that new interactions involving intrinsically disordered proteins may evolve via a low-affinity complex which is optimized by modulating direct interactions as well as dynamics, while tolerating several potentially disruptive mutations.
Collapse
Affiliation(s)
- Greta Hultqvist
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Emma Åberg
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Carlo Camilloni
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- Department of Chemistry, Technische Universität München, München, Germany
- Institute for Advanced Study, Technische Universität München, München, Germany
| | - Gustav N Sundell
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Eva Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Jakob Dogan
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Celestine N Chi
- Laboratory of Physical Chemistry, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
| | | | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| |
Collapse
|
28
|
Xie L, Liu P, Zhu Z, Zhang S, Zhang S, Li F, Zhang H, Li G, Wei Y, Sun R. Phylogeny and Expression Analyses Reveal Important Roles for Plant PKS III Family during the Conquest of Land by Plants and Angiosperm Diversification. Front Plant Sci 2016; 7:1312. [PMID: 27625671 PMCID: PMC5004622 DOI: 10.3389/fpls.2016.01312] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 08/16/2016] [Indexed: 05/06/2023]
Abstract
Polyketide synthases (PKSs) utilize the products of primary metabolism to synthesize a wide array of secondary metabolites in both prokaryotic and eukaryotic organisms. PKSs can be grouped into three distinct classes, types I, II, and III, based on enzyme structure, substrate specificity, and catalytic mechanisms. The type III PKS enzymes function as homodimers, and are the only class of PKS that do not require acyl carrier protein. Plant type III PKS enzymes, also known as chalcone synthase (CHS)-like enzymes, are of particular interest due to their functional diversity. In this study, we mined type III PKS gene sequences from the genomes of six aquatic algae and 25 land plants (1 bryophyte, 1 lycophyte, 2 basal angiosperms, 16 core eudicots, and 5 monocots). PKS III sequences were found relatively conserved in all embryophytes, but not exist in algae. We also examined gene expression patterns by analyzing available transcriptome data, and identified potential cis-regulatory elements in upstream sequences. Phylogenetic trees of dicots angiosperms showed that plant type III PKS proteins fall into three clades. Clade A contains CHS/STS-type enzymes coding genes with diverse transcriptional expression patterns and enzymatic functions, while clade B is further divided into subclades b1 and b2, which consist of anther-specific CHS-like enzymes. Differentiation regions, such as amino acids 196-207 between clades A and B, and predicted positive selected sites within α-helixes in late appeared branches of clade A, account for the major diversification in substrate choice and catalytic reaction. The integrity and location of conserved cis-elements containing MYB and bHLH binding sites can affect transcription levels. Potential binding sites for transcription factors such as WRKY, SPL, or AP2/EREBP may contribute to tissue- or taxon-specific differences in gene expression. Our data shows that gene duplications and functional diversification of plant type III PKS enzymes played a critical role in the ancient conquest of the land by early plants and angiosperm diversification.
Collapse
Affiliation(s)
- Lulu Xie
- Department of Chinese Cabbage, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - Pingli Liu
- College of Biological Sciences and Biotechnology, Beijing Forestry UniversityBeijing, China
| | - Zhixin Zhu
- College of Horticulture and Landscape Architecture, Hainan UniversityHaikou, China
| | - Shifan Zhang
- Department of Chinese Cabbage, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - Shujiang Zhang
- Department of Chinese Cabbage, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - Fei Li
- Department of Chinese Cabbage, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - Hui Zhang
- Department of Chinese Cabbage, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - Guoliang Li
- Department of Chinese Cabbage, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - Yunxiao Wei
- Department of Chinese Cabbage, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - Rifei Sun
- Department of Chinese Cabbage, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| |
Collapse
|
29
|
Abstract
Alignment-free sequence comparison methods are attracting persistent interest, driven by data-intensive applications in genome-wide molecular taxonomy and phylogenetic reconstruction. Among all the methods based on substring composition, the average common substring (ACS) measure admits a straightforward linear time sequence comparison algorithm, while yielding impressive results in multiple applications. An important direction of this research is to extend the approach to permit a bounded edit/hamming distance between substrings, so as to reflect more accurately the evolutionary process. To date, however, algorithms designed to incorporate k ≥ 1 mismatches have O(n(2)) worst-case time complexity, where n is the total length of the input sequences. On the other hand, accounting for mismatches has shown to lead to much improved classification, while heuristics can improve practical performance. In this article, we close the gap by presenting the first provably efficient algorithm for the k-mismatch average common string (ACSk) problem that takes O(n) space and O(n log(k) n) time in the worst case for any constant k. Our method extends the generalized suffix tree model to incorporate a carefully selected bounded set of perturbed suffixes, and can be applied to other complex approximate sequence matching problems.
Collapse
Affiliation(s)
| | - Alberto Apostolico
- College of Computing, Georgia Institute of Technology , Atlanta, Georgia
| | - Srinivas Aluru
- College of Computing, Georgia Institute of Technology , Atlanta, Georgia
| |
Collapse
|
30
|
Carmel A, Musa-Lempel N, Tsur D, Ziv-Ukelson M. The worst case complexity of maximum parsimony. J Comput Biol 2014; 21:799-808. [PMID: 25302568 DOI: 10.1089/cmb.2014.0128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
One of the core classical problems in computational biology is that of constructing the most parsimonious phylogenetic tree interpreting an input set of sequences from the genomes of evolutionarily related organisms. We reexamine the classical maximum parsimony (MP) optimization problem for the general (asymmetric) scoring matrix case, where rooted phylogenies are implied, and analyze the worst case bounds of three approaches to MP: The approach of Cavalli-Sforza and Edwards, the approach of Hendy and Penny, and a new agglomerative, "bottom-up" approach we present in this article. We show that the second and third approaches are faster than the first one by a factor of Θ(√n) and Θ(n), respectively, where n is the number of species.
Collapse
Affiliation(s)
- Amir Carmel
- Department of Computer Science, Ben-Gurion University of the Negev , Beer Sheva, Israel
| | | | | | | |
Collapse
|
31
|
Abstract
Heterogeneity among life traits in mammals has resulted in considerable phylogenetic conflict, particularly concerning the position of the placental root. Layered upon this are gene- and lineage-specific variation in amino acid substitution rates and compositional biases. Life trait variations that may impact upon mutational rates are longevity, metabolic rate, body size, and germ line generation time. Over the past 12 years, three main conflicting hypotheses have emerged for the placement of the placental root. These hypotheses place the Atlantogenata (common ancestor of Xenarthra plus Afrotheria), the Afrotheria, or the Xenarthra as the sister group to all other placental mammals. Model adequacy is critical for accurate tree reconstruction and by failing to account for these compositional and character exchange heterogeneities across the tree and data set, previous studies have not provided a strongly supported hypothesis for the placental root. For the first time, models that accommodate both tree and data set heterogeneity have been applied to mammal data. Here, we show the impact of accurate model assignment and the importance of data sets in accommodating model parameters while maintaining the power to reject competing hypotheses. Through these sophisticated methods, we demonstrate the importance of model adequacy, data set power and provide strong support for the Atlantogenata over other competing hypotheses for the position of the placental root.
Collapse
Affiliation(s)
- Claire C Morgan
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin, Ireland
| | | | | | | | | | | |
Collapse
|
32
|
Rossi CC, de Araújo EF, de Queiroz MV, Bazzolli DMS. Characterization of the omlA gene from different serotypes of Actinobacillus pleuropneumoniae: A new insight into an old approach. Genet Mol Biol 2013; 36:243-51. [PMID: 23885207 PMCID: PMC3715291 DOI: 10.1590/s1415-47572013005000012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 01/29/2013] [Indexed: 11/22/2022] Open
Abstract
The OmlA protein is a virulence factor of Actinobacillus pleuropneumoniae, an important pathogen in pigs. The polymorphisms present in the omlA gene sequence of 15 reference serotypes of A. pleuropneumoniae and non-serotypable isolates were assessed to determine the possible evolutionary relationship among them and to validate the importance of this gene as a molecular marker for the characterization of this bacterium. Divergence among the 15 serotypes of A. pleuropneumoniae probably resulted initially from two major evolutionary events that led to subsequent differentiation into nine groups. This differentiation makes it possible to characterize most of the serotypes by using bionformatics, thereby avoiding problems with immunological cross-reactivity. A conserved α-helix common to all the serotypes was most likely involved in connecting the protein to the outer membrane and acting as a signal peptide. A previously unknown gene duplication was also identified and could contribute to the genetic variability that makes it difficult to serotype some isolates. Our data support the importance of the omlA gene in the biology of A. pleuropneumoniae and provide a new area of research into the OmlA protein.
Collapse
Affiliation(s)
- Ciro César Rossi
- Laboratório de Genética Molecular de Micro-organismos, Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | | | | | | |
Collapse
|
33
|
Lin Y, Hu F, Tang J, Moret BM. Maximum likelihood phylogenetic reconstruction from high-resolution whole-genome data and a tree of 68 eukaryotes. Pac Symp Biocomput 2013:285-96. [PMID: 23424133 PMCID: PMC3712796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The rapid accumulation of whole-genome data has renewed interest in the study of the evolution of genomic architecture, under such events as rearrangements, duplications, losses. Comparative genomics, evolutionary biology, and cancer research all require tools to elucidate the mechanisms, history, and consequences of those evolutionary events, while phylogenetics could use whole-genome data to enhance its picture of the Tree of Life. Current approaches in the area of phylogenetic analysis are limited to very small collections of closely related genomes using low-resolution data (typically a few hundred syntenic blocks); moreover, these approaches typically do not include duplication and loss events. We describe a maximum likelihood (ML) approach for phylogenetic analysis that takes into account genome rearrangements as well as duplications, insertions, and losses. Our approach can handle high-resolution genomes (with 40,000 or more markers) and can use in the same analysis genomes with very different numbers of markers. Because our approach uses a standard ML reconstruction program (RAxML), it scales up to large trees. We present the results of extensive testing on both simulated and real data showing that our approach returns very accurate results very quickly. In particular, we analyze a dataset of 68 high-resolution eukaryotic genomes, with from 3,000 to 42,000 genes, from the eGOB database; the analysis, including bootstrapping, takes just 3 hours on a desktop system and returns a tree in agreement with all well supported branches, while also suggesting resolutions for some disputed placements.
Collapse
Affiliation(s)
- Yu Lin
- Laboratory for Computational Biology and Bioinformatics, EPFL, Lausanne VD, CH-1015, Switzerland
| | - Fei Hu
- Department of Computer Science and Engineering, University of South Carolina, Columbia, SC 29208, USA
| | - Jijun Tang
- Department of Computer Science and Engineering, University of South Carolina, Columbia, SC 29208, USA
| | - Bernard M.E. Moret
- Laboratory for Computational Biology and Bioinformatics, EPFL, Lausanne VD, CH-1015, Switzerland
| |
Collapse
|
34
|
Bryner SF, Rigling D, Brunner PC. Invasion history and demographic pattern of Cryphonectria hypovirus 1 across European populations of the chestnut blight fungus. Ecol Evol 2012; 2:3227-41. [PMID: 23301186 PMCID: PMC3539014 DOI: 10.1002/ece3.429] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Revised: 10/09/2012] [Accepted: 10/13/2012] [Indexed: 01/16/2023] Open
Abstract
We reconstructed the invasion history of the fungal virus Cryphonectria hypovirus 1 (CHV-1) in Europe, which infects the chestnut blight fungus Cryphonectria parasitica. The pattern of virus evolution was inferred based on nucleotide sequence variation from isolates sampled across a wide area in Europe at different points in time. Phylogeny and time estimates suggested that CHV-1 was introduced together with its fungal host to Europe and that it rapidly colonized the central range along the south facing slopes of the Alps and the north-east facing slopes of the Dinaric Alps. These central populations were the source for two waves of simultaneous invasions toward the southern Balkans and Turkey, as indicated by migration rates. Our results showed that the evolutionary scenarios for CHV-1 and C. parasitica were spatially congruent. As infection with CHV-1 reduces the pathogenicity of C. parasitica toward the chestnut tree, CHV-1 invasions of the newly established C. parasitica populations probably prevented the development of devastating chestnut blight epidemics in Europe. We propose that in this, and supposedly in other pathosystems, geographic, vegetation-related, demographic, economic, and political factors may help explain the correlated invasion pattern of a parasite and its host.
Collapse
Affiliation(s)
- Sarah F Bryner
- WSL Swiss Federal Research Institute CH-8903, Birmensdorf, Switzerland
| | | | | |
Collapse
|
35
|
Abstract
BACKGROUND Large-scale sequencing of genomes has enabled the inference of phylogenies based on the evolution of genomic architecture, under such events as rearrangements, duplications, and losses. Many evolutionary models and associated algorithms have been designed over the last few years and have found use in comparative genomics and phylogenetic inference. However, the assessment of phylogenies built from such data has not been properly addressed to date. The standard method used in sequence-based phylogenetic inference is the bootstrap, but it relies on a large number of homologous characters that can be resampled; yet in the case of rearrangements, the entire genome is a single character. Alternatives such as the jackknife suffer from the same problem, while likelihood tests cannot be applied in the absence of well established probabilistic models. RESULTS We present a new approach to the assessment of distance-based phylogenetic inference from whole-genome data; our approach combines features of the jackknife and the bootstrap and remains nonparametric. For each feature of our method, we give an equivalent feature in the sequence-based framework; we also present the results of extensive experimental testing, in both sequence-based and genome-based frameworks. Through the feature-by-feature comparison and the experimental results, we show that our bootstrapping approach is on par with the classic phylogenetic bootstrap used in sequence-based reconstruction, and we establish the clear superiority of the classic bootstrap for sequence data and of our corresponding new approach for rearrangement data over proposed variants. Finally, we test our approach on a small dataset of mammalian genomes, verifying that the support values match current thinking about the respective branches. CONCLUSIONS Our method is the first to provide a standard of assessment to match that of the classic phylogenetic bootstrap for aligned sequences. Its support values follow a similar scale and its receiver-operating characteristics are nearly identical, indicating that it provides similar levels of sensitivity and specificity. Thus our assessment method makes it possible to conduct phylogenetic analyses on whole genomes with the same degree of confidence as for analyses on aligned sequences. Extensions to search-based inference methods such as maximum parsimony and maximum likelihood are possible, but remain to be thoroughly tested.
Collapse
Affiliation(s)
- Yu Lin
- Laboratory for Computational Biology and Bioinformatics, EPFL, EPFL-IC-LCBB INJ230, Station 14, CH-1015 Lausanne, Switzerland
| | - Vaibhav Rajan
- Laboratory for Computational Biology and Bioinformatics, EPFL, EPFL-IC-LCBB INJ230, Station 14, CH-1015 Lausanne, Switzerland
| | - Bernard ME Moret
- Laboratory for Computational Biology and Bioinformatics, EPFL, EPFL-IC-LCBB INJ230, Station 14, CH-1015 Lausanne, Switzerland
| |
Collapse
|
36
|
Abstract
The chordate proteome history database (http://ioda.univ-provence.fr) comprises some 20,000 evolutionary analyses of proteins from chordate species. Our main objective was to characterize and study the evolutionary histories of the chordate proteome, and in particular to detect genomic events and automatic functional searches. Firstly, phylogenetic analyses based on high quality multiple sequence alignments and a robust phylogenetic pipeline were performed for the whole protein and for each individual domain. Novel approaches were developed to identify orthologs/paralogs, and predict gene duplication/gain/loss events and the occurrence of new protein architectures (domain gains, losses and shuffling). These important genetic events were localized on the phylogenetic trees and on the genomic sequence. Secondly, the phylogenetic trees were enhanced by the creation of phylogroups, whereby groups of orthologous sequences created using OrthoMCL were corrected based on the phylogenetic trees; gene family size and gene gain/loss in a given lineage could be deduced from the phylogroups. For each ortholog group obtained from the phylogenetic or the phylogroup analysis, functional information and expression data can be retrieved. Database searches can be performed easily using biological objects: protein identifier, keyword or domain, but can also be based on events, eg, domain exchange events can be retrieved. To our knowledge, this is the first database that links group clustering, phylogeny and automatic functional searches along with the detection of important events occurring during genome evolution, such as the appearance of a new domain architecture.
Collapse
Affiliation(s)
- Anthony Levasseur
- INRA, UMR1163 Biotechnologie des Champignons Filamenteux, Aix Marseille Université, ESIL Polytech, 163 avenue de Luminy, CP 925, 13288 Marseille Cedex 09, France
| | | | | | | | | | | | | |
Collapse
|
37
|
Ferrero V, Arroyo J, Castro S, Navarro L. Unusual heterostyly: style dimorphism and self-incompatibility are not tightly associated in Lithodora and Glandora (Boraginaceae). Ann Bot 2012; 109:655-65. [PMID: 21985797 PMCID: PMC3278292 DOI: 10.1093/aob/mcr222] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2011] [Accepted: 06/24/2011] [Indexed: 05/14/2023]
Abstract
BACKGROUND AND AIMS Heterostyly is a floral polymorphism characterized by the reciprocal position of stamens and stigmas in different flower morphs in a population. This reciprocal herkogamy is usually associated with an incompatibility system that prevents selfing and intra-morph fertilization, termed a heteromorphic incompatibility system. In different evolutionary models explaining heterostyly, it has been alternately argued that heteromorphic incompatibility either preceded or followed the evolution of reciprocal herkogamy. In some models, reciprocal herkogamy and incompatibility have been hypothesized to be linked together during the evolution of the heterostylous system. METHODS We examine the incompatibility systems in species with different stylar polymorphisms from the genera Lithodora and Glandora (Boraginaceae). We then test whether evolution towards reciprocal herkogamy is associated with the acquisition of incompatibility. To this end, a phylogeny of these genera and related species is reconstructed and the morphological and reproductive changes that occurred during the course of evolution are assessed. KEY RESULTS Both self-compatibility and self-incompatibility are found within the studied genera, along with different degrees of intra-morph compatibility. We report for the first time extensive variability among members of the genus Glandora and related species in terms of the presence or absence of intraspecies polymorphism and heteromorphic incompatibility. Overall, our results do not support a tight link between floral polymorphism and incompatibility systems. CONCLUSIONS The independent evolution of stylar polymorphism and incompatibility appears to have occurred in this group of plants. This refutes the canonical view that there is strong linkage between these reproductive traits.
Collapse
Affiliation(s)
- V Ferrero
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal.
| | | | | | | |
Collapse
|
38
|
ZHAO YINHE, WANG GUOYING, ZHANG JINPENG, YANG JUNBO, PENG SHANG, GAO LIANMING, LI CHENGYUN, HU JINYONG, LI DEZHU, GAO LIZHI. Expressed sequence tags (ESTs) and phylogenetic analysis of floral genes from a paleoherb species, Asarum caudigerum. Ann Bot 2006; 98:157-63. [PMID: 16675604 PMCID: PMC2803548 DOI: 10.1093/aob/mcl081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
BACKGROUND AND AIMS Asarum caudigerum (Aristolochiaceae) is an important species of paleoherb in relation to understanding the origin and evolution of angiosperm flowers, due to its basal position in the angiosperms. The aim of this study was to isolate floral-related genes from A. caudigerum, and to infer evolutionary relationships among florally expression-related genes, to further illustrate the origin and diversification of flowers in angiosperms. METHODS A subtracted floral cDNA library was constructed from floral buds using suppression subtractive hybridization (SSH). The cDNA of floral buds and leaves at the seedling stage were used as a tester and a driver, respectively. To further identify the function of putative MADS-box transcription factors, phylogenetic trees were reconstructed in order to infer evolutionary relationships within the MADS-box gene family. KEY RESULTS In the forward-subtracted floral cDNA library, 1920 clones were randomly sequenced, from which 567 unique expressed sequence tags (ESTs) were obtained. Among them, 127 genes failed to show significant similarity to any published sequences in GenBank and thus are putatively novel genes. CONCLUSIONS Phylogenetic analysis indicated that a total of 29 MADS-box transcription factors were members of the APETALA3(AP3) subfamily, while nine others were putative MADS-box transcription factors that formed a cluster with MADS-box genes isolated from Amborella, the basal-most angiosperm, and those from the gymnosperms. This suggests that the origin of A. caudigerum is intermediate between the angiosperms and gymnosperms.
Collapse
Affiliation(s)
- YINHE ZHAO
- Laboratory of Biodiversity and Plant Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China, State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 10-Institute for Plant Breeding Research, Carl-von-Linn0094, China, College of Agronomy and Key Laboratory for Plant Pathology of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China, Max-Plancke Weg 10, Koeln 50829, Germany and Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
| | - GUOYING WANG
- Laboratory of Biodiversity and Plant Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China, State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 10-Institute for Plant Breeding Research, Carl-von-Linn0094, China, College of Agronomy and Key Laboratory for Plant Pathology of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China, Max-Plancke Weg 10, Koeln 50829, Germany and Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
| | - JINPENG ZHANG
- Laboratory of Biodiversity and Plant Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China, State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 10-Institute for Plant Breeding Research, Carl-von-Linn0094, China, College of Agronomy and Key Laboratory for Plant Pathology of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China, Max-Plancke Weg 10, Koeln 50829, Germany and Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
| | - JUNBO YANG
- Laboratory of Biodiversity and Plant Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China, State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 10-Institute for Plant Breeding Research, Carl-von-Linn0094, China, College of Agronomy and Key Laboratory for Plant Pathology of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China, Max-Plancke Weg 10, Koeln 50829, Germany and Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
| | - SHANG PENG
- Laboratory of Biodiversity and Plant Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China, State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 10-Institute for Plant Breeding Research, Carl-von-Linn0094, China, College of Agronomy and Key Laboratory for Plant Pathology of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China, Max-Plancke Weg 10, Koeln 50829, Germany and Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
| | - LIANMING GAO
- Laboratory of Biodiversity and Plant Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China, State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 10-Institute for Plant Breeding Research, Carl-von-Linn0094, China, College of Agronomy and Key Laboratory for Plant Pathology of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China, Max-Plancke Weg 10, Koeln 50829, Germany and Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
| | - CHENGYUN LI
- Laboratory of Biodiversity and Plant Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China, State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 10-Institute for Plant Breeding Research, Carl-von-Linn0094, China, College of Agronomy and Key Laboratory for Plant Pathology of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China, Max-Plancke Weg 10, Koeln 50829, Germany and Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
| | - JINYONG HU
- Laboratory of Biodiversity and Plant Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China, State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 10-Institute for Plant Breeding Research, Carl-von-Linn0094, China, College of Agronomy and Key Laboratory for Plant Pathology of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China, Max-Plancke Weg 10, Koeln 50829, Germany and Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
| | - DEZHU LI
- Laboratory of Biodiversity and Plant Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China, State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 10-Institute for Plant Breeding Research, Carl-von-Linn0094, China, College of Agronomy and Key Laboratory for Plant Pathology of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China, Max-Plancke Weg 10, Koeln 50829, Germany and Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
- For correspondence. E-mail
| | - LIZHI GAO
- Laboratory of Biodiversity and Plant Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China, State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 10-Institute for Plant Breeding Research, Carl-von-Linn0094, China, College of Agronomy and Key Laboratory for Plant Pathology of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China, Max-Plancke Weg 10, Koeln 50829, Germany and Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
| |
Collapse
|