De Novo Assembly of Expressed Transcripts and Global Transcriptomic Analysis from Seedlings of the Paper Mulberry (Broussonetia kazinoki x Broussonetia papyifera)

Abstract

The paper mulberry is one of the multifunctional tree species in agroforestry systems and is also commonly utilized in traditional medicine in China and other Asian countries. However, little is known about its molecular genetics, which hinders research on and exploitation of this valuable resource. To discern the correlation between gene expression and the essential properties of the paper mulberry, we performed a transcriptomics analysis, assembling a total of 37,725 unigenes from 54,638,676 reads generated by RNA-seq. Among these, 22,692 unigenes showed greater than 60% similarity with genes from other species. The lengths of 13,566 annotated unigenes were longer than 1,000 bp. Functional clustering analysis with COG (Cluster of Orthologous Groups) revealed that 17,184 unigenes are primarily involved in transcription, translation, signal transduction, carbohydrate metabolism, secondary metabolism, and energy metabolism. GO (Gene Ontology) annotation suggests enrichment of genes encoding antioxidant activity, transporter activity, biosynthesis, metabolism and stress response, with a total of 30,659 unigenes falling in these categories. KEGG (Kyoto Encyclopedia of Genes and Genomes) metabolic pathway analysis showed that 7,199 unigenes are associated with 119 metabolic pathways. In addition to the basic metabolism, these genes are enriched for plant pathogen interaction, flavonoid metabolism and other secondary metabolic processes. Furthermore, differences in the transcriptomes of leaf, stem and root tissues were analyzed and 7,233 specifically expressed unigenes were identified. This global expression analysis provided novel insights about the molecular mechanisms of the biosynthesis of flavonoid, lignin and cellulose, as well as on the response to biotic and abiotic stresses including the remediation of contaminated soil by the paper mulberry.

The complete chloroplast genome of an economic and ecological plant, paper mulberry (Broussonetia kazinoki × Broussonetia papyifera)

“…The complete chloroplast genome of an economic and ecological plant, paper mulberry (Broussonetia kazinoki 3 Broussonetia papyifera) The paper mulberry, hybridized by Broussonetia kazinoki  Broussonetia papyifera, is a species of Moraceae, which is distributed in Eastern Asia and pacific countries (Xianjun et al 2014). The species has important economic values and ecological values.…”

Global transcriptomics identification and analysis of transcriptional factors in different tissues of the paper mulberry

“…In our study, a total of 1,337 TFs identified from the transcriptome data of the paper mulberry could be classified into 55 families and 578 TFs of them had complete ORF. These TFs comprised of more than 3.5% of the genes of this plant [ 22 ]. Although the genome of paper mulberry has not been sequenced and its genes number might be underestimated, this ratio was much closed to that of other genome known plants, such as C. sativa , Fragaria vesca and Vitis vinifera (Figure 6 ) and it is less than that of Arabidopsis and rice.…”

“…Raw sequence data were generated by Illumina pipeline and have been available in NCBI’s Short Read Archive (SRA) database ( http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi ) under accession number SRP029966. All of the Illumina reads generated from different cDNA libraries were de novo assembled with Trinity program to form the global transcriptome of the paper mulberry [ 22 ]. For the functional annotation, unigenes were firstly aligned by Blastx to protein databases nr (E ≤ 1e-5), retrieving proteins with the highest sequence similarity to the given unigenes along with their functional annotations.…”

The Chloroplast Genome Comparative Characteristic of Artificial Breeding Tree, a Case About Broussonetia Kazinoki × Broussonetia Papyifera

“…Paper mulberry, Broussonetia papyifera, B. kazinoki × B. papyifera are all used to called the tree, while it may not the same tree [36]. In recent year, a hybrid variety for paper mulberry was bred [15,37]. The breeding process is showed in Fig.…”