Phylotranscriptomic analysis of the origin and early diversification of land plants

Abstract

Reconstructing the origin and evolution of land plants and their algal relatives is a fundamental problem in plant phylogenetics, and is essential for understanding how critical adaptations arose, including the embryo, vascular tissue, seeds, and flowers. Despite advances in molecular systematics, some hypotheses of relationships remain weakly resolved. Inferring deep phylogenies with bouts of rapid diversification can be problematic; however, genome-scale data should significantly increase the number of informative characters for analyses. Recent phylogenomic reconstructions focused on the major divergences of plants have resulted in promising but inconsistent results. One limitation is sparse taxon sampling, likely resulting from the difficulty and cost of data generation. To address this limitation, transcriptome data for 92 streptophyte taxa were generated and analyzed along with 11 published plant genome sequences. Phylogenetic reconstructions were conducted using up to 852 nuclear genes and 1,701,170 aligned sites. Sixty-nine analyses were performed to test the robustness of phylogenetic inferences to permutations of the data matrix or to phylogenetic method, including supermatrix, supertree, and coalescent-based approaches, maximumlikelihood and Bayesian methods, partitioned and unpartitioned analyses, and amino acid versus DNA alignments. Among other results, we find robust support for a sister-group relationship between land plants and one group of streptophyte green algae, the Zygnematophyceae. Strong and robust support for a clade comprising liverworts and mosses is inconsistent with a widely accepted view of early land plant evolution, and suggests that phylogenetic hypotheses used to understand the evolution of fundamental plant traits should be reevaluated.land plants | Streptophyta | phylogeny | phylogenomics | transcriptome T he origin of embryophytes (land plants) in the Ordovician period roughly 480 Mya (1-4) marks one of the most important events in the evolution of life on Earth. The early evolution of embryophytes in terrestrial environments was facilitated by numerous innovations, including parental protection for the developing embryo, sperm and egg production in multicellular protective structures, and an alternation of phases (often referred to as generations) in which a diploid sporophytic life history stage gives rise to a multicellular haploid gametophytic phase. With Significance Early branching events in the diversification of land plants and closely related algal lineages remain fundamental and unresolved questions in plant evolutionary biology. Accurate reconstructions of these relationships are critical for testing hypotheses of character evolution: for example, the origins of the embryo, vascular tissue, seeds, and flowers. We investigated relationships among streptophyte algae and land plants using the largest set of nuclear genes that has been applied to this problem to date. Hypothesized relationships were rigorously tested through a series of analyses to assess systematic er...

The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae)

“…A phylogenomic approach targeting thousands of independently evolved nuclear loci may be the only way to assess the current taxonomy of this group, and dissect the roles of hybridization and introgression in the origin and rapid diversification of this insular lineage. Phylogenomic methods based on markers identified from, e.g., restriction site associated DNA sequencing (RADseq) (Cruaud et al, 2014;Eaton and Ree, 2013;Smith et al, 2014), targeted enrichment of ultraconserved elements (UCEs) or conserved ortholog sequences (COS) (Mandel et al, 2014;Smith et al, 2014), and RNA-Seq (Wen et al, 2013;Wickett et al, 2014) could be suitable methods to resolve Hawaiian mint relationships. However, these approaches are also associated with challenges, including accurately inferring orthology in high polyploid plants, slow mutation rates in exonic regions, which may be too low to resolve recent radiations (Giarla and Esselstyn, 2015), and the need to obtaining high quality RNA and DNA.…”

Genome of the pitcher plant Cephalotus reveals genetic changes associated with carnivory

“…The reported placement of P. persica (Rosales) is discrepant between plastid-54 and nuclear-based analyses 52,53 .…”

“…We estimated the divergence times of the surveyed species using RAxML version 8 51 , employing tree topologies published previously [52][53][54] . The reported placement of P. persica (Rosales) is discrepant between plastid-54 and nuclear-based analyses 52,53 .…”

On plant defense signaling networks and early land plant evolution

“…We review what is known about the recurrent evolution of plant defense signaling networks across streptophyte evolution (Figure 1). In so doing, we span the trajectory from streptophyte algae (the closest extant relatives to land plants [3-5]), mosses, gymnosperms, and angiosperms. Since most data have been gathered for angiosperms, we will use them primarily for comparative purposes.

10.1080/19420889.2018.1486168-F0001Figure 1.Key phytopathogen interaction factors across the trajectory of streptophyte evolution.

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