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Li ZC, Xie TC, Feng XL, Wang ZX, Lin C, Li GM, Li XZ, Qi J. The First Five Mitochondrial Genomes for the Family Nidulariaceae Reveal Novel Gene Rearrangements, Intron Dynamics, and Phylogeny of Agaricales. Int J Mol Sci 2023; 24:12599. [PMID: 37628782 PMCID: PMC10454537 DOI: 10.3390/ijms241612599] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
The family Nidulariaceae, consisting of five genera including Cyathus, is a unique group of mushrooms commonly referred to as bird's nest fungi due to their striking resemblance to bird's nests. These mushrooms are considered medicinal mushrooms in Chinese medicine and have received attention in recent years for their anti-neurodegenerative properties. However, despite the interest in these mushrooms, very little is known about their mitochondrial genomes (mitogenomes). This study is the first comprehensive investigation of the mitogenomes of five Nidulariaceae species with circular genome structures ranging in size from 114,236 bp to 129,263 bp. Comparative analyses based on gene content, gene length, tRNA, and codon usage indicate convergence within the family Nidulariaceae and heterogeneity within the order Agaricales. Phylogenetic analysis based on a combined mitochondrial conserved protein dataset provides a well-supported phylogenetic tree for the Basidiomycetes, which clearly demonstrates the evolutionary relationships between Nidulariaceae and other members of Agaricales. Furthermore, phylogenetic inferences based on four different gene sets reveal the stability and proximity of evolutionary relationships within Agaricales. These results reveal the uniqueness of the family Nidulariaceae and its similarity to other members of Agaricales; provide valuable insights into the origin, evolution, and genetics of Nidulariaceae species; and enrich the fungal mitogenome resource. This study will help to expand the knowledge and understanding of the mitogenomes in mushrooms.
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Affiliation(s)
- Zhao-chen Li
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Tian-chen Xie
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Xi-long Feng
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Zhen-xin Wang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Chao Lin
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Guo-ming Li
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Xiu-Zhang Li
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai Academy of Animal and Veterinary Sciences, Qinghai University, Xining 810016, China
| | - Jianzhao Qi
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
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Kolařík M, Wei IC, Hsieh SY, Piepenbring M, Kirschner R. Nucleotide composition bias of rDNA sequences as a source of phylogenetic artifacts in Basidiomycota—a case of a new lineage of a uredinicolous Ramularia-like anamorph with affinities to Ustilaginomycotina. Mycol Prog 2021. [DOI: 10.1007/s11557-021-01749-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Li Q, Yang M, Chen C, Xiong C, Jin X, Pu Z, Huang W. Characterization and phylogenetic analysis of the complete mitochondrial genome of the medicinal fungus Laetiporus sulphureus. Sci Rep 2018; 8:9104. [PMID: 29904057 PMCID: PMC6002367 DOI: 10.1038/s41598-018-27489-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 05/24/2018] [Indexed: 12/22/2022] Open
Abstract
The medicinal fungus Laetiporus sulphureus is widely distributed worldwide. To screen for molecular markers potentially useful for phylogenetic analyses of this species and related species, the mitochondrial genome of L. sulphureus was sequenced and assembled. The complete circular mitochondrial genome was 101,111 bp long, and contained 38 protein-coding genes (PCGs), 2 rRNA genes, and 25 tRNA genes. Our BLAST search aligned about 6.1 kb between the mitochondrial and nuclear genomes of L. sulphureus, indicative of possible gene transfer events. Both the GC and AT skews in the L. sulphureus mitogenome were negative, in contrast to the other seven Polyporales species tested. Of the 15 PCGs conserved across the seven species of Polyporales, the lengths of 11 were unique in the L. sulphureus mitogenome. The Ka/Ks of these 15 PCGs were all less than 1, indicating that PCGs were subject to purifying selection. Our phylogenetic analysis showed that three single genes (cox1, cob, and rnl) were potentially useful as molecular markers. This study is the first publication of a mitochondrial genome in the family Laetiporaceae, and will facilitate the study of population genetics and evolution in L. sulphureus and other species in this family.
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Affiliation(s)
- Qiang Li
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, P.R. China.,Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, P.R. China
| | - Mei Yang
- Panzhihua City Academy of Agricultural and Forest Sciences, Panzhihua, 617061, Sichuan, P.R. China
| | - Cheng Chen
- Institute of plant protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, P.R. China
| | - Chuan Xiong
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, P.R. China
| | - Xin Jin
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, P.R. China
| | - Zhigang Pu
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, P.R. China. .,Sichuan Academy of Agricultural Sciences, 106 # Shizishan Rd, Chengdu, 610061, Sichuan, China.
| | - Wenli Huang
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, P.R. China. .,Sichuan Academy of Agricultural Sciences, 106 # Shizishan Rd, Chengdu, 610061, Sichuan, China.
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Wahba L, Costantino L, Tan FJ, Zimmer A, Koshland D. S1-DRIP-seq identifies high expression and polyA tracts as major contributors to R-loop formation. Genes Dev 2017; 30:1327-38. [PMID: 27298336 PMCID: PMC4911931 DOI: 10.1101/gad.280834.116] [Citation(s) in RCA: 180] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 05/11/2016] [Indexed: 12/16/2022]
Abstract
In this study, Wahba et al. investigate how and where DNA–RNA hybrids, which form when an RNA molecule hybridizes to the complementary genomic locus, appear throughout the genome. They present a novel whole-genome method, S1-DRIP-seq, for mapping hybrid-prone regions in S. cerevisiae and identify the first global genomic features that play a causal role in R-loop formation in yeast. R loops form when transcripts hybridize to homologous DNA on chromosomes, yielding a DNA:RNA hybrid and a displaced DNA single strand. R loops impact the genome of many organisms, regulating chromosome stability, gene expression, and DNA repair. Understanding the parameters dictating R-loop formation in vivo has been hampered by the limited quantitative and spatial resolution of current genomic strategies for mapping R loops. We report a novel whole-genome method, S1-DRIP-seq (S1 nuclease DNA:RNA immunoprecipitation with deep sequencing), for mapping hybrid-prone regions in budding yeast Saccharomyces cerevisiae. Using this methodology, we identified ∼800 hybrid-prone regions covering 8% of the genome. Given the pervasive transcription of the yeast genome, this result suggests that R-loop formation is dictated by characteristics of the DNA, RNA, and/or chromatin. We successfully identified two features highly predictive of hybrid formation: high transcription and long homopolymeric dA:dT tracts. These accounted for >60% of the hybrid regions found in the genome. We demonstrated that these two factors play a causal role in hybrid formation by genetic manipulation. Thus, the hybrid map generated by S1-DRIP-seq led to the identification of the first global genomic features causal for R-loop formation in yeast.
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Affiliation(s)
- Lamia Wahba
- Department of Cell and Molecular Biology, University of California at Berkeley, Berkeley, California 94720, USA
| | - Lorenzo Costantino
- Department of Cell and Molecular Biology, University of California at Berkeley, Berkeley, California 94720, USA
| | - Frederick J Tan
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland 21218, USA
| | - Anjali Zimmer
- Department of Cell and Molecular Biology, University of California at Berkeley, Berkeley, California 94720, USA
| | - Douglas Koshland
- Department of Cell and Molecular Biology, University of California at Berkeley, Berkeley, California 94720, USA
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Lubberts B, Mellema JJ, Janssen SJ, Ring D. Fracture line distribution of olecranon fractures. Arch Orthop Trauma Surg 2017; 137:37-42. [PMID: 27832347 DOI: 10.1007/s00402-016-2593-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Indexed: 02/09/2023]
Abstract
PURPOSE The association between specific olecranon fracture characteristics (e.g., displacement, fragmentation, subluxation) and fracture line distribution might help surgeons predict intra-articular fracture location based on fracture characteristics that can be determined on radiographs. We hypothesized that fracture mapping techniques would reveal different fracture patterns for minimally displaced fractures, displaced fractures, and fracture-dislocations of the olecranon. METHODS A consecutive series of 78 patients with olecranon fractures were evaluated using initial radiographs and computed tomography scans and characterized according to the Mayo classification. Fracture lines were identified based on reduced three-dimensional computed tomography reconstructions and graphically superimposed onto a standard template to create two-dimensional fracture maps. The fracture maps were then converted into fracture heat maps. Based on fracture and heat maps, fracture line location and patterns were determined. RESULTS Six (7.7%) patients had a non- or minimally displaced fracture, 22 (28%) a displaced fracture, and 50 (64%) a fracture-dislocation of the olecranon. There were 27 (54%) anterior and 23 (46%) posterior olecranon fracture-dislocations. Fracture lines of non- or minimally displaced fractures and posterior fracture-dislocations enter and exit the trochlear notch at the base of the coronoid, while fracture lines of displaced fractures and anterior fracture-dislocations were spread more broadly over the depths of the trochlear notch. CONCLUSIONS Based on fracture characteristics depicted on radiographs, one can anticipate the amount of the olecranon involved (how close is the fracture line to the coronoid) and the orientation of the fracture line. Computer tomography could be reserved for when more specific knowledge of the fracture line might affect treatment. LEVEL OF EVIDENCE III.
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Affiliation(s)
- Bart Lubberts
- Orthopaedic Hand and Upper Extremity Service, Massachusetts General Hospital, Harvard Medical School, Boston, USA
| | - Jos J Mellema
- Orthopaedic Hand and Upper Extremity Service, Massachusetts General Hospital, Harvard Medical School, Boston, USA
| | - Stein J Janssen
- Orthopaedic Hand and Upper Extremity Service, Massachusetts General Hospital, Harvard Medical School, Boston, USA
| | - David Ring
- Massachusetts General Hospital, Harvard Medical School, Boston, USA. .,Dell Medical School, University of Texas at Austin, Austin, USA.
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Mellema JJ, Doornberg JN, Dyer GSM, Ring D. Distribution of coronoid fracture lines by specific patterns of traumatic elbow instability. J Hand Surg Am 2014; 39:2041-6. [PMID: 25070699 DOI: 10.1016/j.jhsa.2014.06.123] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 06/22/2014] [Accepted: 06/24/2014] [Indexed: 02/02/2023]
Abstract
PURPOSE To determine if specific coronoid fractures relate to specific overall traumatic elbow instability injury patterns and to depict any relationship on fracture maps and heat maps. METHODS We collected 110 computed tomography (CT) studies from patients with coronoid fractures. Fracture types and pattern of injury were characterized based on anteroposterior and lateral radiographs, 2- and 3-dimensional CT scans, and intraoperative findings as described in operative reports. Using quantitative 3-dimensional CT techniques we were able to reconstruct the coronoid and reduce fracture fragments. Based on these reconstructions, fracture lines were identified and graphically superimposed onto a standard template in order to create 2-dimensional fracture maps. To further emphasize the fracture maps, the initial diagrams were converted into fracture heat maps following arbitrary units of measure. The Fisher exact test was used to evaluate the association between coronoid fracture types and elbow fracture-dislocation patterns. RESULTS Forty-seven coronoid fractures were associated with a terrible triad fracture dislocation, 30 with a varus posteromedial rotational injury, 1 with a anterior olecranon fracture dislocation, 22 with a posterior olecranon fracture dislocation, and 7 with a posterior Monteggia injury associated with terrible triad fracture dislocation of the elbow. The association between coronoid fracture types and elbow fracture-dislocation patterns, as shown on 2-dimensional fracture and heat maps, was strongly significant. CONCLUSIONS Our fracture maps and heat maps support the observation that specific patterns of traumatic elbow instability have correspondingly specific coronoid fracture patterns. Knowledge of these patterns is useful for planning management because it directs exposure and fixation and helps identify associated ligament injuries and fractures that might benefit from treatment. CLINICAL RELEVANCE Two-dimensional fracture and heat mapping techniques may help surgeons to predict the distribution of coronoid fracture lines associated with specific injury patterns.
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Affiliation(s)
- Jos J Mellema
- Orthopaedic Hand and Upper Extremity Service, Massachusetts General Hospital, Boston, MA; Department of Orthopaedic Surgery, Brigham and Women's Hospital, Boston, MA; Orthotrauma Research Center Amsterdam, Academic Medical Center, Amsterdam, The Netherlands
| | - Job N Doornberg
- Orthopaedic Hand and Upper Extremity Service, Massachusetts General Hospital, Boston, MA; Department of Orthopaedic Surgery, Brigham and Women's Hospital, Boston, MA; Orthotrauma Research Center Amsterdam, Academic Medical Center, Amsterdam, The Netherlands
| | - George S M Dyer
- Orthopaedic Hand and Upper Extremity Service, Massachusetts General Hospital, Boston, MA; Department of Orthopaedic Surgery, Brigham and Women's Hospital, Boston, MA; Orthotrauma Research Center Amsterdam, Academic Medical Center, Amsterdam, The Netherlands
| | - David Ring
- Orthopaedic Hand and Upper Extremity Service, Massachusetts General Hospital, Boston, MA; Department of Orthopaedic Surgery, Brigham and Women's Hospital, Boston, MA; Orthotrauma Research Center Amsterdam, Academic Medical Center, Amsterdam, The Netherlands.
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