Rhoads A, Au KF. PacBio sequencing and its applications. Genom Proteome Bioinf. 2015;13(5):278–89.
Bayega A, Fahiminiya S, Oikonomopoulos S, Ragoussis J. Current and future methods for mRNA analysis: a drive toward single molecule sequencing//gene expression analysis. New York: Humana Press; 2018. p. 209–41.
Gonzalez-Garay ML. Introduction to isoform sequencing using pacific biosciences technology (Iso-Seq)//Transcriptomics and Gene Regulation. Dordrecht: Springer; 2016. p. 141–60.
Abdel-Ghany SE, Hamilton M, Jacobi JL, Ngam P, Devitt N, Schilkey F, Ben-Hur A, Reddy ASN. A survey of the sorghum transcriptome using single-molecule long reads. Nat Commun. 2016;7:11706.
Wang T, Wang H, Cai D, Gao Y, Zhang H, Wang Y, Lin C, Ma L, Gu L. Comprehensive profiling of rhizome-associated alternative splicing and alternative polyadenylation in moso bamboo (Phyllostachys edulis). Plant J. 2017;91(4):684–99.
Li S, Yamada M, Han X, Ohler U, Benfey PN. High-resolution expression map of the Arabidopsis root reveals alternative splicing and lincRNA regulation. Dev Cell. 2016;39(4):508–22.
Sharon D, Tilgner H, Grubert F, Snyder M. A single-molecule long-read survey of the human transcriptome. Nat Biotechnol. 2013;31(11):1009.
Thomas S, Underwood JG, Tseng E, Holloway AK. Long-read sequencing of chicken transcripts and identification of new transcript isoforms. PLoS ONE. 2014;9(4):e94650.
Wang B, Tseng E, Regulski M, Clark TA, Hon T, Jiao Y, Lu Z, Olson A, Stein JC, Ware D. Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing. Nat Commun. 2016;7:11708.
Jain M, Koren S, Miga KH, Quick J, Rand A, Sasani TA, Tyson JR, Beggs AD, et al. Nanopore sequencing and assembly of a human genome with ultra-long reads. Nat Biotech. 2018;36(4):338.
Michael TP, Jupe F, Bemm F, Motley ST, Sandoval JP, Lanz C, Loudet O, Weigel D, Ecker JR. High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell. Nat Commun. 2018;9(1):541.
Schmidt MHW, Vogel A, Denton AK, Istace B, Wormit A, Geest H, Bolger ME, Alseekh S, Maß J, Pfaff C, Schurr U, Chetelat R, Maumus F, Aury JM, Koren S, Fernie AR, Zamir D, Bolger AM, Usadel B. De novo assembly of a new Solanum pennellii accession using nanopore sequencing. Plant Cell. 2017;29(10):2336–48.
Treutlein B, Gokce O, Quake SR, Südhof TC. Cartography of neurexin alternative splicing mapped by single-molecule long-read mRNA sequencing. P Natl Acad Sci. 2014;111(13):E1291–9.
Byrne A, Beaudin AE, Olsen HE, Jain M, Cole C, Palmer T, DuBois RM, Forsberg EC, Akeson M, Vollmers C. Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells. Nat Commun. 2017;8:16027.
Weirather JL, de Cesare M, Wang Y, Piazza P, Sebastiano V, Wang XJ, Buck D, Au K. Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis. F100Res. 2017;6:100.
Wang Z, Zhang H, Gong W. Genome-wide identification and comparative analysis of alternative splicing across four legume species. Planta. 2019;249(4):1133–42.
Laurent GS, Wahlestedt C, Kapranov P. The Landscape of long noncoding RNA classification. Trends Genet. 2015;31(5):239–51.
Liu J, Wang H, Chua NH. Long noncoding RNA transcriptome of plants. Plant Biotechnol J. 2015;13(3):319–28.
Chao Q, Gao ZF, Zhang D, Zhao BG, Dong FQ, Fu C, Liu L, Wang B. The developmental dynamics of the Populus stem transcriptome. Plant Biotechnol J. 2019;17(1):206–19.
Chao Y, Yuan J, Li S, Jia S, Han S, Xu L. Analysis of transcripts and splice isoforms in red clover (Trifolium pratense L.) by single-molecule long-read sequencing. BMC Plant Biol. 2018;18(1):300.
Seki M, Katsumata E, Suzuki A, Sereewattanawoot S, Sakamoto Y, Mizushima-Sugano J, Sugano S, Kohno T, Frith MC, Tsuchihara K. Evaluation and application of RNA-Seq by MinION. DNA Res. 2018;26(1):55–65.
Jin B, Wang L, Wang J, Jiang KZ, Wang Y, Jiao XX, Ni CY, Wang YL, Teng NJ. The effect of experimental warming on leaf functional traits, leaf structure and leaf biochemistry in Arabidopsis thaliana. BMC Plant Biol. 2011;11(1):35.
Kong L, Zhang Y, Ye ZQ, Liu XQ, Zhao SQ, Wei L, Gao G. CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res. 2007;36:W345–9.
Sun L, Luo HT, Bu DC, Zhao GG, Yu KT, Zhang CG, Liu YN, Chen RS, Zhao Y. Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts. Nucleic Acids Res. 2013;17:e166.
Wang L, Park HJ, Dasari S, Wang S, Kocher JP, Li W. CPAT: coding-Potential Assessment Tool using an alignment-free logistic regression model. Nucleic Acids Res. 2013;41:e74.
Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M. Pfam: the protein families database. Nucleic Acids Res. 2014;42:D222–30.
Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL. Transcript-level expression analysis of RNA-seq experiments with HISAT. StringTie and Ballgown. Nat Protoc. 2016;11(9):1650–67.
Zhou X, Lindsay H, Robinson MD. Robustly detecting differential expression in RNA sequencing data using observation weights. Nucleic Acids Res. 2014;42(11):e91.