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Research: Multiple Pristionchus pacificus genomes reveal distinct evolutionary dynamics between de novo candidates and duplicated genes
- Neel Prabh and
- Christian Rödelsperger
Genome Res. July 2022 32: 1315-1327; Published in Advance May 26, 2022, doi:10.1101/gr.276431.121
...likely from a duplication and divergence mechanism; that is, if rapidly evolving members of large superfamilies diverge beyond a certain level, they will appear as a new gene family. Note that there are also duplications within orthogroups that give rise to multiple paralogs. These duplicates...
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Resource: Indels, structural variation, and recombination drive genomic diversity in Plasmodium falciparum
- Alistair Miles,
- Zamin Iqbal,
- Paul Vauterin,
- Richard Pearson,
- Susana Campino,
- Michel Theron,
- Kelda Gould,
- Daniel Mead,
- Eleanor Drury,
- John O'Brien,
- Valentin Ruano Rubio,
- Bronwyn MacInnis,
- Jonathan Mwangi,
- Upeka Samarakoon,
- Lisa Ranford-Cartwright,
- Michael Ferdig,
- Karen Hayton,
- Xin-zhuan Su,
- Thomas Wellems,
- Julian Rayner,
- Gil McVean,
- and Dominic Kwiatkowski
Genome Res. September 2016 26: 1288-1299; Published in Advance August 16, 2016, doi:10.1101/gr.203711.115
...coding indels are size multiples of 3, preserving the reading frame. Most noncoding indels are size multiples of 2, reflecting the abundance of poly(AT) repeats in noncoding regions. (B) Amino acids inserted and deleted (relative to the 3D7 reference ). (C) Indel diversity in intergenic regions relative...
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Research: Coding and noncoding variants in HFM1, MLH3, MSH4, MSH5, RNF212, and RNF212B affect recombination rate in cattle
- Naveen Kumar Kadri,
- Chad Harland,
- Pierre Faux,
- Nadine Cambisano,
- Latifa Karim,
- Wouter Coppieters,
- Sébastien Fritz,
- Erik Mullaart,
- Denis Baurain,
- Didier Boichard,
- Richard Spelman,
- Carole Charlier,
- Michel Georges,
- and Tom Druet
Genome Res. October 2016 26: 1323-1332; Published in Advance August 11, 2016, doi:10.1101/gr.204214.116
..., and noncoding variants (3) in RNF212B for 1/7 QTL. This suggests that this RNF212 paralog might also be involved in recombination. Most of the identified mutations had significant effects in both sexes, with three of them each accounting for ∼10% of the genetic variance in males. Footnotes...
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Research: Independent expansion, selection, and hypervariability of the TBC1D3 gene family in humans
- Xavi Guitart,
- David Porubsky,
- DongAhn Yoo,
- Max L. Dougherty,
- Philip C. Dishuck,
- Katherine M. Munson,
- Alexandra P. Lewis,
- Kendra Hoekzema,
- Jordan Knuth,
- Stephen Chang,
- Tomi Pastinen,
- and Evan E. Eichler
Genome Res. November 2024 34: 1798-1810; Published in Advance August 6, 2024, doi:10.1101/gr.279299.124
...pluripotent stem cells (iPSCs) (Cheung et al. 2023). We mapped FLNC reads to both haplotypes of the respective species of origin assemblies, allowing only high-quality mappings and tracking all best map assignments versus multiple mappings among the paralogous copies for each species (Methods) (Fig. 4A...
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Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
- Daniela M. Riley,
- Randa Elsayed,
- Mark D. Walsh,
- Simaran Johal,
- Ying Lin,
- Harry Walton,
- Till Bretschneider,
- Sascha Ott,
- and Andrew C. Nelson
Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
.... Zebrafish have multiple orthologs of mammalian TF genes owing to the additional whole and other small duplications during teleost evolution. Where present, a, b, and c paralogs are depicted. (∗) Although the enriched motif is FOXA2:EBOX FPKM, heatmap indicates FOXA2 expression alone. Riley et al. 8 Genome...
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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
...45S rDNA loci and all 5S rDNA genes to evaluate a possible intragenomic variation. 45S rDNA loci identified from contig 16 to contig 29 are highly homogenized, without any insertions or deletions and only seven positions harboring variants unique or shared across paralog copies (Fig. 2D). Instead...
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Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
- Dongying Xie,
- Pohao Ye,
- Yiming Ma,
- and Zhongying Zhao
Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
..., and inverted translocation/duplication, whereas small-scale variations included SNPs, tandem duplications, copy number gains or losses, and insertions and deletions (indels) (Goel et al. 2019). Notably, although both small and large indels were characterized (see Methods), those <100 bp predominated between...
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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
...are major components of many eukaryotic s (Richard et al. 2008) and play vital roles in both biology (Gemayel et al. 2010; Hannan 2012) and disease (Hannan 2018). Loci encoding components of important cellular processes are sometimes present in multiple copies and are often clustered in tandem, including...
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Editorial: Long reads decipher genomes and transcriptomes and offer novel insights into biology and diseases
- Ana Conesa,
- Alexander Hoischen,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: xi-xiv; doi:10.1101/gr.280665.125
.... Genome Res (this issue) 35: 810–823. doi:10.1101/gr.279491.124 ↵Vervoort L, Dierckxsens N, Sousa Santos M, Meynants S, Souche E, Cools R, Heung T, Devriendt K, Peeters H, McDonald-McGinn DM, et al. 2025. Multiple paralogs and recombination mechanisms contribute to the high incidence of 22q11.2 deletion...
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Research: Unraveling the architecture of major histocompatibility complex class II haplotypes in rhesus macaques
- Nanine de Groot,
- Marit van der Wiel,
- Ngoc Giang Le,
- Natasja G. de Groot,
- Jesse Bruijnesteijn,
- and Ronald E. Bontrop
Genome Res. November 2024 34: 1811-1824; Published in Advance October 23, 2024, doi:10.1101/gr.278968.124
...) in concert with adaptive sampling. In particular, the expansion and contraction of the primate DRB-region appear to be a dynamic process that involves the rearrangement of different cassettes of paralogous genes. These chromosomal recombination events are propagated by a conserved pseudogene, DRB6, which...
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