Plastid phylogenomics and cytonuclear discordance in Rubioideae, Rubiaceae

• Published in: PloS one Vol. 19; no. 5; p. e0302365
• Main Authors: Thureborn, Olle, Wikström, Niklas, Razafimandimbison, Sylvain G, Rydin, Catarina
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 20-05-2024; Public Library of Science (PLoS)
• Subjects: Biology and Life Sciences; Botanical research; Cell nuclei; Cell Nucleus - genetics; Chloroplasts; Computer and Information Sciences; Cytoplasm; Datasets; Discordance; Diversity of life; Evolution, Molecular; Flowering; Flowering plants; Gene order; Genes; Genetic aspects; Genome, Plant; Genome, Plastid; Genomes; Genomics; Genomics - methods; Hybridization; Identification and classification; Interspecific hybridization; Livets mångfald; Mitochondrial DNA; Phylogenetics; Phylogeny; Plants (botany); Plastids; Plastids - genetics; Plastomes; Research and Analysis Methods; Ribosomal DNA; Rubiaceae; Rubiaceae - classification; Rubiaceae - genetics; Simulation analysis; Sweden; United States > US
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0302365

In this study of evolutionary relationships in the subfamily Rubioideae (Rubiaceae), we take advantage of the off-target proportion of reads generated via previous target capture sequencing projects based on nuclear genomic data to build a plastome phylogeny and investigate cytonuclear discordance. The assembly of off-target reads resulted in a comprehensive plastome dataset and robust inference of phylogenetic relationships, where most intratribal and intertribal relationships are resolved with strong support. While the phylogenetic results were mostly in agreement with previous studies based on plastome data, novel relationships in the plastid perspective were also detected. For example, our analyses of plastome data provide strong support for the SCOUT clade and its sister relationship to the remaining members of the subfamily, which differs from previous results based on plastid data but agrees with recent results based on nuclear genomic data. However, several instances of highly supported cytonuclear discordance were identified across the Rubioideae phylogeny. Coalescent simulation analysis indicates that while ILS could, by itself, explain the majority of the discordant relationships, plastome introgression may be the better explanation in some cases. Our study further indicates that plastomes across the Rubioideae are, with few exceptions, highly conserved and mainly conform to the structure, gene content, and gene order present in the majority of the flowering plants.