ArticleAnnals of botany2019
Molecular phylogenomics of the tribe Shoreeae (Dipterocarpaceae) using whole plastid genomes.
Article in Annals of botany, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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19 citing papers in PubMed.
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- Plastome structure, phylogeny and evolution of plastid genes in Reevesia (Helicteroideae, Malvaceae).Journal of plant research · 2024Article
- Complete chloroplast genome of endangered speciesMitochondrial DNA. Part B, Resources · 2024Article
- Pervasive Introgression During Rapid Diversification of the European Mountain Genus Soldanella (L.) (Primulaceae).Systematic biology · 2023Article
- Applying molecular and genetic methods to trees and their fungal communities.Applied microbiology and biotechnology · 2023Review
- Plastome evolution in the East Asian lobelias (Lobelioideae) using phylogenomic and comparative analyses.Frontiers in plant science · 2023Article
- Comparative Analyses of Complete Chloroplast Genomes and Karyotypes of AllotetraploidInternational journal of molecular sciences · 2022Article
- Complete pan-plastome sequences enable high resolution phylogenetic classification of sugar beet and closely related crop wild relatives.BMC genomics · 2022Article
- The Evolutionary History of New ZealandBiology · 2021Article
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- A Cautionary Note on the Use of Genotype Callers in Phylogenomics.Systematic biology · 2021Article
- Plastome phylogenomics of Cephalotaxus (Cephalotaxaceae) and allied genera.Annals of botany · 2021Article
- Article
- Resolving Recalcitrant Clades in the Pantropical Ochnaceae: Insights From Comparative Phylogenomics of Plastome and Nuclear Genomic Data Derived From Targeted Sequencing.Frontiers in plant science · 2021Article
- Plastome phylogenomics, biogeography, and clade diversification of Paris (Melanthiaceae).BMC plant biology · 2019Article
- Integrating DNA Barcoding and Traditional Taxonomy for the Identification of Dipterocarps in Remnant Lowland Forests of Sumatra.Plants (Basel, Switzerland) · 2019Article
- Exploring evolution and diversity of Chinese Dipterocarpaceae using next-generation sequencing.Scientific reports · 2019Article
- Whole genomes: the holy grail. A commentary on: 'Molecular phylogenomics of the tribe Shoreeae (Dipterocarpaceae) using whole plastidgenomes'.Annals of botany · 2019Article
- Analyses of Plastome Sequences Improve Phylogenetic Resolution and Provide New Insight Into the Evolutionary History of Asian Sonerileae/Dissochaeteae.Frontiers in plant science · 2019Article
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Abstract
BACKGROUND AND
aimsPhylogenetic relationships within tribe Shoreeae, containing the main elements of tropical forests in Southeast Asia, present a long-standing problem in the systematics of Dipterocarpaceae. Sequencing whole plastomes using next-generation sequencing- (NGS) based genome skimming is increasingly employed for investigating phylogenetic relationships of plants. Here, the usefulness of complete plastid genome sequences in resolving phylogenetic relationships within Shoreeae is evaluated.
methodsA pipeline to obtain alignments of whole plastid genome sequences across individuals with different amounts of available data is presented. In total, 48 individuals, representing 37 species and four genera of the ecologically and economically important tribe Shoreeae sensu Ashton, were investigated. Phylogenetic trees were reconstructed using maximum parsimony, maximum likelihood and Bayesian inference. KEY
resultsHere, the first fully sequenced plastid genomes for the tribe Shoreeae are presented. Their size, GC content and gene order are comparable with those of other members of Malvales. Phylogenomic analyses demonstrate that whole plastid genomes are useful for inferring phylogenetic relationships among genera and groups of Shorea (Shoreeae) but fail to provide well-supported phylogenetic relationships among some of the most closely related species. Discordance in placement of Parashorea was observed between phylogenetic trees obtained from plastome analyses and those obtained from nuclear single nucleotide polymorphism (SNP) data sets identified in restriction-site associated sequencing (RADseq).
conclusionsPhylogenomic analyses of the entire plastid genomes are useful for inferring phylogenetic relationships at lower taxonomic levels, but are not sufficient for detailed phylogenetic reconstructions of closely related species groups in Shoreeae. Discordance in placement of Parashorea was further investigated for evidence of ancient hybridization.
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