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The developmental dynamics of the Populus stem transcriptome
Chao, Qing; Gao, Zhi-Fang; Zhang, Dong2; Zhao, Biligen-Gaowa; Dong, Feng-Qin; Fu, Chun-Xiang; Liu, Li-Jun; Wang, Bai-Chen
2019
发表期刊PLANT BIOTECHNOLOGY JOURNAL
ISSN1467-7644
卷号17期号:1页码:206-219
摘要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.
关键词PacBio Iso-Seq stem cell maintenance primary growth secondary growth transcription factor
学科领域Biotechnology & Applied Microbiology ; Plant Sciences
DOI10.1111/pbi.12958
收录类别SCI
语种英语
WOS关键词SHOOT APICAL MERISTEM ; LONG NONCODING RNAS ; SECONDARY GROWTH ; WOOD FORMATION ; CELL-DIFFERENTIATION ; ARABIDOPSIS GENE ; DNA METHYLATION ; WALL SYNTHESIS ; PLANT ; ROOT
WOS研究方向Biotechnology & Applied Microbiology ; Plant Sciences
WOS记录号WOS:000455486500018
出版者WILEY
文献子类Article
出版地HOBOKEN
EISSN1467-7652
资助机构National High Technology Research and Development Program of ChinaNational High Technology Research and Development Program of China [2013AA102701]
作者邮箱wangbc@ibcas.ac.cn
作品OA属性Green Published, hybrid
引用统计
被引频次:94[WOS]   [WOS记录]     [WOS相关记录]
文献类型期刊论文
条目标识符http://ir.ibcas.ac.cn/handle/2S10CLM1/19572
专题中科院光生物学重点实验室
作者单位1.Chinese Acad Sci, Inst Bot, Photosynth Res Ctr, Key Lab Photobiol, Beijing, Peoples R China
2.Univ Chinese Acad Sci, Beijing, Peoples R China
3.Biomarker Technol Corp, Beijing, Peoples R China
4.Chinese Acad Sci, Inst Bot, Key Lab Plant Mol Physiol, Beijing, Peoples R China
5.Chinese Acad Sci, Qingdao Inst Bioenergy & Bioproc Technol, Qingdao Engn Res Ctr Biomass Resources & Environm, Key Lab Biofuels, Qingdao, Shandong, Peoples R China
6.Shandong Agr Univ, Coll Forestry, Tai An, Shandong, Peoples R China
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GB/T 7714
Chao, Qing,Gao, Zhi-Fang,Zhang, Dong,et al. The developmental dynamics of the Populus stem transcriptome[J]. PLANT BIOTECHNOLOGY JOURNAL,2019,17(1):206-219.
APA Chao, Qing.,Gao, Zhi-Fang.,Zhang, Dong.,Zhao, Biligen-Gaowa.,Dong, Feng-Qin.,...&Wang, Bai-Chen.(2019).The developmental dynamics of the Populus stem transcriptome.PLANT BIOTECHNOLOGY JOURNAL,17(1),206-219.
MLA Chao, Qing,et al."The developmental dynamics of the Populus stem transcriptome".PLANT BIOTECHNOLOGY JOURNAL 17.1(2019):206-219.
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