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Research: Ancestral aneuploidy and stable chromosomal duplication resulting in differential genome structure and gene expression control in trypanosomatid parasites
- João L. Reis-Cunha,
- Samuel A. Pimenta-Carvalho,
- Laila V. Almeida,
- Anderson Coqueiro-dos-Santos,
- Catarina A. Marques,
- Jennifer A. Black,
- Jeziel Damasceno,
- Richard McCulloch,
- Daniella C. Bartholomeu,
- and Daniel C. Jeffares
Genome Res. March 2024 34: 441-453; Published in Advance April 11, 2024, doi:10.1101/gr.278550.123
...-celled parasites from the kinetoplastid order (phylum Euglenozoa), are an interesting group to study aneuploidies. Throughout their life cycles, they are exposed to several stressors, to which chromosome instability (CIN), having a persistent rate of chromosome duplication and loss that generates intra...
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Resource: Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveal expanded transporter repertoire and duplication of entire chromosome ends including subtelomeric regions
- Rodrigo P. Baptista,
- Yiran Li,
- Adam Sateriale,
- Mandy J. Sanders,
- Karen L. Brooks,
- Alan Tracey,
- Brendan R.E. Ansell,
- Aaron R. Jex,
- Garrett W. Cooper,
- Ethan D. Smith,
- Rui Xiao,
- Jennifer E. Dumaine,
- Peter Georgeson,
- Bernard J. Pope,
- Matthew Berriman,
- Boris Striepen,
- James A. Cotton,
- and Jessica C. Kissinger
Genome Res. January 2022 32: 203-213; Published in Advance November 11, 2021, doi:10.1101/gr.275325.121
..., (CpIRef), was assembled with a limited physical map (Abrahamsen et al. 2004) and a few hundred ESTs for training gene finders. Genomic, transcriptomic, and proteomic work has been lacking owing to the obligate quasi-intracellular nature of portions of the parasite's life cycle, the historical lack...
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Resource: CGC1, a new reference genome for Caenorhabditis elegans
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Dae-Eun Jeong,
- Chie Owa,
- Haruka Kobayashi,
- Yoshihiko Suzuki,
- Manami Kanamori,
- Yu Toyoshima,
- Yuichi Iino,
- Ann E. Rougvie,
- Lamia Wahba,
- Andrew Z. Fire,
- Erich M. Schwarz,
- and Shinichi Morishita
Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
...and a second subtelomeric repeat region, it was also possible (unlike in the earlier VC2010 assembly) to fully assemble telomeric repeats at both ends of all chromosomes of CGC1. To illustrate this, Supplemental Figure S14 displays dot plots between pairs of 10 kb genomic sequences taken from the left end...
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Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
- Kevin Moyung,
- Yulong Li,
- Heather K. MacAlpine,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
...length as a function of the location of the midpoint of each fragment and colored the points based on their local density. The result is a near-nucleotide-resolution -wide view of chromatin occupancy for each deletion strain (Fig. 1D–F).View larger version: In this window In a new window Figure 1. Genome...
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Research: Stable genome structures in living fossil fishes
- Cheng Wang,
- Chase D. Brownstein,
- Wenjun Chen,
- Zufa Ding,
- Dan Yu,
- Yu Deng,
- Chenguang Feng,
- Thomas J. Near,
- Shunping He,
- and Liandong Yang
Genome Res. February 2026 36: 318-329; Published in Advance January 13, 2026, doi:10.1101/gr.280800.125
...of genomic structural stability and sequence conservation than other vertebrates.Abundance and activity of transposable elements in gar sTransposable elements (TEs) are DNA sequences in the that can replicate themselves or move between chromosomes. TE activity can lead to genomic instability (Bourque et al...
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Mini-Review: The paradox of R-loops: guardians of the genome or drivers of disease?
- Shachinthaka D. Dissanayaka Mudiyanselage,
- Phillip Wulfridge,
- and Kavitha Sarma
Genome Res. September 2025 35: 1919-1928; Published in Advance August 6, 2025, doi:10.1101/gr.278992.124
...is unclear.When not properly regulated, R-loops can become a significant source of genomic instability and can activate inflammatory immune responses (Brickner et al. 2022). However, R-loops also play roles in cellular processes, including transcription, DNA replication, DNA repair, and chromosome...
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Method: Capturing in vivo RNA transcriptional dynamics from the malaria parasite Plasmodium falciparum
- Heather J. Painter,
- Manuela Carrasquilla,
- and Manuel Llinás
Genome Res. June 2017 27: 1074-1086; Published in Advance April 17, 2017, doi:10.1101/gr.217356.116
..., the human malaria parasite, Plasmodium falciparum, is incapable of pyrimidine salvage for mRNA biogenesis. To capture cellular mRNA dynamics during Plasmodium development, we engineered parasites that can salvage pyrimidines through the expression of a single bifunctional yeast fusion gene, cytosine...
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Research: Transcriptional variation in the malaria parasite Plasmodium falciparum
- Núria Rovira-Graells,
- Archna P. Gupta,
- Evarist Planet,
- Valerie M. Crowley,
- Sachel Mok,
- Lluís Ribas de Pouplana,
- Peter R. Preiser,
- Zbynek Bozdech,
- and Alfred Cortés
Genome Res. May 2012 22: 925-938; Published in Advance March 13, 2012, doi:10.1101/gr.129692.111
...Malaria genetic variation has been extensively characterized, but the level of epigenetic plasticity remains largely unexplored. Here we provide a comprehensive characterization of transcriptional variation in the most lethal malaria parasite, Plasmodium falciparum, based on highly accurate transcriptional...
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Research: Interactive transcriptome analysis of malaria patients and infecting Plasmodium falciparum
- Junya Yamagishi,
- Anna Natori,
- Mohammed E.M. Tolba,
- Arthur E. Mongan,
- Chihiro Sugimoto,
- Toshiaki Katayama,
- Shuichi Kawashima,
- Wojciech Makalowski,
- Ryuichiro Maeda,
- Yuki Eshita,
- Josef Tuda,
- and Yutaka Suzuki
Genome Res. September 2014 24: 1433-1444; Published in Advance August 4, 2014, doi:10.1101/gr.158980.113
...the transcriptomes of the human hosts and the infecting parasites affect one another. Here we report the RNA-seq analysis of 116 Indonesian patients infected with the malaria parasite Plasmodium falciparum (Pf). We extracted RNAs from their peripheral blood as a mixture of host and parasite transcripts and mapped...
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Research: Mutational scanning of CRX classifies clinical variants and reveals biochemical properties of the transcriptional effector domain
- James L. Shepherdson,
- David M. Granas,
- Jie Li,
- Zara Shariff,
- Stephen P. Plassmeyer,
- Alex S. Holehouse,
- Michael A. White,
- and Barak A. Cohen
Genome Res. October 2024 34: 1540-1552; Published in Advance September 25, 2024, doi:10.1101/gr.279415.124
...for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA; 3Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA; 4Center for Biomolecular Condensates...
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