Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences

By Tarjei S. Mikkelsen, M. Wakefield, Bronwen L. Aken, C. Amemiya, Jean L. Chang, Shannon E. Duke, Manuel Garber, Andrew J. Gentles, L. Goodstadt, Andreas Heger and 52 more. Nature, 2007

750 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/ab580d585b369a1f951e906f130f378844a05ce2

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Citations in the corpus

Retrotransposons revisited: the restraint and rehabilitation of parasites. (2008, positive): “Low-copy number and degenerate CR1/L3 clade members form only 0.05%, 0.3%, and 0.5% of mouse, human, and platypus genomes, respectively, but have expanded to 2.3% of opossum DNA (Jurka et al., 2005; Gentles et al., 2007; Mikkelsen et al., 2007; Warren et al., 2008).”
The Genome 10K Project: A Way Forward (2015, neutral): “Passerine birds (5756, 127) Parrots (367, 5) Falcons (64, 2) Seriemas (2, 1) Kingfisher and allies (152, 9) Woodpeckers (406, 8) Hornbills (62, 2) Trogons (44, 1) Cuckoo roller (1, 1) Mousebirds (5, 1) Owls (213, 2) Hawks, eagles, vultures (249, 4) Pelicans, frigatebirds, cormorants (174, 4) Petrels”
Repetitive Elements May Comprise Over Two-Thirds of the Human Genome (2011, methodology): “Motivated by these arguments, we developed a novel approach to identify and demarcate likely repetitive regions in large genomes”
Phylogenetic Relationships and Classification of Didelphid Marsupials, an Extant Radiation of New World Metatherian Mammals (2009, background): “Of the many genes that have been sequenced to date from one or more didelphid marsupials (including the entire genome of Monodelphis domestica; Mikkelsen et al., 2007), only a few have been sequenced from enough taxa to be useful for phylogenetic inference.”
Weird Animal Genomes and the Evolution of Vertebrate Sex and Sex Chromosomes (2008, background): “The opossum was sequenced to a depth of sixfold (48), and a twofold sequence of a model kangaroo, the tammar wallaby, is now available and in assembly.”
Biased gene conversion and the evolution of mammalian genomic landscapes. (2009, background): “The most striking example of intensive fusions is the genome of the marsupial Monodelphis domestica, which consists of only 8 giant autosomes and one small X chromosome (96).”
Molecular Mechanisms of Ultraviolet Radiation-Induced DNA Damage and Repair (2010, neutral): “Eukaryotes Monodelphis domestica + − [134]”
DNA methylation: superior or subordinate in the epigenetic hierarchy? (2011, background): “However, about 40% of ESC bivalent domains are preserved upon differentiation, indicating that most genes harboring bivalent modifications are driven into either an active or an inactive state.(66,74) Thus, genes that are silenced by this mechanism maintain the possibility of being readily activated”
A Methodological Framework for the Reconstruction of Contiguous Regions of Ancestral Genomes and Its Application to Mammalian Genomes (2008, methodology): “N We first downloaded the chained and netted pairwise alignments from the UCSC Genome Bioinformatics site [32] and the coordinates of all the alignments of the human genome (build hg18, March 2006 [60]) against respectively macaca (build rheMac2, January 2006 [61]), mouse (build mm9, July 2007 [62])”
Computational methods for transcriptome annotation and quantification using RNA-seq (2011, methodology): “Seed-extend methods perform better than exon-first approaches when mapping reads from polymorphic species 52 .”