caa a22 4500 606208623 CHVBK 20210128101023.0 cr unu---uuuuu 210128e20150101xx s 000 0 eng 10.1007/s00425-014-2168-1 doi (NATIONALLICENCE)springer-10.1007/s00425-014-2168-1 Genome-wide identification of novel long non-coding RNAs in Populus tomentosa tension wood, opposite wood and normal wood xylem by RNA-seq [Elektronische Daten] [Jinhui Chen, Mingyang Quan, Deqiang Zhang] Increasing evidence shows that long non-coding RNAs (lncRNAs) function as important regulatory factors during plant development, but few reports have examined lncRNAs in trees. Here, we report our genome-scale identification and characterization of lncRNAs differentially expressed in the xylem of tension wood, opposite wood and normal wood in Populus tomentosa, by high-throughput RNA sequencing. We identified 1,377 putative lncRNAs by computational analysis, and expression and structure analyses showed that the lncRNAs had lower expression levels and shorter lengths than protein-coding transcripts in Populus. Of the 776 differently expressed (log2FC ≥1 or ≤-1, FDR ≤0.01) lncRNAs, 389 could potentially target 1,151 genes via trans-regulatory effects. Functional annotation of these target genes demonstrated that they are involved in fundamental processes, and in specific mechanisms such as response to stimuli. We also identified 16 target genes involved in wood formation, including cellulose and lignin biosynthesis, suggesting a potential role for lncRNAs in wood formation. In addition, three lncRNAs harbor precursors of four miRNAs, and 25 were potentially targeted by 44 miRNAs where a negative expression relationship between them was detected by qRT-PCR. Thus, a network of interactions among the lncRNAs, miRNAs and mRNAs was constructed, indicating widespread regulatory interactions between non-coding RNAs and mRNAs. Lastly, qRT-PCR validation confirmed the differential expression of these lncRNAs, and revealed that they have tissue-specific expression in P. tomentosa. This study presents the first global identification of lncRNAs and their potential functions in wood formation, providing a starting point for detailed dissection of the functions of lncRNAs in Populus. Springer-Verlag Berlin Heidelberg, 2014 Long non-coding RNAs nationallicence Populus nationallicence Tension wood nationallicence Wood formation nationallicence lncRNAs : Long non-coding RNAs nationallicence 4CL : 4-Coumarate-CoA ligase nationallicence CCOMT : Caffeoyl-CoA 3-O-methyltransferase nationallicence CESA : Cellulose synthase nationallicence CSLD4 : Cellulose synthase-like protein D4 nationallicence CW : Compression wood nationallicence GA2ox : Gibberellin 2-oxidase nationallicence GO : Gene ontology nationallicence NW : Normal wood nationallicence OW : Opposite wood nationallicence ppo : Polyphenol oxidase nationallicence TF : Transcription factor nationallicence TW : Tension wood nationallicence Chen Jinhui National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, 100083, Beijing, People's Republic of China aut Quan Mingyang National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, 100083, Beijing, People's Republic of China aut Zhang Deqiang National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, 100083, Beijing, People's Republic of China aut Planta Springer Berlin Heidelberg 241/1(2015-01-01), 125-143 0032-0935 241:1<125 2015 241 425 https://doi.org/10.1007/s00425-014-2168-1 text/html Onlinezugriff via DOI BK010053 XK010053 XK010000 Metadata rights reserved Springer special CC-BY-NC licence nationallicence 1 research-article jats NATIONALLICENCE NATIONALLICENCE NL-springer NATIONALLICENCE 856 40 https://doi.org/10.1007/s00425-014-2168-1 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Chen Jinhui National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, 100083, Beijing, People's Republic of China aut NATIONALLICENCE 700 1- Quan Mingyang National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, 100083, Beijing, People's Republic of China aut NATIONALLICENCE 700 1- Zhang Deqiang National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, 100083, Beijing, People's Republic of China aut NATIONALLICENCE 773 0- Planta Springer Berlin Heidelberg 241/1(2015-01-01), 125-143 0032-0935 241:1<125 2015 241 425