Transcriptomic Analysis Reveals Differential Gene Expressions for Cell Growth and Functional Secondary Metabolites in Induced Autotetraploid of Chinese Woad (Isatis indigotica Fort.)

Abstract

The giant organs and enhanced concentrations of secondary metabolites realized by autopolyploidy are attractive for breeding the respective medicinal and agricultural plants and studying the genetic mechanisms. The traditional medicinal plant Chinese woad (Isatis indigotica Fort., 2n = 2x = 14) is now still largely used for the diseases caused by bacteria and viruses in China. In this study, its autopolyploids (3x, 4x) were produced and characterized together with the 2x donor for their phenotype and transcriptomic alterations by using high-throughput RNA sequencing. With the increase of genome dosage, the giantism in cells and organs was obvious and the photosynthetic rate was higher. The 4x plants showed predominantly the normal meiotic chromosome pairing (bivalents and quadrivalents) and equal segregation and then produced the majority of 4x progeny. The total 70136 All-unigenes were de novo assembled, and 56,482 (80.53%) unigenes were annotated based on BLASTx searches of the public databases. From pair-wise comparisons between transcriptomic data of 2x, 3x, 4x plants, 1856 (2.65%)(2x vs 4x), 693(0.98%)(2x vs 3x), 1045(1.48%)(3x vs 4x) unigenes were detected to differentially expressed genes (DEGs), including both up- and down-regulated ones. These DEGs were mainly involved in cell growth (synthesis of expansin and pectin), cell wall organization, secondary metabolite biosynthesis, response to stress and photosynthetic pathways. The up-regulation of some DEGs for metabolic pathways of functional compounds in the induced autotetraploids substantiates the promising new type of this medicinal plant with the increased biomass and targeted metabolites.

Molecular basis underlying the successful invasion of hexaploid cytotypes ofSolidago canadensisL.: Insights from integrated gene and miRNA expression profiling

“…These assembled unigenes were pooled together and further clustered into a reference transcriptome (116,801 “All‐Unigene”) with an average length of 1,056 bp, a N50 value of 1,610 bp, and a GC content of 39.20% (Table A2 in Appendix). These numbers are comparable to those generated in other polyploid studies (e.g., Vigna et al, ; Zhou et al, ) and imply a high‐quality assembly. Furthermore, we also found that the length distribution of the assembled “All‐Unigene” ranged from 224 to 23,608 bp with a total length of 123,376,557 bp, of which 32,942 (28.20%) unigenes ranged from 300 to 500 bp, 32,696 (27.99%) unigenes ranged from 500 to 1,000 bp, 33,468 (28.65%) unigenes ranged from 1,000 to 2,000 bp, and 17,695 (15.15%) unigenes had lengths longer than 2,000 bp (Figure A2 in Appendix).…”

Transcriptome analysis of neo-tetraploid rice reveals specific differential gene expressions associated with fertility and heterosis

“…The differential gene expressions for cell growth and functional secondary metabolites were found in induced autotetraploid of Chinese Woad ( Isatis indigotica Fort.) by transcriptomic analysis30.…”

Dynamic metabolic and transcriptomic profiling of methyl jasmonate‐treated hairy roots reveals synthetic characters and regulators of lignan biosynthesis in Isatis indigotica Fort

“…According to the recent transcriptome annotation of I. indigotica, putative lignan biosynthesis pathway in I. indigotica was depicted (Chen et al, 2013;Tang et al, 2014;Zhou et al, 2015). Biosynthesis of lignans shared a common upstream pathway with lignins and branched after the synthesis of coniferyl alcohol.…”