Chloroplast genomes of Rubiaceae: Comparative genomics and molecular phylogeny in subfamily Ixoroideae.

Autor: Ly SN; Institut de Recherche pour le Développement, UMR DIADE, Université de Montpellier, Montpellier, France., Garavito A; Departamento Ciencias Biológicas, Universidad de Caldas, Manizales, Colombia., De Block P; Meise Botanic Garden, Meise, Belgium., Asselman P; Meise Botanic Garden, Meise, Belgium.; University of Ghent, Ghent, Belgium., Guyeux C; Femto-ST Institute, UMR 6174 CNRS, Université de Bourgogne Franche-Comté, Besançon, France., Charr JC; Femto-ST Institute, UMR 6174 CNRS, Université de Bourgogne Franche-Comté, Besançon, France., Janssens S; Meise Botanic Garden, Meise, Belgium., Mouly A; Laboratory Chrono-Environment, UMR CNRS 6249, Université de Bourgogne Franche-Comté, Besançon, France.; Besançon Botanic Garden, Université de Bourgogne Franche-Comté, Besançon, France., Hamon P; Institut de Recherche pour le Développement, UMR DIADE, Université de Montpellier, Montpellier, France., Guyot R; Institut de Recherche pour le Développement, UMR DIADE, Université de Montpellier, Montpellier, France.; Department of Electronics and Automatization, Universidad Autónoma de Manizales, Manizales, Colombia.
Jazyk: angličtina
Zdroj: PloS one [PLoS One] 2020 Apr 30; Vol. 15 (4), pp. e0232295. Date of Electronic Publication: 2020 Apr 30 (Print Publication: 2020).
DOI: 10.1371/journal.pone.0232295
Abstrakt: In Rubiaceae phylogenetics, the number of markers often proved a limitation with authors failing to provide well-supported trees at tribal and generic levels. A robust phylogeny is a prerequisite to study the evolutionary patterns of traits at different taxonomic levels. Advances in next-generation sequencing technologies have revolutionized biology by providing, at reduced cost, huge amounts of data for an increased number of species. Due to their highly conserved structure, generally recombination-free, and mostly uniparental inheritance, chloroplast DNA sequences have long been used as choice markers for plant phylogeny reconstruction. The main objectives of this study are: 1) to gain insight in chloroplast genome evolution in the Rubiaceae (Ixoroideae) through efficient methodology for de novo assembly of plastid genomes; and, 2) to test the efficiency of mining SNPs in the nuclear genome of Ixoroideae based on the use of a coffee reference genome to produce well-supported nuclear trees. We assembled whole chloroplast genome sequences for 27 species of the Rubiaceae subfamily Ixoroideae using next-generation sequences. Analysis of the plastid genome structure reveals a relatively good conservation of gene content and order. Generally, low variation was observed between taxa in the boundary regions with the exception of the inverted repeat at both the large and short single copy junctions for some taxa. An average of 79% of the SNP determined in the Coffea genus are transferable to Ixoroideae, with variation ranging from 35% to 96%. In general, the plastid and the nuclear genome phylogenies are congruent with each other. They are well-resolved with well-supported branches. Generally, the tribes form well-identified clades but the tribe Sherbournieae is shown to be polyphyletic. The results are discussed relative to the methodology used and the chloroplast genome features in Rubiaceae and compared to previous Rubiaceae phylogenies.
Competing Interests: The authors have declared that no competing interests exist.
Databáze: MEDLINE
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