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  1. Letter: Comparative genomics of the fungal pathogens Candida dubliniensis and Candida albicans
    • Andrew P. Jackson,
    • John A. Gamble,
    • Tim Yeomans,
    • Gary P. Moran,
    • David Saunders,
    • David Harris,
    • Martin Aslett,
    • Jamie F. Barrell,
    • Geraldine Butler,
    • Francesco Citiulo,
    • David C. Coleman,
    • Piet W.J. de Groot,
    • Tim J. Goodwin,
    • Michael A. Quail,
    • Jacqueline McQuillan,
    • Carol A. Munro,
    • Arnab Pain,
    • Russell T. Poulter,
    • Marie-Adèle Rajandream,
    • Hubert Renauld,
    • Martin J. Spiering,
    • Adrian Tivey,
    • Neil A.R. Gow,
    • Barclay Barrell,
    • Derek J. Sullivan,
    • and Matthew Berriman
    Genome Res. December 2009 19: 2231-2244; Published in Advance September 10, 2009, doi:10.1101/gr.097501.109
    ...) and a subclass of RecQ-like helicase pseudogenes, which are most similar to the Saccharomyces cerevisiae Y9 helicase (as well as homologous subtelomeric RecQ helicases in C. albicans), rather than to internally located helicases. However, all but one RecQhelicase inC. dubliniensiswere gene relics; the intact...
  2. LETTER: Correlations Between Gene Expression and Gene Conservation in Fission Yeast
    • Juan Mata and
    • Jürg Bähler
    Genome Res. December 2003 13: 2686-2690; Published in Advance January 1, 2003, doi:10.1101/gr.1420903
    ...: 241 -256. ↵ Braun, E.L., Halpern, A.L., Nelson, M.A., and Natvig, D.O. 2000 . Large-scale comparison of fungal sequence information: Mechanisms of innovation in Neurospora crassa and gene loss in Saccharomyces cerevisiae. Genome Res. 10 : 416 -430. ↵ The C. elegans Sequencing Consortium. 1998 . Genome...
  3. Resource: High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae
    • Jacopo Martelossi,
    • Jacopo Vujovic,
    • Yue Huang,
    • Alessia Tatti,
    • Kaiwei Xu,
    • Federico Puliga,
    • Yuanxue Chen,
    • Omar Rota Stabelli,
    • Fabrizio Ghiselli,
    • Xiaoping Zhang,
    • and Alessandra Zambonelli
    Genome Res. November 2025 35: 2601-2616; Published in Advance August 21, 2025, doi:10.1101/gr.280368.124
    .... panzhihuanense and other true truffles will be necessary to confirm our findings and assess the impact of large-scale genomic rearrangements on Tuberaceae evolution.The preferential localization of multicopy gene families within TE-rich genomic regions supports the idea that these regions act as hotspots...
  4. LETTER: The Role of Lineage-Specific Gene Family Expansion in the Evolution of Eukaryotes
    • Olivier Lespinet,
    • Yuri I. Wolf,
    • Eugene V. Koonin,
    • and L. Aravind
    Genome Res. July 1, 2002 12: 1048-1059; doi:10.1101/gr.174302
    ...– 269 . ↵ Braun E.L. , Halpern A.L. , Nelson M.A. , Natvig D.O. ( 2000 ) Large-scale comparison of fungal sequence information: Mechanisms of innovation in Neurospora crassa and gene loss in Saccharomyces cerevisiae. Genome Res. 10 : 416 – 430 . ↵ Chervitz S.A. , Aravind L. , Sherlock G. , Ball C...
  5. RESOURCE: Comparative genome analysis across a kingdom of eukaryotic organisms: Specialization and diversification in the Fungi
    • Michael J. Cornell,
    • Intikhab Alam,
    • Darren M. Soanes,
    • Han Min Wong,
    • Cornelia Hedeler,
    • Norman W. Paton,
    • Magnus Rattray,
    • Simon J. Hubbard,
    • Nicholas J. Talbot,
    • and Stephen G. Oliver
    Genome Res. December 2007 17: 1809-1822; Published in Advance November 5, 2007, doi:10.1101/gr.6531807
    ...removal of duplicated sequences) has been identified. The sequencing of the Neurospora crassa has shown that RIP activity has resulted in the presence of very few duplicated genes ( Galagan and Selker 2004 ). A previous study ( Dujon et al. 2004 ) analyzed redundancy in five Saccharomycotina yeast s ( S...
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