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202. A transposon surveillance mechanism that safeguards plant male fertility during stress

Author

Lee, Yang-Seok, primary, Maple, Robert, additional, Dürr, Julius, additional, Dawson, Alexander, additional, Tamim, Saleh, additional, Genio, Charo del, additional, Papareddy, Ranjith, additional, Luo, Anding, additional, Lamb, Jonathan C., additional, Sylvester, Anne W., additional, Birchler, James A., additional, Meyers, Blake C., additional, Nodine, Michael D., additional, Rouster, Jacques, additional, and Gutierrez-Marcos, Jose, additional

Published
2020
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214. A new Spirodela polyrhiza genome and proteome reveal a conserved chromosomal structure with high abundances of proteins favoring energy production

Author

Harkess, Alex, primary, McLoughlin, Fionn, additional, Bilkey, Natasha, additional, Elliott, Kiona, additional, Emenecker, Ryan, additional, Mattoon, Erin, additional, Miller, Kari, additional, Czymmek, Kirk, additional, Vierstra, Richard, additional, Meyers, Blake C., additional, and Michael, Todd P., additional

Published
2020
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222. Genome sequencing and analysis of the model grass Brachypodium distachyon

Author

Vogel, John P., Garvin, David F., Mockler, Todd C., Schmutz, Jeremy, Rokhsar, Dan, Bevan, Michael W., Barry, Kerrie, Lucas, Susan, Harmon-Smith, Miranda, Lail, Kathleen, Tice, Hope, Schmutz (Leader), Jeremy, Grimwood, Jane, McKenzie, Neil, Huo, Naxin, Gu, Yong Q., Lazo, Gerard R., Anderson, Olin D., Vogel (Leader), John P., You, Frank M., Luo, Ming-Cheng, Dvorak, Jan, Wright, Jonathan, Febrer, Melanie, Idziak, Dominika, Hasterok, Robert, Lindquist, Erika, Wang, Mei, Fox, Samuel E., Priest, Henry D., Filichkin, Sergei A., Givan, Scott A., Bryant, Douglas W., Chang, Jeff H., Mockler (Leader), Todd C., Wu, Haiyan, Wu, Wei, Hsia, An-Ping, Schnable, Patrick S., Kalyanaraman, Anantharaman, Barbazuk, Brad, Michael, Todd P., Hazen, Samuel P., Bragg, Jennifer N., Laudencia-Chingcuanco, Debbie, Weng, Yiqun, Haberer, Georg, Spannagl, Manuel, Mayer (Leader), Klaus, Rattei, Thomas, Mitros, Therese, Lee, Sang-Jik, Rose, Jocelyn K. C., Mueller, Lukas A., York, Thomas L., Wicker (Leader), Thomas, Buchmann, Jan P., Tanskanen, Jaakko, Schulman (Leader), Alan H., Gundlach, Heidrun, Bevan, Michael, Costa de Oliveira, Antonio, da C. Maia, Luciano, Belknap, William, Jiang, Ning, Lai, Jinsheng, Zhu, Liucun, Ma, Jianxin, Sun, Cheng, Pritham, Ellen, Salse (Leader), Jerome, Murat, Florent, Abrouk, Michael, Mayer, Klaus, Bruggmann, Remy, Messing, Joachim, Fahlgren, Noah, Sullivan, Christopher M., Carrington, James C., Chapman, Elisabeth J., May, Greg D., Zhai, Jixian, Ganssmann, Matthias, Guna Ranjan Gurazada, Sai, German, Marcelo, Meyers, Blake C., Green (Leader), Pamela J., Tyler, Ludmila, Wu, Jiajie, Thomson, James, Chen, Shan, Scheller, Henrik V., Harholt, Jesper, Ulvskov, Peter, Kimbrel, Jeffrey A., Bartley, Laura E., Cao, Peijian, Jung, Ki-Hong, Sharma, Manoj K, Vega-Sanchez, Miguel, Ronald, Pamela, Dardick, Christopher D., De Bodt, Stefanie, Verelst, Wim, Inzé, Dirk, Heese, Maren, Schnittger, Arp, Yang, Xiaohan, Kalluri, Udaya C., Tuskan, Gerald A., Hua, Zhihua, Vierstra, Richard D., Cui, Yu, Ouyang, Shuhong, Sun, Qixin, Liu, Zhiyong, Yilmaz, Alper, Grotewold, Erich, Sibout, Richard, Hematy, Kian, Mouille, Gregory, Höfte, Herman, Michael, Todd, Pelloux, Jérome, OʼConnor, Devin, Schnable, James, Rowe, Scott, Harmon, Frank, Cass, Cynthia L., Sedbrook, John C., Byrne, Mary E., Walsh, Sean, Higgins, Janet, Li, Pinghua, Brutnell, Thomas, Unver, Turgay, Budak, Hikmet, Belcram, Harry, Charles, Mathieu, Chalhoub, Boulos, and Baxter, Ivan

Published
2010
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223. Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans

Author

Haas, Brian J., Kamoun, Sophien, Zody, Michael C., Jiang, Rays H. Y., Handsaker, Robert E., Cano, Liliana M., Grabherr, Manfred, Kodira, Chinnappa D., Raffaele, Sylvain, Torto-Alalibo, Trudy, Bozkurt, Tolga O., Ah-Fong, Audrey M. V., Alvarado, Lucia, Anderson, Vicky L., Armstrong, Miles R., Avrova, Anna, Baxter, Laura, Beynon, Jim, Boevink, Petra C., Bollmann, Stephanie R., Bos, Jorunn I. B., Bulone, Vincent, Cai, Guohong, Cakir, Cahid, Carrington, James C., Chawner, Megan, Conti, Lucio, Costanzo, Stefano, Ewan, Richard, Fahlgren, Noah, Fischbach, Michael A., Fugelstad, Johanna, Gilroy, Eleanor M., Gnerre, Sante, Green, Pamela J., Grenville-Briggs, Laura J., Griffith, John, Grünwald, Niklaus J., Horn, Karolyn, Horner, Neil R., Hu, Chia-Hui, Huitema, Edgar, Jeong, Dong-Hoon, Jones, Alexandra M. E., Jones, Jonathan D. G., Jones, Richard W., Karlsson, Elinor K., Kunjeti, Sridhara G., Lamour, Kurt, Liu, Zhenyu, Ma, LiJun, MacLean, Daniel, Chibucos, Marcus C., McDonald, Hayes, McWalters, Jessica, Meijer, Harold J. G., Morgan, William, Morris, Paul F., Munro, Carol A., O’Neill, Keith, Ospina-Giraldo, Manuel, Pinzón, Andrés, Pritchard, Leighton, Ramsahoye, Bernard, Ren, Qinghu, Restrepo, Silvia, Roy, Sourav, Sadanandom, Ari, Savidor, Alon, Schornack, Sebastian, Schwartz, David C., Schumann, Ulrike D., Schwessinger, Ben, Seyer, Lauren, Sharpe, Ted, Silvar, Cristina, Song, Jing, Studholme, David J., Sykes, Sean, Thines, Marco, van de Vondervoort, Peter J. I., Phuntumart, Vipaporn, Wawra, Stephan, Weide, Rob, Win, Joe, Young, Carolyn, Zhou, Shiguo, Fry, William, Meyers, Blake C., van West, Pieter, Ristaino, Jean, Govers, Francine, Birch, Paul R. J., Whisson, Stephen C., Judelson, Howard S., and Nusbaum, Chad

Published
2009
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225. The Rice Annotation Project Database (RAP-DB): 2008 update*

Author

Tanaka, Tsuyoshi, Antonio, Baltazar A., Kikuchi, Shoshi, Matsumoto, Takashi, Nagamura, Yoshiaki, Numa, Hisataka, Sakai, Hiroaki, Wu, Jianzhong, Itoh, Takeshi, Sasaki, Takuji, Aono, Ryo, Fujii, Yasuyuki, Habara, Takuya, Harada, Erimi, Kanno, Masako, Kawahara, Yoshihiro, Kawashima, Hiroaki, Kubooka, Hiromi, Matsuya, Akihiro, Nakaoka, Hajime, Saichi, Naomi, Sanbonmatsu, Ryoko, Sato, Yoshiharu, Shinso, Yuji, Suzuki, Mami, Takeda, Jun-ichi, Tanino, Motohiko, Todokoro, Fusano, Yamaguchi, Kaori, Yamamoto, Naoyuki, Yamasaki, Chisato, Imanishi, Tadashi, Okido, Toshihisa, Tada, Masahito, Ikeo, Kazuho, Tateno, Yoshio, Gojobori, Takashi, Lin, Yao-Cheng, Wei, Fu-Jin, Hsing, Yue-ie, Zhao, Qiang, Han, Bin, Kramer, Melissa R., McCombie, Richard W., Lonsdale, David, O’Donovan, Claire C., Whitfield, Eleanor J., Apweiler, Rolf, Koyanagi, Kanako O., Khurana, Jitendra P., Raghuvanshi, Saurabh, Singh, Nagendra K., Tyagi, Akhilesh K., Haberer, Georg, Fujisawa, Masaki, Hosokawa, Satomi, Ito, Yukiyo, Ikawa, Hiroshi, Shibata, Michie, Yamamoto, Mayu, Bruskiewich, Richard M., Hoen, Douglas R., Bureau, Thomas E., Namiki, Nobukazu, Ohyanagi, Hajime, Sakai, Yasumichi, Nobushima, Satoshi, Sakata, Katsumi, Barrero, Roberto A., Sato, Yutaka, Souvorov, Alexandre, Smith-White, Brian, Tatusova, Tatiana, An, Suyoung, An, Gynheung, OOta, Satoshi, Fuks, Galina, Messing, Joachim, Christie, Karen R., Lieberherr, Damien, Kim, HyeRan, Zuccolo, Andrea, Wing, Rod A., Nobuta, Kan, Green, Pamela J., Lu, Cheng, Meyers, Blake C., Chaparro, Cristian, Piegu, Benoit, Panaud, Olivier, and Echeverria, Manuel

Published
2008

227. Table S1: sRNA-Seq mapping data from Construction and characterization of a knock-down RNA interference line of OsNRPD1 in rice (Oryza sativa ssp japonica cv Nipponbare)

Author

Debladis, Emilie, Tzuu-Fen Lee, Yan-Jiun Huang, Jui-Hsien Lu, Mathioni, Sandra M., Marie-Christine Carpentier, Llauro, Christel, Pierron, Davy, Mieulet, Delphine, Guiderdoni, Emmanuel, Pao-Yang Chen, Meyers, Blake C., Panaud, Olivier, and Lasserre, Eric

Subjects
food and beverages
Abstract

In plants, RNA-directed DNA methylation (RdDM) is a silencing mechanism relying on the production of 24-nt small interfering RNAs (siRNAs) by RNA POLYMERASE IV (Pol IV) to trigger methylation and inactivation of transposable elements (TEs). We present the construction and characterization of osnrpd1, a knock-down RNA interference line of OsNRPD1 gene that encodes the largest subunit of Pol IV in rice (Oryza sativa ssp japonica cv Nipponbare). We show that osnrpd1 displays a lower accumulation of OsNRPD1 transcripts, associated with an overall reduction of 24-nt siRNAs and DNA methylation level in all three contexts, CG, CHG and CHH. We uncovered new insertions of known active TEs, the LTR retrotransposons Tos17 and Lullaby and the long interspersed nuclear element-type retrotransposon Karma. However, we did not observe any clear developmental phenotype, contrary to what was expected for a mutant severely affected in RdDM. In addition, despite the presence of many putatively functional TEs in the rice genome, we found no evidence of in planta global reactivation of transposition. This knock-down of OsNRPD1 likely led to a weakly affected line, with no effect on development and a limited effect on transposition. We discuss the possibility that a knock-out mutation of OsNRPD1 would cause sterility in rice.This article is part of the discussion meeting issue ‘Crossroads between transposons and gene regulation’.

Published
2019
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231. Arabidopsis bioinformatics resources: The current state, challenges, and priorities for the future

Author

Doherty, Colleen, Friesner, Joanna, Gregory, Brian, Loraine, Ann, Megraw, Molly, Meyers, Blake C., Provart, Nicholas J., Slotkin, R. Keith, Town, Chris, Assmann, Sarah M., Axtell, Michael J., Berardini, Tanya, Chen, Sixue, Gehan, Malia, Huala, Eva, Jaiswal, Pankaj, Larson, Stephen, Li, Song, May, Sean, Michael, Todd, Pires, J. Chris, Topp, Chris, Walley, Justin, Wurtele, Eve, Doherty, Colleen, Friesner, Joanna, Gregory, Brian, Loraine, Ann, Megraw, Molly, Meyers, Blake C., Provart, Nicholas J., Slotkin, R. Keith, Town, Chris, Assmann, Sarah M., Axtell, Michael J., Berardini, Tanya, Chen, Sixue, Gehan, Malia, Huala, Eva, Jaiswal, Pankaj, Larson, Stephen, Li, Song, May, Sean, Michael, Todd, Pires, J. Chris, Topp, Chris, Walley, Justin, and Wurtele, Eve

Abstract

Effective research, education, and outreach efforts by the Arabidopsis thaliana community, as well as other scientific communities that depend on Arabidopsis resources, depend vitally on easily available and publicly-shared resources. These resources include reference genome sequence data and an ever-increasing number of diverse data sets and data types. TAIR (The Arabidopsis Information Resource) and Araport (originally named the Arabidopsis Information Portal) are community informatics resources that provide tools, data, and applications to the more than 30,000 researchers worldwide that use in their work either Arabidopsis as a primary system of study or data derived from Arabidopsis. Four years after Araport's establishment, the IAIC held another workshop to evaluate the current status of Arabidopsis Informatics and chart a course for future research and development. The workshop focused on several challenges, including the need for reliable and current annotation, community-defined common standards for data and metadata, and accessible and user-friendly repositories/tools/methods for data integration and visualization. Solutions envisioned included (a) a centralized annotation authority to coalesce annotation from new groups, establish a consistent naming scheme, distribute this format regularly and frequently, and encourage and enforce its adoption. (b) Standards for data and metadata formats, which are essential, but challenging when comparing across diverse genotypes and in areas with less-established standards (e.g., phenomics, metabolomics). Community-established guidelines need to be developed. (c) A searchable, central repository for analysis and visualization tools. Improved versioning and user access would make tools more accessible. Workshop participants proposed a "one-stop shop" website, an Arabidopsis "Super-Portal" to link tools, data resources, programmatic standards, and best practice descriptions for each data type. This must have community buy

Published
2019
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236. Transgenerational conditioned male fertility of HD-ZIP IV transcription factor mutant ocl4: impact on 21-nt phasiRNA accumulation in pre-meiotic maize anthers.

Author

Yadava, Pranjal, Tamim, Saleh, Zhang, Han, Teng, Chong, Zhou, Xue, Meyers, Blake C., and Walbot, Virginia

Subjects
PLANT fertility, FERTILITY, TRANSCRIPTION factors, ANTHER, SMALL interfering RNA, CORN
Abstract

Key message: Maize Outer cell layer 4 (ocl4) encodes an HD-ZIP IV transcription factor required for robust male fertility and 21-nt phasiRNA biogenesis. ocl4 fertility is favored in warm conditions, and phasiRNAs are partially restored. Environment-sensitive male-sterile plants have been described before and can result from different molecular mechanisms and biological processes, but putative environment-conditioned, transgenerational rescue of their male fertility is a rather new mystery. Here, we report a derivative line of the male-sterile outer cell layer 4 (ocl4) mutant of maize, in which fertility was restored and perpetuated over several generations. Conditioned fertile ocl4 anthers exhibit the anatomical abnormality of a partially duplicated endothecial layer, just like their sterile counterparts. We profiled the dynamics of phased, small interfering RNAs (phasiRNAs) during pre-meiotic development in fully sterile and various grades of semi-fertile ocl4 anthers. The conditioned fertile anthers accumulated significantly higher 21-nt phasiRNAs compared to ocl4 sterile samples, suggesting a partial restoration of phasiRNAs in conditioned fertility. We found that the biogenesis of 21-nt phasiRNAs is largely dependent on Ocl4 at three key steps: (1) production of PHAS precursor transcripts, (2) expression of miR2118 that modulates precursor processing, and (3) accumulation of 21-nt phasiRNAs. [ABSTRACT FROM AUTHOR]

Published
2021
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238. Atypical DNA methylation of genes encoding cysteine-rich peptides in Arabidopsis thaliana

Author

You Wanhui, Tyczewska Agata, Spencer Matthew, Daxinger Lucia, Schmid Marc W, Grossniklaus Ueli, Simon Stacey A, Meyers Blake C, Matzke Antonius JM, and Matzke Marjori

Subjects
Botany, QK1-989
Abstract

Abstract Background In plants, transposons and non-protein-coding repeats are epigenetically silenced by CG and non-CG methylation. This pattern of methylation is mediated in part by small RNAs and two specialized RNA polymerases, termed Pol IV and Pol V, in a process called RNA-directed DNA methylation. By contrast, many protein-coding genes transcribed by Pol II contain in their gene bodies exclusively CG methylation that is independent of small RNAs and Pol IV/Pol V activities. It is unclear how the different methylation machineries distinguish between transposons and genes. Here we report on a group of atypical genes that display in their coding region a transposon-like methylation pattern, which is associated with gene silencing in sporophytic tissues. Results We performed a methylation-sensitive amplification polymorphism analysis to search for targets of RNA-directed DNA methylation in Arabidopsis thaliana and identified several members of a gene family encoding cysteine-rich peptides (CRPs). In leaves, the CRP genes are silent and their coding regions contain dense, transposon-like methylation in CG, CHG and CHH contexts, which depends partly on the Pol IV/Pol V pathway and small RNAs. Methylation in the coding region is reduced, however, in the synergid cells of the female gametophyte, where the CRP genes are specifically expressed. Further demonstrating that expressed CRP genes lack gene body methylation, a CRP4-GFP fusion gene under the control of the constitutive 35 S promoter remains unmethylated in leaves and is transcribed to produce a translatable mRNA. By contrast, a CRP4-GFP fusion gene under the control of a CRP4 promoter fragment acquires CG and non-CG methylation in the CRP coding region in leaves similar to the silent endogenous CRP4 gene. Conclusions Unlike CG methylation in gene bodies, which does not dramatically affect Pol II transcription, combined CG and non-CG methylation in CRP coding regions is likely to contribute to gene silencing in leaves because loss of this methylation in synergid cells is associated with CRP gene expression. We discuss this unusual methylation pattern and its alteration in synergid cells as well as the possible retrogene origin and evolutionary significance of CRP genes that are methylated like transposons.

Published
2012
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239. Efficiency and precision of miRNA biogenesis modes in plants

Author

Moro, Belén, Chorostecki, Uciel, Arikit, Siwaret, Suarez, Irina P., Höbartner, Claudia, Rasia, Rodolfo M., Meyers, Blake C., and Palatnik, Javier F.

Subjects
Small RNA, RNA silencing, microRNA, Mutant, Computational biology, Biology, MiRNA processing, Cleavage (embryo), MiRNA biogenesis, Transcription factor
Abstract

Many evolutionary conserved microRNAs (miRNAs) in plants regulate transcription factors with key functions in development. Hence, mutations in the core components of the miRNA biogenesis machinery cause strong growth defects. An essential aspect of miRNA biogenesis is the precise excision of the small RNA from its precursor. In plants, miRNA precursors are largely variable in size and shape and can be processed by different modes. Here, we optimized an approach to detect intermediates during miRNA biogenesis. We characterized a miRNA whose processing is triggered by a terminal branched loop. Plant miRNA processing can be initiated by internal bubbles, small terminal loops or branched loops followed by dsRNA segments of 15-17 bp. Interestingly, precision and efficiency vary with the processing modes. Despite the various potential structural determinants present in a single a miRNA precursor, DCL1 is mostly guided by a predominant structural region in each precursor in wild-type plants. However, our studies in fiery1, hyl1 and se mutants revealed the existence of cleavage signatures consistent with the recognition of alternative processing determinants. The results provide a general view of the mechanisms underlying the specificity of miRNA biogenesis in plants.

Published
2018

240. CRISPR/Cas9-mediated resistance to cauliflower mosaic virus

Author

Liu, Haijie, Soyars, Cara L., Li, Jianhui, Fei, Qili, Peterson, Brenda A., Meyers, Blake C., Nimchuk, Zachary L., and Wang, Xiaofeng

Subjects
cauliflower mosaic virus, virus resistance, virus escape, food and beverages, small RNA, CRISPR-Cas9
Abstract

Viral diseases are a leading cause of worldwide yield losses in crop production. Breeding of resistance genes (R gene) into elite crop cultivars has been the standard and most cost-effective practice. However, R gene-mediated resistance is limited by the available R genes within genetic resources and in many cases, by strain specificity. Therefore, it is important to generate new and broad-spectrum antiviral strategies. The CRISPR-Cas9 (clustered regularly interspaced palindromic repeat, CRISPR-associated) editing system has been employed to confer resistance to human viruses and several plant single-stranded DNA geminiviruses, pointing out the possible application of the CRISPR-Cas9 system for virus control. Here, we demonstrate that strong viral resistance to cauliflower mosaic virus (CaMV), a pararetrovirus with a double-stranded DNA genome, can be achieved through Cas9-mediated multiplex targeting of the viral coat protein sequence. We further show that small interfering RNAs (siRNA) are produced and mostly map to the 30 end of single-guide RNAs (sgRNA), although very low levels of siRNAs map to the spacer region as well. However, these siRNAs are not responsible for the inhibited CaMV infection because there is no resistance if Cas9 is not present. We have also observed edited viruses in systematically infected leaves in some transgenic plants, with short deletions or insertions consistent with Cas9-induced DNA breaks at the sgRNA target sites in coat protein coding sequence. These edited coat proteins, in most cases, led to earlier translation stop and thus, nonfunctional coat proteins. We also recovered wild-type CP sequence in these infected transgenic plants, suggesting these edited viral genomes were packaged by wild-type coat proteins. Our data demonstrate that the CRISPR-Cas9 system can be used for virus control against plant pararetroviruses with further modifications. Virginia Tech University of North Carolina at Chapel Hill National Science Foundation, Grant/Award Number: 1455607, 1546837 Virginia Agricultural Experiment Station Hatch Program of NIFA, USDA and NSF, Grant/Award Number: 1645749

Published
2018

243. Variation and Inheritance of Small RNAs in Maize Inbreds and F1 Hybrids

Author

Crisp, Peter A., primary, Hammond, Reza, additional, Zhou, Peng, additional, Vaillancourt, Brieanne, additional, Lipzen, Anna, additional, Daum, Chris, additional, Barry, Kerrie, additional, de Leon, Natalia, additional, Buell, C. Robin, additional, Kaeppler, Shawn M., additional, Meyers, Blake C., additional, Hirsch, Candice N., additional, and Springer, Nathan M., additional

Published
2019
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