Assembly and characterization of the complete mitogenome of Bauhinia purpurea (Leguminosae)

Abstract

Objective

Mitochondrial genome sequences are very useful for understanding the mitogenome evolution itself and reconstructing phylogeny of different plant lineages. Bauhinia purpurea, a species from the legume family Leguminosae, is widely distributed in South China and has high ornamental value. Here, we sequenced and assembled the mitogenome of B. purpurea to provide a useful genetic resource for further evolutionary studies.

Data description

We assembled and characterized the complete mitogenome of B. purpurea based on Illumina sequence data. The mitogenome size was 525,727 bp, and its GC content was 45.38%. A total of 35 protein-coding genes, 16 tRNA genes, and 3 rRNA genes were identified in the mitogenome. We also identified 124 pairs of repeats and 6 mitogenome sequences of plastid origin (MTPTs). These MTPTs range from 108 bp to 751 bp, covering 0.65% of the mitogenome.

Objective

The legume family (Leguminosae) ranks the third place in species richness across angiosperms, with about 20,000 species [1]. Many important crops or landscape trees are members of this family. Bauhinia is the largest genus in Cercidoideae, one of six subfamilies of Leguminosae [1]. Three species, B. purpurea, B. variegata and their hybrid B. × blakeana, in this genus have high horticultural values and are widely cultivated in South China [2, 3].

Although mitogenomes of more than 400 seed plants have been published, most focus on one species or distantly related species in a family, which hinders the study of evolution of mitogenome size and sequence, especially intergenic regions that show rapid divergence between closely related species. Comparing mitogenomes of closely related species within a genus may provide useful information on mitogenome size and sequence evolution [4,5,6]. Recently, the mitogenome of B. variegata has been published [7]. In this study, we assembled and characterized the complete mitogenome of its congeneric species, B. purpurea, based on Illumina sequencing data. Then, we made a preliminary mitogenome collinear analysis between the two species. The B. purpurea mitogenome sequence should be a useful resource for comparative mitogenome study in Bauhinia.

Data description

The fresh young leaves of an individual of B. purpurea were collected from Sun Yat-sen University campus, Guangzhou, China. Fresh leaves were used for DNA extraction with a HiPure Plant DNA Mini Kit (Magen, Guangzhou, China). A genome library with an insert size of 350 bp was constructed and then sequenced on Illumina NovaSeq platform with paired-end reads of 150 bp. A total of 8 Gb raw data were generated. Clean data were obtained using Trimmomatic v0.39 [8] with default parameters. GetOrganelle v1.6.4 [9] with default parameters was used to assemble the mitogenome of B. purpurea. The protein-coding genes were annotated using GeSeq [10]. Annotation of ribosomal RNA and transfer RNA genes was carried out using RNammer v1.2 [11] and tRNAscan-SE v2.0 [12] with the “organelle” mode, respectively. All annotated genes were manually adjusted and confirmed. Repeats were identified using a python script ROUSFinder.py [13] with the minimal repeat size set to 30. Gene map of the mitogenome was drawn by PMGmap [14]. To identify the mitochondrial sequences of plastid origin (MTPTs), we compared the chloroplast genome sequence (GenBank accession number: NC_061218.1) and the mitogenome of B. purpurea using BLASTN [15] with evalue set to 1e-5. To construct the phylogenetic tree for 14 species from the four subfamilies of Leguminosae, these sequences of 23 shared mitochondrial protein-coding genes were concatenated and then aligned using MAFFT v7.520 [16]. The maximum likelihood (ML) method was implemented to build a phylogenetic tree in RAxML v8.2.12 [17] with a GAMMAAUTO substitution model and 1000 bootstrap replications.

The assembled circular mitogenome of B. purpurea is 525,727 bp in length and 45.38% in GC content. A total of 54 genes were annotated in the genome, including 35 protein-coding genes, 16 tRNA genes, and 3 rRNA genes. The protein-coding genes have a total length of 37,281 bp and account for 7.09% of the whole mitogenome (Table 1, Data files 1–2). The sequencing depth was relatively even across the mitogenome, with an average depth of 969.4 × (Table 1, Data file 3). A total of 124 repeat pairs were identified in the B. purpurea mitochondrial genome, and the longest repeat pairs are unusually large (60,619 bp). There are many collinear blocks and rearrangements between the mitogenomes of B. purpurea and B. variegata. The longest homologous block is about 57,198 bp (Table 1, Data file 4).

There are six highly homologous fragments between the mitochondrial and chloroplast genomes of B. purpurea, ranging from 108 bp to 751 bp in size and totally accounting for 0.65% of the mitogenome. Four complete genes of chloroplast origin (two trnD-GUC copies and two trnW-CCA copies) were identified on these six fragments (Table 1, Data file 5). In the maximum likelihood tree based on the 23 concatenated mitochondrial genes, B. purpurea is sister to B. variegata with 100% bootstrap support (Table 1, Data file 6).

The unusual large repeat identified in the mitogenome of B. purpurea has not been found in its congeneric species B. variegata, suggesting large repeats can be generated rapidly. The datasets produced in this study, along with available mitogenomes from three other subfamilies of Leguminosae, will benefit for phylogenetic studies of Leguminosae.

Table 1 Overview of data files/data sets

Limitations

Plant mitogenomes evolved rapidly in structure but slowly in sequence [25]. In the rate of synonymous substitutions, the mitochondrial genome evolved at a rate less than one-sixth that of the nuclear genome [26]. Therefore, it is not suitable for studying variation within species.