Whole-transcriptome sequencing of Pinellia ternata using the Illumina platform

Huang, Xiaosheng; Yan, Jun; Liu, D.J.; Yang, Bo; Chen, H.; Li, M.

doi:10.4238/gmr.15028062

Cited by 5 publications

(2 citation statements)

References 36 publications

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“…Herein, we rst report the most comprehensive transcriptome analysis of four genotypes of P. ternate (Shaoye, Taoye, Zhuye and Liuye Type) using the Illumina platform. In our transcriptome analysis, the obtained total clean reads nucleotides, length distribution pattern and unigene lengths were similar to the previous Illumina based sequencing studies [34], indicating an effective de novo assembly of four genotypes of P. ternate transcriptome sequencing data. Among the 126,391…”

Section: Discussionsupporting

confidence: 83%

Illumina-Based Transcriptome Analysis of Four Genotypes of Pinellia ternata (Thunb.) Breit.

Lai

Wan

et al. 2020

Preprint

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Background Pinellia ternate (Thunb.) Breit. ( P. ternate ), a weed species distributed in Eastern Asia, has been widely used as a Chinese herbal medicine. Currently, four genotypes of P. ternate have been identified according to their different leaf shapes, including Shaoye, Taoye, Zhuye and Liuye Type. In addition, the total alkaloids and organic acids content in tuber, tuber yields and other physiology and agronomic characteristics were significant difference. However, little is known about the evolution and genetic diversity of four genotypes of P. ternate . Moreover, the genomics of P. ternate remains uncharacterized. The recent development of RNA-Seq, a next generation sequencing technology, provides an opportunity to expand the identification of P. ternate genes through in-depth transcript profiling. Methods In this study, we presented a comprehensive landscape of the transcriptome profiles of four genotypes of P. ternate using Illumina paired-end sequencing technology. Results Totally, 70,491,871, 72,819,035, 73,159,913 and 71,612,115 reads were achieved in four genotypes of P. ternate , respectively. A total number of 126,391 assembled unigenes were identified. After aligning the sequences to the public protein databases, 82,998 unigenes were annotated. Among these, 15,534 were assigned to Gene Ontology categories, 41,216 to Clusters of Orthologous Groups, and 46,053 to Kyoto Encyclopedia of Genes and Genomes pathways. In addition, 23,678 simple sequence repeats (SSRs) and 65,527 Single Nucleotide Polymorphism (SNP) variations were detected. Conclusion This study provides abundant genomic data and comprehensive transcriptome for P. ternate . We envision that these transcriptome datasets will serve as an important public information platform to accelerate further studies of the P. ternate and the identification of genes that potentially involving in the biosynthesis of total alkaloids, acid and other active ingredients among different genotypes P. ternate .

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Section: Discussionsupporting

confidence: 83%

Illumina-Based Transcriptome Analysis of Four Genotypes of Pinellia ternata (Thunb.) Breit.

Lai

Wan

et al. 2020

Preprint

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“…The first transcriptome database of PT was built by Huang [ 31 ] to research the whole transcriptome information, but he has not built PT resistance to soft rot pathogens transcriptome database to reveal the molecular mechanism to prevent the soft rot disease. PT2P line is a unique chromosome-doubling strain in the laboratory, with many excellent characteristics, such as high volume, disease resistance, and high photosynthetic efficiency.…”

Section: Introductionmentioning

confidence: 99%

Transcriptomic analysis of Pinellia ternata (Thunb.) Breit T2 plus line provides insights in host responses resist Pectobacterium carotovorum infection

et al. 2021

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Transcriptome is used to determine the induction response of Pinellia ternata (Thunb.) Breit T2 plus line (abbreviated as PT2P line) infected with Pectobacterium carotovorum. The main objective of the study was to deal with the transcriptome database of PT2P line resistance to soft rot pathogens to provide a new perspective for identifying the resistance-related genes and understanding the molecular mechanism. Results indicated that water soaking and tissue collapse started at 20 h after PT2P line was infected by P. carotovorum. A total of 1360 and 5768 differentially expressed genes (DEGs) were identified at 0 h and 20 h, respectively. After 20 h of infection, growth and development-related pathways were inhibited. Meanwhile, DEGs were promoted the colonization of P. carotovorum pathogens in specific cell wall modification processes at the early infected stage. A shift to a defensive response was triggered at 0 h. A large number of DEGs were mainly upcontrolled at 20 h and were substantially used in the pathogen recognition and the introduction of signal transformation cascades, secondary metabolites biosynthesis, pathogenic proteins activation, transcription aspects and numerous transporters. Furthermore, our data provided novel insights into the transcript reprogramming of PT2P line in response to P. carotovorum infestation.

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Pinellia ternata PtZS1 contributes to abiotic stress responses via the antioxidant pathway

Guo

et al. 2023

J. Plant Biochem. Biotechnol.

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Whole-transcriptome sequencing of Pinellia ternata using the Illumina platform

Cited by 5 publications

References 36 publications

Illumina-Based Transcriptome Analysis of Four Genotypes of Pinellia ternata (Thunb.) Breit.

Illumina-Based Transcriptome Analysis of Four Genotypes of Pinellia ternata (Thunb.) Breit.

Transcriptomic analysis of Pinellia ternata (Thunb.) Breit T2 plus line provides insights in host responses resist Pectobacterium carotovorum infection

Pinellia ternata PtZS1 contributes to abiotic stress responses via the antioxidant pathway

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