ArticlePlant biotechnology journal2019
The developmental dynamics of the Populus stem transcriptome.
Article in Plant biotechnology journal, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers.
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Who cites it
76 citing papers in PubMed, 199 citations in OpenAlex.
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- Genome-Wide Identification and Salt Stress-Responsive Expression Analysis of thePlants (Basel, Switzerland) · 2025Article
- The developmental transcriptome dynamics of current-year shoot utilized as scion in Camellia chekiangoleosa.BMC plant biology · 2025Article
- Physiological changes and full-length transcriptome of Artemisia sphaerocephala in response to drought stress.BMC plant biology · 2025Article
- Genome-wide identification and analysis of GH1-containing H1 histones among poplar species.BMC genomics · 2025Article
- Insights into Molecular Mechanism of Secondary Xylem Rapid Growth inPlants (Basel, Switzerland) · 2025Article
- Metabolism-Based Herbicide Resistance to Mesosulfuron-methyl and Identification of Candidate Genes inPlants (Basel, Switzerland) · 2024Article
- GhiPLATZ17 and GhiPLATZ22, zinc-dependent DNA-binding transcription factors, promote salt tolerance in upland cotton.Plant cell reports · 2024Article
- Transcriptome analysis of the transition from primary to secondary growth of vertical stem in Eucalyptus grandis.BMC plant biology · 2024Article
- Full-length transcriptome and RNA-Seq analyses reveal the resistance mechanism of sesame in response to Corynespora cassiicola.BMC plant biology · 2024Article
- A protocol for identifying universal reference genes within a genus based on RNA-Seq data: a case study of poplar stem gene expression.Forestry research · 2024Article
- Growth-regulating factor 15-mediated vascular cambium differentiation positively regulates wood formation in hybrid poplar (Frontiers in plant science · 2024Article
- Transcriptome and miRNAs Profiles Reveal Regulatory Network and Key Regulators of Secondary Xylem Formation in "84K" Poplar.International journal of molecular sciences · 2023Article
- Selection, Identification, and Transcript Expression Analysis of Antioxidant Enzyme Genes inAntioxidants (Basel, Switzerland) · 2023Article
- Comprehensive Profiling of Alternative Splicing and Alternative Polyadenylation during Fruit Ripening in Watermelon (International journal of molecular sciences · 2023Article
- Genes expression profiles in vascular cambium of Eucalyptus urophylla × Eucalyptus grandis at different ages.BMC plant biology · 2023Article
- Integrating ATAC-seq and RNA-seq to identify differentially expressed genes with chromatin-accessible changes during photosynthetic establishment in Populus leaves.Plant molecular biology · 2023Article
- Uncovering genomic and transcriptional variations facilitates utilization of wild resources in cotton disease resistance improvement.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- Genome-Wide Identification and Expression Analysis of the PLATZ Transcription Factor in Tomato.Plants (Basel, Switzerland) · 2023Article
16 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
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 short-read sequencing for cataloguing and quantifying eukaryotic transcripts and increase our understanding of the vital and dynamic process of shoot development.
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