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Research: Candida albicans isolates contain frequent heterozygous structural variants and transposable elements within genes and centromeres
- Ursula Oggenfuss,
- Robert T. Todd,
- Natthapon Soisangwan,
- Bailey Kemp,
- Alison Guyer,
- Annette Beach,
- and Anna Selmecki
Genome Res. April 2025 35: 824-838; Published in Advance October 22, 2024, doi:10.1101/gr.279301.124
...12504, USA Corresponding author: selmecki@umn.eduAbstractThe human fungal pathogen Candida albicans poses a significant burden on global health, causing high rates of mortality and antifungal drug resistance. C. albicans is a heterozygous diploid organism that reproduces asexually. Structural variants...
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Research: Confounding factors in assessing the enriched expression of somatic mutant alleles in bulk tumor samples
- Kohei Hagiwara,
- Andrew Thrasher,
- Nadezhda V. Terekhanova,
- and Jinghui Zhang
Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.281003.125
...on oncogenes as in-frame indels accounted for a much higher proportion of somatic indels than in TSGs (41.51% [247/595] vs. 7.86% [403/ 5127], Fisher’s exact P<2.2×10−16), and included them for analysis if the locus was covered with one ormore RNA-seq reads (238 in oncogenes and 5673 in nondrivers...
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Research: Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster
- Anna Grandchamp,
- Lucas Kühl,
- Marie Lebherz,
- Kathrin Brüggemann,
- John Parsch,
- and Erich Bornberg-Bauer
Genome Res. June 2023 33: 872-890; Published in Advance July 13, 2023, doi:10.1101/gr.277482.122
...sister s. So far, most studies do not detect noncoding homologs of de novo genes because of incomplete assemblies and annotations, and long evolutionary distances separating s. Here, we overcome these issues by searching for de novo expressed open reading frames (neORFs), the not-yet fixed precursors...
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Method: Ultra-long sequencing for contiguous haplotype resolution of the human immunoglobulin heavy-chain locus
- Mari B. Gornitzka,
- Egil Røsjø,
- Uddalok Jana,
- Easton E. Ford,
- Alan Tourancheau,
- William D. Lees,
- Zachary Vanwinkle,
- Melissa L. Smith,
- Corey T. Watson,
- and Andreas Lossius
Genome Res. October 2025 35: 2240-2251; Published in Advance August 21, 2025, doi:10.1101/gr.280400.125
...responsible for antigen binding. The IGH locus exhibits high levels of structural variation (SV) and allelic diversity, contributing to significant variability in the germline repertoire within a population and between the haplotypes in the same individual (Rodriguez et al. 2023). During B cell development...
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Research: Polymorphic centromere locations in the pathogenic yeast Candida parapsilosis
- Mihaela Ola,
- Caoimhe E. O'Brien,
- Aisling Y. Coughlan,
- Qinxi Ma,
- Paul D. Donovan,
- Kenneth H. Wolfe,
- and Geraldine Butler
Genome Res. May 2020 30: 684-696; Published in Advance May 18, 2020, doi:10.1101/gr.257816.119
...following damage is particularly well studied in the yeast Candida albicans (Burrack and Berman 2012). Koren et al. (2010) suggested that, in this species, centromeres are associated with the presence of early origins of replication and that the formation of neocentromeres changes the activity of nearby...
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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
...-associated factors. This picture of the relative complement of specific gene families was produced Table 4. Comparative genomics of IFA gene family loci in Candida spp. Locus Alias Chromosome Species identifier C. albicans C. dubliniensis C. tropicalis 1 IFA10 1 orf19.4549 Cd36_01600a x 1 orf19.2430 Cd36_05810 x IFA...
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Research: Genetic and phenotypic intra-species variation in Candida albicans
- Matthew P. Hirakawa,
- Diego A. Martinez,
- Sharadha Sakthikumar,
- Matthew Z. Anderson,
- Aaron Berlin,
- Sharvari Gujja,
- Qiandong Zeng,
- Ethan Zisson,
- Joshua M. Wang,
- Joshua M. Greenberg,
- Judith Berman,
- Richard J. Bennett,
- and Christina A. Cuomo
Genome Res. March 2015 25: 413-425; Published in Advance December 11, 2014, doi:10.1101/gr.174623.114
...Genetic and phenotypic intra-species variation in Candida albicans Matthew P. Hirakawa 1 , Diego A. Martinez 2 , 5 , Sharadha Sakthikumar 2 , 5 , Matthew Z. Anderson 1 , 3 , Aaron Berlin 2 , Sharvari Gujja 2...
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Research: A novel quantitative trait locus implicates Msh3 in the propensity for genome-wide short tandem repeat expansions in mice
- Mikhail O. Maksimov,
- Cynthia Wu,
- David G. Ashbrook,
- Flavia Villani,
- Vincenza Colonna,
- Nima Mousavi,
- Nichole Ma,
- Lu Lu,
- Jonathan K. Pritchard,
- Alon Goren,
- Robert W. Williams,
- Abraham A. Palmer,
- and Melissa Gymrek
Genome Res. May 2023 33: 689-702; Published in Advance May 1, 2023, doi:10.1101/gr.277576.122
...by SIFT (Sim et al. 2012), one low impact synonymous variant, and a multiallelic coding sequence insertion (Supplemental Table S2), with a common allele resulting in an in-frame insertion (rs230013535) and a rarer allele causing a frameshift. Closer inspection of the frameshift allele revealed that all...
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Research: Locus-resolution analysis of L1 regulation and retrotransposition potential in mouse embryonic development
- Patricia Gerdes,
- Dorothy Chan,
- Mischa Lundberg,
- Francisco J. Sanchez-Luque,
- Gabriela O. Bodea,
- Adam D. Ewing,
- Geoffrey J. Faulkner,
- and Sandra R. Richardson
Genome Res. September 2023 33: 1465-1481; Published in Advance October 5, 2023, doi:10.1101/gr.278003.123
...the general shift to upstream TSSs during differentiation. We also examined 5′RACE reads uniquely mapping to a full-length L1 TF element with intact open reading frames (Chr 6: 22,125,162–22,131,805) situated in sense orientation within an intron of the gene Cped1 (Supplemental Fig. S11B). For this locus, we...
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Method: A HIT-trapping strategy for rapid generation of reversible and conditional alleles using a universal donor
- Hengxing Lu,
- Jun Liu,
- Tao Feng,
- Zihang Guo,
- Yunjun Yin,
- Fei Gao,
- Gengsheng Cao,
- Xuguang Du,
- and Sen Wu
Genome Res. May 2021 31: 900-909; Published in Advance April 1, 2021, doi:10.1101/gr.271312.120
.... A common gene knockout strategy is to introduce random indels into the exon of the gene of interest by CRISPR-Cas9-induced NHEJ repair, resulting in coding frameshifts and loss-of-function mutations. However, either the in-frame mutations caused by random indels or incomplete degradation...

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