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Research: Dynamic evolution of satellite DNAs drastically differentiates the genomes of Tribolium sibling species
- Damira Veseljak,
- Evelin Despot-Slade,
- Marin Volarić,
- Lucija Horvat,
- Tanja Vojvoda Zeljko,
- Nevenka Meštrović,
- and Brankica Mravinac
Genome Res. November 2025 35: 2445-2460; Published in Advance September 16, 2025, doi:10.1101/gr.280516.125
...orthologous organization characterized by totally different major satDNAs but related minor satDNAs. The T. freemani male sex chromosome, which lacks the major satDNA but contains a minor-like satDNA, further highlights the question of which satDNA is centromere-competent. By analyzing the long...
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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
...identity with available Phytobacter s of 90.6% and 96%, respectively. We hypothesized that these bacterial strains could either represent novel isolates or have no associated whole- sequencing data in the NCBI database. Therefore, we searched the literature for recent, comprehensive phylogenies...
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Research: Limited allele-specific gene expression in highly polyploid sugarcane
- Gabriel Rodrigues Alves Margarido,
- Fernando Henrique Correr,
- Agnelo Furtado,
- Frederik C. Botha,
- and Robert James Henry
Genome Res. February 2022 32: 297-308; Published in Advance December 23, 2021, doi:10.1101/gr.275904.121
...in maize is a cause of ASE, and although not frequent, it can arise from nonsyntenic genes and contribute to hybrid vigour (Baldauf et al. 2020). There is also evidence of conserved ASE between maize and rice orthologs, with accompanying evidence of positive selection (Waters et al. 2013). The joint...
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12 Drosophila Genomes/Methods: Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes
- Matthew D. Rasmussen and
- Manolis Kellis
Genome Res. December 2007 17: 1932-1942; Published in Advance November 7, 2007, doi:10.1101/gr.7105007
.... The availability of many related genomes enables more powerful analyses, but requires rigorous phylogenetic methods to resolve orthologous genes and regions. Here, we use 12 recently sequenced Drosophila genomes and nine fungal genomes to address the problem of accurate gene-tree reconstruction across many...
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Perspective: Comparative genomics as a tool to understand evolution and disease
- Jessica Alföldi and
- Kerstin Lindblad-Toh
Genome Res. July 2013 23: 1063-1068; doi:10.1101/gr.157503.113
.... The comparative ENCODE project demonstrated the presence of widespread orthology between species, high levels of conservation within genes, as well as extensive signals of conservation outside genes. Noncoding features lacking experimental validation, however, were harder to interpret than protein-coding genes...
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ARTICLE: Genome sequence of Haloarcula marismortui: A halophilic archaeon from the Dead Sea
- Nitin S. Baliga,
- Richard Bonneau,
- Marc T. Facciotti,
- Min Pan,
- Gustavo Glusman,
- Eric W. Deutsch,
- Paul Shannon,
- Yulun Chiu,
- Rueyhung Sting Weng,
- Rueichi Richie Gan,
- Pingliang Hung,
- Shailesh V. Date,
- Edward Marcotte,
- Leroy Hood,
- and Wailap Victor Ng
Genome Res. November 2004 14: 2221-2234; doi:10.1101/gr.2700304
...in the denitrification process, see below) ( Marcotte et al. 1999 ; Bonneau et al. 2004 ). In summary, BLASTP identified orthologs for 3099 proteins in the GenBank non-redundant protein, SWISS-PROT, and EMBL-EBI proteome analysis databases. Of these, 1667 (∼39.3%) matched characterized proteins and were assigned...
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Research: Combinatorial binding of transcription factors in the pluripotency control regions of the genome
- Luciana Ferraris,
- Allan P. Stewart,
- Jinsuk Kang,
- Alec M. DeSimone,
- Matthew Gemberling,
- Dean Tantin,
- and William G. Fairbrother
Genome Res. July 2011 21: 1055-1064; Published in Advance April 28, 2011, doi:10.1101/gr.115824.110
...proteins that have similar specificity. POU binding can be influenced by POU factor–specific interactions with other DNA binding proteins. The human protein reference database reports 36 DNA binding proteins that interact with POU2F1 and 10 that interact with POU5F1, suggesting a large repertoire...
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Research: Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88
- Mikael R. Andersen,
- Margarita P. Salazar,
- Peter J. Schaap,
- Peter J.I. van de Vondervoort,
- David Culley,
- Jette Thykaer,
- Jens C. Frisvad,
- Kristian F. Nielsen,
- Richard Albang,
- Kaj Albermann,
- Randy M. Berka,
- Gerhard H. Braus,
- Susanna A. Braus-Stromeyer,
- Luis M. Corrochano,
- Ziyu Dai,
- Piet W.M. van Dijck,
- Gerald Hofmann,
- Linda L. Lasure,
- Jon K. Magnuson,
- Hildegard Menke,
- Martin Meijer,
- Susan L. Meijer,
- Jakob B. Nielsen,
- Michael L. Nielsen,
- Albert J.J. van Ooyen,
- Herman J. Pel,
- Lars Poulsen,
- Rob A. Samson,
- Hein Stam,
- Adrian Tsang,
- Johannes M. van den Brink,
- Alex Atkins,
- Andrea Aerts,
- Harris Shapiro,
- Jasmyn Pangilinan,
- Asaf Salamov,
- Yigong Lou,
- Erika Lindquist,
- Susan Lucas,
- Jane Grimwood,
- Igor V. Grigoriev,
- Christian P. Kubicek,
- Diego Martinez,
- Noël N.M.E. van Peij,
- Johannes A. Roubos,
- Jens Nielsen,
- and Scott E. Baker
Genome Res. June 2011 21: 885-897; Published in Advance May 4, 2011, doi:10.1101/gr.112169.110
...to be involved in a recent duplication recombination event to ChrVII, (Fig. 2C). Thus, the CBS 513.88 harbors two additional alpha-amylase-encoding genes that are orthologs to the alpha-amylase-encoding genes (AO090023000944, AO090120000196) of A. oryzae RIB40. These findings suggest that CBS 513...
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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
...of these potential lineage-specific expansions, all clusters were reanalyzed using the best hits (BeTs) approach that underlies the construction of clusters of orthologous groups of proteins (COGs; Tatusov et al. 1997 , 2000 ). A BeT is the best BLAST hit (highest score or lowest e value) retrieved from a single...

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