Click
here to close Hello! We notice that
you are using Internet Explorer, which is not supported by Echinobase
and may cause the site to display incorrectly. We suggest using a
current version of Chrome,
FireFox,
or Safari.
BMC Genomics
2018 May 09;191:343. doi: 10.1186/s12864-018-4707-9.
Show Gene links
Show Anatomy links
Transcriptome sequencing and analysis during seed growth and development in Euryale ferox Salisb.
Liu X
,
He Z
,
Yin Y
,
Xu X
,
Wu W
,
Li L
.
???displayArticle.abstract???
BACKGROUND: Euryale ferox Salisb., an annual aquatic plant, is the only species in the genus Euryale in the Nymphaeaceae. Seeds of E. ferox are a nutritious food and also used in traditional Chinese medicine (Qian Shi in Mandarin). The molecular events that occurred during seed development in E. ferox have not yet been characterized. In this study, we performed transcriptomic analysis of four developmental stages (T1, T2, T3, and T4) in E. ferox seeds with three biological replicates per developmental stage to understand the physiological and biochemical processes during E. ferox seeds development.
RESULTS: 313,844,425 clean reads were assembled into 160,107 transcripts and 85,006 unigenes with N50 lengths of 2052 bp and 1399 bp, respectively. The unigenes were annotated using five public databases (NR, COG, Swiss-Prot, KEGG, and GO). In the KEGG database, all of the unigenes were assigned to 127 pathways, of which phenylpropanoid biosynthesis was associated with the synthesis of secondary metabolites during E. ferox seed growth and development. Phenylalanine ammonia-lyase (PAL) as the first key enzyme catalyzed the conversion of phenylalanine to trans-cinnamic acid, then was related to the synthesis of flavonoids, lignins and alkaloid. The expression of PAL1 reached its peak at T3 stage, followed by a slight decrease at T4 stage. Cytochrome P450 (P450), encoded by CYP84A1 (which also called ferulate-5-hydroxylase (F5H) in Arabidopsis), was mainly involved in the biosynthesis of lignins.
CONCLUSIONS: Our study provides a transcriptomic analysis to better understand the morphological changes and the accumulation of medicinal components during E. ferox seed development. The increasing expression of PAL and P450 encoded genes in phenylpropanoid biosynthesis may promote the maturation of E. ferox seed including size, color, hardness and accumulation of medicinal components.
Fig. 1. The leaves and flower of Euryale ferox Salisb. in shallow body of water
Fig. 2. The fruit, the longitudinal section of fruit, seed and kernel of Euryale ferox Salisb. during four development stages (T1, T2, T3 and T4). a Fruit; (b) The longitudinal section of fruit; (c) Seed; (d) Kernel
Fig. 3. Venn diagram of Euryale ferox Salisb. seed unigenes. Functional annotation was done using five public databases; NCBI non-redundant protein sequences (NR), Swiss-Prot, COG, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG). The shared unigenes are indicated in the intersections
Fig. 4. Histogram of clusters of orthologous groups (COG) classification. A total of 11,304 unigenes with lengths more than 300 bp were divided into 25 COG categories
Fig. 5. Functional annotation of assembled sequences based on gene ontology (GO) categorization. 15,827 unigenes were grouped into the three main GO domains: “cellular component”, “molecular function”, and “biological process”
Fig. 6. Simplified scheme of phenylpropanoid biosynthesis. Two key enzymes are PAL (phenylalanine ammonia-lyase) and F5H (ferulate-5-hydroxylase) which called the CYP84A1 gene of cytochrome P450
Fig. 7. A phylogenetic tree depicting the relationships among the CYP84A1s in angiosperm. Forty-two CYP84A1 genes from angiosperms with Ginkgo biloba as a outgroup were used in this study
Fig. 8. Relative expression levels of six DEGs in four developmental stages of Euryale ferox Salisb. seed. We compared expression levels determined by RNA-seq and qRT-PCR analyses for each DEG
Ahmed,
Antidiabetic, antioxidant, antihyperlipidemic effect of extract of Euryale ferox salisb. with enhanced histopathology of pancreas, liver and kidney in streptozotocin induced diabetic rats.
2015, Pubmed,
Echinobase
Ahmed,
Antidiabetic, antioxidant, antihyperlipidemic effect of extract of Euryale ferox salisb. with enhanced histopathology of pancreas, liver and kidney in streptozotocin induced diabetic rats.
2015,
Pubmed
,
Echinobase
Apweiler,
UniProt: the Universal Protein knowledgebase.
2004,
Pubmed
Ashburner,
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
2000,
Pubmed
Boerjan,
Lignin biosynthesis.
2003,
Pubmed
Chang,
Tomato phenylalanine ammonia-lyase gene family, highly redundant but strongly underutilized.
2009,
Pubmed
Cheng,
Transcriptome Analysis of Gene Expression during Chinese Water Chestnut Storage Organ Formation.
2017,
Pubmed
Das,
The effect of Euryale ferox (Makhana), an herb of aquatic origin, on myocardial ischemic reperfusion injury.
2006,
Pubmed
,
Echinobase
Du,
Genome-Wide Analysis, Classification, Evolution, and Expression Analysis of the Cytochrome P450 93 Family in Land Plants.
2017,
Pubmed
Grabherr,
Full-length transcriptome assembly from RNA-Seq data without a reference genome.
2012,
Pubmed
Hou,
The phenylalanine ammonia-lyase gene family in Salvia miltiorrhiza: genome-wide characterization, molecular cloning and expression analysis.
2014,
Pubmed
Ivamoto,
Diterpenes biochemical profile and transcriptional analysis of cytochrome P450s genes in leaves, roots, flowers, and during Coffea arabica L. fruit development.
2017,
Pubmed
Kanehisa,
The KEGG resource for deciphering the genome.
2004,
Pubmed
Kao,
Differential expression of two distinct phenylalanine ammonia-lyase genes in condensed tannin-accumulating and lignifying cells of quaking aspen.
2003,
Pubmed
Kumar,
MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.
2017,
Pubmed
Kumar,
RAPD and ISSR Marker-Based Comparative Evaluation of Genetic Diversity Among Indian Germplasms of Euryale ferox: an Aquatic Food Plant.
2017,
Pubmed
,
Echinobase
Langmead,
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
2009,
Pubmed
Leng,
EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments.
2013,
Pubmed
Lepelley,
Characterization, high-resolution mapping and differential expression of three homologous PAL genes in Coffea canephora Pierre (Rubiaceae).
2012,
Pubmed
Li,
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome.
2011,
Pubmed
Liang,
Identification of differentially expressed genes related to aphid resistance in cucumber (Cucumis sativus L.).
2016,
Pubmed
Liu,
De novo assembly and characterization of germinating lettuce seed transcriptome using Illumina paired-end sequencing.
2016,
Pubmed
Ma,
Expression of TaCYP78A3, a gene encoding cytochrome P450 CYP78A3 protein in wheat (Triticum aestivum L.), affects seed size.
2016,
Pubmed
Mach,
Unpuréeing the tomato: layers of information revealed by microdissection and high-throughput transcriptome sequencing.
2012,
Pubmed
Nelson,
The cytochrome p450 homepage.
2010,
Pubmed
Nelson,
Comparative genomics of rice and Arabidopsis. Analysis of 727 cytochrome P450 genes and pseudogenes from a monocot and a dicot.
2004,
Pubmed
Okuda,
Systematics and health effects of chemically distinct tannins in medicinal plants.
2006,
Pubmed
Pombo,
Cloning of FaPAL6 gene from strawberry fruit and characterization of its expression and enzymatic activity in two cultivars with different anthocyanin accumulation.
2012,
Pubmed
Quan,
Polymorphic microsatellite markers in Euryale ferox Salisb. (Nymphaeaceae).
2013,
Pubmed
,
Echinobase
Raes,
Genome-wide characterization of the lignification toolbox in Arabidopsis.
2004,
Pubmed
Reichert,
Phenylalanine ammonia-lyase (PAL) from tobacco (Nicotiana tabacum): characterization of the four tobacco PAL genes and active heterotetrameric enzymes.
2009,
Pubmed
Ruegger,
Regulation of ferulate-5-hydroxylase expression in Arabidopsis in the context of sinapate ester biosynthesis.
1999,
Pubmed
Shang,
Multiple tandem duplication of the phenylalanine ammonia-lyase genes in Cucumis sativus L.
2013,
Pubmed
Song,
Isolation and identification of compounds responsible for antioxidant capacity of Euryale ferox seeds.
2011,
Pubmed
,
Echinobase
Tang,
Whole transcriptome sequencing reveals genes involved in plastid/chloroplast division and development are regulated by the HP1/DDB1 at an early stage of tomato fruit development.
2014,
Pubmed
Tatusov,
The COG database: a tool for genome-scale analysis of protein functions and evolution.
2000,
Pubmed
Trapnell,
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.
2010,
Pubmed
Wanner,
The phenylalanine ammonia-lyase gene family in Arabidopsis thaliana.
1995,
Pubmed
Wu,
Transcriptome profile analysis of floral sex determination in cucumber.
2010,
Pubmed
Wu,
Antioxidant and anti-fatigue activities of phenolic extract from the seed coat of Euryale ferox Salisb. and identification of three phenolic compounds by LC-ESI-MS/MS.
2014,
Pubmed
,
Echinobase
Yin,
De novo assembly of the peanut (Arachis hypogaea L.) seed transcriptome revealed candidate unigenes for oil accumulation pathways.
2014,
Pubmed
Yu,
De novo Taproot Transcriptome Sequencing and Analysis of Major Genes Involved in Sucrose Metabolism in Radish (Raphanus sativus L.).
2016,
Pubmed
Zhao,
New cerebrosides from Euryale ferox.
1994,
Pubmed
,
Echinobase