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Resource: The PanOryza pangene catalog of Asian cultivated rice
- Bruno Contreras-Moreira,
- Eshan Sharma,
- Shradha Saraf,
- Guy Naamati,
- Parul Gupta,
- Justin Elser,
- Dmytro Chebotarov,
- Kapeel Chougule,
- Zhenyuan Lu,
- Sharon Wei,
- Andrew Olson,
- Ian Tsang,
- Disha Lodha,
- Yong Zhou,
- Zhichao Yu,
- Wen Zhao,
- Jianwei Zhang,
- Sandeep Amberkar,
- Kawinnat Sue-Ob,
- Zhi Sun,
- Maria Martin,
- Kenneth L. McNally,
- Doreen Ware,
- Eric W. Deutsch,
- Dario Copetti,
- Rod A. Wing,
- Pankaj Jaiswal,
- Sarah Dyer,
- and Andrew R. Jones
Genome Res. January 2026 36: 226-238; Published in Advance December 12, 2025, doi:10.1101/gr.280790.125
...showing the counts of orthologs derived from Ensembl Compara (see Methods). (E) Boxplot showing counts of paralogs. (F) Boxplot of mean quantitative gene expression data log2(FPKM + 1), sourced from 11,726 rice RNA-seq samples. (G) Boxplot of mean prediction score (pLDDT) from the corresponding AlphaFold2...
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Resource: The ggRibo single-gene viewer reveals insights into translatome and other nucleotide-resolution omics data
- Hsin-Yen Larry Wu,
- Isaiah D. Kaufman,
- and Polly Yingshan Hsu
Genome Res. September 2025 35: 2130-2142; Published in Advance July 22, 2025, doi:10.1101/gr.280480.125
...and (optional) extra ORFs, and mapped RNA-seq file(s). Other omics data presented with single-nucleotide resolution (SNR) can be input and visualized in parallel or independently. To visualize DNA and/or amino acid sequences, users can optionally provide the corresponding sequence file. Output plots can...
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Perspective: Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation
- Carolina Monzó,
- Adam Frankish,
- and Ana Conesa
Genome Res. April 2025 35: 583-592; Published in Advance March 3, 2025, doi:10.1101/gr.279865.124
...data to perform gene-level transcriptomic analysis, a maximal representation of transcriptomic complexity is beneficial to ensure that as many RNA-seq reads as possible are correctly assigned to their gene of origin. This would require that the annotation captures the maximal extent of the gene even...
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Research: High resolution genomes of multiple Xiphophorus species provide new insights into microevolution, hybrid incompatibility, and epistasis
- Yuan Lu,
- Edward Rice,
- Kang Du,
- Susanne Kneitz,
- Magali Naville,
- Corentin Dechaud,
- Jean-Nicolas Volff,
- Mikki Boswell,
- William Boswell,
- LaDeana Hillier,
- Chad Tomlinson,
- Kremitzki Milin,
- Ronald B. Walter,
- Manfred Schartl,
- and Wesley C. Warren
Genome Res. April 2023 33: 557-571; Published in Advance May 5, 2023, doi:10.1101/gr.277434.122
...predictions and RNA sequencing (RNA-seq) evidence-supported gene model building. Gene annotation relied on an extensive variety of public RNA-seq data from various tissues to improve gene model accuracy. The RefSeq gene annotation reports for each species provide a full accounting of all methodology deployed...
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Resource: Genome-wide dynamics of alternative polyadenylation in rice
- Haihui Fu,
- Dewei Yang,
- Wenyue Su,
- Liuyin Ma,
- Yingjia Shen,
- Guoli Ji,
- Xinfu Ye,
- Xiaohui Wu,
- and Qingshun Q. Li
Genome Res. December 2016 26: 1753-1760; Published in Advance October 12, 2016, doi:10.1101/gr.210757.116
...(A) sites of PAT-seq data were confirmed by previously collected rice EST data (often sequenced by low throughput and Sanger method). There are ∼70% of the intergenic PACs that are confirmed by EST. Second, single-nucleotide profiles of these intergenic PACs surrounding the poly(A) sites (Supplemental Fig...
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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
...and used Cufflink (Roberts et al. 2011) to call the expression values (FPKM) of annotated rice genes and to detect differentially expressed genes. We obtained 40.1 M of RNA-seq reads from seedlings, and 89.2% of them were mapped to the rice (Tigr release 5). Similarly, we obtained 29.6million reads from...
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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
..., comprehensive studies of transcriptomes at single base resolution are rare, even for modern organisms, and lacking for rice. Here, we present the first transcriptome atlas for eight organs of cultivated rice. Using high-throughput paired-end RNA-seq, we unambiguously detected transcripts expressing...
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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 therefore may play a fundamental role in the establishment of organismal complexity (Black 2003; Mudge et al. 2011; La Cognata et al. 2014). The -wide analysis of AS has been done primarily using exon microarrays first and, more recently, short-read RNA-seq. These two methods are effective...
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Research: Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals
- Alexis Battle,
- Sara Mostafavi,
- Xiaowei Zhu,
- James B. Potash,
- Myrna M. Weissman,
- Courtney McCormick,
- Christian D. Haudenschild,
- Kenneth B. Beckman,
- Jianxin Shi,
- Rui Mei,
- Alexander E. Urban,
- Stephen B. Montgomery,
- Douglas F. Levinson,
- and Daphne Koller
Genome Res. January 2014 24: 14-24; Published in Advance October 3, 2013, doi:10.1101/gr.155192.113
...(Supplemental Fig. S11), suggesting that statistical power along with the resolution of RNA-seq is a contributor to finding eQTLs unique to this study. Genetic variants near each gene also affect alternative splicing; using isoform ratio (the fraction of a gene’s expression arising from each isoform) (Methods...
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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
.... Altogether, our results show that at least 61% of intron-containing genes are alternatively spliced under normal growth conditions, which indicates a high complexity of the Arabidopsis transcriptome. Results RNA-seq of a normalized cDNA library improves gene representation To facilitate the discovery...
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