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Title: Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing

Abstract

Switchgrass ( Panicum virgatum L.) is an important bioenergy crop widely used for lignocellulosic research. While extensive transcriptomic analyses have been conducted on this species using short read-based sequencing techniques, very little has been reliably derived regarding alternatively spliced (AS) transcripts. Here, we present an analysis of transcriptomes of six switchgrass tissue types pooled together, sequenced using Pacific Biosciences (PacBio) single-molecular long-read technology. Our analysis identified 105,419 unique transcripts covering 43,570 known genes and 8795 previously unknown genes. 45,168 are novel transcripts of known genes. A total of 60,096 AS transcripts are identified, 45,628 being novel. We have also predicted 1549 transcripts of genes involved in cell wall construction and remodeling, 639 being novel transcripts of known cell wall genes. Most of the predicted transcripts are validated against Illumina-based short reads. Specifically, 96% of the splice junction sites in all the unique transcripts are validated by at least five Illumina reads. Comparisons between genes derived from our identified transcripts and the current genome annotation revealed that among the gene set predicted by both analyses, 16,640 have different exon-intron structures. Overall, substantial amount of new information is derived from the PacBio RNA data regarding both the transcriptome and the genome ofmore » switchgrass.« less

Authors:
 [1];  [2];  [3];  [2];  [2];  [4];  [4];  [2];  [2];  [2];  [4];  [5];  [6];  [1]
  1. Jilin Univ., Changchun (China); Univ. of Georgia, Athens, GA (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  2. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  3. HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)
  4. Noble Research Institute, LLC, Ardmore, OK (United States)
  5. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)
  6. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Noble Research Institute, LLC, Ardmore, OK (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1477307
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Biotechnology for Biofuels
Additional Journal Information:
Journal Volume: 11; Journal Issue: 1; Journal ID: ISSN 1754-6834
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
09 BIOMASS FUELS; Switchgrass; PacBio sequencing; Transcriptomic analysis; Alternative splicing; Plant cell wall

Citation Formats

Zuo, Chunman, Blow, Matthew, Sreedasyam, Avinash, Kuo, Rita C., Ramamoorthy, Govindarajan Kunde, Torres-Jerez, Ivone, Li, Guifen, Wang, Mei, Dilworth, David, Barry, Kerrie, Udvardi, Michael, Schmutz, Jeremy, Tang, Yuhong, and Xu, Ying. Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing. United States: N. p., 2018. Web. doi:10.1186/s13068-018-1167-z.
Zuo, Chunman, Blow, Matthew, Sreedasyam, Avinash, Kuo, Rita C., Ramamoorthy, Govindarajan Kunde, Torres-Jerez, Ivone, Li, Guifen, Wang, Mei, Dilworth, David, Barry, Kerrie, Udvardi, Michael, Schmutz, Jeremy, Tang, Yuhong, & Xu, Ying. Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing. United States. doi:10.1186/s13068-018-1167-z.
Zuo, Chunman, Blow, Matthew, Sreedasyam, Avinash, Kuo, Rita C., Ramamoorthy, Govindarajan Kunde, Torres-Jerez, Ivone, Li, Guifen, Wang, Mei, Dilworth, David, Barry, Kerrie, Udvardi, Michael, Schmutz, Jeremy, Tang, Yuhong, and Xu, Ying. Wed . "Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing". United States. doi:10.1186/s13068-018-1167-z. https://www.osti.gov/servlets/purl/1477307.
@article{osti_1477307,
title = {Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing},
author = {Zuo, Chunman and Blow, Matthew and Sreedasyam, Avinash and Kuo, Rita C. and Ramamoorthy, Govindarajan Kunde and Torres-Jerez, Ivone and Li, Guifen and Wang, Mei and Dilworth, David and Barry, Kerrie and Udvardi, Michael and Schmutz, Jeremy and Tang, Yuhong and Xu, Ying},
abstractNote = {Switchgrass (Panicum virgatum L.) is an important bioenergy crop widely used for lignocellulosic research. While extensive transcriptomic analyses have been conducted on this species using short read-based sequencing techniques, very little has been reliably derived regarding alternatively spliced (AS) transcripts. Here, we present an analysis of transcriptomes of six switchgrass tissue types pooled together, sequenced using Pacific Biosciences (PacBio) single-molecular long-read technology. Our analysis identified 105,419 unique transcripts covering 43,570 known genes and 8795 previously unknown genes. 45,168 are novel transcripts of known genes. A total of 60,096 AS transcripts are identified, 45,628 being novel. We have also predicted 1549 transcripts of genes involved in cell wall construction and remodeling, 639 being novel transcripts of known cell wall genes. Most of the predicted transcripts are validated against Illumina-based short reads. Specifically, 96% of the splice junction sites in all the unique transcripts are validated by at least five Illumina reads. Comparisons between genes derived from our identified transcripts and the current genome annotation revealed that among the gene set predicted by both analyses, 16,640 have different exon-intron structures. Overall, substantial amount of new information is derived from the PacBio RNA data regarding both the transcriptome and the genome of switchgrass.},
doi = {10.1186/s13068-018-1167-z},
journal = {Biotechnology for Biofuels},
issn = {1754-6834},
number = 1,
volume = 11,
place = {United States},
year = {2018},
month = {6}
}

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Figures / Tables:

Fig. 1 Fig. 1 : The percentage of the G1 transcripts satisfying each of the six thresholds defined along the x‑axis. The four thresholds marked as a, b, c, d, are for high‑quality alignment in human, maize, Amborella, and PacBio tutorial Iso‑Seq analysis, respectively

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