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Research: Deep taxon sampling reveals the evolutionary dynamics of novel gene families in Pristionchus nematodes
- Neel Prabh,
- Waltraud Roeseler,
- Hanh Witte,
- Gabi Eberhardt,
- Ralf J. Sommer,
- and Christian Rödelsperger
Genome Res. November 2018 28: 1664-1674; Published in Advance September 19, 2018, doi:10.1101/gr.234971.118
...-specific expression of the lsy-6 microRNA. Development 132: 5451–5460. ↵Juan D, Rico D, Marques-Bonet T, Fernández-Capetillo O, Valencia A. 2014. Late-replicating CNVs as a source of new genes. Biol Open 3: 231. ↵Katju V, Lynch M. 2003. The structure and early evolution of recently arisen gene duplicates...
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Research: Birth and expression evolution of mammalian microRNA genes
- Julien Meunier,
- Frédéric Lemoine,
- Magali Soumillon,
- Angélica Liechti,
- Manuela Weier,
- Katerina Guschanski,
- Haiyang Hu,
- Philipp Khaitovich,
- and Henrik Kaessmann
Genome Res. January 2013 23: 34-45; Published in Advance October 3, 2012, doi:10.1101/gr.140269.112
...Research 35 www..org Evolution of mammalian microRNA genes miRNAgenes are overlappingwith introns of protein-coding genes in the different species, although annotated introns only constitute ;22%–45% of the entire (Table 2). The overrepresentation of miRNA families in introns is highly significant in all...
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Research: Multiple RNA recognition patterns during microRNA biogenesis in plants
- Nicolás G. Bologna,
- Arnaldo L. Schapire,
- Jixian Zhai,
- Uciel Chorostecki,
- Jerome Boisbouvier,
- Blake C. Meyers,
- and Javier F. Palatnik
Genome Res. October 2013 23: 1675-1689; Published in Advance August 29, 2013, doi:10.1101/gr.153387.112
...Multiple RNA recognition patterns during microRNA biogenesis in plants Nicolás G. Bologna 1 , 4 , Arnaldo L. Schapire 1 , Jixian Zhai 2 , Uciel Chorostecki 1 , Jerome Boisbouvier 3 , Blake C. Meyers 2 and Javier F. Palatnik...
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LETTER: Genomic evolution of the placenta using co-option and duplication and divergence
- Kirstin Knox and
- Julie C. Baker
Genome Res. May 2008 18: 695-705; Published in Advance March 13, 2008, doi:10.1101/gr.071407.107
...Genomic evolution of the placenta using co-option and duplication and divergence Kirstin Knox and Julie C. Baker 1 Department of Genetics, Stanford University, Stanford, California 94062, USA Abstract The invention of the placenta facilitated...
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Research: A role for palindromic structures in the cis-region of maize Sirevirus LTRs in transposable element evolution and host epigenetic response
- Alexandros Bousios,
- Concepcion M. Diez,
- Shohei Takuno,
- Vojtech Bystry,
- Nikos Darzentas,
- and Brandon S. Gaut
Genome Res. February 2016 26: 226-237; Published in Advance December 2, 2015, doi:10.1101/gr.193763.115
...for sequence evolution. Supporting this conjecture, we found that the LTRs of the three lower copy families exhibited similar correspondences between indel size and location, GC content, and siRNA targeting (Supplemental Fig. S5A–C). Moreover, analysis of the cross-mapping siRNAs among all families revealed...
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LETTER: A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains
- Qian-Hao Zhu,
- Andrew Spriggs,
- Louisa Matthew,
- Longjiang Fan,
- Gavin Kennedy,
- Frank Gubler,
- and Chris Helliwell
Genome Res. September 2008 18: 1456-1465; Published in Advance August 7, 2008, doi:10.1101/gr.075572.107
...duplication of target gene sequences in Arabidopsis thaliana . Nat. Genet. 36 : 1282 – 1290 . ↵ Arazi, T. , Talmor-Neiman, M. , Stav, R. , Riese, M. , Huijser, P. , Baulcombe, D.C. ( 2005 ) Cloning and characterization of microRNAs from moss . Plant J. 43 : 837 – 848 . ↵ Axtell, M.J. , Snyder, J.A. , Bartel...
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Methods: Computational prediction of miRNAs in Arabidopsis thaliana
- Alex Adai,
- Cameron Johnson,
- Sizolwenkosi Mlotshwa,
- Sarah Archer-Evans,
- Varun Manocha,
- Vicki Vance,
- and Venkatesan Sundaresan
Genome Res. January 2005 15: 78-91; doi:10.1101/gr.2908205
...(candidate microRNA 214) miRNA sequence had a predicted target sequence that was conserved across four Arabidopsis transcripts, and the cmr6 candidate miRNA sequence had five target sites within the untranslated leader of the target transcript within Arabidopsis . These sequences are unlikely to occur...
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PERSPECTIVE: The Arabidopsis genome: A foundation for plant research
- Michael Bevan and
- Sean Walsh
Genome Res. December 2005 15: 1632-1642; doi:10.1101/gr.3723405
.... 2004 ), as did whole- arrays ( Yamada et al. 2003 ). These data also revealed extensive antisense transcription of genes ( Wang et al. 2005 ) and microRNAs, most of which appear to be encoded in non-gene space and may act as regulators of gene expression ( Reinhart et al. 2002 ). They may serve...
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LETTER: A Large Imprinted microRNA Gene Cluster at the Mouse Dlk1-Gtl2 Domain
- Hervé Seitz,
- Hélène Royo,
- Marie-Line Bortolin,
- Shau-Ping Lin,
- Anne C. Ferguson-Smith,
- and Jérôme Cavaillé
Genome Res. September 2004 14: 1741-1748; Published in Advance August 12, 2004, doi:10.1101/gr.2743304
.... 2002 . RNA-directed DNA methylation in Arabidopsis . Proc. Natl. Acad. Sci. 99 : 16499 -16506. ↵ Aukerman, M.J. and Sakai, H. 2003 . Regulation of flowering time and floral organ identity by a MicroRNA and its APETALA2-like target genes. Plant Cell 15 : 2730 -2741. ↵ Barlow, D.P. 1993 . Methylation...
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Research: Analysis of Arabidopsis genome-wide variations before and after meiosis and meiotic recombination by resequencing Landsberg erecta and all four products of a single meiosis
- Pingli Lu,
- Xinwei Han,
- Ji Qi,
- Jiange Yang,
- Asela J. Wijeratne,
- Tao Li,
- and Hong Ma
Genome Res. March 2012 22: 508-518; Published in Advance November 21, 2011, doi:10.1101/gr.127522.111
...- -Total 656 1002 1658 542 158 700 aIndels were detected within the UTR region of a 59 or 39 terminal exon. bA portion of a coding region within an exon was deleted from the Ler when compared with Col. cFor cases when a single exon is affected. dncRNA: nonprotein-coding RNA; miRNA: microRNA. Lu et al. 512...
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