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

  title={Chloroplast genomes of Rubiaceae: Comparative genomics and molecular phylogeny in subfamily Ixoroideae},
  author={S. N. Ly and Andr{\'e}a Garavito and P. De Block and Pieter Asselman and C. Guyeux and Jean-Claude Charr and S. Janssens and A. Mouly and P. Hamon and R. Guyot},
  journal={PLoS ONE},
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… Expand
2 Citations
Complex evolutionary history of coffees revealed by full plastid genomes and 28,800 nuclear SNP analyses, with particular emphasis on Coffea canephora (Robusta coffee).
In this study, similar global features of the plastid genomes of Psilanthus and Coffea are observed and, in agreement with morphological and physiological traits, the nuclear phylogenetic tree clearly separates PsilAnthus from CoffeA and is considered to be undergoing a long process of speciation with an intermediate step of (sub-)speciation. Expand
The absence of the caffeine synthase gene is involved in the naturally decaffeinated status of Coffea humblotiana, a wild species from Comoro archipelago
The 422-Mb chromosome-level assembly of the Coffea humblotiana genome, a wild and endangered, naturally caffeine-free, species from the Comoro archipelago, revealed an extensive genome conservation, despite an estimated 11 million years of divergence and a broad diversity of genome sizes within the Coffeea genus. Expand


Comparative Analysis of the Complete Chloroplast Genomes of Five Quercus Species
The phylogenetic relationships of the Quercus species inferred from the chloroplast genomes obtained moderate-to-high support, indicating thatchloroplast genome data may be useful in resolving relationships in this genus. Expand
The complete chloroplast genome of the miracle tree Neolamarckia cadamba and its comparison in Rubiaceae family
This complete chloroplast genome will offer valuable information for the development of highly variable DNA markers for future conservation, genetic engineering studies and variety selection of this miracle tree. Expand
Towards a Phylogeny for Coffea (Rubiaceae): identifying well-supported lineages based on nuclear and plastid DNA sequences.
Several major lineages with geographical coherence, as identified in previous studies based on smaller data sets, are supported and others with either geographical or ecological correspondence are recognized for the first time. Expand
Characterization of the complete chloroplast genome of Emmenopterys henryi (Gentianales: Rubiaceae), an endangered relict tree species endemic to China
The chloroplast genome sequence of an endangered relict tree species endemic to China, Emmenopterys henryi, was determined based on the Illumina data and indicates that E. Henryi is most closely related to coffeea arabica and coffea canephora. Expand
Evaluation of chloroplast genome annotation tools and application to analysis of the evolution of coffee species
Eight genes in the plant chloroplast pan genome (consisting of 92 genes) were always absent in the coffee species analyzed, suggesting that the annotation of most of the previously annotated chloroplow genomes should now be updated. Expand
Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns
Phylogenetic trees from multiple methods provide strong support for the position of Amborella as the earliest diverging lineage of flowering plants, followed by Nymphaeales and Austrobaileyales, and the plastid genome trees also provide strongSupport for a sister relationship between eudicots and monocots, and this group is sister to a clade that includes Chloranthales and magnoliids. Expand
Chloroplast genomic data provide new and robust insights into the phylogeny and evolution of the Ranunculaceae.
It is hypothesize that global warming and the associated decrease in the type and number of animal pollinators may have been the main reason why taxa with highly elaborate petals as well as those without petal were generated during each of the two waves of radiation. Expand
Highly accelerated rates of genomic rearrangements and nucleotide substitutions in plastid genomes of Passiflora subgenus Decaloba.
The most highly rearranged lineage was subgenus Decaloba, which experienced extensive IR expansion that incorporated up to 25 protein-coding genes usually located in large single copy region, making it an ideal system to investigate the dynamic evolution of angiosperm plastomes. Expand
Conflicting results from mitochondrial genomic data challenge current views of Rubiaceae phylogeny.
It is shown that the mitochondrial genome can provide structured and statistically significant information on plant phylogeny and demonstrates with striking clarity that the phylogeny of Rubiaceae is far from resolved. Expand
Exceptional reduction of the plastid genome of saguaro cactus (Carnegiea gigantea): Loss of the ndh gene suite and inverted repeat.
The saguaro plastid genome is the smallest known for an obligately photosynthetic angiosperm, having lost the IR and plastsid ndh genes, and this loss supports a statistically strong association across seed plants between the loss of n Dh genes and the Loss of the inverted repeat (IR). Expand