Insights into phylogenetic relationships in Pinus inferred from a comparative analysis of complete chloroplast genomes.
Comparative analysis
Complete chloroplast genome
Phylogenetic relationships
Pinus
Journal
BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258
Informations de publication
Date de publication:
22 Jun 2023
22 Jun 2023
Historique:
received:
02
08
2022
accepted:
09
06
2023
medline:
26
6
2023
pubmed:
23
6
2023
entrez:
22
6
2023
Statut:
epublish
Résumé
Pinus is the largest genus of Pinaceae and the most primitive group of modern genera. Pines have become the focus of many molecular evolution studies because of their wide use and ecological significance. However, due to the lack of complete chloroplast genome data, the evolutionary relationship and classification of pines are still controversial. With the development of new generation sequencing technology, sequence data of pines are becoming abundant. Here, we systematically analyzed and summarized the chloroplast genomes of 33 published pine species. Generally, pines chloroplast genome structure showed strong conservation and high similarity. The chloroplast genome length ranged from 114,082 to 121,530 bp with similar positions and arrangements of all genes, while the GC content ranged from 38.45 to 39.00%. Reverse repeats showed a shrinking evolutionary trend, with IRa/IRb length ranging from 267 to 495 bp. A total of 3,205 microsatellite sequences and 5,436 repeats were detected in the studied species chloroplasts. Additionally, two hypervariable regions were assessed, providing potential molecular markers for future phylogenetic studies and population genetics. Through the phylogenetic analysis of complete chloroplast genomes, we offered novel opinions on the genus traditional evolutionary theory and classification. We compared and analyzed the chloroplast genomes of 33 pine species, verified the traditional evolutionary theory and classification, and reclassified some controversial species classification. This study is helpful in analyzing the evolution, genetic structure, and the development of chloroplast DNA markers in Pinus.
Sections du résumé
BACKGROUND
BACKGROUND
Pinus is the largest genus of Pinaceae and the most primitive group of modern genera. Pines have become the focus of many molecular evolution studies because of their wide use and ecological significance. However, due to the lack of complete chloroplast genome data, the evolutionary relationship and classification of pines are still controversial. With the development of new generation sequencing technology, sequence data of pines are becoming abundant. Here, we systematically analyzed and summarized the chloroplast genomes of 33 published pine species.
RESULTS
RESULTS
Generally, pines chloroplast genome structure showed strong conservation and high similarity. The chloroplast genome length ranged from 114,082 to 121,530 bp with similar positions and arrangements of all genes, while the GC content ranged from 38.45 to 39.00%. Reverse repeats showed a shrinking evolutionary trend, with IRa/IRb length ranging from 267 to 495 bp. A total of 3,205 microsatellite sequences and 5,436 repeats were detected in the studied species chloroplasts. Additionally, two hypervariable regions were assessed, providing potential molecular markers for future phylogenetic studies and population genetics. Through the phylogenetic analysis of complete chloroplast genomes, we offered novel opinions on the genus traditional evolutionary theory and classification.
CONCLUSION
CONCLUSIONS
We compared and analyzed the chloroplast genomes of 33 pine species, verified the traditional evolutionary theory and classification, and reclassified some controversial species classification. This study is helpful in analyzing the evolution, genetic structure, and the development of chloroplast DNA markers in Pinus.
Identifiants
pubmed: 37349702
doi: 10.1186/s12864-023-09439-6
pii: 10.1186/s12864-023-09439-6
pmc: PMC10286357
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
346Subventions
Organisme : National Key R&D Plan for the Fourteenth Five Year Plan
ID : 2022YFD2200304
Organisme : National Key R&D Plan for the Fourteenth Five Year Plan
ID : 2022YFD2200304
Organisme : National Key R&D Plan for the Fourteenth Five Year Plan
ID : 2022YFD2200304
Organisme : National Key R&D Plan for the Fourteenth Five Year Plan
ID : 2022YFD2200304
Organisme : National Key R&D Plan for the Fourteenth Five Year Plan
ID : 2022YFD2200304
Informations de copyright
© 2023. The Author(s).
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