The developmental dynamics of the Populus stem transcriptome

Plant Biotechnology Journal
Qing ChaoBai-Chen Wang

Abstract

The Populus shoot undergoes primary growth (longitudinal growth) followed by secondary growth (radial growth), which produces biomass that is an important source of energy worldwide. We adopted joint PacBio Iso-Seq and RNA-seq analysis to identify differentially expressed transcripts along a developmental gradient from the shoot apex to the fifth internode of Populus Nanlin895. We obtained 87 150 full-length transcripts, including 2081 new isoforms and 62 058 new alternatively spliced isoforms, most of which were produced by intron retention, that were used to update the Populus annotation. Among these novel isoforms, there are 1187 long non-coding RNAs and 356 fusion genes. Using this annotation, we found 15 838 differentially expressed transcripts along the shoot developmental gradient, of which 1216 were transcription factors (TFs). Only a few of these genes were reported previously. The differential expression of these TFs suggests that they may play important roles in primary and secondary growth. AP2, ARF, YABBY and GRF TFs are highly expressed in the apex, whereas NAC, bZIP, PLATZ and HSF TFs are likely to be important for secondary growth. Overall, our findings provide evidence that long-read sequencing can complement s...Continue Reading

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Citations

Oct 15, 2019·Frontiers in Genetics·Deborah WeighillDaniel Jacobson
Dec 29, 2020·Mitochondrial DNA. Part B, Resources·Tao SuYuxin Liu
Jun 26, 2021·Frontiers in Microbiology·Xinhong PengXiliang Jiang
Jul 29, 2021·Plant Science : an International Journal of Experimental Plant Biology·Yuhan DongShenchun Qu
Jul 28, 2021·Journal of Experimental Botany·Zhen HanLi-Jun Liu

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Methods Mentioned

BETA
Illumina sequencing
PCR
RNA Assay
Assay

Software Mentioned

AStalavista
‐ Analysis
BLAST
Tophat2
bowtie
R
DESeq
CNCI
bowtie2
cBot Cluster Generation System

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