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Research: Distinct types of short open reading frames are translated in plant cells
- Igor Fesenko,
- Ilya Kirov,
- Andrey Kniazev,
- Regina Khazigaleeva,
- Vassili Lazarev,
- Daria Kharlampieva,
- Ekaterina Grafskaia,
- Viktor Zgoda,
- Ivan Butenko,
- Georgy Arapidi,
- Anna Mamaeva,
- Vadim Ivanov,
- and Vadim Govorun
Genome Res. September 2019 29: 1464-1477; Published in Advance August 6, 2019, doi:10.1101/gr.253302.119
...author: fesigor@gmail.comAbstractGenomes contain millions of short (<100 codons) open reading frames (sORFs), which are usually dismissed during gene annotation. Nevertheless, peptides encoded by such sORFs can play important biological roles, and their impact on cellular processes has long been...
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Research: Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster
- Anna Grandchamp,
- Lucas Kühl,
- Marie Lebherz,
- Kathrin Brüggemann,
- John Parsch,
- and Erich Bornberg-Bauer
Genome Res. June 2023 33: 872-890; Published in Advance July 13, 2023, doi:10.1101/gr.277482.122
...novo gene to emerge, at least two events must occur: the emergence of a new open reading frame (ORF), and the gain of transcription. Nonetheless, s and synteny between two closely related species can be extensively reshuffled during evolution.The extensive divergence of noncoding regions because...
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Research: Genome-wide mapping reveals R-loops associated with centromeric repeats in maize
- Yang Liu,
- Qian Liu,
- Handong Su,
- Kunpeng Liu,
- Xue Xiao,
- Wei Li,
- Qianwen Sun,
- James A. Birchler,
- and Fangpu Han
Genome Res. August 2021 31: 1409-1418; Published in Advance July 9, 2021, doi:10.1101/gr.275270.121
...the 5.8S, 18S, and 25S rDNA genes, the internal transcribed spacer (ITS1 and ITS2), and the intergenic spacer IGS. To determine which structural elements in 45S are the major contributors for R-loop formation, we used consensus sequences for the 45S rDNA to query trimmed ssDRIP-seq and input reads using...
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Research: Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis
- Huan Wang,
- Pil Joong Chung,
- Jun Liu,
- In-Cheol Jang,
- Michelle J. Kean,
- Jun Xu,
- and Nam-Hai Chua
Genome Res. March 2014 24: 444-453; Published in Advance January 8, 2014, doi:10.1101/gr.165555.113
...transcription regulation and the generation of cellular complexity. Depending on their genomic origins, lncRNAs can be transcribed from intergenic or intragenic regions or from introns of protein-coding genes. We have recently reported more than 6000 intergenic lncRNAs in Arabidopsis . Here, we systematically...
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LETTER: Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana
- Takeshi Itoh,
- Tsuyoshi Tanaka,
- Roberto A. Barrero,
- Chisato Yamasaki,
- Yasuyuki Fujii,
- Phillip B. Hilton,
- Baltazar A. Antonio,
- Hideo Aono,
- Rolf Apweiler,
- Richard Bruskiewich,
- Thomas Bureau,
- Frances Burr,
- Antonio Costa de Oliveira,
- Galina Fuks,
- Takuya Habara,
- Georg Haberer,
- Bin Han,
- Erimi Harada,
- Aiko T. Hiraki,
- Hirohiko Hirochika,
- Douglas Hoen,
- Hiroki Hokari,
- Satomi Hosokawa,
- Yue Hsing,
- Hiroshi Ikawa,
- Kazuho Ikeo,
- Tadashi Imanishi,
- Yukiyo Ito,
- Pankaj Jaiswal,
- Masako Kanno,
- Yoshihiro Kawahara,
- Toshiyuki Kawamura,
- Hiroaki Kawashima,
- Jitendra P. Khurana,
- Shoshi Kikuchi,
- Setsuko Komatsu,
- Kanako O. Koyanagi,
- Hiromi Kubooka,
- Damien Lieberherr,
- Yao-Cheng Lin,
- David Lonsdale,
- Takashi Matsumoto,
- Akihiro Matsuya,
- W. Richard McCombie,
- Joachim Messing,
- Akio Miyao,
- Nicola Mulder,
- Yoshiaki Nagamura,
- Jongmin Nam,
- Nobukazu Namiki,
- Hisataka Numa,
- Shin Nurimoto,
- Claire O’Donovan,
- Hajime Ohyanagi,
- Toshihisa Okido,
- Satoshi OOta,
- Naoki Osato,
- Lance E. Palmer,
- Francis Quetier,
- Saurabh Raghuvanshi,
- Naomi Saichi,
- Hiroaki Sakai,
- Yasumichi Sakai,
- Katsumi Sakata,
- Tetsuya Sakurai,
- Fumihiko Sato,
- Yoshiharu Sato,
- Heiko Schoof,
- Motoaki Seki,
- Michie Shibata,
- Yuji Shimizu,
- Kazuo Shinozaki,
- Yuji Shinso,
- Nagendra K. Singh,
- Brian Smith-White,
- Jun-ichi Takeda,
- Motohiko Tanino,
- Tatiana Tatusova,
- Supat Thongjuea,
- Fusano Todokoro,
- Mika Tsugane,
- Akhilesh K. Tyagi,
- Apichart Vanavichit,
- Aihui Wang,
- Rod A. Wing,
- Kaori Yamaguchi,
- Mayu Yamamoto,
- Naoyuki Yamamoto,
- Yeisoo Yu,
- Hao Zhang,
- Qiang Zhao,
- Kenichi Higo,
- Benjamin Burr,
- Takashi Gojobori,
- Takuji Sasaki,
- and for the Rice Annotation Project
Genome Res. February 2007 17: 175-183; Published in Advance January 8, 2007, doi:10.1101/gr.5509507
...a quarter of the rice appears to contain transcribed regions, while about half of the A. thaliana appears to be transcribed (Supplemental Table 2). This difference can perhaps be explained by the presence of transposable elements inserted among the intergenic regions of rice, which are greater in number...
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RESOURCE: Large-Scale Identification and Analysis of Genome-Wide Single-Nucleotide Polymorphisms for Mapping in Arabidopsis thaliana
- Karl J. Schmid,
- Thomas Rosleff Sörensen,
- Ralf Stracke,
- Ottó Törjék,
- Thomas Altmann,
- Tom Mitchell-Olds,
- and Bernd Weisshaar
Genome Res. June 2003 13: 1250-1257; doi:10.1101/gr.728603
.... Sequence variation and haplotype structure surrounding the flowering time locus FRI in Arabidopsis thaliana. Genetics 161 : 289 –298. ↵ Haubold, B., Kroymann, J., Ratzka, A., Mitchell-Olds, T., and Wiehe, T. 2002 . Recombination and gene conversion in a 170 kb genomic region of Arabidopsis thaliana...
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Resource: Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines
- Wen Huang,
- Andreas Massouras,
- Yutaka Inoue,
- Jason Peiffer,
- Miquel Ràmia,
- Aaron M. Tarone,
- Lavanya Turlapati,
- Thomas Zichner,
- Dianhui Zhu,
- Richard F. Lyman,
- Michael M. Magwire,
- Kerstin Blankenburg,
- Mary Anna Carbone,
- Kyle Chang,
- Lisa L. Ellis,
- Sonia Fernandez,
- Yi Han,
- Gareth Highnam,
- Carl E. Hjelmen,
- John R. Jack,
- Mehwish Javaid,
- Joy Jayaseelan,
- Divya Kalra,
- Sandy Lee,
- Lora Lewis,
- Mala Munidasa,
- Fiona Ongeri,
- Shohba Patel,
- Lora Perales,
- Agapito Perez,
- LingLing Pu,
- Stephanie M. Rollmann,
- Robert Ruth,
- Nehad Saada,
- Crystal Warner,
- Aneisa Williams,
- Yuan-Qing Wu,
- Akihiko Yamamoto,
- Yiqing Zhang,
- Yiming Zhu,
- Robert R.H. Anholt,
- Jan O. Korbel,
- David Mittelman,
- Donna M. Muzny,
- Richard A. Gibbs,
- Antonio Barbadilla,
- J. Spencer Johnston,
- Eric A. Stone,
- Stephen Richards,
- Bart Deplancke,
- and Trudy F.C. Mackay
Genome Res. July 2014 24: 1193-1208; Published in Advance April 8, 2014, doi:10.1101/gr.171546.113
..., large and small introns, and intergenic regions, while the size distribution of indels in coding regions has discrete ‘‘peaks’’ for indel sizes inmultiples of 3 bp (Supplemental Fig. S7). This pattern suggests strongnegative selectionagainst frame-shifting indels compared to more relaxed selection...
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Resource: Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis
- Yamile Marquez,
- John W.S. Brown,
- Craig Simpson,
- Andrea Barta,
- and Maria Kalyna
Genome Res. June 2012 22: 1184-1195; Published in Advance March 5, 2012, doi:10.1101/gr.134106.111
...(Supplemental Fig. S1). Sequencing resulted in nearly 116 million paired-end reads (75-nt read length). To our knowledge, this is the first time that a normalized cDNA library of Arabidopsis has been subjected to high-throughput sequencing. Paired-end reads were aligned to the Arabidopsis thaliana reference...
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Methods: Whole Genome Sequence Comparisons and “Full-Length” cDNA Sequences: A Combined Approach to Evaluate and Improve Arabidopsis Genome Annotation
- Vanina Castelli,
- Jean-Marc Aury,
- Olivier Jaillon,
- Patrick Wincker,
- Christian Clepet,
- Manuella Menard,
- Corinne Cruaud,
- Francis Quétier,
- Claude Scarpelli,
- Vincent Schächter,
- Gary Temple,
- Michel Caboche,
- Jean Weissenbach,
- and Marcel Salanoubat
Genome Res. March 2004 14: 406-413; doi:10.1101/gr.1515604
..., Carlsbad, California 92008 USA Abstract To evaluate the existing annotation of the Arabidopsis genome further, we generated a collection of evolutionary conserved regions (ecores) between Arabidopsis and rice. The ecore analysis provides evidence that the gene catalog of Arabidopsis...
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LETTER: Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses
- Besma Ben Amor,
- Sonia Wirth,
- Francisco Merchan,
- Philippe Laporte,
- Yves d’Aubenton-Carafa,
- Judith Hirsch,
- Alexis Maizel,
- Allison Mallory,
- Antoine Lucas,
- Jean Marc Deragon,
- Herve Vaucheret,
- Claude Thermes,
- and Martin Crespi
Genome Res. January 2009 19: 57-69; Published in Advance November 7, 2008, doi:10.1101/gr.080275.108
...are mainly transcribed by RNA polymerase II from intergenic regions, although few miRNA genes are located in introns of protein-coding genes. It has been estimated that miRNA genes could represent more than 1% of the expressed in worms and humans where it has been proposed that a single miRNA could regulate...

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