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RNA Biology Volume 20, 2023 - Issue 1
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Research Paper

PacBio full-length transcriptome analysis provides new insights into transcription of chloroplast genomes

Jinsong Shia College of Life Sciences, Nankai University, Tianjin, P.R.China;b National Clinical Research Center of Kidney Disease, Jinling Hospital, Nanjing University School of Medicine, Nanjing, ChinaORCID Iconhttps://orcid.org/0000-0001-7250-8813View further author information
ORCID Icon,
Shuangyong Yanc Tianjin Institute of Crop Research, Tianjin Academy of Agricultural Sciences, Tianjin, P.R.ChinaORCID Iconhttps://orcid.org/0000-0002-9696-4984View further author information
ORCID Icon,
Wenjing Lid Qinghai Provincial Key Laboratory of Qinghai-Tibet Plateau Biological Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, P.R.China;e Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, P.R.ChinaORCID Iconhttps://orcid.org/0000-0002-8931-5433View further author information
ORCID Icon,
Xiurong Yangf Institute of Plant Protection, Tianjin Academy of Agricultural Sciences, Tianjin, P.R.ChinaORCID Iconhttps://orcid.org/0000-0002-9489-9445View further author information
ORCID Icon,
Zhongqiu Cuic Tianjin Institute of Crop Research, Tianjin Academy of Agricultural Sciences, Tianjin, P.R.ChinaORCID Iconhttps://orcid.org/0009-0006-6081-5342View further author information
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Junling Lic Tianjin Institute of Crop Research, Tianjin Academy of Agricultural Sciences, Tianjin, P.R.ChinaORCID Iconhttps://orcid.org/0009-0005-6847-6229View further author information
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Guangsheng Lif Institute of Plant Protection, Tianjin Academy of Agricultural Sciences, Tianjin, P.R.ChinaORCID Iconhttps://orcid.org/0009-0008-6465-2290View further author information
ORCID Icon,
Yuejiao Lif Institute of Plant Protection, Tianjin Academy of Agricultural Sciences, Tianjin, P.R.ChinaORCID Iconhttps://orcid.org/0000-0002-2181-2484View further author information
ORCID Icon,
Yanping Hud Qinghai Provincial Key Laboratory of Qinghai-Tibet Plateau Biological Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, P.R.ChinaCorrespondence[email protected]
ORCID Iconhttps://orcid.org/0000-0002-5770-2527View further author information
ORCID Icon &
Shan Gaoa College of Life Sciences, Nankai University, Tianjin, P.R.ChinaCorrespondence[email protected]
ORCID Iconhttps://orcid.org/0000-0002-8919-1338View further author information
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Pages 248-256 | Accepted 13 Apr 2023, Published online: 25 May 2023

References

  • Ren Y, Jiaqing Z, Sun Y, et al. Full-length transcriptome sequencing on PacBio platform (in Chinese). Chinese Sci Bull. 2016;61(11):1250–1254.
  • Gao S, Ren Y, Sun Y, et al. PacBio Full-length transcriptome profiling of insect mitochondrial gene expression. RNA Biol. 2016;13(9):820–825.
  • Xu X, Ji H, Jin X, et al. Using pan RNA-seq analysis to reveal the ubiquitous existence of 5‘and 3’ end small RNAs. Front Genet. 2019;10:1–11.
  • Gao S, Tian X, Chang H, et al. Two novel lncRnas discovered in human mitochondrial DNA using PacBio full-length transcriptome data. Mitochondrion. 2017;38:41–47.
  • Jin X, Cheng Z, Wang B, et al. Precise annotation of human, chimpanzee, rhesus macaque and mouse mitochondrial genomes leads to insight into mitochondrial transcription in mammals. RNA Biol. 2020;17(1):1–8.
  • Shi C, Wang S, Xia E-H, et al. Full transcription of the chloroplast genome in photosynthetic eukaryotes. Sci Rep. 2016;6(1):30135.
  • Liang J, Chen R, Zhang F, et al. Full-length chloroplast genome of Dongxiang wild rice reveals small single-copy region switching. Front Plant Sci. 2022;13. DOI:10.3389/fpls.2022.929352
  • Swiatecka-Hagenbruch M, Liere K, Börner T. High diversity of plastidial promoters in Arabidopsis thaliana. Mol Genet Genomics. 2007;277(6):725–734.
  • Hildebrand M, Hallick RB, Passavant CW, et al. Trans-splicing in chloroplasts: the rps 12 loci of Nicotiana tabacum. Proc Natl Acad Sci USA. 1988;85(2):372–376.
  • Liang G, Mi D, Chang J, et al. Precise annotation of Drosophila mitochondrial genomes leads to insights into AT-rich regions. Mitochondrion. 2022;65:145–149.
  • Adiconis X, Haber AL, Simmons SK, et al. Comprehensive comparative analysis of 3-end RNA-sequencing methods. Nature Methods 2018. 2018;15:505–511.
  • Dombrowski B. 3’ inverted repeats in plant mitochondrial mRnas act as processing and stabilizing elements but do not terminate transcription. Embo J. 1997;16(16):5069–5076.
  • Zhang M, Zhan F, Sun H, et al. Fastq_clean: an optimized pipeline to clean the Illumina sequencing data with quality control. Bioinformatics and Biomedicine (BIBM), 2014 IEEE International Conference on; Belfast, UK: IEEE; 2014. p. 44–48.
  • Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010;26:589–595.
  • Gao S, Ou J, Xiao K. R language and Bioconductor in bioinformatics applications. Chinese ed. Tianjin: Tianjin Science and Technology Translation Publishing Ltd; 2014.
  • Milne I, Stephen G, Bayer M, et al. Using Tablet for visual exploration of second-generation sequencing data. Brief Bioinform. 2013;14(2):193–202.

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