Comparative and phylogenetic analysis of chloroplast genomes from four species in Quercus section Cyclobalanopsis.
Quercus blakei
Quercus dinghuensis
Quercus disciformis
Quercus hui
Chloroplast (cp) genome
Phylogenetic analysis
Journal
BMC genomic data
ISSN: 2730-6844
Titre abrégé: BMC Genom Data
Pays: England
ID NLM: 101775394
Informations de publication
Date de publication:
10 Jun 2024
10 Jun 2024
Historique:
received:
29
06
2023
accepted:
21
05
2024
medline:
11
6
2024
pubmed:
11
6
2024
entrez:
10
6
2024
Statut:
epublish
Résumé
The Quercus L. species is widely recognized as a significant group in the broad-leaved evergreen forests of tropical and subtropical East Asia. These plants hold immense economic value for their use as firewood, furniture, and street trees. However, the identification of Quercus species is considered challenging, and the relationships between these species remain unclear. In this study, we sequenced and assembled the chloroplast (cp.) genomes of four Quercus section Cyclobalanopsis species (Quercus disciformis, Quercus dinghuensis, Quercus blackei, and Quercus hui). Additionally, we retrieved six published cp. genome sequences of Cyclobalanopsis species (Quercus fleuryi, Quercus pachyloma, Quercus ningangensis, Quercus litseoides, Quercus gilva, and Quercus myrsinifolia). Our aim was to perform comparative genomics and phylogenetic analyses of the cp. whole genome sequences of ten Quercus section Cyclobalanopsis species. The results revealed that: (1) Quercus species exhibit a typical tetrad structure, with the cp. genome lengths of the newly sequenced species (Q. disciformis, Q. dinghuensis, Q. blakei, and Q. hui) being 160,805 bp, 160,801 bp, 160,787 bp, and 160,806 bp, respectively; (2) 469 SSRs were detected, among which A/T base repeats were the most common; (3) no rearrangements or inversions were detected within the chloroplast genomes. Genes with high nucleotide polymorphism, such as rps14-psaB, ndhJ-ndhK, rbcL-accD, and rps19-rpl2_2, provided potential reference loci for molecular identification within the Cyclobalanopsis section; (4) phylogenetic analysis showed that the four sections of Cyclobalanopsis were grouped into sister taxa, with Q. hui being the first to diverge from the evolutionary branch and Q. disciformis being the most closely related to Q. blackei. The results of this study form the basis for future studies on taxonomy and phylogenetics.
Identifiants
pubmed: 38858616
doi: 10.1186/s12863-024-01232-y
pii: 10.1186/s12863-024-01232-y
doi:
Types de publication
Journal Article
Comparative Study
Langues
eng
Sous-ensembles de citation
IM
Pagination
57Informations de copyright
© 2024. The Author(s).
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