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Method: Contrasting and combining transcriptome complexity captured by short and long RNA sequencing reads
- Seong Woo Han,
- San Jewell,
- Andrei Thomas-Tikhonenko,
- and Yoseph Barash
Genome Res. October 2024 34: 1624-1635; Published in Advance September 25, 2024, doi:10.1101/gr.278659.123
...and coverage across the full body of transcripts as important for future improvement, much work has been dedicated to reducing the error rate in long reads. However, the effect of sequencing errors on transcriptome analysis can be complex and context dependent. Correction algorithms like IsoQuant do not alter...
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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
...Technologies to study the transcriptome complexity in Caenorhabditis elegans. We generated approximately six million reads using native poly(A)-tailed mRNAs from three developmental stages, with average read lengths ranging from 900 to 1100 nt. Around half of the reads represent full-length transcripts...
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Resource: RNA sequencing reveals a diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development
- Meng How Tan,
- Kin Fai Au,
- Arielle L. Yablonovitch,
- Andrea E. Wills,
- Jason Chuang,
- Julie C. Baker,
- Wing Hung Wong,
- and Jin Billy Li
Genome Res. January 2013 23: 201-216; Published in Advance September 7, 2012, doi:10.1101/gr.141424.112
...and strongly suggest that even though theXenopus tropicalis is close to being finished, it is still missing hundreds of transcribed sequences. To determine if the Trinity contigs that could not be aligned to the are true transcripts or are simply spurious assemblies, we sought to validate some of them...
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RESOURCE: Versatile Gene-Specific Sequence Tags for Arabidopsis Functional Genomics: Transcript Profiling and Reverse Genetics Applications
- Pierre Hilson,
- Joke Allemeersch,
- Thomas Altmann,
- Sébastien Aubourg,
- Alexandra Avon,
- Jim Beynon,
- Rishikesh P. Bhalerao,
- Frédérique Bitton,
- Michel Caboche,
- Bernard Cannoot,
- Vasil Chardakov,
- Cécile Cognet-Holliger,
- Vincent Colot,
- Mark Crowe,
- Caroline Darimont,
- Steffen Durinck,
- Holger Eickhoff,
- Andéol Falcon de Longevialle,
- Edward E. Farmer,
- Murray Grant,
- Martin T.R. Kuiper,
- Hans Lehrach,
- Céline Léon,
- Antonio Leyva,
- Joakim Lundeberg,
- Claire Lurin,
- Yves Moreau,
- Wilfried Nietfeld,
- Javier Paz-Ares,
- Philippe Reymond,
- Pierre Rouzé,
- Goran Sandberg,
- Maria Dolores Segura,
- Carine Serizet,
- Alexandra Tabrett,
- Ludivine Taconnat,
- Vincent Thareau,
- Paul Van Hummelen,
- Steven Vercruysse,
- Marnik Vuylsteke,
- Magdalena Weingartner,
- Peter J. Weisbeek,
- Valtteri Wirta,
- Floyd R.A. Wittink,
- Marc Zabeau,
- and Ian Small
Genome Res. October 15, 2004 14: 2176-2189; doi:10.1101/gr.2544504
...for large-scale functional surveys. Two key methods have greatly enhanced our ability to assign functions to genes in systematic analyses: microarray transcript profiling ( Holloway et al. 2002 ) and silencing via RNA interference or RNAi ( Hannon 2002 ; Waterhouse and Helliwell 2003 ). Full transcriptome...
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Methods: Using the miraEST Assembler for Reliable and Automated mRNA Transcript Assembly and SNP Detection in Sequenced ESTs
- Bastien Chevreux,
- Thomas Pfisterer,
- Bernd Drescher,
- Albert J. Driesel,
- Werner E.G. Müller,
- Thomas Wetter,
- and Sándor Suhai
Genome Res. June 2004 14: 1147-1159; Published in Advance May 12, 2004, doi:10.1101/gr.1917404
...alone may be not enough, especially if the organism shows a high degree of complexity. Analysis of the must be supported by efforts on understanding its transcription—the transcriptome—occurring in cells. Citing Camargo et al. ( 2001 ), the “most definitive approach to the elucidation of transcripts...
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RESOURCE: Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis reveals post-tetraploidization transcriptome remodeling
- Ryan D. Morin,
- Elbert Chang,
- Anca Petrescu,
- Nancy Liao,
- Malachi Griffith,
- Robert Kirkpatrick,
- Yaron S. Butterfield,
- Alice C. Young,
- Jeffrey Stott,
- Sarah Barber,
- Ryan Babakaiff,
- Mark C. Dickson,
- Corey Matsuo,
- David Wong,
- George S. Yang,
- Duane E. Smailus,
- Keith D. Wetherby,
- Peggy N. Kwong,
- Jane Grimwood,
- Charles P. Brinkley III,
- Mabel Brown-John,
- Natalie D. Reddix-Dugue,
- Michael Mayo,
- Jeremy Schmutz,
- Jaclyn Beland,
- Morgan Park,
- Susan Gibson,
- Teika Olson,
- Gerard G. Bouffard,
- Miranda Tsai,
- Ruth Featherstone,
- Steve Chand,
- Asim S. Siddiqui,
- Wonhee Jang,
- Ed Lee,
- Steven L. Klein,
- Robert W. Blakesley,
- Barry R. Zeeberg,
- Sudarshan Narasimhan,
- John N. Weinstein,
- Christa Prange Pennacchio,
- Richard M. Myers,
- Eric D. Green,
- Lukas Wagner,
- Daniela S. Gerhard,
- Marco A. Marra,
- Steven J.M. Jones,
- and Robert A. Holt
Genome Res. June 2006 16: 796-803; Published in Advance May 3, 2006, doi:10.1101/gr.4871006
...tissues from both X. laevis and X. tropicalis ( Klein et al. 2002 ; Blackshear et al. 2001 ; Gilchrist et al. 2004 ). However, for analysis of transcripts and gene structures, the quality of data and coverage provided by EST reads can be limiting. Sequence-verified full-length cDNA clones are more...
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Chicken Special/Resources: Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags
- Simon J. Hubbard,
- Darren V. Grafham,
- Kevin J. Beattie,
- Ian M. Overton,
- Stuart R. McLaren,
- Michael D.R. Croning,
- Paul E. Boardman,
- James K. Bonfield,
- Joan Burnside,
- Robert M. Davies,
- Elizabeth R. Farrell,
- Matthew D. Francis,
- Sam Griffiths-Jones,
- Sean J. Humphray,
- Christopher Hyland,
- Carol E. Scott,
- Haizhou Tang,
- Ruth G. Taylor,
- Cheryll Tickle,
- William R.A. Brown,
- Ewan Birney,
- Jane Rogers,
- and Stuart A. Wilson
Genome Res. January 2005 15: 174-183; Published in Advance December 8, 2004, doi:10.1101/gr.3011405
...here) as well as protein similarity to build gene models. From this, 24,207 (85%) of the 28,416 Ensembl transcripts were matched, corresponding to 14,685 (83%) of the 17,709 Ensembl genes. The degree of transcriptome/ coverage based on these figures is comparable to that seen for the RIKEN...
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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
...Research Center for Environment and Health, D-85764 Neuherberg, Germany; 2The Plant Genome Initiative at Rutgers (PGIR), Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA; 3Broad Institute of MIT and Harvard, Cambridge, Massachusetts...
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Method: Ultra-long sequencing for contiguous haplotype resolution of the human immunoglobulin heavy-chain locus
- Mari B. Gornitzka,
- Egil Røsjø,
- Uddalok Jana,
- Easton E. Ford,
- Alan Tourancheau,
- William D. Lees,
- Zachary Vanwinkle,
- Melissa L. Smith,
- Corey T. Watson,
- and Andreas Lossius
Genome Res. October 2025 35: 2240-2251; Published in Advance August 21, 2025, doi:10.1101/gr.280400.125
...-seq) on peripheral blood mononuclear cells (PBMCs) from the donor (Ford et al. 2023). Notably, we identified productive transcripts from both copies of IGHA1 and IGHG2 within the duplicated haplotype 1 (Fig. 5C). Because the centromeric copy of IGHG4 on haplotype 1 is identical to that on haplotype 2, calling...
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Resource: CGC1, a new reference genome for Caenorhabditis elegans
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Dae-Eun Jeong,
- Chie Owa,
- Haruka Kobayashi,
- Yoshihiko Suzuki,
- Manami Kanamori,
- Yu Toyoshima,
- Yuichi Iino,
- Ann E. Rougvie,
- Lamia Wahba,
- Andrew Z. Fire,
- Erich M. Schwarz,
- and Shinichi Morishita
Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
..., even though the RNA-seq data were collected in two independent studies, supporting the presence of transcription.DiscussionUsing high-accuracy PacBio HiFi and ultralong Oxford Nanopore long-read sequencing, as well as augmenting our initial HiCanu assembly with manual assembly of 54 tandemly repeated...
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