Dataset Information

Data of de novo assembly and functional annotation of the leaf transcriptome of Impatiens balsamina.

ABSTRACT: Impatiens balsamina is both an ornamental and pharmacologically important plant widely distributed in many Asian countries. The leaf of the plant contains many secondary metabolites possessing anti-microbial, anti-tumour and anti-cancer properties. Though there are many phytochemical studies done on the different natural extracts for this plant, not much of genetic information is currently available. This is the first transcriptome of I. balsamina leaf using paired-end Illumina HiSeq sequencing which generated 10.79?GB of raw data. Information of pre-processing (reads filtering), de novo assembly and functional annotation are presented. This data is accessible via NCBI BioProject (PRJNA505711).

SUBMITTER: Foong LC

PROVIDER: S-EPMC6378892 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature

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Data of de novo assembly and functional annotation of the leaf transcriptome of Impatiens balsamina.

Foong Lian Chee LC Ho Anthony Siong Hock ASH Yeo Brandon Pei Hui BPH Lim Yang Mooi YM Tam Sheh May SM

Data in brief 20181216

Impatiens balsamina is both an ornamental and pharmacologically important plant widely distributed in many Asian countries. The leaf of the plant contains many secondary metabolites possessing anti-microbial, anti-tumour and anti-cancer properties. Though there are many phytochemical studies done on the different natural extracts for this plant, not much of genetic information is currently available. This is the first transcriptome of I. balsamina leaf using paired-end Illumina HiS ...[more]

PMID: 30815523

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Project description: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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Dataset Information

Data of de novo assembly and functional annotation of the leaf transcriptome of Impatiens balsamina.

Publications

Data of <i>de novo</i> assembly and functional annotation of the leaf transcriptome of <i>Impatiens balsamina</i>.

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