Factors contributing to organelle genomes size variation and the intracellular DNA transfer in Polygonaceae.
Ecological niche model
Gene transfer
Organelle genome
Polygonaceae
SV
Tibetan medicines
Journal
BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258
Informations de publication
Date de publication:
23 Oct 2024
23 Oct 2024
Historique:
received:
11
04
2024
accepted:
17
10
2024
medline:
24
10
2024
pubmed:
24
10
2024
entrez:
24
10
2024
Statut:
epublish
Résumé
The use of complete organelle genomes, including chloroplast and mitochondrial genomes, is a powerful molecular method for studying biological evolution and gene transfer. However, in the case of Polygonaceae, an important family with numerous edible, medicinal, and ornamental species, the mitochondrial genomes of only three species have been sequenced and analyzed. In this study, we present the mitochondrial and chloroplast genomes of two important Tibetan medicinal plants, Bistorta viviparum and B. macrophyllum. All the organelle genomes are assembled into a single circular structure and contain a common set of 32 protein-coding genes (PCGs). Some genes such as rps2 and ndhF were found to have high nucleotide polymorphism (Pi) in the chloroplast genomes, while cox1, mttB and rps12 showed pronounced Pi values in the mitochondrial genomes. Furthermore, our analysis revealed that most chloroplast genes and mitochondrial PCGs in Polygonaceae plants are under purifying selection. However, a few genes, including the chloroplast gene psaJ and the mitochondrial genes ccmFc, atp8 and nad4, showed positive selection in certain Polygonaceae plants, as indicated by a Ka/Ks ratio greater than one. Structural variation analysis revealed a wealth of differences between the mitochondrial genomes of five Polygonaceae species, with a particularly notable large-scale inversion observed between Reynoutria japonica and Fallopia aubertii. Furthermore, an analysis of the homologous sequences in the chloroplast and mitochondrial genomes revealed that the rps7 has been transferred from the chloroplast to the mitochondrial genome in all five Polygonaceae species. Finally, ecological niche models were constructed for B. viviparum and B. macrophyllum, indicating that mean annual temperature and altitude are the main climatic factors influencing the distribution of both species. Although the current distribution of B. viviparum is significantly wider than that of B. macrophyllum, projections suggest that the optimal growth ranges of both species will expand in the future, with B. macrophyllum potentially exceeding B. viviparum. This study not only contributes to the plastid genome database for Polygonaceae plants, but also provides theoretical insights into the adaptive evolution of these plants.
Identifiants
pubmed: 39443865
doi: 10.1186/s12864-024-10914-x
pii: 10.1186/s12864-024-10914-x
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
994Subventions
Organisme : National Natural Science Foundation of China
ID : 32271753
Organisme : Sichuan Province regional innovation cooperation project
ID : 2022YFQ0076
Organisme : Cooperation project of provincial college, and provincial school
ID : 2023YFSY0012
Informations de copyright
© 2024. The Author(s).
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