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3. A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis

Author

Zhang, Runxuan, Kuo, Richard, Coulter, Max, Calixto, Cristiane P. G., Entizne, Juan Carlos, Guo, Wenbin, Marquez, Yamile, Milne, Linda, Riegler, Stefan, Matsui, Akihiro, Tanaka, Maho, Harvey, Sarah, Gao, Yubang, Wießner-Kroh, Theresa, Paniagua, Alejandro, Crespi, Martin, Denby, Katherine, Hur, Asa ben, Huq, Enamul, Jantsch, Michael, Jarmolowski, Artur, Koester, Tino, Laubinger, Sascha, Li, Qingshun Quinn, Gu, Lianfeng, Seki, Motoaki, Staiger, Dorothee, Sunkar, Ramanjulu, Szweykowska-Kulinska, Zofia, Tu, Shih-Long, Wachter, Andreas, Waugh, Robbie, Xiong, Liming, Zhang, Xiao-Ning, Conesa, Ana, Reddy, Anireddy S. N., Barta, Andrea, Kalyna, Maria, and Brown, John W. S.

Published
2022
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8. BaRTv2: a highly resolved barley reference transcriptome for accurate transcript‐specificRNA‐seq quantification

Author

Coulter, Max, primary, Entizne, Juan Carlos, additional, Guo, Wenbin, additional, Bayer, Micha, additional, Wonneberger, Ronja, additional, Milne, Linda, additional, Schreiber, Miriam, additional, Haaning, Allison, additional, Muehlbauer, Gary J., additional, McCallum, Nicola, additional, Fuller, John, additional, Simpson, Craig, additional, Stein, Nils, additional, Brown, John W. S., additional, Waugh, Robbie, additional, and Zhang, Runxuan, additional

Published
2022
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10. Additional file 3 of A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis

Author

Zhang, Runxuan, Kuo, Richard, Coulter, Max, Calixto, Cristiane P. G., Entizne, Juan Carlos, Guo, Wenbin, Marquez, Yamile, Milne, Linda, Riegler, Stefan, Matsui, Akihiro, Tanaka, Maho, Harvey, Sarah, Gao, Yubang, Wießner-Kroh, Theresa, Paniagua, Alejandro, Crespi, Martin, Denby, Katherine, Hur, Asa ben, Huq, Enamul, Jantsch, Michael, Jarmolowski, Artur, Koester, Tino, Laubinger, Sascha, Li, Qingshun Quinn, Gu, Lianfeng, Seki, Motoaki, Staiger, Dorothee, Sunkar, Ramanjulu, Szweykowska-Kulinska, Zofia, Tu, Shih-Long, Wachter, Andreas, Waugh, Robbie, Xiong, Liming, Zhang, Xiao-Ning, Conesa, Ana, Reddy, Anireddy S. N., Barta, Andrea, Kalyna, Maria, and Brown, John W. S.

Abstract

Additional file 3: Figure S18. Comparison of AtIso transcripts and SJs to Araport and AtRTD2.

Published
2022
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11. Additional file 2 of A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis

Author

Zhang, Runxuan, Kuo, Richard, Coulter, Max, Calixto, Cristiane P. G., Entizne, Juan Carlos, Guo, Wenbin, Marquez, Yamile, Milne, Linda, Riegler, Stefan, Matsui, Akihiro, Tanaka, Maho, Harvey, Sarah, Gao, Yubang, Wießner-Kroh, Theresa, Paniagua, Alejandro, Crespi, Martin, Denby, Katherine, Hur, Asa ben, Huq, Enamul, Jantsch, Michael, Jarmolowski, Artur, Koester, Tino, Laubinger, Sascha, Li, Qingshun Quinn, Gu, Lianfeng, Seki, Motoaki, Staiger, Dorothee, Sunkar, Ramanjulu, Szweykowska-Kulinska, Zofia, Tu, Shih-Long, Wachter, Andreas, Waugh, Robbie, Xiong, Liming, Zhang, Xiao-Ning, Conesa, Ana, Reddy, Anireddy S. N., Barta, Andrea, Kalyna, Maria, and Brown, John W. S.

Abstract

Additional file 2: Fig. S1. Iso-seq transcripts contain false SJs prior to accurate SJ determination and filtering. Fig. S2. Determination of TSS and TES sites for genes with high and low abundance reads. Fig. S3. Comparison of AtIso TSSs and TESs with previously published transcript start and end sites. Fig. S4. Generation of high-level transcripts. Fig. S5. Number of genes and transcripts contributed to AtIso from each Iso-seq library. Fig. S6. Saturation curve of increase in unique genes and transcripts added to AtIso with addition of each library. Fig. S7. SQANTI3 assessment of quality of long read transcripts in AtRTD3 and AtIso. Fig. S8. Increased number of transcript isoforms in AtRTD3. Fig. S9. Genes with characterised different TSS. Fig. S10. Genes with characterised alternative TES. Fig. S11. Confirmation of AS variant isoforms in the lncRNA, FLORE. Fig. S12. Novel genes in AtRTD3 – lncRNAs. Fig. S13. Chimeric transcripts. Fig. S14. Correlation of splicing ratios calculated from the RNA-seq and HR RT-PCR data including outliers. Fig. S15. Accurate Iso-seq transcript determination identifies THIC RNAs produced by riboswitch. Fig. S16. Novel cold-induced isoform of CIPK1 from AtRTD3. Fig. S17. Novel transcript isoform in AtRTD3 affects expression levels of main transcripts compared to AtRTD2.

Published
2022
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12. Additional file 4 of A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis

Author

Zhang, Runxuan, Kuo, Richard, Coulter, Max, Calixto, Cristiane P. G., Entizne, Juan Carlos, Guo, Wenbin, Marquez, Yamile, Milne, Linda, Riegler, Stefan, Matsui, Akihiro, Tanaka, Maho, Harvey, Sarah, Gao, Yubang, Wießner-Kroh, Theresa, Paniagua, Alejandro, Crespi, Martin, Denby, Katherine, Hur, Asa ben, Huq, Enamul, Jantsch, Michael, Jarmolowski, Artur, Koester, Tino, Laubinger, Sascha, Li, Qingshun Quinn, Gu, Lianfeng, Seki, Motoaki, Staiger, Dorothee, Sunkar, Ramanjulu, Szweykowska-Kulinska, Zofia, Tu, Shih-Long, Wachter, Andreas, Waugh, Robbie, Xiong, Liming, Zhang, Xiao-Ning, Conesa, Ana, Reddy, Anireddy S. N., Barta, Andrea, Kalyna, Maria, and Brown, John W. S.

Abstract

Additional file 4: Review history.

Published
2022
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13. IDENTIFYING PLANT GENES SHAPING MICROBIOTA COMPOSITION IN THE BARLEY RHIZOSPHERE

Author

Escudero-Martinez, Carmen, primary, Coulter, Max, additional, Terrazas, Rodrigo Alegria, additional, Foito, Alexandre, additional, Kapadia, Rumana, additional, Pietrangelo, Laura, additional, Maver, Mauro, additional, Sharma, Rajiv, additional, Aprile, Alessio, additional, Morris, Jenny, additional, Hedley, Pete E., additional, Maurer, Andreas, additional, Pillen, Klaus, additional, Naclerio, Gino, additional, Mimmo, Tanja, additional, Barton, Geoffrey J., additional, Waugh, Robbie, additional, Abbott, James, additional, and Bulgarelli, Davide, additional

Published
2021
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15. BaRTv2: A highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification

Author

Coulter, Max, primary, Entizne, Juan Carlos, additional, Guo, Wenbin, additional, Bayer, Micha, additional, Wonneberger, Ronja, additional, Milne, Linda, additional, Schreiber, Miriam, additional, Haaning, Allison, additional, Muehlbauer, Gary, additional, McCallum, Nicola, additional, Fuller, John, additional, Simpson, Craig, additional, Stein, Nils, additional, Brown, John W. S., additional, Waugh, Robbie, additional, and Zhang, Runxuan, additional

Published
2021
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16. A high resolution single molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis

Author

Zhang, Runxuan, primary, Kuo, Richard, additional, Coulter, Max, additional, Calixto, Cristiane P.G., additional, Entizne, Juan Carlos, additional, Guo, Wenbin, additional, Marquez, Yamile, additional, Milne, Linda, additional, Riegler, Stefan, additional, Matsui, Akihiro, additional, Tanaka, Maho, additional, Harvey, Sarah, additional, Yubang, Gao, additional, Wiebner-Kroh, Theresa, additional, Crespi, Martin, additional, Denby, Katherine, additional, Hur, Asa ben, additional, Huq, Enamul, additional, Jantsch, Michael F., additional, Jarmolowski, Artur, additional, Koester, Tino, additional, Laubinger, Sascha, additional, Li, Qingshun Quinn, additional, Gu, Lianfeng, additional, Seki, Motoaki, additional, Staiger, Dorothee, additional, Sunkar, Ramanjulu, additional, Szweykowska-Kulinska, Zofia, additional, Tu, Shih-Long, additional, Wachter, Andreas, additional, Waugh, Robbie, additional, Xiong, Liming, additional, Zhang, Xiao-Ning, additional, Reddy, Anireddy S.N., additional, Barta, Andrea, additional, Kalyna, Maria, additional, and Brown, John WS, additional

Published
2021
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17. BaRTv2: a highly resolved barley reference transcriptome for accurate transcript‐specific RNA‐seq quantification.

Author

Coulter, Max, Entizne, Juan Carlos, Guo, Wenbin, Bayer, Micha, Wonneberger, Ronja, Milne, Linda, Schreiber, Miriam, Haaning, Allison, Muehlbauer, Gary J., McCallum, Nicola, Fuller, John, Simpson, Craig, Stein, Nils, Brown, John W. S., Waugh, Robbie, and Zhang, Runxuan

Subjects
*RNA sequencing, *TRANSCRIPTOMES, *GENETIC transcription regulation, *BARLEY, *CULTIVARS, *SCIENTIFIC community
Abstract

SUMMARY: Accurate characterisation of splice junctions (SJs) as well as transcription start and end sites in reference transcriptomes allows precise quantification of transcripts from RNA‐seq data, and enables detailed investigations of transcriptional and post‐transcriptional regulation. Using novel computational methods and a combination of PacBio Iso‐seq and Illumina short‐read sequences from 20 diverse tissues and conditions, we generated a comprehensive and highly resolved barley reference transcript dataset from the European 2‐row spring barley cultivar Barke (BaRTv2.18). Stringent and thorough filtering was carried out to maintain the quality and accuracy of the SJs and transcript start and end sites. BaRTv2.18 shows increased transcript diversity and completeness compared with an earlier version, BaRTv1.0. The accuracy of transcript level quantification, SJs and transcript start and end sites have been validated extensively using parallel technologies and analysis, including high‐resolution reverse transcriptase‐polymerase chain reaction and 5'‐RACE. BaRTv2.18 contains 39 434 genes and 148 260 transcripts, representing the most comprehensive and resolved reference transcriptome in barley to date. It provides an important and high‐quality resource for advanced transcriptomic analyses, including both transcriptional and post‐transcriptional regulation, with exceptional resolution and precision. Significance Statement: We have developed BaRTv2.18, which represents the most comprehensive and resolved reference transcriptome in barley (Hordeum vulgare) to date. Novel methods are applied to analyze Iso‐seq data that accurately determine the transcripts from start to end (splice junctions, transcript start and end sites). It will prove to be an important and high‐quality resource for the barley research community to carry out advanced transcriptomic analyses, including both transcriptional and post‐transcriptional regulation, with exceptional resolution and precision [ABSTRACT FROM AUTHOR]

Published
2022
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20. Genome Sequencing of Xanthomonas vasicola Pathovar vasculorum Reveals Variation in Plasmids and Genes Encoding Lipopolysaccharide Synthesis, Type-IV Pilus and Type-III Secretion Effectors

Author

Wasukira, Arthur, primary, Coulter, Max, additional, Al-Sowayeh, Noorah, additional, Thwaites, Richard, additional, Paszkiewicz, Konrad, additional, Kubiriba, Jerome, additional, Smith, Julian, additional, Grant, Murray, additional, and Studholme, David, additional

Published
2014
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