Dataset Information

Transcriptome Analysis of Storage Roots and Fibrous Roots of the Traditional Medicinal Herb Callerya speciosa (Champ.) ScHot.

ABSTRACT: Callerya speciosa (Champ.) ScHot is a woody perennial plant in Fabaceae, the roots of which are used medicinally. The storage roots of C. speciosa are derived from fibrous roots, but not all fibrous roots can develop into storage roots. To detect key genes involved in storage roots formation, we performed Illumina sequencing of the C. speciosa storage roots and fibrous roots. De novo assembly resulted in 161,926 unigenes, which were subsequently annotated by BLAST, GO and KEGG analyses. After expression profiling, 4538 differentially expressed genes were identified. The KEGG pathway enrichment analysis revealed changes in the biosynthesis of cytokinin, phenylpropanoid, starch, sucrose, flavone and other secondary metabolites. Transcription factor-related differentially expressed genes (DEGs) were also identified, including such gene families as GRAS, COL, MIKC, ERF, LBD, and NAC. The DEGs related to light signaling, starch, sugar, photohormones and cell wall-loosening might be involved in the formation of storage roots. This study provides the first transcriptome profiling of C. speciosa roots, data that will facilitate future research of root development and metabolites with medicinal value as well as the breeding of C. speciosa.

SUBMITTER: Xu L

PROVIDER: S-EPMC4972434 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Transcriptome Analysis of Storage Roots and Fibrous Roots of the Traditional Medicinal Herb Callerya speciosa (Champ.) ScHot.

Xu Li L Wang Jiabin J Lei Ming M Li Li L Fu Yunliu Y Wang Zhunian Z Ao Mengfei M Li Zhiying Z

PloS one 20160803 8

Callerya speciosa (Champ.) ScHot is a woody perennial plant in Fabaceae, the roots of which are used medicinally. The storage roots of C. speciosa are derived from fibrous roots, but not all fibrous roots can develop into storage roots. To detect key genes involved in storage roots formation, we performed Illumina sequencing of the C. speciosa storage roots and fibrous roots. De novo assembly resulted in 161,926 unigenes, which were subsequently annotated by BLAST, GO and KEGG analyses. After ex ...[more]

PMID: 27486800

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Project description:The R2R3-MYB family is one of the largest plant transcription factor (TF) families playing vital roles in defense, plant growth, and secondary metabolism biosynthesis. Although this gene family has been studied in many species, isoflavonoid biosynthesis-related R2R3-MYB TFs in Callerya speciosa (Champ. ex Benth.) Schot, a traditional Chinese medicinal herb, are poorly understood. Here, a total of 101 R2R3-MYB TFs were identified from C. speciosa transcriptome dataset. 25 clades divided into five functional groups were clustered based on the sequence similarity and phylogenetic tree. Conserved motifs and domain distribution, expression patterns, and coexpression networks were also employed to identify the potential R2R3-MYB TFs in the regulation of isoflavonoid biosynthesis. In silico evaluation showed that the deduced R2R3-CsMYB proteins contain highly conserved R2R3 repeat domain at the N-terminal region, that is the signature motif of R2R3-type MYB TFs. Eight potential TFs (CsMYB17, CsMYB36, CsMYB41, CsMYB44, CsMYB45, CsMYB46, CsMYB72, and CsMYB81) had high degrees of coexpression with four key isoflavonoid biosynthetic genes (CsIFS, CsCHS7, CsHID-1, and CsCHI3), in which CsMYB36 as a potential regulator possessed the highest degree. HPLC analysis showed that formononetin and maackiain contents were significantly increased during the development of tuberous roots, which might be controlled by both related R2R3-CsMYBs and structural genes involved in the isoflavonoid biosynthesis pathway. The transcriptome data were further validated by reverse transcription real-time PCR (RT-qPCR) analysis, and similar expression profiles between TFs and key structural genes were identified. This study was the first step toward the understanding of the R2R3-MYB TFs regulating isoflavonoid biosynthesis in C. speciosa. The results will provide information for further functional analysis and quality improvement through genetic manipulation of these potential R2R3-CsMYB genes in C. speciosa.

Project description:Veratrilla baillonii Franch is an important Chinese medicinal herb for treating liver-related diseases, which has been over-collected in the recent decades. However, the effective conservation and related population genetic study has been hindered because of the lack of genome sequences and genetic markers in the natural population. We have conducted RNA-seq on V. baillonii. We performed de novo assembly of these data to characterize the V. baillonii transcriptome, resulting in 133,019 contigs with size >200 bp. These contigs were annotated using the NCBI nonredundant database and Gene Ontology (GO) terms. From these contigs, we developed novel microsatellite simple sequence repeat (SSR) markers, identifying a total of 40,885 SSRs. SSRs with repeat motifs of 1-4 bp (mono-, di-, tri-, and tetranucleotides) accounted for 99.8% of all SSRs, with mononucleotide repeats most common, followed by dinucleotide (16.2%) and trinucleotide repeats (14.7%). We selected 151 SSRs for experimental validation, of which 74 were confirmed by polymerase chain reaction. Fourteen SSRs were determined to be polymorphic by screening 40 individuals from six distant populations. The number of alleles per locus ranged from two to four, and the expected heterozygosity varied from 0.2637 to 0.8571, suggesting that these SSR markers are highly polymorphic and effective for further genetic analysis in the nature population. In addition, we explored the genetic structure of V. baillonii using five SSRs in four geographic populations and found that the identified genotypes were clustered into two phylogenetic clades: the Mekong River clade and Jinsha River clade. This result indicates that these two regions may harbor highly divergent genetic lineages and enriched genetic diversity. The de novo transcriptome sequences and new SSR markers discovered by this study provide an initial step for understanding the population genetics of V. baillonii, and a valuable resource for effective conservation management.

Dataset Information

Transcriptome Analysis of Storage Roots and Fibrous Roots of the Traditional Medicinal Herb Callerya speciosa (Champ.) ScHot.

Publications

Transcriptome Analysis of Storage Roots and Fibrous Roots of the Traditional Medicinal Herb Callerya speciosa (Champ.) ScHot.

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