The complete mitochondrial genome of turnip (Brassica rapa ssp. rapa)

Abstract

Turnip (Brassica rapa ssp. rapa) is one of the most important leaf and root vegetable crop in the Brassicaceae family. In this study, the complete mitochondrial genome sequence was assembled at the first time and a circle form of 219,736 bp in size was obtained. A total of 99 genes were annotated, including 78 protein-coding genes, 18 transfer RNA (tRNA) genes, and three ribosomal RNA (rRNA) genes. The phylogenetic relationship showed that turnip is closely related to subsp. campestris rather than Raphanus staivus.

Keywords:

• Turnip
• complete mitochondrial genome
• Brassica
• phylogenetic relationship

Turnip (Brassica rapa ssp. rapa L. 2n = 2× =20), one of the most important Brassicaceae vegetable crops, is widely cultivated in China and East Asia. Turnip is widely used for human consumption and animal fodder (Zhuang et al. 2019) due to the abundant glucosinolates (Rochfort et al. 2006; Zhang et al. 2008; Chung et al. 2016), dietary phenolic (Chung et al. 2016), dietary fiber, Vitamin C (Fahey et al. 1995), and other bioactive compounds (Thiruvengadam and Chung 2015). In addition, turnip is used for Tibetan medicine due to the flavonoid compound (p coumaric acid-beta-D-glucopyranoside) in Tibetan turnip, which played important role on anti-hypoxia effect (Chu et al. 2017; Li et al. 2018).

Mitochondria (mt) are main organelles responsible for plant energy production, metabolism, cell homeostasis, which play a vital role in development, reproduction, and various biochemical processes in plants by supplying ATP via oxidative phosphorylation (Palmer and Herbon 1988; Sloan et al. 2012; Liao et al. 2018). The length of mt DNA of plants varies greatly in size from 208 to 11.3 Mb (Sloan et al. 2012; Shen et al. 2019). Many mt genome sequences of Brassica crops have been reported (Yang et al. 2016; Hatono et al. 2017; Yang et al. 2018; Wu et al. 2019). However, to our knowledge, this is the first complete mt genome sequences of turnip presented. The complete mt genome sequence of turnip was assembled, which provide the genome information in the genus Brassica.

The fresh and healthy leaf of B. rapa ssp. rapa was collected from an individual turnip plant, W21, which was planted in the field of Qinghai university (N36°42′; E 101°45′), Xining, China, and genomic DNA was stored at Qinghai University. Total genomic DNA of turnip was extracted from fresh and healthy leaves by modified CTAB (Porebski et al. 1997) method. The library was constructed by the Shaanxi Breeding Biotechnologies Co., Ltd (Shaanxi, China) according to the manufacture’s manual and sequenced using Illumina HiSeq2500. A total of 8.38 Gb clean data was obtained and assembled by the MITObim software (Hahn et al. 2013) with the complete mt genome (JF920285) of Brassica rapa subsp. campestris as a reference. The gaps in the mt genome were mapped by manual alignment (overlapping method) and primer walking (Sanger sequencing method). The junctions were validated by Sanger sequencing using specific primers. The complete mt genome was annotated by the DOGMA (Wyman et al. 2004) and Mitofy (Alver Son et al. 2010) software, then complete mt genome of turnip was submitted to the GenBank under the accession number MT409179.

The complete mt genome of turnip was a circle form of 219,736 bp in size and the overall GC content was 45.24%. A total of 99 genes were annotated, including 78 protein-coding genes, 18 tRNA genes, and three rRNA genes. Of them, trnS gene was triplicated and trnH gene was duplicated. Among these protein-coding genes, 43 orf genes, nine NADH-dehydrogenase subunits genes, five ATP synthase subunits genes, five small subunit of ribosome genes, and three large subunit of ribosome genes were identified and annotated.

The phylogenetic relationship of mt complete genomes sequence among ten species was determined by using MEGA 6.0 with the neighbor-joining method. The sequences included Brassica rapa subsp. campestris (JF920285.1), Brassica juncea (NC_016123.1), Brassica oleracea var. botrytis (KJ820683.1), Brassica carinate (JF920287.1), Brassica nigra (NC_029182), Raphanus staivus (NC_018551), Arabidopsis thaliana (JF729201.1), Nicotiana tabacum (NC_006581.1), and Oryza sativa (MH665664.1). The mt genomes sequence of Oryza sativa (MH665664.1) was used as an outgroup for distinguishing the dicotyledonous and monocotyledonous plants. The phylogenetic relationship showed that turnip is closely related to Brassica rapa subsp. campestris (JF920285.1) rather than Raphanus staivus (NC_018551) (Figure 1). These results were consistent with other studies (Jeong et al. 2014; Seol et al. 2015), and supports that turnip is a sub-species of B. rapa.

Figure 1. Phylogenetic analysis of ten species based on the mitochondrial genome sequences. The mitochondrial sequence of Oryza sativa was used as the outgroup.

Disclosure statement

The authors declare that they have no conflict of interest.

Data availability statement

The genome sequence data that support the findings of this study are openly available in GenBank of NCBI at (https://www.ncbi.nlm.nih.gov/) under the accession no. MT409179.

Additional information

Funding

This research was financially supported by The Qinghai Natural Science Foundation [2019-ZJ-979Q], The Project of Qinghai Key Laboratory of Vegetable Genetics and Physiology [2020-ZJ-Y02], and The Special Project of Qinghai Academy of Agriculture and Forestry Sciences [2018-NKY-008].