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PERSPECTIVE: The opossum genome: Insights and opportunities from an alternative mammal
- Paul B. Samollow
Genome Res. August 2008 18: 1199-1215; doi:10.1101/gr.065326.107
...mammalian species. Modern mammals comprise three major lineages ( Fig. 1 ). Judged from multiple nuclear sequence and mtDNA alignments, the most closely related of these, the Metatheria and Eutheria (placental mammals), diverged from their most recent common ancestor ∼173–190 million years ago (Mya) ( Kumar...
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Research: Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements
- Fu Xiang Quah,
- Miguel Vasconcelos Almeida,
- Moritz Blumer,
- Chengwei Ulrika Yuan,
- Bettina Fischer,
- Kirsten See,
- Ben Jackson,
- Richard Zatha,
- Bosco Rusuwa,
- George F. Turner,
- M. Emília Santos,
- Hannes Svardal,
- Martin Hemberg,
- Richard Durbin,
- and Eric Miska
Genome Res. May 2025 35: 1094-1107; Published in Advance April 10, 2025, doi:10.1101/gr.279674.124
..., which have been shown to be sources of phenotypic novelty in cichlid fishes (Santos et al. 2014; Carleton et al. 2020; Munby et al. 2021). About 36.55% of the A. calliptera sequences are annotated by RepeatModeler/RepeatMasker as TEs, of which the biggest classes were DNA transposons (12.09%), LINEs (8...
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LETTER: The 1.4-Mb CMT1A Duplication/HNPP Deletion Genomic Region Reveals Unique Genome Architectural Features and Provides Insights into the Recent Evolution of New Genes
- Ken Inoue,
- Ken Dewar,
- Nicholas Katsanis,
- Lawrence T. Reiter,
- Eric S. Lander,
- Keri L. Devon,
- Dudley W. Wyman,
- James R. Lupski,
- and Bruce Birren
Genome Res. June 1, 2001 11: 1018-1033; doi:10.1101/gr.180401
...in two common inherited peripheral neuropathies, Charcot-Marie-Tooth disease type 1A (CMT1A) and hereditary neuropathy with liability to pressure palsy (HNPP). CMT1A and HNPP exemplify a paradigm for genomic disorders wherein unique genome architectural features result in susceptibility to DNA...
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Resource: Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression
- Ni-Chen Chang,
- Quirze Rovira,
- Jonathan Wells,
- Cédric Feschotte,
- and Juan M. Vaquerizas
Genome Res. July 2022 32: 1408-1423; Published in Advance January 5, 2022, doi:10.1101/gr.275655.121
...% of all TEs in the human but only ∼10% in zebrafish (International Human Genome Sequencing Consortium 2001; Howe et al. 2013). In contrast, ∼40% of the zebrafish comprises DNA transposons, whereas in humans, they occupy just ∼3% (Pace and Feschotte 2007). Overall, all the major lineages of eukaryotic...
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Research: Variation in mutation, recombination, and transposition rates in Drosophila melanogaster and Drosophila simulans
- Yiguan Wang,
- Paul McNeil,
- Rashidatu Abdulazeez,
- Marta Pascual,
- Susan E. Johnston,
- Peter D. Keightley,
- and Darren J. Obbard
Genome Res. April 2023 33: 587-598; Published in Advance April 10, 2023, doi:10.1101/gr.277383.122
...the known differences in the TE community between these species (Mérel et al. 2020), with Helitron elements being the most common TE, followed by Gypsy and Jockey. DNA transposons made up 39% of all TEs in D. melanogaster and 44% in D. simulans; long-terminal repeats (LTRs) made up 36% and 34% in the two...
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LETTER: Additional Complexity on Human Chromosome 15q: Identification of a Set of Newly Recognized Duplicons (LCR15) on 15q11–q13, 15q24, and 15q26
- Miguel Angel Pujana,
- Marga Nadal,
- Mònica Gratacòs,
- Belén Peral,
- Katalin Csiszar,
- Rogelio González-Sarmiento,
- Lauro Sumoy,
- and Xavier Estivill
Genome Res. January 1, 2001 11: 98-111; doi:10.1101/gr.155601
...shown). Southern blot analysis of human genomic DNA revealed several fragments of hybridization with probe REP471 (Fig. 5 A). The analysis of a complete chromosome panel ( Dubois and Naylor 1993 ) revealed two copies of REP471 on chromosome Y, one on chromosomes 2 and 7, and at least eight copies...

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