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Resource: Dynamic transcriptional and chromatin accessibility landscape of medaka embryogenesis
- Yingshu Li,
- Yongjie Liu,
- Hang Yang,
- Ting Zhang,
- Kiyoshi Naruse,
- and Qiang Tu
Genome Res. June 2020 30: 924-937; Published in Advance June 26, 2020, doi:10.1101/gr.258871.119
...relative to that of the zebrafish . The sequence was published in 2007 with a contig N50 of 9.8 kb (Kasahara et al. 2007). Recently a high-quality (HQ) version based on the long-read single-molecule sequencing technology has been released (Ichikawa et al. 2017). The contig N50 is as long as 2.4 Mb...
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Perspective: Challenges in identifying mRNA transcript starts and ends from long-read sequencing data
- Ezequiel Calvo-Roitberg,
- Rachel F. Daniels,
- and Athma A. Pai
Genome Res. November 2024 34: 1719-1734; doi:10.1101/gr.279559.124
...of the relationships between individual exons. The LRS technology space is currently dominated by Pacific Biosciences (PacBio; https://www.pacb.com/products-and-services/applications/rna-sequencing/ [accessed April 25, 2024]) and Oxford Nanopore Technologies (ONT) (Box 1). PacBio utilizes single-molecule real...
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Research: miRNA-like secondary structures in maize (Zea mays) genes and transposable elements correlate with small RNAs, methylation, and expression
- Galen T. Martin,
- Edwin Solares,
- Jeanelle Guadardo-Mendez,
- Aline Muyle,
- Alexandros Bousios,
- and Brandon S. Gaut
Genome Res. November 2023 33: 1932-1946; Published in Advance November 2, 2023, doi:10.1101/gr.277459.122
...in their primary sequence of bases and also by their shape. This shape is primarily defined by the secondary structure of the transcript, a product of the intramolecular hydrogen bonds between RNA bases. Secondary structure can mediate the relationship between genotype and phenotype, because it affects...
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Research: Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize
- Baoxing Song,
- Edward S. Buckler,
- Hai Wang,
- Yaoyao Wu,
- Evan Rees,
- Elizabeth A. Kellogg,
- Daniel J. Gates,
- Merritt Khaipho-Burch,
- Peter J. Bradbury,
- Jeffrey Ross-Ibarra,
- Matthew B. Hufford,
- and M. Cinta Romay
Genome Res. July 2021 31: 1245-1257; Published in Advance May 27, 2021, doi:10.1101/gr.266528.120
...for the study of conserved sequences. Species of the Andropogoneae tribe have diverged in a relatively short time frame, sharing a common ancestor ∼16–20 million years ago (Vicentini et al. 2008). Andropogoneae species include maize, sorghum, sugarcane, and silvergrass, some of the most productive grain, sugar...
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Resource: Long-read RNA sequencing reveals widespread sex-specific alternative splicing in threespine stickleback fish
- Alice S. Naftaly,
- Shana Pau,
- and Michael A. White
Genome Res. August 2021 31: 1486-1497; Published in Advance June 15, 2021, doi:10.1101/gr.274282.120
...contributors to phenotypic diversity across eukaryotes. Although short-read RNA-sequencing has increased our understanding of isoform diversity, it is challenging to accurately detect full-length transcripts, preventing the identification of many alternate isoforms. Long-read sequencing technologies have made...
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Resource: High resolution annotation of zebrafish transcriptome using long-read sequencing
- German Nudelman,
- Antonio Frasca,
- Brandon Kent,
- Kirsten C. Sadler,
- Stuart C. Sealfon,
- Martin J. Walsh,
- and Elena Zaslavsky
Genome Res. September 2018 28: 1415-1425; Published in Advance July 30, 2018, doi:10.1101/gr.223586.117
...QC package. RNA-seq alignment to the GRCz10 RefSeq Danio rerio reference and splice junction identification was done using STAR (Dobin et al. 2013). Isoform quantification was done with kallisto (Bray et al. 2016).Single molecule real-time sequencing (SMRT-Seq)cDNA preparationTotal RNA from 256-cell...
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Resource: Direct full-length RNA sequencing reveals unexpected transcriptome complexity during Caenorhabditis elegans development
- Runsheng Li,
- Xiaoliang Ren,
- Qiutao Ding,
- Yu Bi,
- Dongying Xie,
- and Zhongying Zhao
Genome Res. February 2020 30: 287-298; Published in Advance February 5, 2020, doi:10.1101/gr.251512.119
...centromeres (Jain et al. 2018), improving the existing assembly (Ren et al. 2018), the rapid on-site sequencing of pathogens (Jain et al. 2016), and detecting 5-methylcytosine (5mC) in the s of humans and yeast. Direct sequencing of single-molecule native RNA is expected to benefit transcript integrity...
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Research: The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA
- Michael Regulski,
- Zhenyuan Lu,
- Jude Kendall,
- Mark T.A. Donoghue,
- Jon Reinders,
- Victor Llaca,
- Stephane Deschamps,
- Andrew Smith,
- Dan Levy,
- W. Richard McCombie,
- Scott Tingey,
- Antoni Rafalski,
- James Hicks,
- Doreen Ware,
- and Robert A. Martienssen
Genome Res. October 2013 23: 1651-1662; Published in Advance June 5, 2013, doi:10.1101/gr.153510.112
...to detect DNA methylation demonstrated clear differences between maize inbred lines, lending support to this hypothesis (Eichten et al. 2011). Similarly, studies using -wide sequencing of methylation-dependent restriction fragments have revealed that most methylation is found in transposable elements, prime...
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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
...diversity.There has been increasing interest in the application of single-molecule sequencing to obtain full-length transcripts in animals and plants, as long reads allow direct sequencing and eliminate the need for short-read assembly and transcript reconstruction. Currently, there are three different long...
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Research: SWATH-MS-based proteogenomic analysis reveals the involvement of alternative splicing in poplar upon lead stress
- Fu-Yuan Zhu,
- Xin Chen,
- Yu-Chen Song,
- Lydia Pui Ying Lam,
- Yuki Tobimatsu,
- Bei Gao,
- Mo-Xian Chen,
- and Fu-Liang Cao
Genome Res. March 2023 33: 371-385; Published in Advance March 24, 2023, doi:10.1101/gr.277473.122
...from poplar RNA samples was used for paired-end (2 × 125-bp) sequencing with an Illumina HiSeq 4000 platform by Annogroad Gene Technology Co., Ltd. (Beijing, China). Three replicates of each sample were trimmed to obtain clean reads for subsequent analysis.Single-molecule lrRNA-seq and data analysis...

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