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The developmental dynamics of the Populus stem transcriptome.

Qing Chao1, Zhi-Fang Gao1,2, Dong Zhang3

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Plant Biotechnology Journal
|June 1, 2018
PubMed
Summary

This study reveals new insights into Populus shoot development by identifying novel transcripts and differentially expressed genes, including key transcription factors, using advanced sequencing techniques. These findings enhance our understanding of plant growth and biomass production.

Keywords:
PacBio Iso-Seqprimary growthsecondary growthstem cell maintenancetranscription factor

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Area of Science:

  • Plant biology
  • Genomics
  • Molecular genetics

Background:

  • Populus shoots exhibit primary (longitudinal) and secondary (radial) growth, crucial for biomass production.
  • Accurate transcript annotation is essential for understanding plant development.

Purpose of the Study:

  • To identify and characterize novel transcripts and differentially expressed genes during Populus shoot development.
  • To update the Populus genome annotation using long-read sequencing data.
  • To investigate the roles of transcription factors in primary and secondary shoot growth.

Main Methods:

  • Joint PacBio Iso-Seq and RNA-seq analysis of Populus Nanlin895 shoot apex to the fifth internode.
  • Identification and annotation of full-length transcripts, including novel isoforms, long non-coding RNAs, and fusion genes.
  • Differential expression analysis to identify key genes and transcription factors involved in shoot development.

Main Results:

  • 87,150 full-length transcripts were identified, updating the Populus annotation with 2,081 new isoforms and 62,058 alternatively spliced isoforms.
  • 1,187 long non-coding RNAs and 356 fusion genes were discovered among the novel isoforms.
  • 15,838 differentially expressed transcripts were found, including 1,216 transcription factors (TFs), with distinct TF families associated with different growth stages (e.g., AP2, ARF in apex; NAC, bZIP in secondary growth).

Conclusions:

  • Long-read sequencing complements short-read sequencing for comprehensive transcript cataloging and quantification.
  • The study provides an updated Populus annotation and identifies novel TFs critical for primary and secondary shoot growth.
  • This research deepens the understanding of the molecular mechanisms underlying Populus shoot development and biomass generation.