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BMC Genomics
2018 May 09;191:343. doi: 10.1186/s12864-018-4707-9.
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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
.
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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
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