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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
...genomics and phylogeny-aware statistical methods, we quantify the association between the presence of seven widespread defense systems and the abundance of MGEs in the s of 196 bacterial and one archaeal species. We also calculate the differences in the rates of gene gain and loss between lineages...
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Research: Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements
- Luis E. Valentin-Alvarado,
- Ling-Dong Shi,
- Kathryn E. Appler,
- Alexander Crits-Christoph,
- Valerie De Anda,
- Benjamin A. Adler,
- Michael L. Cui,
- Lynn Ly,
- Pedro Leão,
- Richard J. Roberts,
- Rohan Sachdeva,
- Brett J. Baker,
- David F. Savage,
- and Jillian F. Banfield
Genome Res. October 2024 34: 1595-1609; Published in Advance October 15, 2024, doi:10.1101/gr.279480.124
...-domain horizontal gene transfer (Ghaly et al. 2022). Recent studies identified viruses of Loki-, Odin-, Thor-, and Heimdallarchaeia (Medvedeva et al. 2022; Rambo et al. 2022; Tamarit et al. 2022; Wu et al. 2022), as well as putative transposons carrying cargo genes that replicate within Heimdallarchaeia (Wu et al...
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Review: Accurate and complete genomes from metagenomes
- Lin-Xing Chen,
- Karthik Anantharaman,
- Alon Shaiber,
- A. Murat Eren,
- and Jillian F. Banfield
Genome Res. March 2020 30: 315-333; Published in Advance March 18, 2020, doi:10.1101/gr.258640.119
...to the rest of the because the region has not been encountered previously in s of related organisms, possibly because it was acquired by lateral gene transfer. Thus, the most robust bins will draw on a combination of multiple clear signals.If a study includes a set of samples with related community membership...
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Review: De novo gene birth and the conundrum of ORFan genes in bacteria
- Md. Hassan uz-Zaman and
- Howard Ochman
Genome Res. August 2025 35: 1679-1688; Published in Advance July 10, 2025, doi:10.1101/gr.280157.124
...postulated to originate from either horizontal transfer, rapid divergence from pre-existing genes, or de novo emergence from noncoding sequences. We assess the body of research that explores each of these hypotheses and demonstrate that the mystery of the origin of bacterial ORFans still remains unresolved...
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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
...content estimation lacks synteny information, which can be useful for understanding biological phenomena such as operonic coregulation and horizontal gene transfer. To get around this limitation, we clustered genes based on the Pearson's correlation of their presence and absence across inferred strains...
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Research: Human contamination in bacterial genomes has created thousands of spurious proteins
- Florian P. Breitwieser,
- Mihaela Pertea,
- Aleksey V. Zimin,
- and Steven L. Salzberg
Genome Res. June 2019 29: 954-960; Published in Advance May 7, 2019, doi:10.1101/gr.245373.118
...↵Altemose N, Miga KH, Maggioni M, Willard HF. 2014. Genomic characterization of large heterochromatic gaps in the human assembly. PLoS Comput Biol 10: e1003628. doi:10.1371/journal.pcbi.1003628 ↵Anderson MT, Seifert HS. 2011. Opportunity and means: horizontal gene transfer from the human host to a bacterial...
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LETTER: Phylogenetic analyses of cyanobacterial genomes: Quantification of horizontal gene transfer events
- Olga Zhaxybayeva,
- J. Peter Gogarten,
- Robert L. Charlebois,
- W. Ford Doolittle,
- and R. Thane Papke
Genome Res. September 2006 16: 1099-1108; Published in Advance August 9, 2006, doi:10.1101/gr.5322306
...and Archaeal domains. Phylogenetic analysis of such “extended data sets” identifies putative instances of horizontal gene transfer from/to the cyanobacteria. Out of 1128 data sets, 879 had detectable homologs in selected prokaryotic s, and the remaining 249 data sets were “cyanobacteria-specific” (and...
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LETTER: Lineage-Specific Gene Expansions in Bacterial and Archaeal Genomes
- I. King Jordan,
- Kira S. Makarova,
- John L. Spouge,
- Yuri I. Wolf,
- and Eugene V. Koonin
Genome Res. April 1, 2001 11: 555-565; Published in Advance March 13, 2001, doi:10.1101/gr.166001
.... This matrix was used in parsimony graph reconstruction of the 32 complete archaeal and bacterial s (Fig. 5 ). The resulting graph does not represent a phylogeny in sensu strictu, as the signal in the data may be derived from horizontal transfer and gene loss in addition to the pattern of speciation...
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Method: CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
- Donovan H. Parks,
- Michael Imelfort,
- Connor T. Skennerton,
- Philip Hugenholtz,
- and Gene W. Tyson
Genome Res. July 2015 25: 1043-1055; Published in Advance May 14, 2015, doi:10.1101/gr.186072.114
...of the population s recoding the opal stop codon as CheckM automatically identifies such recodings (see Supplemental Methods). Poor quality estimates are expected for genomic elements such as plasmids or phage as the marker genes used by CheckM are specific to bacterial and archaeal chromosomes. The 10 plasmids...
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Resource: Using populations of human and microbial genomes for organism detection in metagenomes
- Sasha K. Ames,
- Shea N. Gardner,
- Jose Manuel Marti,
- Tom R. Slezak,
- Maya B. Gokhale,
- and Jonathan E. Allen
Genome Res. July 2015 25: 1056-1067; Published in Advance April 29, 2015, doi:10.1101/gr.184879.114
...for all the HMP sequencer runs. Horizontal transfer and replicate sequencing complicate interpretation of plasmid and gene profiles, particularly when the same plasmid or gene is sequenced multiple times but differently named. Since LMAT takes a “best first match” approach, the reported plasmid or gene...
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