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Research: Transcriptomic and proteomic effects of gene deletion are not evolutionarily conserved
- Yang Li and
- Jianzhi Zhang
Genome Res. March 2025 35: 512-521; Published in Advance February 18, 2025, doi:10.1101/gr.280008.124
...sensitivity of these effects to the genetic background, explaining why these effects are not evolutionarily conserved. Together, our results suggest that most transcriptomic and proteomic effects of gene deletion do not inform selected-effect function. This finding has important implications for assessing and...
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Research: Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection
- Jian-Hai Chen,
- Patrick Landback,
- Deanna Arsala,
- Alexander Guzzetta,
- Shengqian Xia,
- Jared Atlas,
- Dylan Sosa,
- Yong E. Zhang,
- Jingqiu Cheng,
- Bairong Shen,
- and Manyuan Long
Genome Res. March 2025 35: 379-392; Published in Advance February 14, 2025, doi:10.1101/gr.279498.124
...(Pandey et al. 2013), and (HOS) the synteny method (orthologous gene order conservation between human and opossum) (Ross et al. 2005). (E) The fraction of disease genes with male-specific reproductive disease phenotypes within each X Chromosomal subregion, as illustrated in D, is presented. The gene...
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Method: Identification of the shortest species-specific oligonucleotide sequences
- Ioannis Mouratidis,
- Maxwell A. Konnaris,
- Nikol Chantzi,
- Candace S.Y. Chan,
- Michail Patsakis,
- Kimonas Provatas,
- Austin Montgomery,
- Fotis A. Baltoumas,
- Congzhou M. Sha,
- Manvita Mareboina,
- Georgios A. Pavlopoulos,
- Dionysios V. Chartoumpekis,
- and Ilias Georgakopoulos-Soares
Genome Res. February 2025 35: 279-295; Published in Advance January 2, 2025, doi:10.1101/gr.280070.124
...the shortest species-specific nucleotide sequences offers insights into species evolution and holds potential practical applications in agriculture, wildlife conservation, and healthcare. We propose a new method for sequence analysis termed nucleic “quasi-primes,” the shortest occurring sequences in each of 45...
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Resource: A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state
- Jack F. Cazet,
- Stefan Siebert,
- Hannah Morris Little,
- Philip Bertemes,
- Abby S. Primack,
- Peter Ladurner,
- Matthias Achrainer,
- Mark T. Fredriksen,
- R. Travis Moreland,
- Sumeeta Singh,
- Suiyuan Zhang,
- Tyra G. Wolfsberg,
- Christine E. Schnitzler,
- Andreas D. Baxevanis,
- Oleg Simakov,
- Bert Hobmayer,
- and Celina E. Juliano
Genome Res. February 2023 33: 283-298; Published in Advance January 13, 2023, doi:10.1101/gr.277040.122
...–J) Predicted domain boundaries fall within regions of heterochromatin. Domain boundaries are associated with reduced chromatin accessibility (F), H3K4me1 (G), and sequence conservation (H) and with elevated repeat element density (I) and H3K27me3 (J).We next explored intra-chromosomal interactions in our Hi...
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Resource: The genome of the colonial hydroid Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals
- Christine E. Schnitzler,
- E. Sally Chang,
- Justin Waletich,
- Gonzalo Quiroga-Artigas,
- Wai Yee Wong,
- Anh-Dao Nguyen,
- Sofia N. Barreira,
- Liam B. Doonan,
- Paul Gonzalez,
- Sergey Koren,
- James M. Gahan,
- Steven M. Sanders,
- Brian Bradshaw,
- Timothy Q. DuBuc,
- Febrimarsa,
- Danielle de Jong,
- Eric P. Nawrocki,
- Alexandra Larson,
- Samantha Klasfeld,
- Sebastian G. Gornik,
- R. Travis Moreland,
- Tyra G. Wolfsberg,
- Adam M. Phillippy,
- James C. Mullikin,
- Oleg Simakov,
- Paulyn Cartwright,
- Matthew Nicotra,
- Uri Frank,
- and Andreas D. Baxevanis
Genome Res. March 2024 34: 498-513; Published in Advance March 20, 2024, doi:10.1101/gr.278382.123
...mitochondrial chromosomes in the absence of telomeric sequences (Supplemental Fig. S10). In addition, the presence of nonfunctional (and gradually degrading) nuclear copies of mtDNA (NUMTs) have previously been identified in H. vulgaris (Song et al. 2013). Sequence similarity searches did not detect NUMTs...
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Research: Ribosomal DNA harbors an evolutionarily conserved clock of biological aging
- Meng Wang and
- Bernardo Lemos
Genome Res. March 2019 29: 325-333; Published in Advance February 14, 2019, doi:10.1101/gr.241745.118
...author: blemos@hsph.harvard.eduAbstractThe ribosomal DNA (rDNA) is the most evolutionarily conserved segment of the and gives origin to the nucleolus, an energy intensive nuclear organelle and major hub influencing myriad molecular processes from cellular metabolism to epigenetic states of the . The r...
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Research: Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize
- Baoxing Song,
- Edward S. Buckler,
- Hai Wang,
- Yaoyao Wu,
- Evan Rees,
- Elizabeth A. Kellogg,
- Daniel J. Gates,
- Merritt Khaipho-Burch,
- Peter J. Bradbury,
- Jeffrey Ross-Ibarra,
- Matthew B. Hufford,
- and M. Cinta Romay
Genome Res. July 2021 31: 1245-1257; Published in Advance May 27, 2021, doi:10.1101/gr.266528.120
...; Ricci et al. 2019), although not all cis-regulatory sequences are evolutionarily conserved (Ross et al. 1994; Wittkopp et al. 2002; McLean et al. 2011). We observed enrichment of lead eQTLs in CNS regions and association between CNS absence and gene expression (Fig. 5C,D). In terms of the regulation...
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Research: RNA editing in bacteria recodes multiple proteins and regulates an evolutionarily conserved toxin-antitoxin system
- Dan Bar-Yaacov,
- Ernest Mordret,
- Ruth Towers,
- Tammy Biniashvili,
- Clara Soyris,
- Schraga Schwartz,
- Orna Dahan,
- and Yitzhak Pilpel
Genome Res. October 2017 27: 1696-1703; Published in Advance September 1, 2017, doi:10.1101/gr.222760.117
...making it the first identified RNA editing enzyme that modifies both tRNAs and mRNAs. Interestingly, several of the editing targets are self-killing toxins that belong to evolutionarily conserved toxin-antitoxin pairs. We focused on hokB, a toxin that confers antibiotic tolerance by growth inhibition...
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Research: The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible
- Yue Hao,
- Makenzie E. Mabry,
- Patrick P. Edger,
- Michael Freeling,
- Chunfang Zheng,
- Lingling Jin,
- Robert VanBuren,
- Marivi Colle,
- Hong An,
- R. Shawn Abrahams,
- Jacob D. Washburn,
- Xinshuai Qi,
- Kerrie Barry,
- Christopher Daum,
- Shengqiang Shu,
- Jeremy Schmutz,
- David Sankoff,
- Michael S. Barker,
- Eric Lyons,
- J. Chris Pires,
- and Gavin C. Conant
Genome Res. May 2021 31: 799-810; Published in Advance April 16, 2021, doi:10.1101/gr.270033.120
...The contributions from the progenitor s of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible Yue Hao1, Makenzie E. Mabry2, Patrick P. Edger3,4, Michael Freeling5, Chunfang Zheng6, Lingling Jin7, Robert VanBuren3,8, Marivi Colle3, Hong An2, R. Shawn Abrahams2...
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Research: Genomic architecture constrained placental mammal X Chromosome evolution
- Wesley A. Brashear,
- Kevin R. Bredemeyer,
- and William J. Murphy
Genome Res. August 2021 31: 1353-1365; Published in Advance July 22, 2021, doi:10.1101/gr.275274.121
...be an indirect result of selection on gene content or selection against rearrangements that might disrupt X-Chromosome inactivation (XCI). Previous comparisons between the human and mouse X Chromosome sequences have suggested that although single-copy X Chromosome genes are conserved between species, most...

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