Abstract
Nelumbo nucifera is an evolutionary relic from the Late Cretaceous period. Sequencing the N. nucifera mitochondrial genome is important for elucidating the evolutionary characteristics of basal eudicots. Here, the N. nucifera mitochondrial genome was sequenced using single molecule real-time sequencing technology (SMRT), and the mitochondrial genome map was constructed after de novo assembly and annotation. The results showed that the 524,797-bp N. nucifera mitochondrial genome has a total of 63 genes, including 40 protein-coding genes, three rRNA genes and 20 tRNA genes. Fifteen collinear gene clusters were conserved across different plant species. Approximately 700 RNA editing sites in the protein-coding genes were identified. Positively selected genes were identified with selection pressure analysis. Nineteen chloroplast-derived fragments were identified, and seven tRNAs were derived from the chloroplast. These results suggest that the N. nucifera mitochondrial genome retains evolutionarily conserved characteristics, including ancient gene content and gene clusters, high levels of RNA editing, and low levels of chloroplast-derived fragment insertions. As the first publicly available basal eudicot mitochondrial genome, the N. nucifera mitochondrial genome facilitates further analysis of the characteristics of basal eudicots and provides clues of the evolutionary trajectory from basal angiosperms to advanced eudicots.
Highlights
The size of the mitochondrial genome differs among angiosperm species, ranging from approximately 220 kb (Brassica napus)[1] to 11.3 Mb (Silene conica)[2], reflecting the insertion of noncoding DNA3, including DNA of plastid and nuclear origin and DNA from horizontal gene transfer (HGT)[4,5]
It is important to sequence the N. nucifera mitochondrial genome to reveal the evolutionary characteristics of this plant and provide clues concerning the evolutionary trajectory from basal angiosperms to advanced eudicots
The results showed that A or U were more frequently used compared with G or C at the third position of N. nucifera mitochondrial codons (Supplementary Table S4), as observed in both chloroplast genomes and plant mitochondria genomes[25,26]
Summary
The size of the mitochondrial genome differs among angiosperm species, ranging from approximately 220 kb (Brassica napus)[1] to 11.3 Mb (Silene conica)[2], reflecting the insertion of noncoding DNA3, including DNA of plastid and nuclear origin and DNA from horizontal gene transfer (HGT)[4,5]. The organization, gene content and RNA editing of the mitochondrial genome differs over a significant scale across seed plants. This variation is useful for studying the evolution of both genome structures and sequences. Third-generation sequencing through single molecule real-time sequencing technology (SMRT)[14,15] produces considerably longer (up to 30 kb) unbiased DNA sequences without PCR amplification[16] This technology has previously been used in de novo assembly through the PacBio RS II platform[17,18,19,20,21]. Our analyses provide insights into the evolution of gene content and order, RNA editing patterns, positively selected sites and chloroplast DNA insertions in core eudicots
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