Transcript Profiling Reveals Auxin and Cytokinin Signaling Pathways and Transcription Regulation during In Vitro Organogenesis of Ramie (Boehmeria nivea L. Gaud)

Abstract

In vitro organogenesis, one of the most common pathways leading to in vitro plant regeneration, is widely used in biotechnology and the fundamental study of plant biology. Although previous studies have constructed a complex regulatory network model for Arabidopsis in vitro organogenesis, no related study has been reported in ramie. To generate more complete observations of transcriptome content and dynamics during ramie in vitro organogenesis, we constructed a reference transcriptome library and ten digital gene expression (DGE) libraries for illumina sequencing. Approximately 111.34 million clean reads were obtained for transcriptome and the DGE libraries generated between 13.5 and 18.8 million clean reads. De novo assembly produced 43,222 unigenes and a total of 5,760 differentially expressed genes (DEGs) were filtered. Searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database, 26 auxin related and 11 cytokinin related DEGs were selected for qRT-PCR validation of two ramie cultivars, which had high (Huazhu No. 5) or extremely low (Dazhuhuangbaima) shoot regeneration abilities. The results revealed differing regulation patterns of auxin and cytokinin in different genotypes. Here we report the first genome-wide gene expression profiling of in vitro organogenesis in ramie and provide an overview of transcription and phytohormone regulation during the process. Furthermore, the auxin and cytokinin related genes have distinct expression patterns in two ramie cultivars with high or extremely low shoot regeneration ability, which has given us a better understanding of the in vitro organogenesis mechanism. This result will provide a foundation for future phytohormone research and lead to improvements of the ramie regeneration system.

Identification and Expression Analysis of the PIN and AUX/LAX Gene Families in Ramie (Boehmeria nivea L. Gaud)

“…Because mulberry (Morus notabilis) and ramie both belong to the order Urticales, the MnPIN and MnAUX/LAX gene sequences were downloaded from the mulberry genome database [56]. All the obtained sequences of the two gene families were used to search three ramie transcriptome databases [57][58][59]. ClustalX [60] was used to align the sequences from the three transcriptome databases according to the nucleotide sequence.…”

Transcriptome Assembly of the Bast Fiber Crop, Ramie, Boehmeria nivea (L.) Gaud. (Urticaceae)

“…Research on ramie has included descriptions of specific genes including transcription factors, expansins, and cellulose synthases, as well as transcriptome-level responses related to water deficit, heavy metals, nematodes, hormones, and developmental processes [8][9][10][11][12][13][14]. However, no assembled transcriptome of ramie has been reported to date.…”

Transcriptome Dataset of Leaf Tissue in Agave H11648

“…Equal mass of the three RNA samples were mixed together and sent to Genoseq Technology Co. Ltd (Wuhan, Hubei, China) for next-generation sequencing. Ten micrograms of RNA were used for cDNA library construction [11,18]. The mRNAs were obtained after purification with poly-T oligo-attached magnetic beads, which were subjected for fragmentation with TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA, USA).…”