Abstract
Eruca sativa Mill. (Brassicaceae) is an important edible vegetable and a potential medicinal plant due to the antibacterial activity of its seed oil. Here, the complete chloroplast (cp) genome of E. sativa was de novo assembled with a combination of long PacBio reads and short Illumina reads. The E. sativa cp genome had a quadripartite structure that was 153,522 bp in size, consisting of one large single-copy region of 83,320 bp and one small single-copy region of 17,786 bp which were separated by two inverted repeat (IRa and IRb) regions of 26,208 bp. This complete cp genome harbored 113 unique genes: 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Forty-nine long repetitive sequences and 69 simple sequence repeats were identified in the E. sativa cp genome. A codon usage analysis of the E. sativa cp genome showed a bias toward codons ending in A/T. The E. sativa cp genome was similar in size, gene composition, and linearity of the structural region when compared with other Brassicaceae cp genomes. Moreover, the analysis of the synonymous (Ks) and non-synonymous (Ka) substitution rates demonstrated that protein-coding genes generally underwent purifying selection pressure, expect ycf1, ycf2, and rps12. A phylogenetic analysis determined that E. sativa is evolutionarily close to important Brassica species, indicating that it may be possible to transfer favorable E. sativa alleles into other Brassica species. Our results will be helpful to advance genetic improvement and breeding of E. sativa, and will provide valuable information for utilizing E. sativa as an important resource to improve other Brassica species.
Highlights
Eruca sativa Mill. is an annual or perennial species of Eruca (Brassicaceae), mainly distributed in Europe and Western Asia
The complete E. sativa cp genome had a quadripartite structure comprised of 153,522 bp, including an small single copy (SSC) region of 17,786 bp and an large single copy (LSC) region of 83,320 bp, which were separated by a pair of inverted repeats (IRa and IRb) of 26,208 bp (Table 1, Fig 1)
The results showed that the average Ka/Ks ratio was 0.17, after removing the genes with Ka or Ks of 0, indicating that the genes in the E. sativa cp genome were subject to strong purifying selection pressures
Summary
Eruca sativa Mill. is an annual or perennial species of Eruca (Brassicaceae), mainly distributed in Europe and Western Asia. Is an annual or perennial species of Eruca (Brassicaceae), mainly distributed in Europe and Western Asia. E. sativa is believed to have originated from the Mediterranean region and has been widely used as an oil crop and edible vegetable [1]. Due to the fragrance of its leaves, E. sativa is a popular salad and spice in Middle Eastern and European countries [2]. The complete chloroplast genome of Eruca sativa. Social Development of Guizhou (QKHZC[2017] 2811) by YWC
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