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Method: Probing the eukaryotic microbes of ruminants with a deep-learning classifier and comprehensive protein databases
- Ming Yan,
- Thea O. Andersen,
- Phillip B. Pope,
- and Zhongtang Yu
Genome Res. February 2025 35: 368-378; Published in Advance December 27, 2024, doi:10.1101/gr.279825.124
...protozoan proteins relative to those of fungal and hindgut eukaryotes highlights the need for further genomic investigations into rumen protozoa. This need is also underscored by their complex functions and implications, such as predation on other rumen microbes, enzymatic breakdown of plant material...
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Research: Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus
- Rita Tam,
- Mareike Möller,
- Runpeng Luo,
- Zhenyan Luo,
- Ashley Jones,
- Sambasivam Periyannan,
- John P. Rathjen,
- and Benjamin Schwessinger
Genome Res. June 2025 35: 1364-1376; Published in Advance April 11, 2025, doi:10.1101/gr.280359.124
...-resolved assemblies have become the norm in eukaryotic genomics with advances in long-read sequencing technologies. Complete assemblies are fundamental for addressing key questions in biology that were previously hidden in the “dark matter” of s. Key breakthroughs have revolved around centromeres and the embedded...
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Method: Transcriptome reconstruction and functional analysis of eukaryotic marine plankton communities via high-throughput metagenomics and metatranscriptomics
- Alexey Vorobev,
- Marion Dupouy,
- Quentin Carradec,
- Tom O. Delmont,
- Anita Annamalé,
- Patrick Wincker,
- and Eric Pelletier
Genome Res. April 2020 30: 647-659; Published in Advance March 23, 2020, doi:10.1101/gr.253070.119
...and catabolism in different oceanic provinces, thus demonstrating the potential of the MGT collection to provide functional insights on eukaryotic plankton. We established the ability of the MGT approach to capture interspecies associations through the analysis of a nitrogen-fixing haptophyte...
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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
...Comparative genomics of the fungal pathogens Candida dubliniensis and Candida albicans Andrew P. Jackson 1 , 8 , John A. Gamble 1 , Tim Yeomans 2 , Gary P. Moran 2 , David Saunders 1 , David Harris 1 , Martin Aslett 1...
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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
...proliferation of genome sequencing in diverse fungal species has provided the first opportunity for comparative genome analysis across a eukaryotic kingdom. Here, we report a comparative study of 34 complete fungal genome sequences, representing a broad diversity of Ascomycete, Basidiomycete, and Zygomycete...
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LETTER: Evolution of Eukaryotic Transcription: Insights From the Genome of Giardia lamblia
- Aaron A. Best,
- Hilary G. Morrison,
- Andrew G. McArthur,
- Mitchell L. Sogin,
- and Gary J. Olsen
Genome Res. August 2004 14: 1537-1547; doi:10.1101/gr.2256604
...Evolution of Eukaryotic Transcription: Insights From the Genome of Giardia lamblia Aaron A. Best 1 , Hilary G. Morrison 2 , Andrew G. McArthur 2 , Mitchell L. Sogin 2 , and Gary J. Olsen 1 , 3 1 Department of Microbiology...
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Research: Evolutionary dynamics of polyadenylation signals and their recognition strategies in protists
- Marcin P. Sajek,
- Danielle Y. Bilodeau,
- Michael A. Beer,
- Emma Horton,
- Yukiko Miyamoto,
- Katrina B. Velle,
- Lars Eckmann,
- Lillian Fritz-Laylin,
- Olivia S. Rissland,
- and Neelanjan Mukherjee
Genome Res. October 2024 34: 1570-1581; Published in Advance September 26, 2024, doi:10.1101/gr.279526.124
...in the eukaryotic kingdom. We use direct RNA sequencing to determine poly(A) signals for four protists within the Metamonada clade (which also contains G. lamblia) and two outgroup protists. These experiments reveal that the AAUAAA hexamer serves as the poly(A) signal in at least four different eukaryotic clades...
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PERSPECTIVE: Insights on biology and evolution from microbial genome sequencing
- Claire M. Fraser-Liggett
Genome Res. December 2005 15: 1603-1610; doi:10.1101/gr.3724205
...design and adaptive evolution of Escherichia coli for production of lactic acid. Biotechnol. Bioeng. 91 : 643 -648. ↵ Galagan, J.E., Henn, M.R., Ma, L.-J., Cuomo, C.A., and Birren, B. 2005 . Genomics of the fungal kingdom: Insights into Eukaryotic biology. Genome Res. (this issue). ↵ Gardner, M...
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LETTER: The Basic Helix-Loop-Helix Protein Family: Comparative Genomics and Phylogenetic Analysis
- Valérie Ledent and
- Michel Vervoort
Genome Res. May 1, 2001 11: 754-770; doi:10.1101/gr.177001
...The Basic Helix-Loop-Helix Protein Family: Comparative Genomics and Phylogenetic Analysis Valérie Ledent 1 and Michel Vervoort 2 , 3 1Belgian EMBnet Node, Bioinformatics Laboratory, Université Libre de Bruxelles, Department of Molecular Biology, B-6041...
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Review: The structure, function, and evolution of plant centromeres
- Matthew Naish and
- Ian R. Henderson
Genome Res. February 2024 34: 161-178; Published in Advance March 14, 2024, doi:10.1101/gr.278409.123
...Matthew Naish and Ian R. Henderson Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom Corresponding author: irh25@cam.ac.ukAbstractCentromeres are essential regions of eukaryotic chromosomes responsible for the formation of kinetochore complexes, which connect...
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