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METHODS: Parallel Construction of Orthologous Sequence-Ready Clone Contig Maps in Multiple Species
- James W. Thomas,
- Arjun B. Prasad,
- Tyrone J. Summers,
- Shih-Queen Lee-Lin,
- Valerie V.B. Maduro,
- Jacquelyn R. Idol,
- Joseph F. Ryan,
- Pamela J. Thomas,
- Jennifer C. McDowell,
- and Eric D. Green
Genome Res. August 1, 2002 12: 1277-1285; doi:10.1101/gr.283202
...analysis, a robust and scalable strategy for simultaneously constructing sequence-ready bacterial artificial chromosome (BAC) contig maps from targeted genomic regions has been developed. Central to this approach is the generation and utilization of “universal” oligonucleotide-based hybridization probes...
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METHODS: Automated Construction of High-Density Comparative Maps Between Rat, Human, and Mouse
- Anne E. Kwitek,
- Peter J. Tonellato,
- Dan Chen,
- Jo Gullings-Handley,
- Yongjian Samuel Cheng,
- Simon Twigger,
- Todd E. Scheetz,
- Thomas L. Casavant,
- Monika Stoll,
- Marcelo A. Nobrega,
- Masahide Shiozawa,
- M. Bento Soares,
- Val C. Sheffield,
- and Howard J. Jacob
Genome Res. November 1, 2001 11: 1935-1943; doi:10.1101/gr.173701
...of radiation hybrid (RH) maps, coupled with the large numbers of available Expressed Sequence Tags (ESTs), has revolutionized the way comparative maps can be built. We used publicly available rat, mouse, and human data to identify genes and ESTs with interspecies sequence identity (homology), identified...
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Review: Advancements in prospective single-cell lineage barcoding and their applications in research
- Xiaoli Zhang,
- Yirui Huang,
- Yajing Yang,
- Qi-En Wang,
- and Lang Li
Genome Res. December 2024 34: 2147-2162; Published in Advance November 21, 2024, doi:10.1101/gr.278944.124
...the LARRY approach to investigate the fate determination map of HSCs using both in vivo mouse models and in vitro cell systems. Employing a “Clone-splitting” strategy, they partitioned barcoded progenitor cells into distinct groups after sufficient expansion and performed scRNA-seq on samples collected...
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Research: Degrees of convergent evolution in rodent adaptations to arid environments
- Domitille Chalopin,
- Carine Rey,
- Jeremy Ganofsky,
- Juliana Blin,
- Pascale Chevret,
- Marion Mouginot,
- Laurent Guéguen,
- Bastien Boussau,
- Sophie Pantalacci,
- and Marie Sémon
Genome Res. March 2026 36: 472-486; Published in Advance January 21, 2026, doi:10.1101/gr.280089.124
...). The quality of the assemblies is summarized in Supplemental Table S13. Expression levels were obtained by mapping the sequence reads against coding sequences from de novo assemblies using kallisto 0.45.1 (Bray et al. 2016) with the default parameters.Annotation of transcriptsWe selected the rodent...
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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
...) (see Fig. 5). Additionally, using only Adnataria s should maximize the occurrence of retained rearrangements, as the phylogenetic distances within the Adnataria group are relatively low, with many species still hybridizing (Delaporte et al. 2001).View larger version: In this window In a new window...
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Research: Hybridization drives mitochondrial DNA degeneration and metabolic shift in a species with biparental mitochondrial inheritance
- Mathieu Hénault,
- Souhir Marsit,
- Guillaume Charron,
- and Christian R. Landry
Genome Res. November/December 2022 32: 2043-2056; Published in Advance November 9, 2022, doi:10.1101/gr.276885.122
...leakage or de novo mutations. mtDNA integrity and the resolution of heteroplasmy have important implications, notably for mitochondrial genetic disorders, speciation, and evolution in hybrids. However, the impact of genetic variation on the transition to homoplasmy from initially heteroplasmic backgrounds...
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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
...within either Hydractinia . This result was confirmed by the lack of sequence variance in Illumina raw reads mapped to their mitochondrial s. Other cnidarians with linear mtDNAs, such as the jellyfish Sanderia malayensis and Rhopilema esculentum, were also shown to not contain NUMTs (Nong et al. 2020...
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Resource: DEAD box RNA helicases are pervasive protein kinase interactors and activators
- Alexander Hirth,
- Edoardo Fatti,
- Eugen Netz,
- Sergio P. Acebron,
- Dimitris Papageorgiou,
- Andrea Švorinić,
- Cristina-Maria Cruciat,
- Emil Karaulanov,
- Alexandr Gopanenko,
- Tianheng Zhu,
- Irmgard Sinning,
- Jeroen Krijgsveld,
- Oliver Kohlbacher,
- and Christof Niehrs
Genome Res. June 2024 34: 952-966; Published in Advance July 10, 2024, doi:10.1101/gr.278264.123
.../MAP2K, and STE20/PAK family members. We identified MARK1 in all screens and validated that DDX proteins accelerate the MARK1 catalytic rate. These findings indicate pervasive interactions between protein kinases and DEAD box RNA helicases, and provide a rich resource to explore their regulatory...
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Method: Variational inference using approximate likelihood under the coalescent with recombination
- Xinhao Liu,
- Huw A. Ogilvie,
- and Luay Nakhleh
Genome Res. November 2021 31: 2107-2119; Published in Advance August 23, 2021, doi:10.1101/gr.273631.120
...conducted inference on each scenario using the combination for coalHMM construction to find the MAP solution and inspected the accuracy. In total, we conducted 3 × 4 × 5 = 60 inferences.Figure 5, A through C, shows inference results for scenarios 1, 2, and 3, respectively. The message is clearest in Figure...
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Research: Rates and spectra of de novo structural mutations in Chlamydomonas reinhardtii
- Eugenio López-Cortegano,
- Rory J. Craig,
- Jobran Chebib,
- Eniolaye J. Balogun,
- and Peter D. Keightley
Genome Res. January 2023 33: 45-60; Published in Advance December 12, 2022, doi:10.1101/gr.276957.122
...individually for each MA line, whereas all MA lines and the ancestor for each strain were analyzed collectively with vg from a single Cactus alignment. We subsequently collated and manually curated all variant calls using a combination of read visualization and mapping approaches (Fig. 1A).View larger version...
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