Analysis of Complete Chloroplast Genome Sequences Improves Phylogenetic Resolution in Paris (Melanthiaceae)

Abstract

The genus Paris in the broad concept is an economically important group in the monocotyledonous family Melanthiaceae (tribe Parideae). The phylogeny of Paris was controversial in previous morphology-based classification and molecular phylogeny. Here, the complete cp genomes of eleven Paris taxa were sequenced, to better understand the evolutionary relationships among these plants and the mutation patterns in their chloroplast (cp) genomes. Comparative analyses indicated that the overall cp genome structure among the Paris taxa is quite similar. The triplication of trnI-CAU was found only in the cp genomes of P. quadrifolia and P. verticillata. Phylogenetic analyses based on the complete cp genomes did not resolve Paris as a monophyletic group, instead providing evidence supporting division of the twelve taxa into two segregate genera: Paris sensu strict and Daiswa. The sister relationship between Daiswa and Trillium was well supported. We recovered two fully supported lineages with divergent distribution in Daiswa; however, none of the previously recognized sections in Daiswa was resolved as monophyletic using plastome data, suggesting that the infrageneric relationships and biogeography of Daiswa species require further investigation. Ten highly divergent DNA regions, suitable for species identification, were detected among the 12 cp genomes. This study is the first successful attempt to provide well-supported evolutionary relationships in Paris based on phylogenomic analyses. The findings highlight the potential of the whole cp genomes for improving resolution in phylogeny as well as species identification in phylogenetically and taxonomically difficult plant genera.

Comparative genomics of figworts (Scrophularia, Scrophulariaceae), with implications for the evolution of Scrophularia and Lamiales

“…Such conservatism is expected considering the low substitution rate in chloroplasts and the presumed recent age of divergence among them. Similar findings have also been detected in many other closely related taxa, such as genera or tribes (Choi et al, 2016;Huang et al, 2016;Kaila et al, 2016;Yang et al, 2016;Li et al, 2017;Zeng et al, 2017).…”

chloroExtractor: extraction and assembly of the chloroplast genome from whole genome shotgun data

“…Such assemblies, can be used to remove chloroplast reads before a genomic assembly of the remaining nuclear DNA. Moreover, chloroplast genomes are useful in phylogenetic reconstruction (Huang et al 2016) or barcoding applications (Coissac et al 2016). A similar tool, aiming the assembly of whole chloroplast genomes is the Python program org.ASM, but it is not production ready, yet.…”

Phylogenomics, biogeography, and clade diversification of Paris (Melanthiaceae)

“…This has offered new approaches to resolve recalcitrant relationships [36][37][38][39][40][41][42][43]. Huang et al [44] and Yang et al [45] attempted to apply plastid genomes (plastomes) to resolve phylogenetic relationships within Paris. Although the plastome data greatly improve phylogenetic resolution and support, limited taxon sampling prevented them from building a robust overall view of the genus.…”

“…Previous phylogenetic analyses based on a small number of DNA loci or limited taxon sampling failed to robustly reconstruct the backbone of the Paris tree [21][22][23][24][44][45]. Including all currently recognized species, the plastome analysis fully resolved interspecific relationships of Paris with strong support at most nodes.…”