The Complete Mitochondrial Genome of Pall. (Saxifragales: Paeoniaceae): Evidence of Gene Transfer from Chloroplast to Mitochondrial Genome

Overview

Journal Genes (Basel)

Publisher MDPI

Date 2024 Feb 24

PMID 38397228

Authors

Pan Tang

Yang Ni

Jingling Li

Qianqi Lu

Chang Liu

Jinlin Guo

Affiliations

Soon will be listed here.

Abstract

(), a perennial plant renowned for its medicinal roots, provides a unique case for studying the phylogenetic relationships of species based on organelle genomes, as well as the transference of DNA across organelle genomes. In order to investigate this matter, we sequenced and characterized the mitochondrial genome (mitogenome) of . Similar to the chloroplast genome (cpgenome), the mitogenome of extends across 181,688 base pairs (bp). Its unique quadripartite structure results from a pair of extensive inverted repeats, each measuring 25,680 bp in length. The annotated mitogenome includes 27 protein-coding genes, 37 tRNAs, 8 rRNAs, and two pseudogenes (, ). Phylogenetic analysis was performed to identify phylogenetic trees consistent with Paeonia species phylogeny in the APG Ⅳ system. Moreover, a total of 12 MTPT events were identified and 32 RNA editing sites were detected during mitogenome analysis of . Our research successfully compiled and annotated the mitogenome of . The study provides valuable insights regarding the taxonomic classification and molecular evolution within the Paeoniaceae family.

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References

Pan H, Xi Z, Wei X, Wang K . A network pharmacology approach to predict potential targets and mechanisms of "" herb pair in the treatment of chronic pain with comorbid anxiety and depression. Ann Med. 2022; 54(1):413-425. PMC: 8812742. DOI: 10.1080/07853890.2022.2031268. View

Sharma A, Sharma S, Kumar N, Rana R, Sharma P, Kumar P . Morpho-molecular genetic diversity and population structure analysis in garden pea (Pisum sativum L.) genotypes using simple sequence repeat markers. PLoS One. 2022; 17(9):e0273499. PMC: 9480992. DOI: 10.1371/journal.pone.0273499. View

Bommer D, Haberhausen G, Zetsche K . A large deletion in the plastid DNA of the holoparasitic flowering plant Cuscuta reflexa concerning two ribosomal proteins (rpl2, rpl23), one transfer RNA (trnI) and an ORF 2280 homologue. Curr Genet. 1993; 24(1-2):171-6. DOI: 10.1007/BF00324682. View

Hatmaker E, Wadl P, Rinehart T, Carroll J, Lane T, Trigiano R . Complete chloroplast genome comparisons for Pityopsis (Asteraceae). PLoS One. 2020; 15(12):e0241391. PMC: 7769439. DOI: 10.1371/journal.pone.0241391. View

Guo Q, Guo L, Li Y, Yang H, Hu X, Song C . Development and Characterization of Microsatellite Markers Based on the Chloroplast Genome of Tree Peony. Genes (Basel). 2022; 13(9). PMC: 9498374. DOI: 10.3390/genes13091543. View

Fang B, Li J, Zhao Q, Liang Y, Yu J . Assembly of the Complete Mitochondrial Genome of Chinese Plum (): Characterization of Genome Recombination and RNA Editing Sites. Genes (Basel). 2021; 12(12). PMC: 8701122. DOI: 10.3390/genes12121970. View

Skuza L, Gastineau R, Sielska A . The complete chloroplast genome of Secale sylvestre (Poaceae: Triticeae). J Appl Genet. 2021; 63(1):115-117. PMC: 8755654. DOI: 10.1007/s13353-021-00656-x. View

Shearman J, Sonthirod C, Naktang C, Sangsrakru D, Yoocha T, Chatbanyong R . Assembly of the durian chloroplast genome using long PacBio reads. Sci Rep. 2020; 10(1):15980. PMC: 7541610. DOI: 10.1038/s41598-020-73549-4. View

Dong W, Xu C, Liu Y, Shi J, Li W, Suo Z . Chloroplast phylogenomics and divergence times of Lagerstroemia (Lythraceae). BMC Genomics. 2021; 22(1):434. PMC: 8191006. DOI: 10.1186/s12864-021-07769-x. View

10.

Tillich M, Lehwark P, Pellizzer T, Ulbricht-Jones E, Fischer A, Bock R . GeSeq - versatile and accurate annotation of organelle genomes. Nucleic Acids Res. 2017; 45(W1):W6-W11. PMC: 5570176. DOI: 10.1093/nar/gkx391. View

11.

Bi C, Qu Y, Hou J, Wu K, Ye N, Yin T . Deciphering the Multi-Chromosomal Mitochondrial Genome of . Front Plant Sci. 2022; 13:914635. PMC: 9240471. DOI: 10.3389/fpls.2022.914635. View

12.

Li Y, Chen X, Wu K, Pan J, Long H, Yan Y . Characterization of Simple Sequence Repeats (SSRs) in Ciliated Protists Inferred by Comparative Genomics. Microorganisms. 2020; 8(5). PMC: 7285179. DOI: 10.3390/microorganisms8050662. View

13.

Modi A, Vai S, Caramelli D, Lari M . The Illumina Sequencing Protocol and the NovaSeq 6000 System. Methods Mol Biol. 2021; 2242:15-42. DOI: 10.1007/978-1-0716-1099-2_2. View

14.

Chan P, Lowe T . tRNAscan-SE: Searching for tRNA Genes in Genomic Sequences. Methods Mol Biol. 2019; 1962:1-14. PMC: 6768409. DOI: 10.1007/978-1-4939-9173-0_1. View

15.

Liu S, Ni Y, Li J, Zhang X, Yang H, Chen H . CPGView: A package for visualizing detailed chloroplast genome structures. Mol Ecol Resour. 2023; 23(3):694-704. DOI: 10.1111/1755-0998.13729. View

16.

Wang X, Chen H, Yang D, Liu C . Diversity of mitochondrial plastid DNAs (MTPTs) in seed plants. Mitochondrial DNA A DNA Mapp Seq Anal. 2017; 29(4):635-642. DOI: 10.1080/24701394.2017.1334772. View

17.

Vilela M, Del Bem L, Van Sluys M, de Setta N, Kitajima J, Cruz G . Analysis of Three Sugarcane Homo/Homeologous Regions Suggests Independent Polyploidization Events of Saccharum officinarum and Saccharum spontaneum. Genome Biol Evol. 2017; 9(2):266-278. PMC: 5381655. DOI: 10.1093/gbe/evw293. View

18.

Ho J, Chang H, Lin C, Liu C, Hsieh C, Horng J . Characterization of the anti-influenza activity of the Chinese herbal plant Paeonia lactiflora. Viruses. 2014; 6(4):1861-75. PMC: 4014724. DOI: 10.3390/v6041861. View

19.

Sloan D, Wu Z . History of plastid DNA insertions reveals weak deletion and at mutation biases in angiosperm mitochondrial genomes. Genome Biol Evol. 2014; 6(12):3210-21. PMC: 4986453. DOI: 10.1093/gbe/evu253. View

20.

Gaeta M, Yuyama P, Sartori D, Helena Pelegrinelli Fungaro M, Vanzela A . Occurrence and chromosome distribution of retroelements and NUPT sequences in Copaifera langsdorffii Desf. (Caesalpinioideae). Chromosome Res. 2010; 18(4):515-24. DOI: 10.1007/s10577-010-9131-1. View