Transcriptome analysis using de novo RNA-seq to compare ginseng roots cultivated in different environments

Yang, Byung Wook; Hahm, Young Tae

doi:10.1007/s10725-017-0328-6

Cited by 14 publications

(18 citation statements)

References 30 publications

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“…Recently, high-throughput RNA sequencing (RNA-seq) technology has become a powerful and costefficient means to facilitate an understanding of differential gene expression and regulatory mechanisms, especially for plant species without a reference genome [8,9]. RNA-seq has been widely used in the study of rhizome transcriptomics, including in various rhizomatous species such as sorghum (Sorghum halepense and Sorghum propinquum) [10,11], bamboo (Phyllostachys praecox) [12], Oryza longIstam-inata [13][14][15], Equisetum hyemale L. [16], Panax ginseng [17], reed (Phragm ites-australis) [18], tropical lotus (Nelumbo nucifera) [19], CangZhu (Atractylodes Lace-a) [20], Ligusticum chuanxiong [21], ginger (Zingiber officinale) [22], and Miscanthus lutarioriparius [8].…”

Section: Introductionmentioning

confidence: 99%

Revealing the full-length transcriptome of caucasian clover rhizome development

Yin

Zhao

et al. 2020

Preprint

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Background: Caucasian clover (Trifolium ambiguum M.Bieb.) is a strongly rhizomatous, low-crowned perennial leguminous and ground-covering grass. The species may be used as an ornamental plant and is resistant to cold, arid temperatures and grazing due to a well-developed underground rhizome system and a strong clonal reproduction capacity. However, the posttranscriptional mechanism of the development of the rhizome system in caucasian clover has not been comprehensively studied. Additionally, a reference genome for this species has not yet been published, which limits further exploration of many important biological processes in this plant. Result: We adopted PacBio Sequencing and Illumina Sequencing to identify differentially expressed transcripts in five tissues taproot (T1), horizontal rhizome (T2), swelling of taproot (T3), rhizome bud (T4) and rhizome bud tip (T5) of the caucasian clover rhizome. In total, we obtained 19.82 GB clean data and 80,654 nonredundant transcripts were analyzed. Additionally, we identified 78,209 open reading frames (ORFs), 65,227 coding sequences (CDSs), 58,276 simple sequence repeats (SSRs), 6,821 alternative splicing (AS) sites, 24,29 long noncoding RNAs (lncRNAs) and 4,501 putative transcription factors (TFs)from 64 different families. Compared with other tissues, T5 exhibited more differentially expressed genes, and co-upregulated genes in T5 are mainly annotated as involved in phenylpropanoid biosynthesis. We also identified betaine aldehyde dehydrogenase (BADH) as a highly expressed gene specific to T5. WGCNA cluster analysis of transcription factors and physiological indicators were combined to reveal 11 candidate genes (MEgreen-GA3), three of which belong to the HB-KNOX family, that are up-regulated in T3. We analyzed 276 differential transcripts involved in hormone signaling and transduction, and the largest number of transcripts are associated with the IAA signaling pathway, with significant upregulation in T2 and T5. Conclusions: Taken together, this study contributes to our understanding of gene expression across five different tissues and provides preliminary insight into rhizome growth and development in caucasian clover.

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Section: Introductionmentioning

confidence: 99%

Revealing the full-length transcriptome of caucasian clover rhizome development

Yin

Zhao

et al. 2020

Preprint

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“…As a functional molecular marker, SSRs generated from expressed sequence tags (EST-SSRs) can investigate the effects of environmental heterogeneity and local adaptation due to its tight linkage with functional genes controlling phenotype [20][21][22]. Up till now numbers of EST-SSRs developed and checked for polymorphism in many species, such as sweet potato [23], Sesamum indicum [24], radish [25], Cymbidium sinense [26], Chinese bayberry [27], Silver r [28], Salix, Populus, Eucalyptus [29]; Rosa roxburghii [30], Neottopteris nidus [16], Lacquar tree [31], Bread wheat [32], Proso Millet [33], Almond [34] and Ginseng [35]. Limited genomic resources have been developed for Panax species so far, e.g., P. vietnamensis var.…”

Section: Introductionmentioning

confidence: 99%

“…Illumina HiSeq TM 4000 is a new-generation method to permit a comprehensive analysis in the gene expression pro le, have provided fascinating opportunities in life sciences and facilitated transcriptomes sequencing at low-cost and rapid identi cation of EST-SSRs [16,22,25,26,34,35,[37][38][39]. Transcriptomes de novo assembly is indispensable for functional genomics or markers mining in non-model plants study, especially when genome sequence is not available [16,23,30,[37][38][39].…”

Section: Introductionmentioning

confidence: 99%

De novo assembly and transcriptome characterization of an endemic species of Vietnam, Panax vietnamensis Ha et Grushv., including the development of EST-SSR markers for population genetics

Shah

Pham

et al. 2020

Preprint

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Abstract Background: Understanding the genetic diversity in endangered species that occur in forest remnants is necessary to establish efficient strategies for the species conservation, restoration and management. Panax vietnamensis Ha et Grushv. is medicinally important, endemic and endangered species of Vietnam. However, genetic diversity and structure of population are unknown due to lack of efficient molecular markers. Results: In this study, we employed Illumina HiSeqTM 4000 sequencing to analyze the transcriptomes of P. vietnamensis (roots, leaves and stems). Raw reads total of 23,741,783 was obtained and then assembled, from which the generated unigenes were 89,271 (average length = 598.3191 nt). The 31,686 unigenes were annotated in different databases i.e. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Nucleotide Collection (NR/NT) and Swiss-Prot for functional annotation. Further, 11,343 EST-SSRs were detected. From 7,774 primer pairs, 101 were selected for polymorphism validation, in which; 20 primer pairs were successfully amplified to DNA fragments and significant amounts of polymorphism was observed within population. The nine polymorphic microsatellite loci were used for population structure and diversity analyses. The obtained results revealed high levels of genetic diversity in populations, the average observed and expected heterozygosity were HO = 0.422 and HE = 0.479, respectively. During the Bottleneck analysis using TPM and SMM models (p < 0.01) shows that targeted population is significantly heterozygote deficient. This suggests sign of the bottleneck in all populations. Genetic differentiation between populations was moderate (FST = 0.133) and indicating slightly high level of gene flow (Nm = 1.63). Analysis of molecular variance (AMOVA) showed 63.17% of variation within individuals and 12.45% among populations. Our results shows two genetic clusters related to geographical distances. Conclusion: Our study will assist conservators in future conservation management, breeding, production and habitats restoration of the species.

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“…Recently, high-throughput RNA sequencing (RNA-seq) technology has become a powerful and costefficient means to facilitate an understanding of differential gene expression and regulatory mechanisms, especially for plant species without a reference genome [12,13,14]. RNA-seq has been widely used in the study of rhizome transcriptomics, including in various rhizomatous species such as sorghum (Sorghum halepense and Sorghum propinquum) [15,16], bamboo (Phyllostachys praecox) [17], Oryza longistaminata [18][19][20], Equisetum hyemale [21], Panax ginseng [22], Phragmites australis [23], tropical lotus (Nelumbo nucifera) [24], CangZhu (Atractylodes lacea) [25], Ligusticum chuanxiong [26], ginger (Zingiber officinale) [27], and Miscanthus lutarioriparius [12]. Identification of the energy, metabolism, hormones and protein genes associated with rhizome development has revealed that plant rhizomes are also rich in growth-related regulatory factors.…”

Section: Introductionmentioning

confidence: 99%

Revealing the full-length transcriptome of caucasian clover rhizome development

Yin

Zhao

et al. 2020

Preprint

View full text Add to dashboard Cite

Background: Caucasian clover (Trifolium ambiguum M. Bieb.) is a strongly rhizomatous, low-crowned perennial leguminous and ground-covering grass. The species may be used as an ornamental plant and is resistant to cold, arid temperatures and grazing due to a well-developed underground rhizome system and a strong clonal reproduction capacity. However, the posttranscriptional mechanism of the development of the rhizome system in caucasian clover has not been comprehensively studied. Additionally, a reference genome for this species has not yet been published, which limits further exploration of many important biological processes in this plant. Result: We adopted PacBio Sequencing and Illumina Sequencing to identify differentially expressed transcripts in five tissues taproot (T1), horizontal rhizome (T2), swelling of taproot (T3), rhizome bud (T4) and rhizome bud tip (T5) of the caucasian clover rhizome. In total, we obtained 19.82 GB clean data and 80,654 nonredundant transcripts were analysed. Additionally, we identified 78,209 open reading frames (ORFs), 65,227 coding sequences (CDSs), 58,276 simple sequence repeats (SSRs), 6,821 alternative splicing (AS) sites, 24,29 long noncoding RNAs (lncRNAs) and 4,501 putative transcription factors (TFs) from 64 different families. Compared with other tissues, T5 exhibited more differentially expressed genes, and co-upregulated genes in T5 are mainly annotated as involved in phenylpropanoid biosynthesis. We also identified betaine aldehyde dehydrogenase (BADH) as a highly expressed gene-specific to T5. A weighted gene co-expression network analysis (WGCNA) cluster analysis of transcription factors and physiological indicators were combined to reveal 11 candidate genes (MEgreen-GA3), three of which belong to the HB-KNOX family, that are up-regulated in T3. We analysed 276 differential transcripts involved in hormone signaling and transduction, and the largest number of transcripts are associated with the IAA signaling pathway, with significant up-regulation in T2 and T5. Conclusions: Taken together, this study contributes to our understanding of gene expression across five different tissues and provides preliminary insight into rhizome growth and development in caucasian clover.

show abstract

Transcriptome analysis using de novo RNA-seq to compare ginseng roots cultivated in different environments

Cited by 14 publications

References 30 publications

Revealing the full-length transcriptome of caucasian clover rhizome development

Revealing the full-length transcriptome of caucasian clover rhizome development

De novo assembly and transcriptome characterization of an endemic species of Vietnam, Panax vietnamensis Ha et Grushv., including the development of EST-SSR markers for population genetics

Revealing the full-length transcriptome of caucasian clover rhizome development

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