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

Mengyao Li,Jie Li,Jiachang Xiao,Yangxia Zheng,Ran Zhang,Kaimin Zheng

doi:10.3390/agronomy11122546

Abstract

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.

Highlights

Our results show the genetic relationship between E. japonicum and its related species and provide a theoretical basis for improving the yield and development of E. japonicum germplasm resources
The rrn16 gene had the highest Pi value (Pi = 0.25499), followed by rrn4.5 (Pi = 0.21805) and rrn23 (Pi = 0.12611), respectively (Figure 4). These findings further indicated that there exists moderate differentiation in the cp genome sequences of the Eutrema species
The sequences exhibited a high degree of collinearity, with differences only in the genome size, intron deletion, and inverted repeats (IR) expansion and contraction (Figure 7). These findings suggested that the cp genome of Eutrema species maintains a high degree of collinearity and conservation during the evolution process

Summary

Introduction

Wasabi japonica (Miq.) Mastum.,) is a perennial herbaceous species of the Brassicaceae family. Contain China and Japan [1]. All parts of wasabi are edible, and it contains many nutrients such as proteins, fats, vitamin C, and natural active ingredients in its rhizomes. Wasabi’s unique isothiocyanate has a bactericidal anti-cancer effect [2,3,4] and is the source of both its spicy taste and aroma [5]. Wasabi has been widely used as an invaluable condiment worldwide.

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