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Research: Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control
- Todd P. Michael,
- Evan Ernst,
- Nolan Hartwick,
- Philomena Chu,
- Douglas Bryant,
- Sarah Gilbert,
- Stefan Ortleb,
- Erin L. Baggs,
- K. Sowjanya Sree,
- Klaus J. Appenroth,
- Joerg Fuchs,
- Florian Jupe,
- Justin P. Sandoval,
- Ksenia V. Krasileva,
- Ljudmylla Borisjuk,
- Todd C. Mockler,
- Joseph R. Ecker,
- Robert A. Martienssen,
- and Eric Lam
Genome Res. February 2021 31: 225-238; Published in Advance December 23, 2020, doi:10.1101/gr.266429.120
...signify an alternative defense system. Diurnal expression analysis revealed that only 13% of Wolffia genes are expressed in a time-of-day (TOD) fashion, which is less than the typical ∼40% found in several model plants under the same condition. In contrast to the model plants Arabidopsis and rice, many...
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Research: Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq
- Tingting Lu,
- Guojun Lu,
- Danlin Fan,
- Chuanrang Zhu,
- Wei Li,
- Qiang Zhao,
- Qi Feng,
- Yan Zhao,
- Yunli Guo,
- Wenjun Li,
- Xuehui Huang,
- and Bin Han
Genome Res. September 2010 20: 1238-1249; Published in Advance July 13, 2010, doi:10.1101/gr.106120.110
.... Abstract The functional complexity of the rice transcriptome is not yet fully elucidated, despite many studies having reported the use of DNA microarrays. Next-generation DNA sequencing technologies provide a powerful approach for mapping and quantifying the transcriptome, termed RNA sequencing (RNA...
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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
...Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis Yamile Marquez 1 , John W.S. Brown 2 , 3 , Craig Simpson 2 , Andrea Barta 1 , 4 and Maria Kalyna 1 , 4 1 Max F...
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Method: SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification
- Manuel Tardaguila,
- Lorena de la Fuente,
- Cristina Marti,
- Cécile Pereira,
- Francisco Jose Pardo-Palacios,
- Hector del Risco,
- Marc Ferrell,
- Maravillas Mellado,
- Marissa Macchietto,
- Kenneth Verheggen,
- Mariola Edelmann,
- Iakes Ezkurdia,
- Jesus Vazquez,
- Michael Tress,
- Ali Mortazavi,
- Lennart Martens,
- Susana Rodriguez-Navarro,
- Victoria Moreno-Manzano,
- and Ana Conesa
Genome Res. March 2018 28: 396-411; Published in Advance February 9, 2018, doi:10.1101/gr.222976.117
...and the preprocessing pipeline using 47 unique descriptors. We apply SQANTI to a neuronal mouse transcriptome using Pacific Biosciences (PacBio) long reads and illustrate how the tool is effective in characterizing and describing the composition of the full-length transcriptome. We perform extensive evaluation of To...
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LETTER: Mapping the C. elegans noncoding transcriptome with a whole-genome tiling microarray
- Housheng He,
- Jie Wang,
- Tao Liu,
- X. Shirley Liu,
- Tiantian Li,
- Yunfei Wang,
- Zuwei Qian,
- Haixia Zheng,
- Xiaopeng Zhu,
- Tao Wu,
- Baochen Shi,
- Wei Deng,
- Wei Zhou,
- Geir Skogerbø,
- and Runsheng Chen
Genome Res. October 2007 17: 1471-1477; Published in Advance September 4, 2007, doi:10.1101/gr.6611807
...Mapping the C. elegans noncoding transcriptome with a whole-genome tiling microarray Housheng He 1 , 2 , 8 , Jie Wang 1 , 2 , 8 , Tao Liu 1 , 2 , 8 , X. Shirley Liu 3 , 4 , Tiantian Li 1 , 2 , Yunfei Wang 1 , 2...
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Research: Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome
- Guojie Zhang,
- Guangwu Guo,
- Xueda Hu,
- Yong Zhang,
- Qiye Li,
- Ruiqiang Li,
- Ruhong Zhuang,
- Zhike Lu,
- Zengquan He,
- Xiaodong Fang,
- Li Chen,
- Wei Tian,
- Yong Tao,
- Karsten Kristiansen,
- Xiuqing Zhang,
- Songgang Li,
- Huanming Yang,
- Jian Wang,
- and Jun Wang
Genome Res. May 2010 20: 646-654; Published in Advance March 19, 2010, doi:10.1101/gr.100677.109
...Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome Guojie Zhang 1 , 2 , 6 , Guangwu Guo 1 , 6 , Xueda Hu 1 , 6 , Yong Zhang 1 , 6 , Qiye Li 1 , 3 , Ruiqiang Li 1 , 4...
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Research: Transcriptome dynamics through alternative polyadenylation in developmental and environmental responses in plants revealed by deep sequencing
- Yingjia Shen,
- R.C. Venu,
- Kan Nobuta,
- Xiaohui Wu,
- Varun Notibala,
- Caghan Demirci,
- Blake C. Meyers,
- Guo-Liang Wang,
- Guoli Ji,
- and Qingshun Q. Li
Genome Res. September 2011 21: 1478-1486; Published in Advance August 3, 2011, doi:10.1101/gr.114744.110
...parallel signature sequencing (MPSS-DGE) and the Illumina sequencingby-synthesis (SBS-DGE) sequencing platforms. The data offer a global view of APA and how it contributes to transcriptome dynamics. Upon analysis of these data, we found that ~60% of Arabidopsis genes have multiple poly(A) sites. Likewise...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...-limited rather than truly discovery-based method. Additionally, probe performance could vary significantly between transcripts, necessitating careful normalization and often validation by qRT-PCR or NB. Despite these limitations, microarrays enabled high-throughput transcriptomic comparisons across conditions...
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Method: Unveiling the functional fate of duplicated genes through expression profiling and structural analysis
- Alex Warwick Vesztrocy,
- Natasha Glover,
- Paul D. Thomas,
- Christophe Dessimoz,
- and Irene Julca
Genome Res. October 2025 35: 2273-2284; Published in Advance August 14, 2025, doi:10.1101/gr.280166.124
...-DNA insertion mutants exhibit no observable phenotype compared to wild-type plants (Kanno et al. 2018). The paralogs LAZY1/LAZY6 in Arabidopsis (Supplemental Fig. S13F) also illustrate this pattern: LAZY1 (LDO) controls shoot orientation as in rice, whereas LAZY6 (MDO) has a different expression profile...
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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
...regions of open chromatin—than ‘‘housekeeping’’ genes that maintain a constant level of expression in all tissues under all conditions. Consist with this hypothesis, we found that the distribution of DH sites is correlated with that of CNSs identified between rice and sorghum. In Arabidopsis thaliana...

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