Complete chloroplast genome sequence and phylogenetic analysis of wasabi (Eutrema japonicum) and its relatives

Haga, Natsuko; Kobayashi, Mariko; Michiki, Nana; Takano, Tomoyuki; Baba, Fujio; Kobayashi, Kazuo; Ohyanagi, Hajime; Ohgane, Jun; Yano, Kentarô; Yamane, Kyoko

doi:10.1038/s41598-019-49667-z

Cited by 15 publications

(27 citation statements)

References 40 publications

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“…In line with previous findings, the results demonstrated a phylogenetically close relationship between W. japonica and other Brassicaceae species, particularly a high genetic similarity between W. japonica and E. salsugineum (Supplementary Fig. S 1 ) [ 19 , 20 ]. Moreover, the analysis indicated that W. japonica follows an independent evolutionary lineage from B. juncea and A. rusticana [ 18 , 21 ].…”

Section: Resultssupporting

confidence: 91%

Myrosinase isogenes in wasabi (Wasabia japonica Matsum) and their putative roles in glucosinolate metabolism

Truong,

Park,

Jeon

et al. 2024

BMC Plant Biol

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Background Wasabi, a Brassicaceae member, is well-known for its unique pungent and hot flavor which is produced from glucosinolate (GSL) degradation. Myrosinase (MYR) is a principle enzyme catalyzing the primary conversion of GSLs to GSL hydrolysis products (GHPs) which is responsible for plant defense system and food quality. Due to the limited information in relation to MYRs present in wasabi (Wasabia japonica M.), this study aimed to identify the MYR isogenes in W. japonica and analyze their roles in relation to GSL metabolism. Results In results, WjMYRI-1 was abundantly expressed in all organs, whereas WjMYRI-2 showed only trace expression levels. WjMYRII was highly expressed in the aboveground tissues. Interestingly, WjMYRII expression was significantly upregulated by certain abiotic factors, such as methyl jasmonate (more than 40-fold in petioles and 15-fold in leaves) and salt (tenfold in leaves). Young leaves and roots contained 97.89 and 91.17 µmol‧g−1 of GSL, whereas less GSL was produced in mature leaves and petioles (38.36 and 44.79 µmol‧g−1, respectively). Similar pattern was observed in the accumulation of GHPs in various plant organs. Notably, despite the non-significant changes in GSL production, abiotic factors treated samples enhanced significantly GHP content. Pearson’s correlation analysis revealed that WjMYRI-1 expression significantly correlated with GSL accumulation and GHP formation, suggesting the primary role of WjMYRI-1-encoding putative protein in GSL degradation. In contrast, WjMYRII expression level showed no correlation with GSL or GHP content, suggesting another physiological role of WjMYRII in stress-induced response. Conclusions In conclusions, three potential isogenes (WjMYRI-1, WjMYRI-2, and WjMYRII) encoding for different MYR isoforms in W. japonica were identified. Our results provided new insights related to MYR and GSL metabolism which are important for the implications of wasabi in agriculture, food and pharmaceutical industry. Particularly, WjMYRI-1 may be primarily responsible for GSL degradation, whereas WjMYRII (clade II) may be involved in other regulatory pathways induced by abiotic factors.

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Section: Resultssupporting

confidence: 91%

Myrosinase isogenes in wasabi (Wasabia japonica Matsum) and their putative roles in glucosinolate metabolism

Truong,

Park,

Jeon

et al. 2024

BMC Plant Biol

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“…In recent years, studies of wasabi have primarily focused on its nutritional components and cultivation techniques [15,16]. A previous study sequenced the cp genome of E. japonicum, revealing that E. tenue (Gifu) had a close relationship with E. yunnanense, and asserted that they should be considered as a different species from other E. tenue species [17]. However, it only studied the phylogenetic relationships of Eutrema species.…”

Section: Introductionmentioning

confidence: 99%

Analyses of Chloroplast Genome of Eutrema japonicum Provide New Insights into the Evolution of Eutrema Species

Zhang

et al. 2021

Agronomy

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Wasabi (Eutrema japonicum) is a vegetable of Brassicaceae family, currently cultivated in Southwest Asia. It is rich in nutritional and has a spicy flavour. It is regarded as a rare condiment worldwide. Its genetic profile for yield improvement and the development of E. japonicum germplasm resources remains unknown. Cognizant of this, this study sequenced and assembled the chloroplast (cp) genome of E. japonicum to enrich our genomic information of wasabi and further understand genetic relationships within the Eutrema species. The structural characteristics, phylogeny, and evolutionary relationship of cp genomes among other Brassicaceae plants were analyzed and compared to those of Eutrema species. The cp genome of E. japonicum has 153,851 bp with a typical quadripartite structure, including 37 tRNA genes, 8 rRNA genes, and 87 protein-coding genes. It contains 290 simple sequence repeats and prefers to end their codons with an A or T, which is the same as other Brassicaceae species. Moreover, the cp genomes of the Eutrema species had a high degree of collinearity and conservation during the evolution process. Nucleotide diversity analysis revealed that genes in the IR regions had higher Pi values than those in LSC (Large single copy) and SSC (Small single copy) regions, making them potential molecular markers for wasabi diversity studies. The analysis of genetic distance between Eutrema plants and other Brassicacea plants showed that intraspecies variation was found to be low, while large differences were found between genera and species. Phylogenetic analysis based on 29 cp genomes revealed the existence of a close relationship amongst the Eutrema species. Overall, this study provides baseline information for cp genome-based molecular breeding and genetic transformation studies of Eutrema plants.

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“…A scaffold of over 500 bp was used for further analysis. Prokka (v1.13.7) was used for genome prediction and annotation and RepeatMasker (v4.0.9) was used for repeat sequence analysis which has been applied in chloroplast and mitochondrion genomes in many plants (Haga et al., 2019; Lemieux, Otis, & Turmel, 2014; Zhang et al., 2012). Non‐coding RNA prediction was conducted by rRNAmmer (Lagesen et al., 2007) and tRNAscan‐SE (Chan & Loew, 2019).…”

Section: Methodsmentioning

confidence: 99%

“…• Wetland plants are used to treat waste and contaminated waters and landscape reintegration. genomes in many plants (Haga et al, 2019;Lemieux, Otis, & Turmel, 2014;Zhang et al, 2012). Non-coding RNA prediction was conducted by rRNAmmer (Lagesen et al, 2007) and tRNAscan-SE (Chan & Loew, 2019).…”

Section: Core Ideasmentioning

confidence: 99%

Complete chloroplast genome sequences and codon usage pattern among three wetland plants

Deng¹,

Liu²,

Tian³

et al. 2020

Agronomy Journal

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Artificial wetlands are now constructed to be used for wastewater treatment, water quality improvement of reservoirs, and landscape reintegration purposes. The removal and degradation of enriched nutrients and pollutants from them are efficiently done by the activity of wetland plants. Most studies are focused on the purification capacity; the identification and classification of these species are lacking.In the present research, chloroplast genomes (cp genome) of three wetland plants namely, Cyperus alternifolius L., Thalia dealbata Fraser, and Canna indica L. were examined. The cp genomes of these species were sampled and sequenced using Illumina HiSeq platform with a 300-bp paired-end sequencing followed by the analysis of codon usage pattern. In the experiment, 3.86 Gb clean data were obtained and 310 genes from each of C. alternifolius and T. dealbata and 62 genes in C. indica were predicted. In the optimal codons analysis, showed that three cp genome preferred A/U-ending and 3, 11, and 14 were identified in the C. alternifolius, T. dealbata, and C. indica cp genomes, respectively. Advanced analysis indicated that other factors (e.g., natural selection) play a major role in shaping codon usage pattern rather than mutation pressure. These results extend the codon usage bias study of plants and provide genetic data for further identification and phylogenetic studies.Abbreviations: CAI, codon adaptation index; CBI, codon bias index; CDS, protein-coding sequences; COA, correspondence analysis; cp genome, chloroplast genome sequences; ENC, effective number of codons; Fop, frequency of optimal codons; GC3s, GC content at the third synonymous codon positions; RSCU, relative synonymous codon usage

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Complete chloroplast genome sequence and phylogenetic analysis of wasabi (Eutrema japonicum) and its relatives

Cited by 15 publications

References 40 publications

Myrosinase isogenes in wasabi (Wasabia japonica Matsum) and their putative roles in glucosinolate metabolism

Myrosinase isogenes in wasabi (Wasabia japonica Matsum) and their putative roles in glucosinolate metabolism

Analyses of Chloroplast Genome of Eutrema japonicum Provide New Insights into the Evolution of Eutrema Species

Complete chloroplast genome sequences and codon usage pattern among three wetland plants

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