Transcriptome profiling of PeCRY1 transgenic Populus tomentosa
Cryptochromes, a class of blue light photoreceptors, play vital roles in regulating growth and development in higher plants. Despite their control over various important traits, there have been few studies focusing on cryptochromes in forest trees to date. In this study, the Euphrates poplar (Populus euphratica) gene PeCRY1 (cryptochrome 1 of Populus euphratica) was isolated and heterologously expressed in Populus tomentosa. Three biological replicates of each of the PeCRY1 transgenic P. tomentosa (CRY1) and wild-type (WT) plants were processed for transcriptome profiling. We found 34792 commonly expressed transcripts among the 93868 detected unigenes. Using R package DESeq, we identified 357 differentially expressed genes (DEGs), including 132 upregulated and 225 downregulated genes. Gene ontology (GO) enrichment and KEGG pathway enrichment were used to better understand the functions of detected DEGs. Biosynthetic processes, such as starch and sucrose metabolism, which are closely related to growth and development, were highly enriched. Organic cyclic compound biosynthesis was downregulated, whereas carbohydrate metabolism was upregulated. Through KEGG pathway enrichment, we observed that the pentose phosphate pathway, photosynthesis, and circadian rhythm were significantly enriched. Another method of expression analysis based on quantitative reverse transcription polymerase chain reaction (qRT-PCR) validated our RNA sequencing (RNA-seq) results.
KeywordsTranscriptome Populus tomentosa Euphrates poplar RNA-seq Cryptochromes
This work is supported by Special Fund for Forest Scientific Research in the Public Welfare (201404102), Changjiang Scholars Award and “Thousand-person Plan” Award and the Fundamental Research Funds for the Central Universities (NO.BLX2014-22).
RW and WB conceived and designed the experiments. LW performed the experiments, analyzed the data and wrote the paper. WB contributed reagents/materials/analysis tools.
Compliance with ethical standards
Conflict of interest
All of the authors Wenhao Bo, Rongling Wu and Wang Lina declare no competing financial interests.
The subject of this study is the forest tree Euphrates poplar, which grows widely in Northwest China. The transgenic receptor is Populus tomentosa, which is distributed throughout most of China. Neither is an endangered species. The transgenic plants were all cultured in a laboratory setting, and the laboratory is not personally owned. There was no permit required for this study.
Research involving human and animal rights
The article does not contain any studies with human participants performed by any of the authors.
- Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S et al (2008) The Pfam protein families database. Nucl Acids Res 36(264):263–266Google Scholar
- Giliberto L, Perrotta G, Pallara P, Weller JL, Fraser PD, Bramley PM, Fiore A, Tavazza M, Giuliano G (2005) Manipulation of the blue light photoreceptor cryptochrome 2 in tomato affects vegetative development, flowering time, and fruit antioxidant content. Plant Physiol 137:199–208CrossRefPubMedPubMedCentralGoogle Scholar
- Jeong R-D, Chandra-Shekara A, Barman SR, Navarre D, Klessig DF, Kachroo A, Kachroo P (2010) Cryptochrome 2 and phototropin 2 regulate resistance protein-mediated viral defense by negatively regulating an E3 ubiquitin ligase. Proc Natl Acad Sci USA 107:13538–13543CrossRefPubMedPubMedCentralGoogle Scholar
- Liu PX (2011) Study on population structure and dynamics of Populus euphratica in the middle and lower reaches of the Shule River Basin Oasis, Hexi Corridor. J Nat Resources 26:429–439Google Scholar
- Monte E, Tepperman JM, Al-Sady B, Kaczorowski KA, Alonso JM, Ecker JR, Li X, Zhang Y, Quail PH (2004) The phytochrome-interacting transcription factor, PIF3, acts early, selectively, and positively in light-induced chloroplast development. Proc Natl Acad Sci USA 101:16091–16098CrossRefPubMedPubMedCentralGoogle Scholar
- Xie XZ, Chen ZP, Wang XJ (2005) Cloning and expression analysis of CRY2 gene in Sorghum bicolor. J Plant Physiol Mol Biol 31:261Google Scholar