Dataset Information

Comparative Transcriptome Analysis of Isoetes Sinensis Under Terrestrial and Submerged Conditions.

ABSTRACT: Isoetes L. is an ancient genus of heterosporous lycopsids with a unique phylogenetic position. Repeated adaptations to environmental changes over time have contributed to occupying a variety of niches in Isoetes. However, we know little about how they adapt to the environmental changes, and the sequence resources are very limited in public databases. Isoetes sinensis is an amphibious plant in this genus, alternating frequently between terrestrial and aquatic environments. In this study, I. sinensis was applied to investigate the adaptations under terrestrial (TC) and submerged (ST) conditions using Illumina RNA-sequencing technology. Approximately 87 million high-quality reads were yielded and assembled into 31,619 unigenes with an average length of 1618 bp. Overall, 28,208 unigenes were annotated against the National Center of Biotechnology Information (NCBI), Non-redundant (Nr), Cluster of Orthologous Groups (COG), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Moreover, we identified 1740 differentially expressed genes with 1146 up-regulated and 594 down-regulated genes under TC. GO annotation revealed that stress-relevant categories were remarkably enriched, and KEGG enrichment analysis showed that the phytohormone signalings and carbohydrate metabolism were significantly influenced. Furthermore, a total of 1646 transcription factors (TF) were identified and classified into 54 TF families; among them, 180 TFs were dynamic between terrestrial and submerged conditions. This study is the first report for Isoetes to generate numerous sequences and establish general understandings about the adaptations in the changing environments. The dataset provides a foundation for novel gene discoveries, comparative genomics, functional genomics, and phylogenetics in Isoetes.

SUBMITTER: Yang T

PROVIDER: S-EPMC4722078 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Comparative Transcriptome Analysis of Isoetes Sinensis Under Terrestrial and Submerged Conditions.

Yang Tao T Liu Xing X

Plant molecular biology reporter 20150627

Isoetes L. is an ancient genus of heterosporous lycopsids with a unique phylogenetic position. Repeated adaptations to environmental changes over time have contributed to occupying a variety of niches in Isoetes. However, we know little about how they adapt to the environmental changes, and the sequence resources are very limited in public databases. Isoetes sinensis is an amphibious plant in this genus, alternating frequently between terrestrial and aquatic environments. In ...[more]

PMID: 26843780

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Project description:Cordycepin is a crucial bioactive compound produced by the fungus Cordyceps spp. Its therapeutic potential has been recognized for a wide range of biological properties such as anticancer, anti-diabetic, antidepressant, antioxidant, immunomodulation, etc. Moreover, its human random clinical trials depicted a promising anti-inflammatory activity that reduced the airway inflammation remarkably in asthmatic patients. But its overexploitation and low production of cordycepin in naturally growing biomass are insufficient to meet its existing market demand for its therapeutic use. Therefore, strategies for enhancement of cordycepin production in Cordyceps spp. are warranted. However, specifically, wild type Ophiocordyceps sinensis possesses a very low content of cordycepin and has restricted growth in natural mycelial biomass. To overcome these limitations, this study attempted to enhance cordycepin production in its mycelial biomass in vitro under submerged conditions by adding various growth supplements. The effect of these growth supplements was evaluated by reversed-phase high-performance liquid chromatography (RP-HPLC) which demonstrated that among nucleosides- hypoxanthine and adenosine; amino acids-glycine and glutamine; plant hormones- 1-naphthaleneacetic acid (NAA) and 3-indoleacetic acid (IAA); vitamin-thiamine (B1) from each group of growth supplements yielded a higher amount of cordycepin with 466.48?±?3.88, 380.23?±?1.78, 434.97?±?2.32, 269.78?±?2.92, 227.61?±?2.34, 226.02?±?1.69 and 185.26?±?2.35?mg/L respectively as compared to control with 13.66?±?0.64?mg/L. Further, at the transcriptional level, quantitative real time-polymerase chain reaction (qRT-PCR) analysis of genes associated with metabolism and cordycepin biosynthesis depicted significant upregulation of major downstream genes- NT5E, RNR, purA, and ADEK which corroborated well with RP-HPLC analysis. Taken together, the present study identified growth supplements as potential precursors to activate the cordycepin biosynthesis pathway leading to improved cordycepin production in O. sinensis.

Dataset Information

Comparative Transcriptome Analysis of Isoetes Sinensis Under Terrestrial and Submerged Conditions.

Publications

Comparative Transcriptome Analysis of <i>Isoetes Sinensis</i> Under Terrestrial and Submerged Conditions.

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