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Research: Proteome-wide structural analysis quantifies structural conservation across distant species
- Shijie Zhang,
- Teng Zhang,
- and Yuan Fu
Genome Res. November 2023 33: 1975-1993; Published in Advance November 22, 2023, doi:10.1101/gr.277771.123
...such as rhodopsin, the phylogenetic relationships between the prokaryotic 7TM proteins and eukaryotic GPCR proteins cannot be inferred unambiguously from sequence similarity alone (Strotmann et al. 2011). However, by referencing protein structures, a previous study has provided evidence that eukaryotic GPCR may...
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Research: Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements
- Fu Xiang Quah,
- Miguel Vasconcelos Almeida,
- Moritz Blumer,
- Chengwei Ulrika Yuan,
- Bettina Fischer,
- Kirsten See,
- Ben Jackson,
- Richard Zatha,
- Bosco Rusuwa,
- George F. Turner,
- M. Emília Santos,
- Hannes Svardal,
- Martin Hemberg,
- Richard Durbin,
- and Eric Miska
Genome Res. May 2025 35: 1094-1107; Published in Advance April 10, 2025, doi:10.1101/gr.279674.124
...similarity between the two Rhamphochromis individuals is expected as they belong to the same species and might have exhibited structural changes independently of the other cichlids. This is consistent with the SNP-based Lake Malawi cichlid phylogeny in which the pelagic group that contains the Rhamphochromis...
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Method: Robust analysis of prokaryotic pangenome gene gain and loss rates with Panstripe
- Gerry Tonkin-Hill,
- Rebecca A. Gladstone,
- Anna K. Pöntinen,
- Sergio Arredondo-Alonso,
- Stephen D. Bentley,
- and Jukka Corander
Genome Res. January 2023 33: 129-140; Published in Advance January 20, 2023, doi:10.1101/gr.277340.122
...pans.ResultsOverviewPanstripe accepts a phylogeny produced using standard pipelines and a corresponding gene presence/absence matrix as produced by most pan inference tools (Page et al. 2015; Lees et al. 2018; Tonkin-Hill et al. 2020). The length of each branch in the phylogeny is then compared...
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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
...as structural variants (SVs) (Rieseberg 2001). Species-specific sequences resulting from the insertion, deletion, or localized divergence of sequence appear as unaligned regions when s are analyzed. The true origin of unaligned regions is more difficult to infer than rearrangements or syntenic regions (Weisman...
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Research: Evolutionary assembly patterns of prokaryotic genomes
- Maximilian O. Press,
- Christine Queitsch,
- and Elhanan Borenstein
Genome Res. June 2016 26: 826-833; Published in Advance April 14, 2016, doi:10.1101/gr.200097.115
...-based dependencies among prokaryotic genes, analyze the obtained set of epistatic interactions, and identify patterns in the evolution of prokaryotic s.ResultsPGCE inferenceWe first set out to detect pairs of genes for which the presence of one gene in the promotes the gain of the other gene (though not necessarily...
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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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Research: Timescale and genetic linkage explain the variable impact of defense systems on horizontal gene transfer
- Yang Liu,
- João Botelho,
- and Jaime Iranzo
Genome Res. February 2025 35: 268-278; Published in Advance January 10, 2025, doi:10.1101/gr.279300.124
...-quality genomic data, phylogenomic methods, and phylogeny-aware statistical inference, our study aimed to shed light on the nuanced consequences of the interplay between defense systems and MGEs on bacterial evolution across timescales.ResultsAssociation between defense systems and MGE abundance is MGE and taxon...
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Resource: Interspecies systems biology links bacterial metabolic pathways to nematode gene expression, chemotaxis behavior, and survival
- Marina Athanasouli,
- Tobias Loschko,
- and Christian Rödelsperger
Genome Res. October 2025 35: 2363-2374; Published in Advance August 5, 2025, doi:10.1101/gr.280848.125
...intestinal- and detoxification-related modules as components of the primary response layer to diverse microbiota. This further supports the general structure of our interactome as the module labels were inferred independently from the cross-species interactions. Furthermore, overlaying the number...
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Research: Contiguous and complete assemblies of Blastocystis gut microbiome–associated protists reveal evolutionary diversification to host ecology
- Abigail L. Lind,
- Nathan A. McDonald,
- Elias R. Gerrick,
- Ami S. Bhatt,
- and Katherine S. Pollard
Genome Res. June 2025 35: 1377-1390; Published in Advance April 22, 2025, doi:10.1101/gr.279080.124
...-read, short-read, and Hi-C DNA sequencing, alongside gene annotation and RNA sequencing. Comparative genomic analyses reveal significant variation in gene content and structure across Blastocystis. Notably, three strains from herbivorous tortoises, phylogenetically distant from human subtypes, have markedly...
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Method: Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC
- Byron J. Smith,
- Chunyu Zhao,
- Veronika Dubinkina,
- Xiaofan Jin,
- Liron Zahavi,
- Saar Shoer,
- Jacqueline Moltzau-Anderson,
- Eran Segal,
- and Katherine S. Pollard
Genome Res. May 2025 35: 1247-1260; Published in Advance April 10, 2025, doi:10.1101/gr.279543.124
...sources of error in quantifying gene depth, a second algorithm is needed to infer which genes are actually present in a specific strain's , a step that we call gene content estimation. Because this strain is never directly observed in isolation—indeed, it is only a hypothesis—we refer to it as an inferred...
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