Complete mitochondrial genome assembly of Zizania latifolia and comparative genome analysis

Abstract

Zizania latifolia (Griseb.) Turcz. ex Stapf has been cultivated as a popular aquatic vegetable in China due to its important nutritional, medicinal, ecological, and economic values. The complete mitochondrial genome (mitogenome) of Z. latifolia has not been previously studied and reported, which has hindered its molecular systematics and understanding of evolutionary processes. Here, we assembled the complete mitogenome of Z. latifolia and performed a comprehensive analysis including genome organization, repetitive sequences, RNA editing event, intercellular gene transfer, phylogenetic analysis, and comparative mitogenome analysis. The mitogenome of Z. latifolia was estimated to have a circular molecule of 392,219 bp and 58 genes consisting of three rRNA genes, 20 tRNA genes, and 35 protein-coding genes (PCGs). There were 46 and 20 simple sequence repeats (SSRs) with different motifs identified from the mitogenome and chloroplast genome of Z. latifolia, respectively. Furthermore, 49 homologous fragments were observed to transfer from the chloroplast genome to the mitogenome of Z. latifolia, accounting for 47,500 bp, presenting 12.1% of the whole mitogenome. In addition, there were 11 gene-containing homologous regions between the mitogenome and chloroplast genome of Z. latifolia. Also, approximately 85% of fragments from the mitogenome were duplicated in the Z. latifolia nuclear genome. Selection pressure analysis revealed that most of the mitochondrial genes were highly conserved except for ccmFc, ccmFn, matR, rps1, and rps3. A total of 93 RNA editing sites were found in the PCGs of the mitogenome. Z. latifolia and Oryza minuta are the most closely related, as shown by collinear analysis and the phylogenetic analysis. We found that repeat sequences and foreign sequences in the mitogenomes of Oryzoideae plants were associated with genome rearrangements. In general, the availability of the Z. latifolia mitogenome will contribute valuable information to our understanding of the molecular and genomic aspects of Zizania.

Keywords: Oryzoideae; RNA editing; Zizania latifolia; mitochondrial genome; phylogenetic; repeat sequence; synteny.

Figure 1

Zizania latifolia mitogenome circular map.

Figure 2

Repeat sequences in the mitogenome of Zizania latifolia. (A) Type and proportion of simple sequence repeats (SSRs). (B) The length distribution of dispersed repeat.

Figure 3

Relative synonymous codon usage (RSCU) of Zizania latifolia mitogenome.

Figure 4

The distribution of RNA editing sites in 21 genes of the mitogenome of Zizania latifolia.

Figure 5

Gene map of the Zizania latifolia chloroplast genome.

Figure 6

Chloroplast-derived and nuclear-derived sequences in Zizania latifolia. (A) Schematic representation of transfers between chloroplast and mitogenome (MTPTs) of Z. latifolia. (B) Distribution of the sequences homologous with nuclear genome in chloroplast genome (MUPTs) in Z. latifolia. (C) Distribution of the sequences homologous with nuclear genome (NUMTs) in mitogenome in Z. latifolia.

Figure 7

Collinearity and gene rearrangement analysis of Zizania latifolia. (A) Mauve alignments of Z. latifolia mitogenome with seven closed species. (B) The gene arrangement of mitogenomes in Oryzoideae; the boxes under corresponding mitogenome refer to annotated genes, and the boxes refer to CDS, tRNA, or rRNA.

Figure 8

Phylogenetic tree of 30 species. Outgroup: Ginkgo biloba and Amborella trichopoda.

Figure 9

Nucleotide diversity (Pi) analysis of 26 protein-coding genes (PCGs) in the mitogenome of Zizania latifolia and seven species (Oryza sativa, Oryza coarctata, Zea perennis, Zea luxurians, Oryza rufipogon, Oryza minuta, and Triticum aestivum).

Figure 10

Non-synonymous and synonymous substitution (Ka/Ks) of 26 protein-coding genes (PCGs) in Zizania latifolia, Oryza coarctata, Triticum aestivum, Oryza sativa, and Zea perennis.

Figure 11

Gene content (GC %) and genome size (kb) of 30 plant mitochondrial genomes.