title: 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.
authors.affiliation: State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, China.
authors.forename: Songtao
authors.initials: S
authors.lastname: Gui
authors.affiliation: State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, China.
authors.forename: Zhihua
authors.initials: Z
authors.lastname: Wu
authors.affiliation: State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, China.
authors.forename: Hongyuan
authors.initials: H
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, China.
authors.forename: Yinzhen
authors.initials: Y
authors.lastname: Zheng
authors.affiliation: State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, China.
authors.forename: Zhixuan
authors.initials: Z
authors.lastname: Zhu
authors.affiliation: Nextomics Biosciences Co., Ltd., Wuhan, 430075, China.
authors.forename: Dequan
authors.initials: D
authors.lastname: Liang
authors.affiliation: State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, China.
authors.forename: Yi
authors.initials: Y
authors.lastname: Ding
mesh_terms: D001483:Base Sequence; D002736:Chloroplasts / Q000235:genetics; D002874:Chromosome Mapping / Q000379:methods; D019143:Evolution, Molecular; D054629:Genome, Mitochondrial / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics*; D008928:Mitochondria / Q000235:genetics*; D005810:Multigene Family / Q000235:genetics; D031653:Nelumbo / Q000235:genetics*; D010802:Phylogeny; D017393:RNA Editing / Q000235:genetics; D012335:RNA, Ribosomal / Q000235:genetics; D012343:RNA, Transfer / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D012335:RNA, Ribosomal; D012343:RNA, Transfer