The mitochondrial genome map of Nelumbo nucifera reveals ancient evolutionary features

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.

Improving Nelumbo nucifera genome assemblies using high‐resolution genetic maps and BioNano genome mapping reveals ancient chromosome rearrangements

“…Based on the anchored N. nucifera pseudo-chromosomes in the present study, we were able to infer the possible chromosome rearrangements of N. nucifera. In contrast with the low mutation rate of N. nucifera when compared with core eudicots as reported in its nuclear genome (Ming et al, 2013;Wang et al, 2013) and organelle genomes (Wu et al, 2014b;Gui et al, 2016), the ancient chromosome rearrangements happened more frequently in N. nucifera than that in many core eudicots. Considering that the lotus-specific WGD event occurred between 76 and 54 MYA (Ming et al, 2013), the ancient chromosome rearrangements in N. nucifera may be caused by changes in climate during the Cretaceous-Paleogene transition.…”

“…In contrast with the low mutation rate of N . nucifera when compared with core eudicots as reported in its nuclear genome (Ming et al ., ; Wang et al ., ) and organelle genomes (Wu et al ., ; Gui et al ., ), the ancient chromosome rearrangements happened more frequently in N . nucifera than that in many core eudicots.…”

Assembly and Analysis of the Complete Mitochondrial Genome of Capsella bursa-pastoris

“…Plant mitochondrial DNA (mtDNA) contains many repeats as well as inserts of nuclear and chloroplast origin, which makes mitogenome assembly difficult [8]. However, the development of long-read third-generation sequencing technologies (PacBio in particular) improves and simplifies assembly of such complex molecules, greatly facilitating the research of plant mitogenomes [9][10][11][12][13].…”

Mitochondrial genome sequencing and phylogenetic analysis of Cynodondactylon × Cynodontransvaalensis

“…Repetitive genes are prevalent in vascular plants (Goremykin et al, 2009); e.g., Nelumbo nucifera Gaertn. and maize (CMS-C) contain 6 and 10 duplicated protein genes, respectively (Allen et al, 2007;Gui et al, 2016). In the mitochondrial genome of Cynodon dactylon × C. transvaalensis, psaB (a chloroplast encoding gene) and 2 rRNA genes (rrn18 and rrn5) have 2 copies.…”

“…The protein-coding genes transferred from the plastid seem to be nonfunctional. However, tRNAs of plastid origin are likely to be functional (Gui et al, 2016;Nakazono and Hirai, 1993).…”