Assembly and comparative analysis of complete mitochondrial genome sequence of an economic plant Salix suchowensis

Abstract

Willow is a widely used dioecious woody plant of Salicaceae family in China. Due to their high biomass yields, willows are promising sources for bioenergy crops. In this study, we assembled the complete mitochondrial (mt) genome sequence of S. suchowensis with the length of 644,437 bp using Roche-454 GS FLX Titanium sequencing technologies. Base composition of the S. suchowensis mt genome is A (27.43%), T (27.59%), C (22.34%), and G (22.64%), which shows a prevalent GC content with that of other angiosperms. This long circular mt genome encodes 58 unique genes (32 protein-coding genes, 23 tRNA genes and 3 rRNA genes), and 9 of the 32 protein-coding genes contain 17 introns. Through the phylogenetic analysis of 35 species based on 23 protein-coding genes, it is supported that Salix as a sister to Populus. With the detailed phylogenetic information and the identification of phylogenetic position, some ribosomal protein genes and succinate dehydrogenase genes are found usually lost during evolution. As a native shrub willow species, this worthwhile research of S. suchowensis mt genome will provide more desirable information for better understanding the genomic breeding and missing pieces of sex determination evolution in the future.

Keywords: Assembly; Mitochondrial genome; Phylogenetic analysis; Repeats; Salix suchowensis.

Figure 1. The circular mitochondrial genome of S. suchowensis.

Genomic features on transcriptionally clockwise and counter-clockwise strands are drawn on the inside and outside of the circle, respectively. Genes belonging to different functional groups are color-coded. GC content is represented on the inner circle by the dark gray plot.

Figure 2. The distribution of SSRs in the S. suchowensis mt genome.

The colors represent different types of SSRs. The percentages of SSRs are also provided on the pie chart.

Figure 3. The frequency distribution of repeat lengths in the S. suchowensis mt genome.

The number shown in histogram represents the specific frequency of each repeat length.

Figure 4. The distribution of RNA editing sites in the S. suchowensis mt protein-coding genes.

The number shown by gray box represents the RNA editing sites of each gene.

Figure 5. The Ka/Ks values of 32 protein-coding genes of S. suchowensi s versus G. raimondii.

The red, blue, green and purple genes indicate Complex genes, Cytochrome c biogenesis, Transport membrane protein and Ribosomal proteins, respectively.

Figure 6. The Neighbor-Joining tree was constructed based on 23 conserved genes of 35 representative plant mt genomes.

The colors of red, blue, green and black circles represent the classes of rosids, asterids, monocots and gymnosperms. Numbers at the nodes are bootstrap support values.

Figure 7. Comparison of sizes and GC contents within 22 land plant mt genomes.

The blue and green broken lines represent the sizes and GC contents, respectively. The colors of green, black, blue and red indicate different species in Bryophyte, Gymnospermae, Monocotyledoneae and Dicotledonae, respectively.