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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
...clonality. Generally, rDNA tandem repeats are thought to undergo concerted evolution toward sequence homogenization via repeated homologous recombination, namely, unequal crossovers and gene conversion (Symonová 2019; Mullis et al. 2020; Garcia et al. 2024). Because Pst104E has genetically distinct nuclei...
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Research: Historical RNA expression profiles from the extinct Tasmanian tiger
- Emilio Mármol-Sánchez,
- Bastian Fromm,
- Nikolay Oskolkov,
- Zoé Pochon,
- Panagiotis Kalogeropoulos,
- Eli Eriksson,
- Inna Biryukova,
- Vaishnovi Sekar,
- Erik Ersmark,
- Björn Andersson,
- Love Dalén,
- and Marc R. Friedländer
Genome Res. August 2023 33: 1299-1316; Published in Advance July 18, 2023, doi:10.1101/gr.277663.123
....marmol.sanchez@gmail.comAbstractPaleogenomics continues to yield valuable insights into the evolution, population dynamics, and ecology of our ancestors and other extinct species. However, DNA sequencing cannot reveal tissue-specific gene expression, cellular identity, or gene regulation, which are only attainable at the transcriptional level...
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Research: The genomic basis of evolutionary differentiation among honey bees
- Bertrand Fouks,
- Philipp Brand,
- Hung N. Nguyen,
- Jacob Herman,
- Francisco Camara,
- Daniel Ence,
- Darren E. Hagen,
- Katharina J. Hoff,
- Stefanie Nachweide,
- Lars Romoth,
- Kimberly K.O. Walden,
- Roderic Guigo,
- Mario Stanke,
- Giuseppe Narzisi,
- Mark Yandell,
- Hugh M. Robertson,
- Nikolaus Koeniger,
- Panuwan Chantawannakul,
- Michael C. Schatz,
- Kim C. Worley,
- Gene E. Robinson,
- Christine G. Elsik,
- and Olav Rueppell
Genome Res. July 2021 31: 1203-1215; Published in Advance May 4, 2021, doi:10.1101/gr.272310.120
...-seq tracks in the A. mellifera Apollo browser (Dunn et al. 2019) available at the Hymenoptera Genome Database (Elsik et al. 2016). Four of the GR gene models were supported by RNA-seq reads spanning predicted exon–intron boundaries, indicating they are actively transcribed and thus functional receptors...
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Research: Comprehensive global genome dynamics of Chlamydia trachomatis show ancient diversification followed by contemporary mixing and recent lineage expansion
- James Hadfield,
- Simon R. Harris,
- Helena M.B. Seth-Smith,
- Surendra Parmar,
- Patiyan Andersson,
- Philip M. Giffard,
- Julius Schachter,
- Jeanne Moncada,
- Louise Ellison,
- María Lucía Gallo Vaulet,
- Marcelo Rodríguez Fermepin,
- Frans Radebe,
- Suyapa Mendoza,
- Sander Ouburg,
- Servaas A. Morré,
- Konrad Sachse,
- Mirja Puolakkainen,
- Suvi J. Korhonen,
- Chris Sonnex,
- Rebecca Wiggins,
- Hamid Jalal,
- Tamara Brunelli,
- Patrizia Casprini,
- Rachel Pitt,
- Cathy Ison,
- Alevtina Savicheva,
- Elena Shipitsyna,
- Ronza Hadad,
- Laszlo Kari,
- Matthew J. Burton,
- David Mabey,
- Anthony W. Solomon,
- David Lewis,
- Peter Marsh,
- Magnus Unemo,
- Ian N. Clarke,
- Julian Parkhill,
- and Nicholas R. Thomson
Genome Res. July 2017 27: 1220-1229; Published in Advance June 6, 2017, doi:10.1101/gr.212647.116
...history of this pathogen. Here, we analyze 563 full s, 455 of which are novel, to show that the history of the species comprises two phases, and conclude that the currently circulating lineages are the result of evolution in different genomic ecotypes. Temporal analysis indicates these lineages have...
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Perspective: On the origin of prokaryotic species
- W. Ford Doolittle and
- Olga Zhaxybayeva
Genome Res. May 2009 19: 744-756; doi:10.1101/gr.086645.108
...on concatenated gene sequences)—or comparable collections of genomically similar individuals—should be described as species depends on the degree of clustering one requires before making such designation. No one’s model of prokaryotic evolution would predict gene sequence data that lack all structure, so without...
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Method: A Bayesian framework for inferring dynamic intercellular interactions from time-series single-cell data
- Cameron Park,
- Shouvik Mani,
- Nicolas Beltran-Velez,
- Katie Maurer,
- Teddy Huang,
- Shuqiang Li,
- Satyen Gohil,
- Kenneth J. Livak,
- David A. Knowles,
- Catherine J. Wu,
- and Elham Azizi
Genome Res. September 2024 34: 1384-1396; Published in Advance September 5, 2024, doi:10.1101/gr.279126.124
...interactions in scRNA-seq data from nonuniformly sampled time points, incorporates prior knowledge on R–L complexes, and quantifies uncertainty in both its predictions and interpretations. Unlike previous methods, DIISCO can be trained on temporal data to learn how interactions change over time between samples...
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Perspective: The impact of long-read sequencing on human population-scale genomics
- Tobias Rausch,
- Tobias Marschall,
- and Jan O. Korbel
Genome Res. April 2025 35: 593-598; doi:10.1101/gr.280120.124
...using language models for variant effect prediction (Ji et al. 2021; Rozowsky et al. 2023), hold promise in overcoming some of the expected downstream challenges with interpreting variant data from long-read sequencing studies.Methylation as a parallel readout for assessing genetic variant consequences...
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Research: Alternative polyadenylation drives oncogenic gene expression in pancreatic ductal adenocarcinoma
- Swati Venkat,
- Arwen A. Tisdale,
- Johann R. Schwarz,
- Abdulrahman A. Alahmari,
- H. Carlo Maurer,
- Kenneth P. Olive,
- Kevin H. Eng,
- and Michael E. Feigin
Genome Res. March 2020 30: 347-360; Published in Advance February 6, 2020, doi:10.1101/gr.257550.119
...the TCGA and GTEx data sets, and these 3′-UTR forms can be detected in cell models and patient samples.3′-UTR changes are widespread among PDAC patients and enriched in PDAC pathwaysTo visualize the landscape of APA across PDAC, we clustered patients (columns) based on change in PDUI score (tumor − normal...
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Research: Tracing human stem cell lineage during development using DNA methylation
- Lucas A. Salas,
- John K. Wiencke,
- Devin C. Koestler,
- Ze Zhang,
- Brock C. Christensen,
- and Karl T. Kelsey
Genome Res. September 2018 28: 1285-1295; Published in Advance August 2, 2018, doi:10.1101/gr.233213.117
...al. 2014), and let-7b miRNA (Copley et al. 2013; Rowe et al. 2016). Direct tracking of stem cell lineage and diversity has been achieved in experimental animal models by enumerating chromosomal translocations, retroviral insertions, and molecular barcodes in repopulating cells during hematopoietic...
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Perspective: From human genome to cancer genome: The first decade
- David A. Wheeler and
- Linghua Wang
Genome Res. July 2013 23: 1054-1062; doi:10.1101/gr.157602.113
...Cancer 4: 177–183. Garraway LA, Lander ES. 2013. Lessons from the cancer . Cell 153: 17–37. Gerlinger M, Swanton C. 2010. How Darwinian models inform therapeutic failure initiated by clonal heterogeneity in cancer medicine. Br J Cancer 103: 1139–1143. Gerlinger M, Rowan AJ, Horswell S, Larkin J...

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