De novo transcriptome analysis using 454 pyrosequencing of the Himalayan Mayapple, Podophyllum hexandrum

Bhattacharyya, Dipto; Sinha, Ragini; Hazra, Saptarshi; Datta, R. K.; Chattopadhyay, Sharmila

doi:10.1186/1471-2164-14-748

Cited by 44 publications

(18 citation statements)

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“…Further TFs are also known to regulate secondary metabolism in plants at the gene and protein levels as well (Vom Endt et al, 2002 ). TFs that are known to regulate plant secondary metabolism include R2R3-MYB, basic helix-loop-helix (bHLH) proteins like CrMYC2, AP2/ERF family proteins, WRKY, NAC, DOF, bZIP, HD-ZIP, and TFIIIA zinc finger TFs (Bhattacharyya et al, 2013 ). A total of 16,344 P. amarus unitranscripts could be annotated at the Plant TF database (PlnTFDB; http://plntfdb.bio.uni-potsdam.de/v3.0/downloads.php ) (Pérez-Rodríguez et al, 2009 ) and categorized into 59 TF categories (Figure 10 ).…”

Section: Resultsmentioning

confidence: 99%

Sequencing, De novo Assembly, Functional Annotation and Analysis of Phyllanthus amarus Leaf Transcriptome Using the Illumina Platform

Mazumdar

Chattopadhyay

2016

Front. Plant Sci.

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Phyllanthus amarus Schum. and Thonn., a widely distributed annual medicinal herb has a long history of use in the traditional system of medicine for over 2000 years. However, the lack of genomic data for P. amarus, a non-model organism hinders research at the molecular level. In the present study, high-throughput sequencing technology has been employed to enhance better understanding of this herb and provide comprehensive genomic information for future work. Here P. amarus leaf transcriptome was sequenced using the Illumina Miseq platform. We assembled 85,927 non-redundant (nr) “unitranscript” sequences with an average length of 1548 bp, from 18,060,997 raw reads. Sequence similarity analyses and annotation of these unitranscripts were performed against databases like green plants nr protein database, Gene Ontology (GO), Clusters of Orthologous Groups (COG), PlnTFDB, KEGG databases. As a result, 69,394 GO terms, 583 enzyme codes (EC), 134 KEGG maps, and 59 Transcription Factor (TF) families were generated. Functional and comparative analyses of assembled unitranscripts were also performed with the most closely related species like Populus trichocarpa and Ricinus communis using TRAPID. KEGG analysis showed that a number of assembled unitranscripts were involved in secondary metabolites, mainly phenylpropanoid, flavonoid, terpenoids, alkaloids, and lignan biosynthetic pathways that have significant medicinal attributes. Further, Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values of the identified secondary metabolite pathway genes were determined and Reverse Transcription PCR (RT-PCR) of a few of these genes were performed to validate the de novo assembled leaf transcriptome dataset. In addition 65,273 simple sequence repeats (SSRs) were also identified. To the best of our knowledge, this is the first transcriptomic dataset of P. amarus till date. Our study provides the largest genetic resource that will lead to drug development and pave the way in deciphering various secondary metabolite biosynthetic pathways in P. amarus, especially those conferring the medicinal attributes of this potent herb.

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Section: Resultsmentioning

confidence: 99%

Sequencing, De novo Assembly, Functional Annotation and Analysis of Phyllanthus amarus Leaf Transcriptome Using the Illumina Platform

Mazumdar

Chattopadhyay

2016

Front. Plant Sci.

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“…High-throughput sequencing technology has been widely used in various plants to obtain transcript coverage even without a reference genome. 454 sequencing is a reasonably low cost [ 28 ] transcriptome profiling method, and its novel and efficient high throughput approach has been used on the olive [ 29 ], Leymus chinensis [ 21 ], orchids [ 30 ], Podophyllum hexandrum [ 31 ], plum [ 32 ], Lonicera japonica Thunb. [ 33 ] and Vicia faba L. [ 34 ].…”

Section: Discussionmentioning

confidence: 99%

De Novo Sequencing and Analysis of the Safflower Transcriptome to Discover Putative Genes Associated with Safflor Yellow in Carthamus tinctorius L.

Liu

Dong

Yao

et al. 2015

IJMS

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Safflower (Carthamus tinctorius L.), an important traditional Chinese medicine, is cultured widely for its pharmacological effects, but little is known regarding the genes related to the metabolic regulation of the safflower’s yellow pigment. To investigate genes related to safflor yellow biosynthesis, 454 pyrosequencing of flower RNA at different developmental stages was performed, generating large databases.In this study, we analyzed 454 sequencing data from different flowering stages in safflower. In total, 1,151,324 raw reads and 1,140,594 clean reads were produced, which were assembled into 51,591 unigenes with an average length of 679 bp and a maximum length of 5109 bp. Among the unigenes, 40,139 were in the early group, 39,768 were obtained from the full group and 28,316 were detected in both samples. With the threshold of “log2 ratio ≥ 1”, there were 34,464 differentially expressed genes, of which 18,043 were up-regulated and 16,421 were down-regulated in the early flower library. Based on the annotations of the unigenes, 281 pathways were predicted. We selected 12 putative genes and analyzed their expression levels using quantitative real time-PCR. The results were consistent with the 454 sequencing results. In addition, the expression of chalcone synthase, chalcone isomerase and anthocyanidin synthase, which are involved in safflor yellow biosynthesis and safflower yellow pigment (SYP) content, were analyzed in different flowering periods, indicating that their expression levels were related to SYP synthesis. Moreover, to further confirm the results of the 454 pyrosequencing, full-length cDNA of chalcone isomerase (CHI) and anthocyanidin synthase (ANS) were cloned from safflower petal by RACE (Rapid-amplification of cDNA ends) method according to fragment of the transcriptome.

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“…A number of key lignan biosynthetic enzymes remain to be identified. Over the past few years, however, the genomes or transcriptomes of lignan-rich plants including Linum [ 77 , 78 , 79 ], Sesamum [ 72 , 73 , 74 ], and Podophyllum [ 71 , 80 , 81 ] have been documented, followed by in silico detection of functional genes. Particularly, Next-generation sequencing (NGS) is a promising approach for the molecular characterization of lignan biosynthetic enzymes; indeed, CYP719A23 and its homolog were identified by NGS-based transcriptome [ 71 ].…”

Section: Lignan Biosynthesis Pathwaysmentioning

confidence: 99%

Essences in Metabolic Engineering of Lignan Biosynthesis

et al. 2015

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Lignans are structurally and functionally diverse phytochemicals biosynthesized in diverse plant species and have received wide attentions as leading compounds of novel drugs for tumor treatment and healthy diets to reduce of the risks of lifestyle-related non-communicable diseases. However, the lineage-specific distribution and the low-amount of production in natural plants, some of which are endangered species, hinder the efficient and stable production of beneficial lignans. Accordingly, the development of new procedures for lignan production is of keen interest. Recent marked advances in the molecular and functional characterization of lignan biosynthetic enzymes and endogenous and exogenous factors for lignan biosynthesis have suggested new methods for the metabolic engineering of lignan biosynthesis cascades leading to the efficient, sustainable, and stable lignan production in plants, including plant cell/organ cultures. Optimization of light conditions, utilization of a wide range of elicitor treatments, and construction of transiently gene-transfected or transgenic lignan-biosynthesizing plants are mainly being attempted. This review will present the basic and latest knowledge regarding metabolic engineering of lignans based on their biosynthetic pathways and biological activities, and the perspectives in lignan production via metabolic engineering.

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De novo transcriptome analysis using 454 pyrosequencing of the Himalayan Mayapple, Podophyllum hexandrum

Cited by 44 publications

References 50 publications

Sequencing, De novo Assembly, Functional Annotation and Analysis of Phyllanthus amarus Leaf Transcriptome Using the Illumina Platform

Sequencing, De novo Assembly, Functional Annotation and Analysis of Phyllanthus amarus Leaf Transcriptome Using the Illumina Platform

De Novo Sequencing and Analysis of the Safflower Transcriptome to Discover Putative Genes Associated with Safflor Yellow in Carthamus tinctorius L.

Essences in Metabolic Engineering of Lignan Biosynthesis

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