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McCarthy CGP, Fitzpatrick DA. Multiple Approaches to Phylogenomic Reconstruction of the Fungal Kingdom. ADVANCES IN GENETICS 2017; 100:211-266. [PMID: 29153401 DOI: 10.1016/bs.adgen.2017.09.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Fungi are possibly the most diverse eukaryotic kingdom, with over a million member species and an evolutionary history dating back a billion years. Fungi have been at the forefront of eukaryotic genomics, and owing to initiatives like the 1000 Fungal Genomes Project the amount of fungal genomic data has increased considerably over the last 5 years, enabling large-scale comparative genomics of species across the kingdom. In this chapter, we first review fungal evolution and the history of fungal genomics. We then review in detail seven phylogenomic methods and reconstruct the phylogeny of 84 fungal species from 8 phyla using each method. Six methods have seen extensive use in previous fungal studies, while a Bayesian supertree method is novel to fungal phylogenomics. We find that both established and novel phylogenomic methods can accurately reconstruct the fungal kingdom. Finally, we discuss the accuracy and suitability of each phylogenomic method utilized.
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Engel SR, Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight SS, Hitz BC, Karra K, Nash RS, Weng S, Wong ED, Lloyd P, Skrzypek MS, Miyasato SR, Simison M, Cherry JM. The reference genome sequence of Saccharomyces cerevisiae: then and now. G3 (BETHESDA, MD.) 2014; 4:389-98. [PMID: 24374639 PMCID: PMC3962479 DOI: 10.1534/g3.113.008995] [Citation(s) in RCA: 255] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 12/21/2013] [Indexed: 11/18/2022]
Abstract
The genome of the budding yeast Saccharomyces cerevisiae was the first completely sequenced from a eukaryote. It was released in 1996 as the work of a worldwide effort of hundreds of researchers. In the time since, the yeast genome has been intensively studied by geneticists, molecular biologists, and computational scientists all over the world. Maintenance and annotation of the genome sequence have long been provided by the Saccharomyces Genome Database, one of the original model organism databases. To deepen our understanding of the eukaryotic genome, the S. cerevisiae strain S288C reference genome sequence was updated recently in its first major update since 1996. The new version, called "S288C 2010," was determined from a single yeast colony using modern sequencing technologies and serves as the anchor for further innovations in yeast genomic science.
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Affiliation(s)
- Stacia R. Engel
- Department of Genetics, Stanford University, Stanford, California 94305
| | - Fred S. Dietrich
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina 27710
| | - Dianna G. Fisk
- Department of Genetics, Stanford University, Stanford, California 94305
| | - Gail Binkley
- Department of Genetics, Stanford University, Stanford, California 94305
| | - Rama Balakrishnan
- Department of Genetics, Stanford University, Stanford, California 94305
| | - Maria C. Costanzo
- Department of Genetics, Stanford University, Stanford, California 94305
| | - Selina S. Dwight
- Department of Genetics, Stanford University, Stanford, California 94305
| | - Benjamin C. Hitz
- Department of Genetics, Stanford University, Stanford, California 94305
| | - Kalpana Karra
- Department of Genetics, Stanford University, Stanford, California 94305
| | - Robert S. Nash
- Department of Genetics, Stanford University, Stanford, California 94305
| | - Shuai Weng
- Department of Genetics, Stanford University, Stanford, California 94305
| | - Edith D. Wong
- Department of Genetics, Stanford University, Stanford, California 94305
| | - Paul Lloyd
- Department of Genetics, Stanford University, Stanford, California 94305
| | - Marek S. Skrzypek
- Department of Genetics, Stanford University, Stanford, California 94305
| | | | - Matt Simison
- Department of Genetics, Stanford University, Stanford, California 94305
| | - J. Michael Cherry
- Department of Genetics, Stanford University, Stanford, California 94305
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Abstract
The complete sequencing of the genome of a simple eukaryotic organism - the budding yeast Saccharomyces cerevisiae - is a milestone for biology, and sets the stage for a complete understanding of how a eukaryotic cell functions.
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Affiliation(s)
- M Johnston
- Department of Genetics, Box 8232, Washington University Medical School, 4566 Scott Avenue, St. Louis, Missouri 63110, USA
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Scholler P, Schwarz S, Hoheisel JD. High-resolution cosmid mapping of the left arm of Saccharomyces cerevisiae chromosome XII; a first step towards an ordered sequencing approach. Yeast 1995; 11:659-66. [PMID: 7483838 DOI: 10.1002/yea.320110706] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
For the sequencing of the left arm of chromosome XII of Saccharomyces cerevisiae, we fine-mapped the entire 450 kb fragment between the ribosomal DNA (rDNA) and the left telomere. Total yeast DNA in agarose blocks was digested with I-PpoI, which exclusively cuts once in each repeat unit of the rDNA. The resulting fragment was isolated from pulsed-field gels, together with the equally sized chromosome IX. A cosmid library of some 30-fold chromosome coverage was generated from this material, with the cloning efficiency being around 20,000 clones per microgram genomic DNA. The chromosome XII and IX specific clones were identified by complementary hybridizations with the respective chromosomes. For the left arm of chromosome XII, a contiguous cosmid array (contig) with an average map resolution better than 9 kb was generated by clone hybridization procedures. The ordered library serves as a tool for the physical mapping of genetic markers. Also, a minimal set of 15 clones was selected that covers the entire fragment. This subset forms the basis for the generation of a template map of much higher resolution for a directed sequencing of the left arm of chromosome XII.
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Affiliation(s)
- P Scholler
- German Cancer Research Center, Heidelberg
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Goffeau A, Nakai K, Slonimski P, Risler JL, Slominski P [corrected to Slonimski P]. The membrane proteins encoded by yeast chromosome III genes. FEBS Lett 1993; 325:112-7. [PMID: 8513882 DOI: 10.1016/0014-5793(93)81425-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- A Goffeau
- Unité de Biochimie Physiologique, Université de Louvain, Louvain-la-Neuve, Belgium
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