Plastome phylogenomic study of Gentianeae (Gentianaceae): widespread gene tree discordance and its association with evolutionary rate heterogeneity of plastid genes

Abstract

Background Plastome-scale data have been prevalent in reconstructing the plant Tree of Life. However, phylogenomic studies currently based on plastomes rely primarily on maximum likelihood inference of concatenated alignments of plastid genes, and thus phylogenetic discordance produced by individual plastid genes has generally been ignored. Moreover, structural and functional characteristics of plastomes indicate that plastid genes may not evolve as a single locus and are experiencing different evolutionary forces, yet the genetic characteristics of plastid genes within a lineage remain poorly studied. Results We sequenced and annotated 10 plastome sequences of Gentianeae. Phylogenomic analyses yielded robust relationships among genera within Gentianeae. We detected great variation of gene tree topologies and revealed that more than half of the genes, including one ( atpB ) of the three widely used plastid markers ( rbcL , atpB and matK ) in phylogenetic inference of Gentianeae, are likely contributing to phylogenetic ambiguity of Gentianeae. Estimation of nucleotide substitution rates showed extensive rate heterogeneity among different plastid genes and among different functional groups of genes. Comparative analysis suggested that the ribosomal protein (RPL and RPS) genes and the RNA polymerase (RPO) genes have higher substitution rates and genetic variations among plastid genes in Gentianeae. Our study revealed that just one ( matK ) of the three ( matK, ndhB and rbcL ) widely used markers show high phylogenetic informativeness (PI) value. Due to the high PI and lowest gene-tree discordance, rpoC2 is advocated as a promising plastid DNA barcode for taxonomic studies of Gentianeae. Furthermore, our analyses revealed a positive correlation of evolutionary rates with genetic variation of plastid genes, but a negative correlation with gene-tree discordance under purifying selection. Conclusions Overall, our results demonstrate the heterogeneity of nucleotide substitution rates and genetic characteristics among plastid genes providing new insights into plastome evolution, while highlighting the necessity of considering gene-tree discordance into phylogenomic studies based on plastome-scale data.

Comparative chloroplast genome s: insights into the evolution of the chloroplast genome of Camellia sinensis and the phylogeny of Camellia

“…This might be because the cp gene sequences used in their phylogenetic analysis were incomplete cp genomes (83,585 to 83,835 bp). A recent study had emphasized that the extensive heterogeneity of nucleotide substitution rate among different plastid genes and among different functional groups of genes were likely contributing to phylogenetic ambiguity [94]. In our phylogenetic analysis of the data partitions of cp genome, the sequence variations in the six datasets showed different percentage variation (Supplementary Tab.…”

Comparative chloroplast genomes: insights into the evolution of the chloroplast genome of Camellia sinensis and the phylogeny of Camellia

“…sinensis (natural triploid Chinary type tea) was highlighted with blue circle mark. The ages of stratigraphic boundaries were obtained from the International Chronostratigraphic Chart (Pl, Pliocene; Qu, Quaternary) [95], with a scale as million years ago (Mya). The divergence time of each node among Camellia species was showed in the table below.…”

Comparative chloroplast genomes: insights into the evolution of the chloroplast genome of Camellia sinensis and the phylogeny of Camellia 

“…This might be because the cp gene sequences used in their phylogenetic analysis were incomplete cp genomes (83,585 to 83,835 bp). A recent study had emphasized that the extensive heterogeneity of nucleotide substitution rate among different plastid genes and among different functional groups of genes were likely contributing to phylogenetic ambiguity [90]. In our phylogenetic analysis of the data partitions of cp genome, the sequence variations in the six datasets showed different percentage variation (Supplementary Tab.…”