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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
.... Despite the absence of chromosome-scale assemblies to dissect intra- and inter-chromosomal genomic rearrangements, our results recapitulate the mesosynteny pattern formally described in filamentous fungi (Hane et al. 2011) and observed between T. melanosporum and the Eurotiomycete Coccidioides immitis...
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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
...). There is also evidence for substantial rearrangements of orthologous linkage groups (LGs) during the evolutionary history of the two families, which resulted in differences in karyotype (n = 11 in Cupressaceae; n = 12 in Pinaceae) (De Miguel et al. 2015), size (9–20 Gbp in Cupressaceae; 18–31 Gbp in Pinaceae...
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LETTER: Many or most genes in Arabidopsis transposed after the origin of the order Brassicales
- Michael Freeling,
- Eric Lyons,
- Brent Pedersen,
- Maqsudul Alam,
- Ray Ming,
- and Damon Lisch
Genome Res. December 2008 18: 1924-1937; Published in Advance October 3, 2008, doi:10.1101/gr.081026.108
...an analysis of the evolution of gene chromosomal position. The most recent analyses of intragenomic collinearity within At inferred two sequential tetraploidies (designated α and β), although the timing and exact gene contents of these two events differed markedly when estimated by two independent research...
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ARTICLE: Comparative genomics of Gossypium and Arabidopsis: Unraveling the consequences of both ancient and recent polyploidy
- Junkang Rong,
- John E. Bowers,
- Stefan R. Schulze,
- Vijay N. Waghmare,
- Carl J. Rogers,
- Gary J. Pierce,
- Hua Zhang,
- James C. Estill,
- and Andrew H. Paterson
Genome Res. September 2005 15: 1198-1210; Published in Advance August 18, 2005, doi:10.1101/gr.3907305
...genomics. To explore an approach by which these challenges might be mitigated, genetic maps of extant diploid and tetraploid cottons ( Gossypium spp.) were used to infer the approximate order of 3016 loci along the chromosomes of their hypothetical common ancestor. The inferred Gossypium gene order...
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Resource: The fine-scale recombination rate variation and associations with genomic features in a butterfly
- Aleix Palahí i Torres,
- Lars Höök,
- Karin Näsvall,
- Daria Shipilina,
- Christer Wiklund,
- Roger Vila,
- Peter Pruisscher,
- and Niclas Backström
Genome Res. May 2023 33: 810-823; Published in Advance June 12, 2023, doi:10.1101/gr.277414.122
...and evolutionary forces affecting evolution and divergence in holocentric organisms.Results84 Leptidea sinapis males were sampled across Sweden and used for paired-end Illumina sequencing. Chromosome-specific demographic histories were inferred with SMC++ (Terhorst et al. 2017) using six “distinguished...
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LETTER: Dynamic evolution at pericentromeres
- Anne E. Hall,
- Gregory C. Kettler,
- and Daphne Preuss
Genome Res. March 2006 16: 355-364; Published in Advance February 6, 2006, doi:10.1101/gr.4399206
...and pericentromere evolution—its members have undergone recent polyploidization and hybridization, with close relatives changing in genome size and chromosome number. Through sequence and hybridization analyses, we examined regions from Arabidopsis arenosa, Capsella rubella , and Olimarabidopsis pumila...
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Research: Limited allele-specific gene expression in highly polyploid sugarcane
- Gabriel Rodrigues Alves Margarido,
- Fernando Henrique Correr,
- Agnelo Furtado,
- Frederik C. Botha,
- and Robert James Henry
Genome Res. February 2022 32: 297-308; Published in Advance December 23, 2021, doi:10.1101/gr.275904.121
...guide molecular breeding of this crop (Wang et al. 2013).Genomic analyses in sugarcane (Saccharum spp.) are limited by the unique combination of several layers of genomic complexity. All known Saccharum accessions are highly polyploid (D'Hont et al. 1998), with evidence of both allo- and autopolyploidy...
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ARTICLE: The Bacterial Replicative Helicase DnaB Evolved from a RecA Duplication
- Detlef D. Leipe,
- L. Aravind,
- Nick V. Grishin,
- and Eugene V. Koonin
Genome Res. January 1, 2000 10: 5-16; doi:10.1101/gr.10.1.5
..., previously undetected eukaryotic homologs of DnaB from C. elegans , Arabidopsis thaliana , and Plasmodium chabaudi were retrieved with E values between 10−7 and 10−5; a human homolog of these proteins was detected among EST products by searching the database of expressed sequence tags (dbEST) database (see...
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Research: Causes and consequences of a complex recombinational landscape in the ant Cardiocondyla obscurior
- Mohammed Errbii,
- Jürgen Gadau,
- Kerstin Becker,
- Lukas Schrader,
- and Jan Oettler
Genome Res. June 2024 34: 863-876; Published in Advance June 5, 2024, doi:10.1101/gr.278392.123
..., these studies did not explore the genomic features associated with the -wide variation in recombination rates.Here, we use genetic linkage mapping, a chromosome-level assembly, and extensive population-genomic data of the model species Cardiocondyla obscurior (Oettler 2021) for first analyses of the causes...

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