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Research: Differences in activity and stability drive transposable element variation in tropical and temperate maize
- Shujun Ou,
- Armin Scheben,
- Tyler Collins,
- Yinjie Qiu,
- Arun S. Seetharam,
- Claire C. Menard,
- Nancy Manchanda,
- Jonathan I. Gent,
- Michael C. Schatz,
- Sarah N. Anderson,
- Matthew B. Hufford,
- and Candice N. Hirsch
Genome Res. August 2024 34: 1140-1153; Published in Advance September 9, 2024, doi:10.1101/gr.278131.123
...Community et al. 2022). When compared to the original EDTA pipeline, panEDTA in maize, rice, and Arabidopsis (Supplemental Figs. S1, S2A) annotated a similar number of total bases of TE sequence, but with a substantial improvement in the consistency of element classification across individuals (Supplemental...
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Research: Characterization of DNA methylation reader proteins in Arabidopsis thaliana
- Jonathan Cahn,
- James P.B. Lloyd,
- Ino D. Karemaker,
- Pascal W.T.C. Jansen,
- Jahnvi Pflueger,
- Owen Duncan,
- Jakob Petereit,
- Ozren Bogdanovic,
- A. Harvey Millar,
- Michiel Vermeulen,
- and Ryan Lister
Genome Res. December 2024 34: 2229-2243; Published in Advance December 4, 2024, doi:10.1101/gr.279379.124
...in the vegetative cell of mature pollen (Wang et al. 2024). Considering the specialized function and regulation of DNA methylation in some tissues such as pollen vegetative cell and endosperm, it is likely that the loss of mC readers would only create phenotypes in these specific cell types, or during restricted...
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Research: Genome-wide redistribution of 24-nt siRNAs in rice gametes
- Chenxin Li,
- Hengping Xu,
- Fang-Fang Fu,
- Scott D. Russell,
- Venkatesan Sundaresan,
- and Jonathan I. Gent
Genome Res. February 2020 30: 173-184; Published in Advance January 2, 2020, doi:10.1101/gr.253674.119
...anthers in diverse angiosperms, including rice (Johnson et al. 2009; Zhai et al. 2015b; Fei et al. 2016; Xia et al. 2019). In female reproductive tissues, phasiRNAs are not well characterized, but the argonaute MEL1 binds 21-nt phasiRNAs and is required for both male and female meiosis in rice (Nonomura...
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Research: Resetting of the 24-nt siRNA landscape in rice zygotes
- Chenxin Li,
- Jonathan I. Gent,
- Hengping Xu,
- Hong Fu,
- Scott D. Russell,
- and Venkatesan Sundaresan
Genome Res. February 2022 32: 309-323; Published in Advance December 23, 2021, doi:10.1101/gr.275981.121
...that rice developing endosperm (7–8 d after fertilization) has a unique siRNA profile in which a small number of loci accounts for the majority of siRNAs (Rodrigues et al. 2013). These siRNA loci were termed siren loci (siRNA in the endosperm). A similar phenomenon was recently reported in Brassica rapa...
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Research: Parent-of-origin-dependent nucleosome organization correlates with genomic imprinting in maize
- Xiaomei Dong,
- Jian Chen,
- Tong Li,
- En Li,
- Xiangbo Zhang,
- Mei Zhang,
- Weibin Song,
- Haiming Zhao,
- and Jinsheng Lai
Genome Res. July 2018 28: 1020-1028; Published in Advance June 14, 2018, doi:10.1101/gr.230201.117
...the expression of imprinted genes in maize endosperm. Mol Plant 10: 442–455. ↵Du M, Luo M, Zhang R, Finnegan EJ, Koltunow AM. 2014. Imprinting in rice: the role of DNA and histone methylation in modulating parent-of-origin specific expression and determining transcript start sites. Plant J 79: 232–242. ↵Fincher...
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Resource: A comparative transcriptional landscape of maize and sorghum obtained by single-molecule sequencing
- Bo Wang,
- Michael Regulski,
- Elizabeth Tseng,
- Andrew Olson,
- Sara Goodwin,
- W. Richard McCombie,
- and Doreen Ware
Genome Res. June 2018 28: 921-932; Published in Advance April 30, 2018, doi:10.1101/gr.227462.117
...reproductive tissues, as also hypothesized in rice and Arabidopsis (Wu et al. 2014; Cui et al. 2015). However, we also observed differences among species. For example, in maize unlike in sorghum, endosperm’s transcriptome is younger than in other tissues, including pollen, suggesting that differentmechanisms...
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Resource: High-resolution mapping of open chromatin in the rice genome
- Wenli Zhang,
- Yufeng Wu,
- James C. Schnable,
- Zixian Zeng,
- Michael Freeling,
- Gregory E. Crawford,
- and Jiming Jiang
Genome Res. January 2012 22: 151-162; Published in Advance November 22, 2011, doi:10.1101/gr.131342.111
...High-resolution mapping of open chromatin in the rice genome Wenli Zhang 1 , 4 , Yufeng Wu 1 , 4 , James C. Schnable 2 , Zixian Zeng 1 , Michael Freeling 2 , Gregory E. Crawford 3 and Jiming Jiang 1 , 5...
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Research: Complementation contributes to transcriptome complexity in maize (Zea mays L.) hybrids relative to their inbred parents
- Anja Paschold,
- Yi Jia,
- Caroline Marcon,
- Steve Lund,
- Nick B. Larson,
- Cheng-Ting Yeh,
- Stephan Ossowski,
- Christa Lanz,
- Dan Nettleton,
- Patrick S. Schnable,
- and Frank Hochholdinger
Genome Res. December 2012 22: 2445-2454; Published in Advance October 19, 2012, doi:10.1101/gr.138461.112
...of such genes were reported from different tissues of the rice hybrid LYP9 (Wei et al. 2009), whereas other studies found fewer such genes in maize embryos, endosperm, seedling shoots, and immature ears of hybrids (Stupar and Springer 2006; Swanson-Wagner et al. 2006; Meyer et al. 2007; Stupar et al. 2007...
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LETTER: Uneven chromosome contraction and expansion in the maize genome
- Rémy Bruggmann,
- Arvind K. Bharti,
- Heidrun Gundlach,
- Jinsheng Lai,
- Sarah Young,
- Ana C. Pontaroli,
- Fusheng Wei,
- Georg Haberer,
- Galina Fuks,
- Chunguang Du,
- Christina Raymond,
- Matt C. Estep,
- Renyi Liu,
- Jeffrey L. Bennetzen,
- Agnes P. Chan,
- Pablo D. Rabinowicz,
- John Quackenbush,
- W. Brad Barbazuk,
- Rod A. Wing,
- Bruce Birren,
- Chad Nusbaum,
- Steve Rounsley,
- Klaus F.X. Mayer,
- and Joachim Messing
Genome Res. October 2006 16: 1241-1251; Published in Advance August 10, 2006, doi:10.1101/gr.5338906
.... 2003 ; Lai et al. 2004b ; Messing et al. 2004 ). Thus, maize is expected to have less than double the number of genes that are present in rice, which has an estimated gene number of 37,544 ( International Rice Genome Sequencing Project 2005 ). Based on the size of the transcriptome and the average gene...
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Resource: An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations
- Bernardo J. Clavijo,
- Luca Venturini,
- Christian Schudoma,
- Gonzalo Garcia Accinelli,
- Gemy Kaithakottil,
- Jonathan Wright,
- Philippa Borrill,
- George Kettleborough,
- Darren Heavens,
- Helen Chapman,
- James Lipscombe,
- Tom Barker,
- Fu-Hao Lu,
- Neil McKenzie,
- Dina Raats,
- Ricardo H. Ramirez-Gonzalez,
- Aurore Coince,
- Ned Peel,
- Lawrence Percival-Alwyn,
- Owen Duncan,
- Josua Trösch,
- Guotai Yu,
- Dan M. Bolser,
- Guy Namaati,
- Arnaud Kerhornou,
- Manuel Spannagl,
- Heidrun Gundlach,
- Georg Haberer,
- Robert P. Davey,
- Christine Fosker,
- Federica Di Palma,
- Andrew L. Phillips,
- A. Harvey Millar,
- Paul J. Kersey,
- Cristobal Uauy,
- Ksenia V. Krasileva,
- David Swarbreck,
- Michael W. Bevan,
- and Matthew D. Clark
Genome Res. May 2017 27: 885-896; Published in Advance April 18, 2017, doi:10.1101/gr.217117.116
...relative to other species. These gene sets were analyzed for overrepresented Gene Ontology (GO) terms, shown in Supplemental File S2. Gene families that were significantly expanded in wheat An improved wheat assembly and annotation Genome Research 889 www..org compared with Arabidopsis, rice, sorghum...
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