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. 2021 Mar 11;6(3):723-731.
doi: 10.1080/23802359.2020.1860697.

Complete chloroplast genome sequence and phylogenetic analysis of winter oil rapeseed (Brassica rapa L.)

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Complete chloroplast genome sequence and phylogenetic analysis of winter oil rapeseed (Brassica rapa L.)

Jun Yan Wu et al. Mitochondrial DNA B Resour. .

Abstract

Winter oil rapeseed '18 R-1' (Brassica rapa L.) is a new variety that can survive in northern China where the extreme low temperature is -20 °C to -32 °C. It is different from traditional B. rapa and Brassica napus. In this study, the complete chloroplast (cp) genome of '18 R-1' was sequenced and analyzed to assess the genetic relationship. The size of cp genome is 153,494 bp, including one large single copy (LSC) region of 83,280 bp and one small single copy (SSC) region of 17,776 bp, separated by two inverted repeat (IR) regions of 26,219 bp. The GC content of the whole genome is 36.35%, while those of LSC, SSC, and IR are 34.12%, 29.20%, and 42.32%, respectively. The cp genome encodes 132 genes, including 87 protein-coding genes, eight rRNA genes, and 37 tRNA genes. In repeat structure analysis, 288 simple sequence repeats (SSRs) were identified. Cp genome of '18 R-1' was closely related to Brassica chinensis, B. rapa and Brassica pekinesis.

Keywords: SSRs; Winter oil rapeseed; chloroplast genome; phylogeny.

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Conflict of interest statement

No potential conflict of interest was reported by the author(s).

Figures

Figure 1.
Figure 1.
Cp genome map of 18 R-1. Genes inside the circle are transcribed clockwise, and those outside are transcribed counterclockwise. Genes of different functions are color-coded. The darker gray in the inner circle shows the G + C content, while the lighter gray shows the A + T content.
Figure 2.
Figure 2.
RSCU distribution.
Figure 3.
Figure 3.
Length of repeat (bp) and repeated sequence.
Figure 4.
Figure 4.
SSR sequences of cp genome.
Figure 5.
Figure 5.
Analysis of cp IR scope change.
Figure 6.
Figure 6.
Synteny analysis of chloroplast genomes from nine species in Cruciferae. 1. 18R-1; 2. Brassica loerance; 3. Brassica pekinesis; 4. Brassica napus; 5. Raphanus sativus; 6. Brassica juncea; 7. Brassica nigra; 8. Brassica rapa; 9. Arabidopsis thaliana.
Figure 7.
Figure 7.
Phylogenetic tree constructed from the maximum likelihood and Bayesian inference based on the complete chloroplast genomes. Note: Numbers near each branch is confidence factors in BI.

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Grants and funding

This research was supported by the China Agriculture Research System [CARS-12] and the Natural Science Foundation of Gansu Province [17JR5RA149].

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