Deciphering the Multi-Chromosomal Mitochondrial Genome of Populus simonii

Abstract

Mitochondria, inherited maternally, are energy metabolism organelles that generate most of the chemical energy needed to power cellular various biochemical reactions. Deciphering mitochondrial genome (mitogenome) is important for elucidating vital activities of species. The complete chloroplast (cp) and nuclear genome sequences of Populus simonii (P. simonii) have been reported, but there has been little progress in its mitogenome. Here, we assemble the complete P. simonii mitogenome into three circular-mapping molecules (lengths 312.5, 283, and 186 kb) with the total length of 781.5 kb. All three molecules of the P. simonii mitogenome had protein-coding capability. Whole-genome alignment analyses of four Populus species revealed the fission of poplar mitogenome in P. simonii. Comparative repeat analyses of four Populus mitogenomes showed that there were no repeats longer than 350 bp in Populus mitogenomes, contributing to the stability of genome sizes and gene contents in the genus Populus. As the first reported multi-circular mitogenome in Populus, this study of P. simonii mitogenome are imperative for better elucidating their biological functions, replication and recombination mechanisms, and their unique evolutionary trajectories in Populus.

Keywords: Populus simonii; comparative analysis; fission; mitochondrial genome; multi-circular molecule.

FIGURE 1

The assembly graph of P. simonii mitogenome. The mt contigs chosen from Newbler are represented by different color blocks. The P. simonii mtChr1 is composed of only one contig, while mtChr2 and mt Chr3 are composed of seven and six contigs, respectively.

FIGURE 2

Circular maps of the multi-circular mitogenome of P. simonii. Genomic features on transcriptionally clockwise and counterclockwise strands are drawn on the inside and outside of the three circles, respectively. GC content of each chromosome is represented on the inner circle by the dark gray plot. The asterisks (*) besides genes denote intron-containing genes.

FIGURE 3

Mitogenomic syntenic analyses among four Populus species. The P. tremula mitogenome was set as reference. PsChr1, PsChr2, and PsChr3 represent the three circular chromosomes of P. simonii mitogenome. The green, yellow, and pink rectangular region represent the syntenic regions of P. tremula vs. P. davidiana, P. tremula vs. P. alba, and P. tremula vs. P. simonii, respectively. The red and blue lines refer direct and inverted syntenic regions, respectively.

FIGURE 4

The phylogenetic relationships of P. simonii with other 34 represented land plants. Numbers on each node are bootstrap support values. Colors indicate the families of each species.

FIGURE 5

Mitochondrial tRNA gene contents among 17 representative plants. Black circle, gene is present; White circle, gene is absent. Species names are abbreviated as shown in Supplementary Table S1.