Plastome-Wide Rearrangements and Gene Losses in Carnivorous Droseraceae

Abstract

The plastid genomes of four related carnivorous plants (Drosera regia, Drosera erythrorhiza, Aldrovanda vesiculosa, and Dionaea muscipula) were sequenced to examine changes potentially induced by the transition to carnivory. The plastid genomes of the Droseraceae show multiple rearrangements, gene losses, and large expansions or contractions of the inverted repeat. All the ndh genes are lost or nonfunctional, as well as in some of the species, clpP1, ycf1, ycf2 and some tRNA genes. Uniquely, among land plants, the trnK gene has no intron. Carnivory in the Droseraceae coincides with changes in plastid gene content similar to those induced by parasitism and mycoheterotrophy, suggesting parallel changes in chloroplast function due to the similar switch from autotrophy to (mixo-) heterotrophy. A molecular phylogeny of the taxa based on all shared plastid genes indicates that the “snap-traps” of Aldrovanda and Dionaea have a common origin.

A systematic comparison of chloroplast genome assembly tools

“…Despite the overall high conservation of the genome sequence, there are striking differences in the gene content between different groups (e.g. the loss of the whole ndh gene family in Droseraceae [15]). Even more extreme evolutionary cases, where chloroplasts show a very low GC content and a modified genetic code are described [16].…”

Intraspecific Variation within the Utricularia amethystina Species Morphotypes Based on Chloroplast Genomes

“…The chloroplast genomes of most angiosperms have conserved quadripartite structure separated in Large and Small Single Copy regions (LSC and SSC, respectively) and two inverted repetitive regions (IRs) [16]. However, comparative analyses indicate that some plants, such as parasitic [17], mycoheterotrophic (e.g., in [18,19]), and species of carnivorous plants from the order Caryophyllales [20,21], have suffered substantial rearrangement and gene losses throughout plant evolution. For example, across diverse lineages of plants, chloroplast genomes lack NAD(P)H-dehydrogenase (ndh) complex genes, genes that could have been involved in the transition from aquatic to terrestrial habit thought plant evolutionary history [22,23].…”

Genome-wide signatures of plastid-nuclear coevolution point to repeated perturbations of plastid proteostasis systems across angiosperms

“…Our analysis was conducted on publicly available genomes and transcriptomes. Because the signature of ERC relies on phylogenetic rate heterogeneity, we sampled species that are known to exhibit differences in evolutionary rate for at least some plastid genes, including representatives from accelerated lineages, such as Acacia aulacocarpa, Oenothera biennis, Geranium maderense, Plantago maritima, Lobelia siphilitica, Silene noctiflora, and Oryza sativa (Jansen et al, 2007;Guisinger et al, 2008;Knox, 2014;Sloan, Triant, Forrester, et al, 2014;Dugas et al, 2015;Nevill et al, 2019;Shrestha et al, 2019). We also sampled species that exhibit the slow background rate of plastome evolution typical for most angiosperms.…”

“…Not surprisingly, angiosperms that lose photosynthetic function and transition to parasitic/heterotrophic lifestyles exhibit massive plastome decay and rapid protein sequence evolution (Wicke et al, 2016), in extreme cases resulting in outright loss of the entire plastome (Molina et al, 2014). However, even among angiosperms that remain fully photosynthetic, there have been repeated accelerations in rates of plastid gene evolution (Jansen et al, 2007;Guisinger et al, 2008;Knox, 2014;Sloan, Triant, Forrester, et al, 2014;Dugas et al, 2015;Nevill et al, 2019;Shrestha et al, 2019). These accelerations in angiosperms that retain a photosynthetic lifestyle can be highly gene-specific (Magee et al, 2010) and are often most pronounced in non-photosynthetic genes, such as those that encode ribosomal proteins, RNA polymerase subunits, the plastid caseinolytic protease (Clp) subunit ClpP1, the acetyl-CoA carboxylase (ACCase) subunit AccD, and the essential chloroplast factors Ycf1 and Ycf2 (Guisinger et al, 2008;Sloan, Triant, Forrester, et al, 2014;Seongjun Park et al, 2017;Shrestha et al, 2019).…”