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Assembly and comparative analysis of the complete mitochondrial genome of Brassica rapa var. Purpuraria

BMC Genomics volume 25, Article number: 546 (2024) Cite this article

Abstract

Background

Purple flowering stalk (Brassica rapa var. purpuraria) is a widely cultivated plant with high nutritional and medicinal value and exhibiting strong adaptability during growing. Mitochondrial (mt) play important role in plant cells for energy production, developing with an independent genetic system. Therefore, it is meaningful to assemble and annotate the functions for the mt genome of plants independently. Though there have been several reports referring the mt genome of in Brassica species, the genome of mt in B. rapa var. purpuraria and its functional gene variations when compared to its closely related species has not yet been addressed.

Results

The mt genome of B. rapa var. purpuraria was assembled through the Illumina and Nanopore sequencing platforms, which revealed a length of 219,775 bp with a typical circular structure. The base composition of the whole B. rapa var. purpuraria mt genome revealed A (27.45%), T (27.31%), C (22.91%), and G (22.32%). 59 functional genes, composing of 33 protein-coding genes (PCGs), 23 tRNA genes, and 3 rRNA genes, were annotated. The sequence repeats, codon usage, RNA editing, nucleotide diversity and gene transfer between the cp genome and mt genome were examined in the B. rapa var. purpuraria mt genome. Phylogenetic analysis show that B. rapa var. Purpuraria was closely related to B. rapa subsp. Oleifera and B. juncea. Ka/Ks analysis reflected that most of the PCGs in the B. rapa var. Purpuraria were negatively selected, illustrating that those mt genes were conserved during evolution.

Conclusions

The results of our findings provide valuable information on the B.rapa var. Purpuraria genome, which might facilitate molecular breeding, genetic variation and evolutionary researches for Brassica species in the future.

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Introduction

Purple flowering stalks (Brassica rapa var. purpuraria) is widely distributed in the middle regions of the Yangtze River that belongs to the Cruciferae family [1]. B. rapa var. Purpuraria is an important and popular vegetable for consumers due to its bright color and delicious taste with abundant anthocyanidins, carotenoids, proanthocyanidins, vitamin C and mineral elements [2, 3]. Mitochondria (mt) is important organelles that involve in many metabolic processes related to the synthesis of these nutritional components of amino acids, lipids and vitamins and energy production [4,5,6]. The mt genome of angiosperm Arabidopsis thaliana was first reported in 1997 [7]. Subsequently, the mt genomes of some field crops and fruits, including rice (Oryza sativa L.) [8], rape (Brassica napus L.) [9], corn (Zea mays L.) [10], grape (Vitis vinifera)[11], apple (Malus domestica) [12], and kiwifruit (Actinidia chinensis) [13], have been successively published. The mt genomes have the characteristics of integrity, polymorphism, and semi-autonomy with a unique expression system, they contain a few genes and limited the types of proteins. Therefore, they need to be coordinated with nuclear genes to maintain normal biological functions [14]. The number, arrangement and composition of genes are conserved in the chloroplast (cp) genomes of higher plants [15]. However, Mt genomes have highly conserved characteristics and evolutionary rates that are different from nuclear genes. Therefore, the mt genome is relatively large, which could provide a large amount of genetic information and solve the problem of classification, identification and evolution of related species [14, 16].

The mt genome has significant differences in length, gene sequence, and gene content in different species, and even varies in different cultivars in the same species [17,18,19]. The length of mt genome in plants varies from 66 Kb to 11.7 Mb [18, 20]. The plant mt genomes mainly contain 50–60 conserved genes, which involved in oxidative phosphorylation and protein translation, and many unknown function open reading frames (ORFs) [21]. In addition, Some of ORFs in the mt genome play a key role in cytoplasmic male sterility of species [22,23,24]. Except for the unknown function ORFs, the differences in the number of complex II subunit, ribosomal protein genes, tRNAs and multi-copy genes were the main reason for the difference in the number of mt genes in different species [25]. With the development of sequencing technology and the decreasing of sequencing costs, a variety of mt genomes have been reported. The mt genome of Brassica species including A. thaliana [26], Raphanus sativus L. [27], and B. napus [28] have been reported. In addition, the mt genomes of several varieties of B. rapa species have also been addressed. The mt genomes in the varieties of B. rapa developed with close full length from 219,736 bp to 219,775 bp, with same number of tRNA (18) and rRNA (3); and exhibited minor differences for gene numbers between 54 and 99, and PCGs ranged from 34 to 78 [29,30,31]. The characterized mt genome could help to observe structural variations in the evolutionary history of Brassica species or varieties. Therefore, assembling and analyzing the mt genomes is important to better understanding of their genetic characteristics and for molecular breeding research.

In this work, the whole mt genome of B. rapa var. Purpuraria was sequenced and assembled using the Illumina and Nanopore sequencing platforms. The genomic features, repeat sequences, codon usage, RNA editing sites, and comparative genomics were analyzed. We also conducted phylogenetic analysis to understand the genetic variations in B. rapa var. Purpuraria more effectively. This study enhances our understanding of B. rapa var. Purpuraria genetics and provides useful information for future researches on identification, molecular breeding and system evolution of mt genomes of Brassicaceae species.

Materials and methods

Plant materials, DNA extraction and sequencing

The B. rapa var. Purpuraria seeds were provided by Peng Li (Xiangtan Agricultural Science Research Institute), and cultivated at the Xiangtan Agricultural Science Research Institute (Yuhu District, Xiangtan, Hunan, China; 27°52 N, 112°50E) under natural conditions. Fresh young leaves were collected and quickly frozen in liquid nitrogen, and then stored at 80 °C. Plant specimens were conserved in the Hunan University of Humanities, Science and Technology (accession number: 20231218BRP02). The total DNA isolation from the young leaves was performed using CTAB method [32] and purified using Plant DNA Mini Kit (D311, Genepioneer Biotechnologies, Nanjing, China) according to the manufacturer's protocol. The qualified DNA samples was sequenced with 500 bp paired-end (PE) library construction using the VAHTS Universal DNA Library Prep Kit for IlluminaV3 (Vazyme Biotech Co., Ltd, Nanjing, China). About 29,356,547,400 raw data from B. rapa var. Purpuraria were generated with PE150 sequencing strategy. Subsequently, the qualified DNA was cut into 20-kb fragments using a Covarisg-tube (Covaris) and purified with AMPure beads. The samples were sequenced with Oxford Nanopore library construction.

Mitochondrial genome assembly and annotation

We used the Fastp 0.23.4 ( https://github.com/OpenGene/fastp) software to filter the second-generation raw data. The parameters were set as follows: (1) Cut off the primer and adapters sequences; (2) Filter out the reads with average quality value lower than Q5. (3) Delete the reads with the number of uncertain bases more than 5. Then, the original tri-generational data was filtered using filtlongv0.2.1 (https://link.zhihu.com/?target=https%3A//github.com/rrwick/Filtlong) with parameters set as:–min_length 1000 and –min_mean_q7. The highly quality tri-generational data were aligned with the plant mt gene database (https://github.com/xul962464/plant_mt_ref_gene) using minimap2 [33]. The size of sequence more than 50 bp, containing multiple core genes and higher alignment quality was selected as the seed sequence. Then, the original tri-generational data were compared with the seed sequences using minimap2, and the sequences with overlap more than 1 kb were screened and added to the seed sequences. The original data were compared to the seed sequence iteratively, and all the third-generation sequencing data of the mt genome were obtained. All the third-generation sequencing data were performed self-correction and assembled using the canu v2.0 program [34], and Bowtie2 (v2.3.5.1) was used to align the second-generation data to the corrected sequence. The second-generation data were compared to stitch the corrected third-generation data using Unicycler (v0.4.8) software with default parameters, followed by using Bandage ( v0.8.1) software to visualize and manually adjust the stitching results. The corrected third-generation sequencing data were aligned to the conting obtained by the second step of Unicycler using minimap2, and the branch direction was manually determined to obtain the final assembly result.

The encoded proteins and rRNAs were aligned to reported plant mt sequences using BLAST, and further manually adjusted according to closely related species. The tRNAs were annotated using tRNAscanSE online tool [35] (http://lowelab.ucsc.edu/tRNAscan-SE/). ORFs were annotated using Open Reading Frame Finder (http://www.ncbi.nlm.nih.gov/gorf/gorf.html) with a minimum length of 102 bp. The map of B. rapa var. Purpuraria mt genome was drawn using OGDRAW (https://chlorobox.mpimp-golm.mpg.de/OGDraw.html) software. A single nucleotide polymorphism (SNP) was detected among six Brassica mt genomes using MUMmer and BLAT v35 softwares.

Relative synonymous codon usage (RSCU) analysis.

The codon composition of the mt genome of B. rapa var. Purpuraria was analyzed using a Perl script written by ourselves, to select for a unique coding sequences (CDS) and calculate the RSCU of synonymous codons.

Analysis of repeat sequences

Dispersed repeat sequences, including forward repeats, backward repeats, reverse repeats, and complementary repeats, were detected using blastn v2.10.1 software with parameters set as -word _ size 7 and evalue 1e-5. Tandem repeats were identified using trf409.linux64 software with parameter set as: 2 7 7 80 10 50 2000 -f -d -m. SSRs were identified with the MISA v1.0 tool [36]. The motif length of one- to six- nucleotide SSRs was set as 10, 5, 4, 3, 3 and 3, respectively.

Identification of RNA editing sites

RNA editing sites in the PCGs of B. rapa var. Purpuraria were analyzed using the PmtREP program (http://cloud.genepioneer.com:9929/#/tool/alltool/detail/336) with the cutoff value set as 0.2 [37].

Gene transfer between the cp genome and mt genome

The B. rapa var. Purpuraria mt genome was aligned with its cp genome (PP191173) by blast and the selected parameters were set as the matching rate ≥ 70%, E-value ≤ 1e−5 and length ≥ 30 bp [38].

Ka/Ks and Pi analysis

We analyzed the nonsynonymous (Ka) and synonymous (Ks) substitution rates of each PCG between B. rapa var. Purpuraria and Cucurbita pepo (NC_014050.1), Helianthus grosseserratus (NC_051989.1), Brassica oleracea (NC_016118.1), Brassica juncea (NC_016123.1), Glycyrrhiza uralensis ( NC_053919) and Solanum lycopersicum (MF034192). Homologous gene pairs were aligned in mafft v7.310 ( https://mafft.cbrc.jp/alignment/software/). Ka, Ks, and Ka/Ks values of each PCG were calculated using KaKs_Calculator v2.0 tool (https://sourceforge.net/projects/kakscalculator2/) with MLWL calculation method. Dnasp5 software was used to calculate the Pi value of each gene.

Phylogenetic analysis

A total of 25 whole mt genomes were used to make sure the phylogenetic position of B. rapa var. Purpuraria. The 31 mt PCG genes (atp1, atp4, atp6, atp8, atp9, ccmB, ccmC, ccmFc, ccmFn, cob, cox1, cox2, cox3, mttB, nad1, nad2, nad3, nad4, nad4L, nad5, nad6, nad7, nad9, rpl16, rpl2, rpl5, rps12, rps14, rps3, rps4, and rps7) conserved across the 25 analyzed species were aligned using Mafft v7.427 software with default parameters. Alignments were trimmed in trimAl with substitution model selecting in ModelFinder [39, 40]. Subsequently, a maximum likelihood tree was constructed by IQ-TREE v1.6.12 software using the mtMet + F + R5 model with a bootstrap of 1000 [41]. Ginkgo biloba (NC_027976) was used as the outgroup in this analysis.

Results

Characteristics of the B. rapa var. Purpuraria mt genome

In this study, the mt genome of B. rapa var. Purpuraria was sequenced 29,356,547,400 raw data and 97,855,158 bp clean data (Q20 = 97.11% and Q30 = 91.81%) were obtained using the Illumina platform (Table S1). Regarding the Nanopore sequencing, a total of 17,960,842,101 bases and 1,417,067 reads were obtained using the Nanopore sequencing platform. The subreads with N50 and the mean read were 27,413 bp and 12,674 bp, respectively (Table S2). The whole mt genome of B. rapa var. Purpuraria was 219,775 bp in length with a typical circular structure (Fig. 1). The nucleotide composition of the whole B. rapa var. Purpuraria mt genome contains 27.45% of A, 27.31% of T, 22.91% of C, and 22.32% of G, with GC and AT contents accounted for 45.23% and 54.77%, respectively (Table S3). PCGs and cis-spliced introns occupied 13.22% and 12.86% of the complete mt genome, whereas tRNA and rRNA genes only made up 0.79% and 2.34%, respectively. A total of 59 genes, comprising 33 PCGs, 3 rRNAs, and 23 tRNAs, were found in the B. rapa var. Purpuraria mt genome (Table 2). Six genes, namely, ccmFc, cox2, rpl2, rps3, trnI-AAT, and trnT-GGT included one intron, genes of nad1, nad2, nad5, and nad7 contained four introns, and one gene of nad4 had three introns. Three tRNA genes were identified in two or three copies (trnH-GTG, trnM-CAT and trnY-GTA) (Fig. 1 and Table 1).

Fig. 1
figure 1

The circular map of the B. rapa var. Purpuraria mt genome

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Table 1 Gene profile and organization of the B. rapa var. Purpuraria mt genome
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Plant mt genomes have significantly different in size, gene order and content [42]. We selected six Brassica mt genomes to compare genome characteristics and determine variability of the mt genome of B. rapa var. Purpuraria (Table 2). The size of selected mt genomes varied from 219,736 bp (B. rapa ssp. rapa) to 232,145 bp (B. nigra). The smallest number of genes (53) was found in B. nigra, and the largest (106) in B. napus. The number of tRNA genes ranged from 17 in B. napus, B. nigra, and B. oleracea to 23 in B. rapa var. Purpuraria. In addition, all the selected mt genomes included 3 rRNA genes (Table 2). Combing our present results, it revealed that B. rapa var. Purpuraria has a high degree of similarity to the mt genome sequences to B. rapa, B. nigra, and B. oleracea. Furthermore, to identify sequence variations in the known genes, SNPs were detected between B. rapa var. Purpuraria and B. juncea, B. napus, B. rapa, B. nigra and B. oleracea. A total of 202 SNPs were found among six mt genomes. 135 SNPs were identified between B. rapa var. Purpuraria and B. rapa ssp. rapa, followed by 62 SNPs in B. rapa var. Purpuraria vs B. nigra group, 4 SNPs (cox2, atp1, and two cox1 genes) in B. rapa var. Purpuraria vs B. napus group, and only one SNP (atp1 gene) in B. rapa var. Purpuraria vs B. oleracea group. But there were no SNPs identified in B. rapa var. Purpuraria vs B. juncea and B. rapa var. Purpuraria vs B. rapa (Table S4).

Table 2 Comparison of gene content among Brassica mt genomes
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Codon preference analysis of PCGs

The total size of PCGs in B. rapa var. Purpuraria was 35,927 bp. Except for nad1 gene with ACG as the start codon, ATG was the start codon for other PCGs, which might be the result of C-to-U RNA editing of the second site (Table 1). Four types of stop codons, including TAA, TGA, TAG, and CGA, were detected, and the C to U for RNA editing phenomenon was discovered in ccmFc gene. We also calculated the RSCU of 33 PCGs in the B. rapa var. Purpuraria mt genome (Fig. 2). The 33 PCGs made up 29,055 bp encoding 9685 codons including termination codons. Leucine (Leu) was the most frequent amino acid, with a total of 1053 codons, accounted for 10.87%, followed by serine (Ser), with a total of 856 codons, accounting for 8.84%, and termination codon (Ter) was the rarest with a total of 33 codons, accounting for 0.034%. We discovered that 30 codons of RSCU value were greater than 1, of which 27 codons (90%) ended with A or U, two codons (6.67%) ended with G, and only one codon (3.33%) ended with C. It illustrated that the A / U preference at the third codon was positioned in the B. rapa var. Purpuraria mt genome (Table S5).

Fig. 2
figure 2

RSCU analysis of the B. rapa var. Purpuraria mt genome

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The prediction of RNA editing

RNA-editing sites are widely distributed in the mt genome of plants. In this study, 379 RNA editing sites within 33 PCGs (Table 3) were predicted in the mt genome of B. rapa var. Purpuraria using PmtREP tool (Figure S1). Among these PCGs, atp6 had one RNA-editing site, whereas the highest was in nad4 with 379 RNA-editing sites (33), of which 30.34% (115 sites) occurred with the first position of the triplet codes, 68.07% (258 sites) located at the second base of the triplet codes. In addition, the first and second bases of the triplet codes were edited, leading to an amino acid change from proline (CCC) to phenylalanine (TTC). There were 45.64% (173 positions) of amino acids hydrophobicity remained unchanged after the RNA editing. Besides, 45.38% (172 positions) of the amino acids were varied from hydrophilic to hydrophobic, while 8.71% (33 positions) were ranged from hydrophobic to hydrophilic. Furthermore, only one amino acid was varied from arginine to stop codon (Table 3). The findings in our study showed that most amino acids were changed from serine to leucine (24.01%, 160 sites), proline to leucine (22.69%, 86 sites), and serine to phenylalanine (12.40%, 47 sites).

Table 3 Prediction of RNA editing sites in the B. rapa var. Purpuraria mt genome
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In addition, we compared the RNA editing sites of B. rapa (AP017996), B. nigra(AP012989), and B.oleracea (AP012988) with representatives from Brassica species (Fig. 3). The highest edited transcripts were ccmB with 32 editing sites in B. nigra, and nad4 with 33 editing sites in B. rapa, B.oleracea and B. rapa var. Purpuraria. From the comparison results of RNA editing sites, we found that B. rapa var. Purpuraria is highly similar to other three closely related Brassica species.

Fig. 3
figure 3

The distribution and comparison of RNA-editing sites in the PCGs of B. rapa var. Purpuraria mt genome and three closely related Brassica mt genomes

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Repeat sequences analysis

Simple sequence repeats (SSRs), also known as microsatellites, are DNA stretches composing of short unit sequence repeats of 1–6 base pairs in length [43]. In this study, a total of 55 SSRs were detected in the mt genome of B. rapa var. Purpuraria, containing 20 (36.36%) monomers, 11 (20.00%) dimers, 5(9.09%) trimers, 18 (32.73%) tetramers, and 1 (1.82%) pentamers (Table 4). No hexanucleotide repeats were detected. Among the 55 SSRs, monomer and tetramer were the main type of SSR motifs, accounting for 69.09% of all detected SSRs. In addition, 90.00% of monomers had A/T contents, and 36.36% of dimers were AT/TA (Table S6). The abundant AT content of SSRs supported with the high AT content (54.77%) of the whole mt genome of B. rapa var. Purpuraria.

Table 4 Frequency of identifed SSR motifs in the B. rapa var. Purpuraria mt genome
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Tandem repeats (satellite DNA) are core repeating units about 1—200 bases [44]. As shown in Table 5, 17 tandem repeats with a matching degree over than ≧84% and length varying from 3 to 39 bp were obtained. A total of 252 dispersed repeats (≧28 bp), of which 144 palindromic (57.54%) and 108 forward repeats (42.46%) were observed, and no reverse and complementary repeats were found (Fig. 4). The total length of the dispersed repeats was 16251 bp, which occupied 7.39% of the whole mt genome. Most repeats were 25–40 bp (169 repeats, 67.06%), while only one was over than 1 kb being 2427 bp (Table S7).

Table 5 The tandem repeats anaysis of B. rapa var. Purpuraria mt genome
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Fig. 4
figure 4

Dispersed repeats analysis in the B. rapa var. Purpuraria mt genome

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Ka/Ks and Pi analysis

The Ka/Ks ratio was used to evaluate selective pressures during the evolutionary dynamics of PCGs among similar species. In this work, B. rapa var. Purpuraria was used as a reference to calculate the Ka/Ks value of 33 PCGs in the B. rapa var. Purpuraria mt genome (Fig. 5). The Ka/Ks values of most of PCGs were less than one, demonstrating that these genes may undergo negative selections during evolution. However, the Ka/Ks value of the atp4 and ccmB genes between B. rapa var. Purpuraria and Cucurbita pepo, the ccmB gene between B. rapa var. Purpuraria and Glycyrrhiza uralensis, the atp4, ccmB, and mttB genes between B. rapa var. Purpuraria and Helianthus grosseserratus, the ccmB gene between B. rapa var. Purpuraria and Solanum lycopersicum were higher than one, implying positive selection for these genes during evolution. Our findings further indicated that these mt genes might be highly conserved during the evolution process in higher plants.

Fig. 5
figure 5

Ka/Ks ratios of 33 PCGs between B. rapa var. Purpuraria and six species

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The nucleotide diversity (Pi) values of 36 PCGs were accounted and varied from 0.01790 to 0.14222, with an average of 0.04417 (Fig. 6 and Table S8). The Pi value of gene3.rpl10 region was largest among these regions being 0.1422, and 0.07436 in gene4.rps4, 0.07195 in gene6.atp8, 0.07182 in gene29.rpl2 and 0.0709 in gene21.atp9 were found The lower Pi values revealed that the mt genome sequences of B. rapa var. Purpuraria were highly conserved.

Fig. 6
figure 6

Nucleotide diversity of B. rapa var. Purpuraria mt genome

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Phylogenetic analysis

To determine the evolutionary status for the mt genome of B. rapa var. Purpuraria, the phylogenetic analyses was carried out on B. rapa var. Purpuraria together with other 24 Cruciferae/Brassica species (Fig. 7). A phylogenetic tree was built based on an aligned data matrix of 31 conserved PCGs, including atp1, atp4, atp6, atp8, atp9, ccmB, ccmC, ccmFc, ccmFn, cob, cox1, cox2, cox3, mttB, nad1, nad2, nad3, nad4, nad4L, nad5, nad6, nad7, nad9, rpl16, rpl2, rpl5, rps12, rps14, rps3, rps4, and rps7, from all tested species. The phylogenetic tree was divided into six groups, being Brassica, Raphanus, Arabis, Arabidopsis, Capsella, and Ginkgo. B. rapa var. Purpuraria was clustered with the species of genus Brassica at first group, and formed sister branches with other related Brassica species within the Cruciferae family clade. Furthermore, B. rapa var. Purpuraria was closely related to B. rapa subsp. Oleifera (NC_016125.1) and B. juncea (NC_016123.1), indicating that B. rapa var. Purpuraria belongs to the Brassica in the Cruciferae family.

Fig. 7
figure 7

Maximum-likelihood phylogenetic tree based on 31 conserved PCGs among 25 species. Ginkgo biloba (NC_027976) used as the out group

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Analysis of homologous fragments of mitochondria and chloroplasts

The total length of homologous sequences on chloroplasts was 13,153 bp, accounting for 8.57% of the whole cp genome. While the total size of homologous sequences on mitochondria was 8961 bp, accounting for 4.08% of the whole mt genome (Table S9). As shown in Table 6, twenty-two homologous fragments with a total length of 13,325 bp were found. The transfer route of the fragments may occur firstly from the chloroplast to nucleus, and then to the mitochondrion in B.rapa var. Purpuraria, accounting for 6.06% of the whole mt genome. Eight annotated genes, namely, trnL-CAA, trnN-GTT, rrn18, trnW-CCA, trnD-GTC, trnM-CAT, ccmC, and trnI-AAT, with high similarity to the mitochondria likely originated from the mt genome. While 17 genes, being rpoB, ycf2, ycf15, trnL-CAA, rbcL, trnN-GUU, ycf1, psaA, rrn23, rrn16, psaB, trnW-CCA, trnD-GUC, trnP-UGG, trnM-CAU, trnI-CAU, and trnI-GAU with high similarity to the cp genes, might be transferred from cp genome, and only partial sequences of those genes were identified in the mt genome (Table 6). Most of transferred genes were tRNA genes, of which those genes were much more conserved in the mt genome than PCGs during the evolution.

Table 6 Fragments transferred from cp to mt in B.rapa var. Purpuraria
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Discussion

Mitochondria is the core of energy source in cells, which exhibited more complex in plant than animals due to its size variations and repetitive sequences [45,46,47]. In this study, we analyzed the characteristics of mt genome in B. rapa var. Purpuraria. The total length of the mt genome of B. rapa var. Purpuraria was similar to that of B. juncea [48], being moderate in genome length compared with other reported mt genomes [49]. The GC content in the B. rapa var. Purpuraria mt genome is 45.23%, which is similar to that of other reported plant mt genomes such as Camellia sinensis var. Assamica cv. Duntsa, 45.62% [50]; Mesona chinensis Benth, 44.21% [51]; B. napus, 45.21% [52], while exhibited greater than the B. rapa var. Purpuraria cp genome (PP191173, 36.36%) assembled by our research group. Non-coding sequence accounted for 71.7% of the whole B. rapa var. Purpuraria mt genome, which is similar to most of plant mt genomes [52,53,54]. In addition, the PCGs occupied 13.22% might be due to the result of increasing sequence repeats during evolution. PCGs usually encoded from initiation codon (ATG) to stop codons (TGA, TAA, and TGA), and the distribution of amino acids compositions was consistent with Acer yangbiense [55] and A. thaliana [56]. The nad1 gene using ACG as start codon in consistent with Salix suchowensis and Phaseolus vulgaris might be induced by RNA editing [46, 47].

Codon usage bias refers that synonymous codons exist in a non-random manner in different species [57]. The analysis of codon usage patterns is helpful to understand the molecular mechanism of biological adaptation and explore the evolutionary relationship among species [58]. Previous studies have shown that codons prefer to use A / U endings in the plant mt genomes [44,45,46,47]. In total of 30 high-frequency codons were detected in the B. rapa var. Purpuraria mt genome, of which 90% codons ended with A or U, which might be the result of natural selection, mutation pressure and genetic drift [59]. In addition, we found that leucine was the most frequently used amino acid, which was consistent with S. glauca [44] and Acer truncatum Bunge [60].

The number of RNA editing sites varies among different plants, and occurred commonly in gymnosperm and angiosperm mt genomes. We obtained 379 RNA editing sites within all the 33 PCGs in the B. rapa var. Purpuraria mt genome, which exhibited much less than those in Diospyros oleifera (515) [61], Bupleurum chinense DC (517) [38], Macadamia integrifolia (688), M. ternifolia (689) and M. tetraphylla (688) [62], and higher than those in S.glauca (261)[44] and Pereskia aculeata (362) [63]. The selection of RNA editing sites in the B. rapa var. Purpuraria genome exhibited a high degree of compositional bias. Most of the RNA editing sites were the C-T editing type, being similar as in other plant mt genomes [64,65,66]. Previous studies showed that about 50% of RNA editing generated at the second bases of the triplet codes [44, 65]. About 68.07% (258) RNA editing sites occurred at the second codon position in the B. rapa var. Purpuraria mt genome, greater than that at the first codon position (115, 30.34%). In addition, 1.58% (6) RNA editing sites occurred at both of the first and second codon position. The similar phenomenon was observed in the D. oleifera mt genome [61]. There is no RNA editing sites predicted at the third codon position in B. rapa var. Purpuraria mt genome [44, 66].

The repeat sequences, including SSR, tandem and dispersed repeats, were widely distributed in the plant mt genomes [8, 67]. Previous studies have reported that repeat sequences were important for intermolecular recombination, which play a vital role in forming the mt genome [68]. Because of its high variability and recessive inheritance, SSR has been widely used to confirm phylogenetic relationships, genetic diversity studies and species identification [69]. The mt genome of B. rapa var. Purpuraria contained 55 SSRs, of which 90.00% of monomers being A or T, resulting 54.77% of AT in the B. rapa var. Purpuraria mt genome. The high AT content in mt genome were also detected in Scutellaria tsinyunensis [70]. and Magnolia biondii [71]. In addition, 252 dispersed repeats were discovered in this study, which was much greater than B. oleracea var. Italica in the genus Brassica [72].

The ratio of Ka/Ks provides useful information for reconstructing phylogenetic relationships, and contributes to understand the evolutionary dynamics of PCGs among closely related species [73]. Most of mt genes with Ka/Ks ratios < 1 exhibited negative selections, and a few genes with Ka/Ks ratios > 1 showed positive selections during the evolution in plants [44, 61]. The Ka/Ks ratio of ccmB gene was greater than 1 in S. glauca mt genome exhibited positive selection [44], whereas Five genes, namely, atp4, nad1, ccmC, mttB, and rpl2, showed positive selections in Capsicum pubescens Ruiz & Pav mt genome [74]. Two genes, being mttB and rpl5 exhibited positive selections in European-Asian species [75]. However, three genes with Ka/Ks ratios > 1, including atp4, ccmB, and mttB, exhibited positive selections in our study in consistent with previous studies [44, 74, 75], illustrating that these genes might be selected for future researches on the gene selection and phylogenetic of Brassica species. Changes in the size and structure of the plant mt genomes have been obviously observed, whereas the functional genes are still conserved [76]. Previous studies indicated that Pi could reveal the variation of nucleic acid sequences in different plants, and the highly variable regions might be selected as potential molecular markers for population genetics [77, 78]. Pi analysis reflected the variation of nucleotide sequences among different species (Fig. 6). Our results revealed that the Pi value of rpl10 gene was the largest in these regions, illustrating that rpl10 gene might be used as molecular markers for the mt genome analysis in B. rapa var. purpuraria. Except for Reclinomonas, plants are the only group of eukaryotes that still remain the rpl10 gene in their mt genomes [48, 49]. However, the mt rpl10 gene has been missed in some Brassicaceae species, and replaced by an additional copy of the nuclear gene that normally encodes cp RPL10 protein [79]. Five highly variable regions, being ccmB, ccmFC, rps1, rps10, and rps14, might be used as molecular markers in Phaseolus vulgaris mt genome. In addtional, the overall low Pi values showed that the mt genome sequences of B. rapa var. Purpuraria were highly conserved.

Phylogenetic analysis of plants have developed to use the complete genome data to construct the relationship among different species [44,45,46,47,48]. Here, the phylogenetic tree was constructed according to the mt genomes of 25 species. B. rapa var. Purpuraria was well clustered with the species of genus Brassica and stayed closely to B. rapa subsp. Oleifera and B. juncea, suggesting that B. rapa var. Purpuraria belongs to the Brassica species in the Cruciferae family. Shao et al. (2021) found that B. oleracea stayed a closely relationship with B. rapa subsp. Campestris with 100% support rate [80]. Brassicaceae is a superfamily containing over 3800 species, in which Brassica is the most important genus as having many important vegetables and oil crops. It has been mentioned that based on cp genome, B. napus always clustered with B. rapa morphotypes, but did not cluster into a monophyletic group, and were distantly separated by B. juncea and B. oleracea. The obtained phylogenetic tree revealed a clear phylogenetic relationship among the species. B. rapa var. Purpuraria as a local vegetable planted around Yangtze River, may also develop some different characteristics in mt genome to regulate the biosynthesis in anthocyanin, and other nutritional compounds. Therefore, assembling and analyzing the mt genomes with those difference genome information will help to better understand their genetic characteristics and selecting their differences for further investigation. DNA sequence transfer between cp and mt genomes has been frequently discovered in plant mt genomes [81]. In higher plants, the total size of transferred DNA ranges from 50 kb (A. thaliana) to 1.1 Mb ( O. sativa subsp.japonica) depending on the plant species [82]. In total, 13,325 bp of cp DNA has been transferred into the mt genome of B. rapa var. Purpuraria, accounting for 6.06% of the B. rapa var. Purpuraria mt genome. In comparison, the proportion in M. integrifolia, Liriodendron tulipifera, and Nicotiana tabacum is 5.4%, 3%, and 2.5%, respectively [38, 71, 83]. About 22 fragments transferred from the cp genome to the mt genome, containing eight annotated genes, with six tRNA genes (trnL-CAA, trnN-GTT, trnW-CCA, trnD-GTC, trnM-CAT, and trnI-AAT), rrn18, and ccmC. The tRNA genes transferred from cp to mt genomes has been commonly discovered in angiosperms [44, 84, 85]. These results were consistent with the previous study, which showed much more conserved for tRNA genes than the PCGs during the evolution, and tRNA genes played indispensable roles in mt genome [46].

Conclusions

In this work, we sequenced and successfully assembled the genome with a circular molecule structure in the mt genome of B. rapa var. Purpuraria. The full length of mt genome for B. rapa var. Purpuraria was 219,775 bp, containing 59 genes with 33 PCGs, 23 tRNA and 3 rRNA genes. The codon preferences, repeat sequences, RNA editing sites in the B. rapa var. Purpuraria mt genome have also been analyzed subsequently. Phylogenetic analysis confirmed that B. rapa var. Purpuraria exhibited a close relationship with B. oleracea. Gene conservation between mt and cp genome was also discovered in B.rapa var. Purpuraria via analyzing gene migration. The Ka/Ks analysis showed that most of the PCGs exhibited negative selections, demonstrating the conservation of these mt genes during the process of evolution. This study provides useful genetic information about the B. rapa var. Purpuraria mt genome and forms an important theoretical might also help to analyze the genetic variation, systematic evolution, and breeding of B. rapa var. Purpuraria.

Availability of data and materials

The B. rapa var. Purpuraria mt genome sequence was uploaded in the GenBank database (accession number PP231953).

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Funding

This work was supported by Hunan Natural Science Regional Joint Fund Project (grant numbers 2024JJ7235).

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Authors and Affiliations

  1. Development and Utilization and Quality and Safety Control of Characteristic Agricultural Resources in Central Hunan, College of Agriculture and Biotechnology , Hunan University of Humanities, Science and Technology, Loudi, 417000, China

    Yihui Gong, Xin Xie, Guihua Zhou, Meiyu Chen & Zhiyin Chen

  2. Institute of Fruit Tree Research, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China

    Hua Huang

  3. Xiangtan Agricultural Science Research Institute, Xiangtan, 411100, China

    Peng Li

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  4. Meiyu Chen
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  5. Zhiyin Chen
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  6. Peng Li
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  7. Hua Huang
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Contributions

Yihui Gong and Hua Huang concieved and designed the project. Xin Xie and Peng Li collected the plant materials. Xin Xie, Guihua Zhou, Meiyu Chen, and Zhiyin Chen performed the experiments and analyzed the data. Yihui Gong and Hua Huang wrote and revised the manuscript. All authors read and approved the final manuscript.

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Correspondence to Yihui Gong or Hua Huang.

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Gong, Y., Xie, X., Zhou, G. et al. Assembly and comparative analysis of the complete mitochondrial genome of Brassica rapa var. Purpuraria. BMC Genomics 25, 546 (2024). https://doi.org/10.1186/s12864-024-10457-1

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Keywords

BMC Genomics

ISSN: 1471-2164

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