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Research: Haplotype-resolved telomere-to-telomere genome of Aphelenchus avenae implicates P5CS in nematode desiccation stress response
- Yali Zhang,
- Yayi Zhou,
- Yangyang Chen,
- Xueyu Wang,
- Boyan Hu,
- Shahid Siddique,
- Romnick A. Latina,
- Veronica I. Casey,
- Dexin Bo,
- Yucheng Liao,
- Min Zhang,
- Ming Sun,
- Fengjuan Zhang,
- and Dadong Dai
Genome Res. March 23, 2026 ; Published in Advance March 23, 2026, doi:10.1101/gr.281016.125
...of conservation between homologous genes. However, with evolution and genomic changes, some gene pairswill have sequence differences or asymmetry between homologous chromosomes. This variation may be related to the adaptive evolution of different species or the functional differentiation of specific genes...
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Research: Plant genome evolution in the genus Eucalyptus is driven by structural rearrangements that promote sequence divergence
- Scott Ferguson,
- Ashley Jones,
- Kevin Murray,
- Rose Andrew,
- Benjamin Schwessinger,
- and Justin Borevitz
Genome Res. April 2024 34: 606-619; Published in Advance April 8, 2024, doi:10.1101/gr.277999.123
...Plant evolution in the genus Eucalyptus is driven by structural rearrangements that promote sequence divergence Scott Ferguson1,4, Ashley Jones1,4, Kevin Murray1,2, Rose Andrew3, Benjamin Schwessinger1 and Justin Borevitz1 1Research School of Biology, Australian National University, Canberra...
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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...of meiotic crossing over, the variation patterns suggest mechanisms such as unequal sister chromatid exchange. We also examine the prevalence and scale of concerted evolution in the histone and Stellate clusters and discuss the mechanisms underlying these observed patterns.Tandem repetitive sequences...
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Method: Genome enrichment of rare and unknown species from complicated microbiomes by nanopore selective sequencing
- Yuhong Sun,
- Zhanwen Cheng,
- Xiang Li,
- Qing Yang,
- Bixi Zhao,
- Ziqi Wu,
- and Yu Xia
Genome Res. April 2023 33: 612-621; Published in Advance April 11, 2023, doi:10.1101/gr.277266.122
...community and 19 nf-MAGs in the human gut microbial community. Even though the structure and composition of communities changed before and after selective sequencing, metaRUpore is unlikely to introduce systematic biases in the genomic content of MAGs retrieved for rare species (Supplemental Fig. S17...
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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
....zambonelli@unibo.itAbstractThe genus Tuber (family: Tuberaceae) includes the most economically valuable ectomycorrhizal (ECM), truffle-forming fungi. Previous genomic analyses revealed that massive transposable element (TE) proliferation represents a convergent genomic feature of ECM fungi, including Tuberaceae. Repetitive sequences...
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Research: Evolution of genome structure in the Drosophila simulans species complex
- Mahul Chakraborty,
- Ching-Ho Chang,
- Danielle E. Khost,
- Jeffrey Vedanayagam,
- Jeffrey R. Adrion,
- Yi Liao,
- Kristi L. Montooth,
- Colin D. Meiklejohn,
- Amanda M. Larracuente,
- and J.J. Emerson
Genome Res. March 2021 31: 380-396; Published in Advance February 9, 2021, doi:10.1101/gr.263442.120
...of repetitive sequences makes up a larger proportion of the than all single-nucleotide variants (SNVs) combined (The 1000 Genomes Project Consortium 2015; Chakraborty et al. 2018). Moreover, repetitive sequence variants can have significant fitness effects, underlie ecological adaptations, drive evolution...
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Research: Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species
- Charles Plessy,
- Michael J. Mansfield,
- Aleksandra Bliznina,
- Aki Masunaga,
- Charlotte West,
- Yongkai Tan,
- Andrew W. Liu,
- Jan Grašič,
- María Sara del Río Pisula,
- Gaspar Sánchez-Serna,
- Marc Fabrega-Torrus,
- Alfonso Ferrández-Roldán,
- Vittoria Roncalli,
- Pavla Navratilova,
- Eric M. Thompson,
- Takeshi Onuma,
- Hiroki Nishida,
- Cristian Cañestro,
- and Nicholas M. Luscombe
Genome Res. March 2024 34: 426-440; Published in Advance April 15, 2024, doi:10.1101/gr.278295.123
...other and facilitating the rapid evolution of adaptations to sudden environmental variations. The description of chromosomal rearrangements associated with adaptive phenotypes (Joron et al. 2011; Lamichhaney et al. 2016) has brought renewed attention to this area, especially given the advent of sequence...
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Resource: A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes
- Jing Liu,
- Zongji Wang,
- Jing Li,
- Luohao Xu,
- Jiaqi Liu,
- Shaohong Feng,
- Chunxue Guo,
- Shengchan Chen,
- Zhanjun Ren,
- Jinpeng Rao,
- Kai Wei,
- Yuezhou Chen,
- Erich D. Jarvis,
- Guojie Zhang,
- and Qi Zhou
Genome Res. March 2021 31: 497-511; Published in Advance January 6, 2021, doi:10.1101/gr.271569.120
...influenced by the spreading of heterochromatin from WS0. These patterns suggest that alteration of chromatin conformation comprises an important early step of sex chromosome evolution. Overall, our results provide novel insights into the evolution of avian structure and sex chromosomes in three...
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Resource: Construction and evaluation of a new rat reference genome assembly, GRCr8, from long reads and long-range scaffolding
- Kai Li,
- Melissa L. Smith,
- J. Chris Blazier,
- Kelli J. Kochan,
- Jonathan M.D. Wood,
- Kerstin Howe,
- Anne E. Kwitek,
- Melinda R. Dwinell,
- Hao Chen,
- Julia L. Ciosek,
- Patrick Masterson,
- Terence D. Murphy,
- Theodore S. Kalbfleisch,
- and Peter A. Doris
Genome Res. November 2024 34: 2081-2093; Published in Advance November 8, 2024, doi:10.1101/gr.279292.124
...for chromosome-scale assembly. PLoS Comput Biol 15: e1007273. doi:10.1371/journal.pcbi.1007273 ↵Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, et al. 2004. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428...
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Method: Assembly-free single-molecule sequencing recovers complete virus genomes from natural microbial communities
- John Beaulaurier,
- Elaine Luo,
- John M. Eppley,
- Paul Den Uyl,
- Xiaoguang Dai,
- Andrew Burger,
- Daniel J. Turner,
- Matthew Pendelton,
- Sissel Juul,
- Eoghan Harrington,
- and Edward F. DeLong
Genome Res. March 2020 30: 437-446; Published in Advance February 19, 2020, doi:10.1101/gr.251686.119
....Viruses impact the ecology and evolution of virtually all cellular lifeforms on Earth. Because of their centrality in early molecular genetic studies and their small size, viruses were the first biological entities whose s were fully sequenced (Fiers et al. 1976; Sanger et al. 1977). More recently, microbial...
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