Dataset Information

Chloroplast genome of Calamus tetradactylus revealed rattan phylogeny.

ABSTRACT:

Background

Calamus tetradactylus, a species primarily distributed in Vietnam, Laos, and southern China, is highly valued for its utilization as a small-diameter rattan material. While its physical and mechanical properties have been extensively studied, the genomic characteristics of C. tetradactylus remain largely unexplored.

Results

To gain a better understanding of its chloroplast genomic features and evolutionary relationships, we conducted sequencing and assembly of the chloroplast genome of C. tetradactylus. The complete chloroplast genome exhibited the typical highly conserved quartile structure, with specific variable regions identified in the single-copy region (like psbF-psbE, π = 0.10327, ndhF-rpl32, π = 0.10195), as well as genes such as trnT-GGU (π = 0.05764) and ycf1 (π = 0.03345) and others. We propose that these regions and genes hold potential as markers for species identification. Furthermore, phylogenetic analysis revealed that C. tetradactylus formed a distinct clade within the phylogenetic tree, alongside other Calamus species, and C. tetradactylus was most closely related to C. walkeri, providing support for the monophyly of the genus.

Conclusion

The analysis of the chloroplast genome conducted in this study provides valuable insights that can contribute to the improvement of rattan breeding programs and facilitate sustainable development in the future.

SUBMITTER: Zhang H

PROVIDER: S-EPMC10962098 | biostudies-literature | 2024 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Chloroplast genome of Calamus tetradactylus revealed rattan phylogeny.

Zhang Haibo H Liu Peng P Zhang Yi Y Sun Huayu H Wang Yue Y Gao Zhimin Z Liu Xin X

BMC genomic data 20240325 1

<h4>Background</h4>Calamus tetradactylus, a species primarily distributed in Vietnam, Laos, and southern China, is highly valued for its utilization as a small-diameter rattan material. While its physical and mechanical properties have been extensively studied, the genomic characteristics of C. tetradactylus remain largely unexplored.<h4>Results</h4>To gain a better understanding of its chloroplast genomic features and evolutionary relationships, we conducted sequencing and assembly of the chlor ...[more]

PMID: 38528505

Similar Datasets

Project description:BackgroundEriocaulon is a wetland plant genus with important ecological value, and one of the famous taxonomically challenging groups among angiosperms, mainly due to the high intraspecific diversity and low interspecific variation in the morphological characters of species within this genus. In this study, 22 samples representing 15 Eriocaulon species from China, were sequenced and combined with published samples of Eriocaulon to test the phylogenetic resolution using the complete chloroplast genome. Furthermore, comparative analyses of the chloroplast genomes were performed to investigate the chloroplast genome evolution of Eriocaulon.ResultsThe 22 Eriocaulon chloroplast genomes and the nine published samples were proved highly similar in genome size, gene content, and order. The Eriocaulon chloroplast genomes exhibited typical quadripartite structures with lengths from 150,222 bp to 151,584 bp. Comparative analyses revealed that four mutation hotspot regions (psbK-trnS, trnE-trnT, ndhF-rpl32, and ycf1) could serve as effective molecular markers for further phylogenetic analyses and species identification of Eriocaulon species. Phylogenetic results supported Eriocaulon as a monophyletic group. The identified relationships supported the taxonomic treatment of section Heterochiton and Leucantherae, and the section Heterochiton was the first divergent group. Phylogenetic tree supported Eriocaulon was divided into five clades. The divergence times indicated that all the sections diverged in the later Miocene and most of the extant Eriocaulon species diverged in the Quaternary. The phylogeny and divergence times supported rapid radiation occurred in the evolution history of Eriocaulon.ConclusionOur study mostly supported the taxonomic treatment at the section level for Eriocaulon species in China and demonstrated the power of phylogenetic resolution using whole chloroplast genome sequences. Comparative analyses of the Eriocaulon chloroplast genome developed molecular markers that can help us better identify and understand the evolutionary history of Eriocaulon species in the future.

Project description:The genus Allium (Amaryllidaceae, Allioideae) is one of the largest monocotyledonous genera and it includes many economically important crops that are cultivated for consumption or medicinal uses. Recent advances in molecular phylogenetics have revolutionized our understanding of Allium taxonomy and evolution. However, the phylogenetic relationships in some Allium sections (such as the Allium section Daghestanica) and the genetic bases of adaptative evolution, remain poorly understood. Here, we newly assembled six chloroplast genomes from Chinese endemic species in Allium section Daghestanica and by combining these genomes with another 35 allied species, we performed a series of analyses including genome structure, GC content, species pairwise Ka/Ks ratios, and the SSR component, nucleotide diversity and codon usage. Positively selected genes (PSGs) were detected in the Allium lineage using the branch-site model. Comparison analysis of Bayesian and ML phylogeny on CCG (complete chloroplast genome), SCG (single copy genes) and CDS (coding DNA sequences) produced a well-resolved phylogeny of Allioideae plastid lineages, which illustrated several novel relationships with the section Daghestanica. In addition, six species in section Daghestanica showed highly conserved structures. The GC content and the GC3s content in Allioideae species exhibited lower values than studied non-Allioideae species, along with elevated pairwise Ka/Ks ratios. The rps2 gene was lost in all examined Allioideae species, and 10 genes with significant posterior probabilities for codon sites were identified in the positive selection analysis, seven of them are associated with photosynthesis. Our study uncovered a new species relationship in section Daghestanica and suggested that the selective pressure has played an important role in Allium adaptation and evolution, these results will facilitate our further understanding of evolution and adaptation of species in the genus Allium.

Dataset Information

Chloroplast genome of Calamus tetradactylus revealed rattan phylogeny.

Background

Results

Conclusion

Publications

Chloroplast genome of Calamus tetradactylus revealed rattan phylogeny.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets