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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
..., with a mean identity of 93.6% (Fig. 2E).Fossil-calibrated and -scale divergence time reveals a late Cretaceous origin and Paleogene radiation of TuberaceaeTo provide a robust timeline for Tuberaceae emergence and diversification as well as a backbone for all comparative genomic analyses, we first produced...
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Resource: The genome of the colonial hydroid Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals
- Christine E. Schnitzler,
- E. Sally Chang,
- Justin Waletich,
- Gonzalo Quiroga-Artigas,
- Wai Yee Wong,
- Anh-Dao Nguyen,
- Sofia N. Barreira,
- Liam B. Doonan,
- Paul Gonzalez,
- Sergey Koren,
- James M. Gahan,
- Steven M. Sanders,
- Brian Bradshaw,
- Timothy Q. DuBuc,
- Febrimarsa,
- Danielle de Jong,
- Eric P. Nawrocki,
- Alexandra Larson,
- Samantha Klasfeld,
- Sebastian G. Gornik,
- R. Travis Moreland,
- Tyra G. Wolfsberg,
- Adam M. Phillippy,
- James C. Mullikin,
- Oleg Simakov,
- Paulyn Cartwright,
- Matthew Nicotra,
- Uri Frank,
- and Andreas D. Baxevanis
Genome Res. March 2024 34: 498-513; Published in Advance March 20, 2024, doi:10.1101/gr.278382.123
...: a DIAMOND hit to NCBI nr, a PANNZER2 hit, or both (Supplemental Table S9).Mitochondrial Cnidarians are characterized by mitochondrial genomic diversity, varying in overall mtDNA conformation (circular or linear), gene content, gene organization, and the number of mitochondrial chromosomes within each...
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Resource: The western redcedar genome reveals low genetic diversity in a self-compatible conifer
- Tal J. Shalev,
- Omnia Gamal El-Dien,
- Macaire M.S. Yuen,
- Shu Shengqiang,
- Shaun D. Jackman,
- René L. Warren,
- Lauren Coombe,
- Lise van der Merwe,
- Ada Stewart,
- Lori B. Boston,
- Christopher Plott,
- Jerry Jenkins,
- Guifen He,
- Juying Yan,
- Mi Yan,
- Jie Guo,
- Jesse W. Breinholt,
- Leandro G. Neves,
- Jane Grimwood,
- Loren H. Rieseberg,
- Jeremy Schmutz,
- Inanc Birol,
- Matias Kirst,
- Alvin D. Yanchuk,
- Carol Ritland,
- John H. Russell,
- and Joerg Bohlmann
Genome Res. October 2022 32: 1952-1964; Published in Advance September 15, 2022, doi:10.1101/gr.276358.121
...duplications, pseudogenes, and gene fragments.However, little genomic research has been completed on conifers of other families. In particular, the Cupressaceae, such as cypresses, junipers, and redwoods, are thought to have undergone a whole- duplication unique from the Pinaceae (Li et al. 2015...
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LETTER: A Genome-Wide Survey of Human Pseudogenes
- David Torrents,
- Mikita Suyama,
- Evgeny Zdobnov,
- and Peer Bork
Genome Res. December 2003 13: 2559-2567; doi:10.1101/gr.1455503
....M., Bertone, P., Echols, N., Johnson, T., and Gerstein, M. 2002 . Molecular fossils in the human : Identification and analysis of the pseudogenes in chromosomes 21 and 22. Genome Res. 12 : 272 -280. ↵ Hattori, M., Fujiyama, A., Taylor, T.D., Watanabe, H., Yada, T., Park, H.S., Toyoda, A., Ishii, K., Totoki, Y...
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ARTICLE: Identification and Analysis of Over 2000 Ribosomal Protein Pseudogenes in the Human Genome
- Zhaolei Zhang,
- Paul Harrison,
- and Mark Gerstein
Genome Res. October 1, 2002 12: 1466-1482; doi:10.1101/gr.331902
...Identification and Analysis of Over 2000 Ribosomal Protein Pseudogenes in the Human Genome Zhaolei Zhang , Paul Harrison , and Mark Gerstein 1 Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA...
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LETTER: Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription, and evolution
- Deyou Zheng,
- Adam Frankish,
- Robert Baertsch,
- Philipp Kapranov,
- Alexandre Reymond,
- Siew Woh Choo,
- Yontao Lu,
- France Denoeud,
- Stylianos E. Antonarakis,
- Michael Snyder,
- Yijun Ruan,
- Chia-Lin Wei,
- Thomas R. Gingeras,
- Roderic Guigó,
- Jennifer Harrow,
- and Mark B. Gerstein
Genome Res. June 2007 17: 839-851; doi:10.1101/gr.5586307
..., pseudogenes are “genomic fossils” valuable for exploring the dynamics and evolution of genes and genomes. Pseudogene identification is an important problem in computational genomics, and is also critical for obtaining an accurate picture of a genome’s structure and function. However, no consensus...
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Research: Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes
- David Thybert,
- Maša Roller,
- Fábio C.P. Navarro,
- Ian Fiddes,
- Ian Streeter,
- Christine Feig,
- David Martin-Galvez,
- Mikhail Kolmogorov,
- Václav Janoušek,
- Wasiu Akanni,
- Bronwen Aken,
- Sarah Aldridge,
- Varshith Chakrapani,
- William Chow,
- Laura Clarke,
- Carla Cummins,
- Anthony Doran,
- Matthew Dunn,
- Leo Goodstadt,
- Kerstin Howe,
- Matthew Howell,
- Ambre-Aurore Josselin,
- Robert C. Karn,
- Christina M. Laukaitis,
- Lilue Jingtao,
- Fergal Martin,
- Matthieu Muffato,
- Stefanie Nachtweide,
- Michael A. Quail,
- Cristina Sisu,
- Mario Stanke,
- Klara Stefflova,
- Cock Van Oosterhout,
- Frederic Veyrunes,
- Ben Ward,
- Fengtang Yang,
- Golbahar Yazdanifar,
- Amonida Zadissa,
- David J. Adams,
- Alvis Brazma,
- Mark Gerstein,
- Benedict Paten,
- Son Pham,
- Thomas M. Keane,
- Duncan T. Odom,
- and Paul Flicek
Genome Res. April 2018 28: 448-459; Published in Advance March 21, 2018, doi:10.1101/gr.234096.117
...lineage-specific characteristics (Kim et al. 2011; Wu et al. 2014; Foote et al. 2015). Indeed, evolutionary comparisons have even enabled the identification of genomic variation, such as repeat expansions, which can explain aspects of and karyotype evolution (Carbone et al. 2014).Even closely related...
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LETTER: Millions of Years of Evolution Preserved: A Comprehensive Catalog of the Processed Pseudogenes in the Human Genome
- Zhaolei Zhang,
- Paul M. Harrison,
- Yin Liu,
- and Mark Gerstein
Genome Res. December 2003 13: 2541-2558; doi:10.1101/gr.1429003
...genes, which are most densely populated in the GC-rich regions ( Mouchiroud et al. 1991 ; International Human Genome Sequencing Consortium 2001 ; Venter et al. 2001 ). We also checked to see whether, in conjunction with the local GC content, there are any pseudogenic “hot spots” on the chromosomes where...
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Research: Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies
- PingHsun Hsieh,
- August E. Woerner,
- Jeffrey D. Wall,
- Joseph Lachance,
- Sarah A. Tishkoff,
- Ryan N. Gutenkunst,
- and Michael F. Hammer
Genome Res. March 2016 26: 291-300; Published in Advance February 17, 2016, doi:10.1101/gr.196634.115
...Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies PingHsun Hsieh 1 , August E. Woerner 2 , 3 , Jeffrey D. Wall 4 , Joseph Lachance 5 , 6 , Sarah A...
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Research: Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary
- Kevin Vanneste,
- Guy Baele,
- Steven Maere,
- and Yves Van de Peer
Genome Res. August 2014 24: 1334-1347; Published in Advance May 16, 2014, doi:10.1101/gr.168997.113
...had a higher chance of establishment in the short term.Most explanations for the success of recently formed polyploids focus on their unstable genomic background which, despite most often leading to negative phenotypic effects through chromosomal abnormalities, also can infer the necessary plasticity...
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