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Method: The multicomparative 2-n-way genome suite
- Gennady Churakov,
- Fengjun Zhang,
- Norbert Grundmann,
- Wojciech Makalowski,
- Angela Noll,
- Liliya Doronina,
- and Jürgen Schmitz
Genome Res. October 2020 30: 1508-1516; Published in Advance July 29, 2020, doi:10.1101/gr.262261.120
...cow, 21 from dog, and eight from opossum. Manual checking of the orthology of the loci (Methods) revealed 87 clear cases of phylogenetically verified intron losses in mammals (Fig. 2, red balls; Supplemental Table S1; Supplemental Data S1).View larger version: In this window In a new window Figure 2...
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Research: Chromosome-wide profiling of X-chromosome inactivation and epigenetic states in fetal brain and placenta of the opossum, Monodelphis domestica
- Xu Wang,
- Kory C. Douglas,
- John L. VandeBerg,
- Andrew G. Clark,
- and Paul B. Samollow
Genome Res. January 2014 24: 70-83; Published in Advance September 24, 2013, doi:10.1101/gr.161919.113
...that thematernal allele was the one preferentially expressed. However, M/P was <1.0 for two genes, Frmd7 and Hmgb3 (Fig. 2E). There was no significant difference in the level of paternal leakage between the two tissues for Genome Research 71 www..org X-inactivation and epigenetic profiles in opossum 17...
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LETTER: Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica
- Andrew J. Gentles,
- Matthew J. Wakefield,
- Oleksiy Kohany,
- Wanjun Gu,
- Mark A. Batzer,
- David D. Pollock,
- and Jerzy Jurka
Genome Res. July 2007 17: 992-1004; Published in Advance May 10, 2007, doi:10.1101/gr.6070707
...and Visualization Center, Center for BioModular Multi-Scale Systems, Louisiana State University, Baton Rouge, Louisiana 70803, USA Abstract The genome of the gray short-tailed opossum Monodelphis domestica is notable for its large size (∼3.6 Gb). We characterized nearly 500 families of interspersed...
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LETTER: Using genomic data to unravel the root of the placental mammal phylogeny
- William J. Murphy,
- Thomas H. Pringle,
- Tess A. Crider,
- Mark S. Springer,
- and Webb Miller
Genome Res. April 2007 17: 413-421; Published in Advance February 23, 2007, doi:10.1101/gr.5918807
..., armadillo, elephant, and opossum to identify informative coding indels that would serve as rare genomic changes to infer early events in placental mammal phylogeny. We also expanded our species sampling by including sequence data from &gt;30 ongoing projects, followed by PCR and sequencing validation...
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Platypus Special/Letter: Bird-like sex chromosomes of platypus imply recent origin of mammal sex chromosomes
- Frédéric Veyrunes,
- Paul D. Waters,
- Pat Miethke,
- Willem Rens,
- Daniel McMillan,
- Amber E. Alsop,
- Frank Grützner,
- Janine E. Deakin,
- Camilla M. Whittington,
- Kyriena Schatzkamer,
- Colin L. Kremitzki,
- Tina Graves,
- Malcolm A. Ferguson-Smith,
- Wes Warren,
- and Jennifer A. Marshall Graves
Genome Res. June 2008 18: 965-973; Published in Advance May 7, 2008, doi:10.1101/gr.7101908
...E Deakin D McMillan Whittington, C Malcolm genome;gr.7101908 10.1101/gr.7101908 1088-9051 Bird-like sex chromosomes of platypus imply recent origin of mammal sex chromosomes Bird-like sex chromosomes of platypus imply recent origin of mammal sex chromosomes Frédéric Veyrunes 1 , 2 , 6 , Paul D. Waters 1...
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Method: Genome-wide characterization of centromeric satellites from multiple mammalian genomes
- Can Alkan,
- Maria Francesca Cardone,
- Claudia Rita Catacchio,
- Francesca Antonacci,
- Stephen J. O'Brien,
- Oliver A. Ryder,
- Stefania Purgato,
- Monica Zoli,
- Giuliano Della Valle,
- Evan E. Eichler,
- and Mario Ventura
Genome Res. January 2011 21: 137-145; Published in Advance November 16, 2010, doi:10.1101/gr.111278.110
...elements correspond to functional centromeric sequences. We analyzed genome datasets from six species of mammals representing the diversity of the mammalian lineage, namely, horse, dog, elephant, armadillo, opossum, and platypus. We define candidate monomer satellite repeats and demonstrate centromeric...
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Resource: Breakpoint graphs and ancestral genome reconstructions
- Max A. Alekseyev and
- Pavel A. Pevzner
Genome Res. May 2009 19: 943-957; Published in Advance February 13, 2009, doi:10.1101/gr.082784.108
..., macaque, mouse, rat, dog, and opossum. MGRA relies on the notion of the multiple breakpoint graphs to overcome some limitations of the existing approaches to ancestral genome reconstructions. MGRA also generates the rearrangement-based characters guiding the phylogenetic tree reconstruction when...
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Research: The recombination landscape of the zebra finch Taeniopygia guttata genome
- Niclas Backström,
- Wolfgang Forstmeier,
- Holger Schielzeth,
- Harriet Mellenius,
- Kiwoong Nam,
- Elisabeth Bolund,
- Matthew T. Webster,
- Torbjörn Öst,
- Melanie Schneider,
- Bart Kempenaers,
- and Hans Ellegren
Genome Res. April 2010 20: 485-495; Published in Advance March 31, 2010, doi:10.1101/gr.101410.109
...eutherian mammals studied so far is in the range of 0.5–1.2 cM/Mb, with mouse and rat in the lower and human in the upper end (Jensen-Seaman et al. 2004;Dumont andPayseur 2007).Marsupials (as represented by opossum) have a much lower rate (»0.2 cM/Mb; Samollow 2008), and this probably holds true for wallaby...
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ARTICLE: Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates
- Yoichiro Nakatani,
- Hiroyuki Takeda,
- Yuji Kohara,
- and Shinichi Morishita
Genome Res. September 2007 17: 1254-1265; Published in Advance July 25, 2007, doi:10.1101/gr.6316407
...Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates Yoichiro Nakatani 1 , 5 , Hiroyuki Takeda 2 , Yuji Kohara 3 , and Shinichi Morishita 1 , 4 , 5 1 Department...
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Methods: Reconstructing contiguous regions of an ancestral genome
- Jian Ma,
- Louxin Zhang,
- Bernard B. Suh,
- Brian J. Raney,
- Richard C. Burhans,
- W. James Kent,
- Mathieu Blanchette,
- David Haussler,
- and Webb Miller
Genome Res. December 2006 16: 1557-1565; Published in Advance September 18, 2006, doi:10.1101/gr.5383506
...rearrangements ( Wienberg 2004 ), the chromosomal painting approach has the advantage that data are available for over 80 mammals (50 primates). Alternatively, computational methods that attempt to identify orthologous genomic intervals have much higher resolution, potentially down to under a kilobase. However...
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