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For: Jiang H, Guan W, Pinney D, Wang W, Gu Z. Relaxation of yeast mitochondrial functions after whole-genome duplication. Genes Dev 2008;18:1466-71. [PMID: 18669479 PMCID: PMC2527710 DOI: 10.1101/gr.074674.107] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2007] [Accepted: 05/14/2008] [Indexed: 12/20/2022]
Number Cited by Other Article(s)
1
Wolters JF, LaBella AL, Opulente DA, Rokas A, Hittinger CT. Mitochondrial genome diversity across the subphylum Saccharomycotina. Front Microbiol 2023;14:1268944. [PMID: 38075892 PMCID: PMC10701893 DOI: 10.3389/fmicb.2023.1268944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/31/2023] [Indexed: 12/20/2023]  Open
2
Wolters JF, LaBella AL, Opulente DA, Rokas A, Hittinger CT. Mitochondrial Genome Diversity across the Subphylum Saccharomycotina. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.28.551029. [PMID: 37577532 PMCID: PMC10418067 DOI: 10.1101/2023.07.28.551029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
3
Masłowska-Górnicz A, van den Bosch MRM, Saccenti E, Suarez-Diez M. A large-scale analysis of codon usage bias in 4868 bacterial genomes shows association of codon adaptation index with GC content, protein functional domains and bacterial phenotypes. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022;1865:194826. [PMID: 35605953 DOI: 10.1016/j.bbagrm.2022.194826] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 05/05/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
4
Hao W. From Genome Variation to Molecular Mechanisms: What we Have Learned From Yeast Mitochondrial Genomes? Front Microbiol 2022;13:806575. [PMID: 35126340 PMCID: PMC8811140 DOI: 10.3389/fmicb.2022.806575] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/03/2022] [Indexed: 11/26/2022]  Open
5
Arella D, Dilucca M, Giansanti A. Codon usage bias and environmental adaptation in microbial organisms. Mol Genet Genomics 2021;296:751-762. [PMID: 33818631 PMCID: PMC8144148 DOI: 10.1007/s00438-021-01771-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 02/22/2021] [Indexed: 01/01/2023]
6
Frankovsky J, Vozáriková V, Nosek J, Tomáška Ľ. Mitochondrial protein phosphorylation in yeast revisited. Mitochondrion 2021;57:148-162. [PMID: 33412333 DOI: 10.1016/j.mito.2020.12.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 12/23/2020] [Accepted: 12/30/2020] [Indexed: 12/16/2022]
7
Discordant evolution of mitochondrial and nuclear yeast genomes at population level. BMC Biol 2020;18:49. [PMID: 32393264 PMCID: PMC7216626 DOI: 10.1186/s12915-020-00786-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 04/22/2020] [Indexed: 12/31/2022]  Open
8
Xiao S, Nguyen DT, Wu B, Hao W. Genetic Drift and Indel Mutation in the Evolution of Yeast Mitochondrial Genome Size. Genome Biol Evol 2018;9:3088-3099. [PMID: 29126284 PMCID: PMC5714193 DOI: 10.1093/gbe/evx232] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2017] [Indexed: 12/27/2022]  Open
9
Lee HY, Chao JC, Cheng KY, Leu JY. Misfolding-prone proteins are reversibly sequestered to an Hsp42-associated granule upon chronological aging. J Cell Sci 2018;131:jcs.220202. [PMID: 30054385 DOI: 10.1242/jcs.220202] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 07/20/2018] [Indexed: 12/19/2022]  Open
10
Cheng J, Guo X, Cai P, Cheng X, Piškur J, Ma Y, Jiang H, Gu Z. Parallel Evolution of Chromatin Structure Underlying Metabolic Adaptation. Mol Biol Evol 2018;34:2870-2878. [PMID: 28961859 DOI: 10.1093/molbev/msx220] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
11
Mobile Introns Shape the Genetic Diversity of Their Host Genes. Genetics 2017;205:1641-1648. [PMID: 28193728 PMCID: PMC5378118 DOI: 10.1534/genetics.116.199059] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 02/07/2017] [Indexed: 12/23/2022]  Open
12
Kuang MC, Hutchins PD, Russell JD, Coon JJ, Hittinger CT. Ongoing resolution of duplicate gene functions shapes the diversification of a metabolic network. eLife 2016;5:e19027. [PMID: 27690225 PMCID: PMC5089864 DOI: 10.7554/elife.19027] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 09/28/2016] [Indexed: 12/23/2022]  Open
13
Sillo F, Garbelotto M, Friedman M, Gonthier P. Comparative Genomics of Sibling Fungal Pathogenic Taxa Identifies Adaptive Evolution without Divergence in Pathogenicity Genes or Genomic Structure. Genome Biol Evol 2015;7:3190-206. [PMID: 26527650 PMCID: PMC4700942 DOI: 10.1093/gbe/evv209] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2015] [Indexed: 12/27/2022]  Open
14
Wolters JF, Chiu K, Fiumera HL. Population structure of mitochondrial genomes in Saccharomyces cerevisiae. BMC Genomics 2015;16:451. [PMID: 26062918 PMCID: PMC4464245 DOI: 10.1186/s12864-015-1664-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 05/29/2015] [Indexed: 12/13/2022]  Open
15
Wu B, Buljic A, Hao W. Extensive Horizontal Transfer and Homologous Recombination Generate Highly Chimeric Mitochondrial Genomes in Yeast. Mol Biol Evol 2015;32:2559-70. [PMID: 26018571 DOI: 10.1093/molbev/msv127] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]  Open
16
Lin Z, Wang TY, Tsai BS, Wu FT, Yu FJ, Tseng YJ, Sung HM, Li WH. Identifying cis-regulatory changes involved in the evolution of aerobic fermentation in yeasts. Genome Biol Evol 2013;5:1065-78. [PMID: 23650209 PMCID: PMC3698916 DOI: 10.1093/gbe/evt067] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
17
Hagman A, Säll T, Compagno C, Piskur J. Yeast "make-accumulate-consume" life strategy evolved as a multi-step process that predates the whole genome duplication. PLoS One 2013;8:e68734. [PMID: 23869229 PMCID: PMC3711898 DOI: 10.1371/journal.pone.0068734] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2013] [Accepted: 06/03/2013] [Indexed: 11/19/2022]  Open
18
Thompson DA, Roy S, Chan M, Styczynsky MP, Pfiffner J, French C, Socha A, Thielke A, Napolitano S, Muller P, Kellis M, Konieczka JH, Wapinski I, Regev A. Evolutionary principles of modular gene regulation in yeasts. eLife 2013;2:e00603. [PMID: 23795289 PMCID: PMC3687341 DOI: 10.7554/elife.00603] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Accepted: 05/02/2013] [Indexed: 12/20/2022]  Open
19
Mitochondrial genome evolution in a single protoploid yeast species. G3-GENES GENOMES GENETICS 2012;2:1103-11. [PMID: 22973548 PMCID: PMC3429925 DOI: 10.1534/g3.112.003152] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 07/09/2012] [Indexed: 12/26/2022]
20
Parallel evolution of the make-accumulate-consume strategy in Saccharomyces and Dekkera yeasts. Nat Commun 2011;2:302. [PMID: 21556056 PMCID: PMC3112538 DOI: 10.1038/ncomms1305] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Accepted: 04/08/2011] [Indexed: 11/24/2022]  Open
21
Botzman M, Margalit H. Variation in global codon usage bias among prokaryotic organisms is associated with their lifestyles. Genome Biol 2011;12:R109. [PMID: 22032172 PMCID: PMC3333779 DOI: 10.1186/gb-2011-12-10-r109] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Revised: 06/16/2011] [Accepted: 10/27/2011] [Indexed: 11/29/2022]  Open
22
Determinants of translation efficiency and accuracy. Mol Syst Biol 2011;7:481. [PMID: 21487400 PMCID: PMC3101949 DOI: 10.1038/msb.2011.14] [Citation(s) in RCA: 345] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Accepted: 02/15/2011] [Indexed: 12/17/2022]  Open
23
Barth D, Berendonk TU. The mitochondrial genome sequence of the ciliate Paramecium caudatum reveals a shift in nucleotide composition and codon usage within the genus Paramecium. BMC Genomics 2011;12:272. [PMID: 21627782 PMCID: PMC3118789 DOI: 10.1186/1471-2164-12-272] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 05/31/2011] [Indexed: 11/10/2022]  Open
24
Lipinski KA, Puchta O, Surendranath V, Kudla M, Golik P. Revisiting the yeast PPR proteins--application of an Iterative Hidden Markov Model algorithm reveals new members of the rapidly evolving family. Mol Biol Evol 2011;28:2935-48. [PMID: 21546354 DOI: 10.1093/molbev/msr120] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]  Open
25
Rozpędowska E, Galafassi S, Johansson L, Hagman A, Piškur J, Compagno C. Candida albicans--a pre-whole genome duplication yeast--is predominantly aerobic and a poor ethanol producer. FEMS Yeast Res 2011;11:285-91. [PMID: 21205163 DOI: 10.1111/j.1567-1364.2010.00715.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]  Open
26
Solieri L. Mitochondrial inheritance in budding yeasts: towards an integrated understanding. Trends Microbiol 2010;18:521-30. [PMID: 20832322 DOI: 10.1016/j.tim.2010.08.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Revised: 07/23/2010] [Accepted: 08/04/2010] [Indexed: 01/08/2023]
27
Lin Z, Li WH. Expansion of hexose transporter genes was associated with the evolution of aerobic fermentation in yeasts. Mol Biol Evol 2010;28:131-42. [PMID: 20660490 DOI: 10.1093/molbev/msq184] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]  Open
28
Jiang H, Guan W, Gu Z. Tinkering evolution of post-transcriptional RNA regulons: puf3p in fungi as an example. PLoS Genet 2010;6:e1001030. [PMID: 20661438 PMCID: PMC2908677 DOI: 10.1371/journal.pgen.1001030] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Accepted: 06/16/2010] [Indexed: 11/19/2022]  Open
29
Chou JY, Leu JY. Speciation through cytonuclear incompatibility: Insights from yeast and implications for higher eukaryotes. Bioessays 2010;32:401-11. [DOI: 10.1002/bies.200900162] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
30
Sun J, Jiang H, Flores R, Wen J. Gene duplication in the genome of parasitic Giardia lamblia. BMC Evol Biol 2010;10:49. [PMID: 20163721 PMCID: PMC2829556 DOI: 10.1186/1471-2148-10-49] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2009] [Accepted: 02/17/2010] [Indexed: 11/23/2022]  Open
31
Presgraves DC. The molecular evolutionary basis of species formation. Nat Rev Genet 2010;11:175-80. [DOI: 10.1038/nrg2718] [Citation(s) in RCA: 407] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
32
John Wiley & Sons, Ltd.. Current awareness on yeast. Yeast 2009. [DOI: 10.1002/yea.1618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]  Open
33
Traba J, Satrústegui J, del Arco A. Transport of adenine nucleotides in the mitochondria of Saccharomyces cerevisiae: interactions between the ADP/ATP carriers and the ATP-Mg/Pi carrier. Mitochondrion 2009;9:79-85. [PMID: 19460304 DOI: 10.1016/j.mito.2009.01.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2008] [Revised: 10/09/2008] [Accepted: 01/05/2009] [Indexed: 01/09/2023]
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