A Phylogenomic Assessment of Ancient Polyploidy and Genome Evolution Across the Poales

Comparisons of flowering plant genomes reveal multiple rounds of ancient polyploidy characterized by large intra-genomic syntenic blocks. Three such whole genome duplication (WGD) events, designated as rho (ρ), sigma (σ), and tau (τ), have been identified in the genomes of cereal grasses. Precise dating of these WGD events is necessary to investigate how they have influenced diversification rates, evolutionary innovations, and genomic characteristics such as the GC profile of protein coding sequences. The timing of these events has remained uncertain due to the paucity of monocot genome sequence data outside the grass family (Poaceae). Phylogenomic analysis of protein coding genes from sequenced genomes and transcriptome assemblies from 35 species, including representatives of all families within the Poales, has resolved the timing ofrho and sigma relative to speciation events and placed tau prior to divergence of Asparagales and the commelinids but after divergence with eudicots. Examination of gene family phylogenies indicates that rhooccurred just prior to the diversification of Poaceae and sigma occurred before early diversification of Poales lineages but after the Poales-commelinid split. Additional lineage specific WGD events were identified on the basis of the transcriptome data. Gene families exhibiting high GC content are underrepresented among those with duplicate genes that persisted following these genome duplications. However, genome duplications had little overall influence on lineage-specific changes in the GC content of coding genes. Improved resolution of the timing of WGD events in monocot history provides evidence for the influence of polyploidization on functional evolution and species diversification

Parallel Loss of Plastid Introns and Their Maturase in the Genus Cuscuta

Plastid genome content and arrangement are highly conserved across most land plants and their closest relatives, streptophyte algae, with nearly all plastid introns having invaded the genome in their common ancestor at least 450 million years ago. One such intron, within the transfer RNA trnK-UUU, contains a large open reading frame that encodes a presumed intron maturase, matK. This gene is missing from the plastid genomes of two species in the parasitic plant genus Cuscuta but is found in all other published land plant and streptophyte algal plastid genomes, including that of the nonphotosynthetic angiosperm Epifagus virginiana and two other species of Cuscuta. By examining matK and plastid intron distribution in Cuscuta, we add support to the hypothesis that its normal role is in splicing seven of the eight group IIA introns in the genome. We also analyze matK nucleotide sequences from Cuscuta species and relatives that retain matK to test whether changes in selective pressure in the maturase are associated with intron deletion. Stepwise loss of most group IIA introns from the plastid genome results in substantial change in selective pressure within the hypothetical RNA-binding domain of matK in both Cuscuta and Epifagus, either through evolution from a generalist to a specialist intron splicer or due to loss of a particular intron responsible for most of the constraint on the binding region. The possibility of intron-specific specialization in the X-domain is implicated by evidence of positive selection on the lineage leading to C. nitida in association with the loss of six of seven introns putatively spliced by matK. Moreover, transfer RNA gene deletion facilitated by parasitism combined with an unusually high rate of intron loss from remaining functional plastid genes created a unique circumstance on the lineage leading to Cuscuta subgenus Grammica that allowed elimination of matK in the most species-rich lineage of Cuscuta

Methods for Obtaining and Analyzing Whole Chloroplast Genome Sequences

During the past decade there has been a rapid increase in our understanding of plastid genome organization and evolution due to the availability of many new completely sequenced genomes. Currently there are 43 complete genomes published and ongoing projects are likely to increase this sampling to nearly 200 genomes during the next five years. Several groups of researchers including ours have been developing new techniques for gathering and analyzing entire plastid genome sequences and details of these developments are summarized in this chapter. The most important recent developments that enhance our ability to generate whole chloroplast genome sequences involve the generation of pure fractions of chloroplast genomes by whole genome amplification using rolling circular amplification, cloning genomes into Fosmid or BAC vectors, and the development of an organellar annotation program (DOGMA). In addition to providing details of these methods, we provide an overview of methods for analyzing complete plastid genome sequences for repeats and gene content, as well as approaches for using gene order and sequence data for phylogeny reconstruction. This explosive increase in the number of sequenced plastid genomes and improved computational tools will provide many insights into the evolution of these genomes and much new data for assessing relationships at deep nodes in plants and other photosynthetic organisms

Analysis of 81 Genes From 64 Plastid Genomes Resolves Relationships in Angiosperms and Identifies Genome-Scale Evolutionary Patterns

Angiosperms are the largest and most successful clade of land plants with \u3e250,000 species distributed in nearly every terrestrial habitat. Many phylogenetic studies have been based on DNA sequences of one to several genes, but, despite decades of intensive efforts, relationships among early diverging lineages and several of the major clades remain either incompletely resolved or weakly supported. We performed phylogenetic analyses of 81 plastid genes in 64 sequenced genomes, including 13 new genomes, to estimate relationships among the major angiosperm clades, and the resulting trees are used to examine the evolution of gene and intron content. Phylogenetic trees from multiple methods, including model-based approaches, provide strong support for the position of Amborella as the earliest diverging lineage of flowering plants, followed by Nymphaeales and Austrobaileyales. The plastid genome trees also provide strong support for a sister relationship between eudicots and monocots, and this group is sister to a clade that includes Chloranthales and magnoliids. Resolution of relationships among the major clades of angiosperms provides the necessary framework for addressing numerous evolutionary questions regarding the rapid diversification of angiosperms. Gene and intron content are highly conserved among the early diverging angiosperms and basal eudicots, but 62 independent gene and intron losses are limited to the more derived monocot and eudicot clades. Moreover, a lineage-specific correlation was detected between rates of nucleotide substitutions, indels, and genomic rearrangements

A genome triplication associated with early diversification of the core eudicots

Background: Although it is agreed that a major polyploidy event, gamma, occurred within the eudicots, the phylogenetic placement of the event remains unclear. Results: To determine when this polyploidization occurred relative to speciation events in angiosperm history, we employed a phylogenomic approach to investigate the timing of gene set duplications located on syntenic gamma blocks. We populated 769 putative gene families with large sets of homologs obtained from public transcriptomes of basal angiosperms, magnoliids, asterids, and more than 91.8 gigabases of new next-generation transcriptome sequences of non-grass monocots and basal eudicots. The overwhelming majority (95%) of well-resolved gamma duplications was placed before the separation of rosids and asterids and after the split of monocots and eudicots, providing strong evidence that the gamma polyploidy event occurred early in eudicot evolution. Further, the majority of gene duplications was placed after the divergence of the Ranunculales and core eudicots, indicating that the gamma appears to be restricted to core eudicots. Molecular dating estimates indicate that the duplication events were intensely concentrated around 117 million years ago. Conclusions: The rapid radiation of core eudicot lineages that gave rise to nearly 75% of angiosperm species appears to have occurred coincidentally or shortly following the gamma triplication event. Reconciliation of gene trees with a species phylogeny can elucidate the timing of major events in genome evolution, even when genome sequences are only available for a subset of species represented in the gene trees. Comprehensive transcriptome datasets are valuable complements to genome sequences for high-resolution phylogenomic analysis

Systematics and plastid genome evolution of the cryptically photosynthetic parasitic plant genus Cuscuta (Convolvulaceae)

<p>Abstract</p> <p>Background</p> <p>The genus <it>Cuscuta </it>L. (Convolvulaceae), commonly known as dodders, are epiphytic vines that invade the stems of their host with haustorial feeding structures at the points of contact. Although they lack expanded leaves, some species are noticeably chlorophyllous, especially as seedlings and in maturing fruits. Some species are reported as crop pests of worldwide distribution, whereas others are extremely rare and have local distributions and apparent niche specificity. A strong phylogenetic framework for this large genus is essential to understand the interesting ecological, morphological and molecular phenomena that occur within these parasites in an evolutionary context.</p> <p>Results</p> <p>Here we present a well-supported phylogeny of <it>Cuscuta </it>using sequences of the nuclear ribosomal internal transcribed spacer and plastid <it>rps2</it>, <it>rbcL </it>and <it>matK </it>from representatives across most of the taxonomic diversity of the genus. We use the phylogeny to interpret morphological and plastid genome evolution within the genus. At least three currently recognized taxonomic sections are not monophyletic and subgenus <it>Cuscuta </it>is unequivocally paraphyletic. Plastid genes are extremely variable with regards to evolutionary constraint, with <it>rbcL </it>exhibiting even higher levels of purifying selection in <it>Cuscuta </it>than photosynthetic relatives. Nuclear genome size is highly variable within <it>Cuscuta</it>, particularly within subgenus <it>Grammica</it>, and in some cases may indicate the existence of cryptic species in this large clade of morphologically similar species.</p> <p>Conclusion</p> <p>Some morphological characters traditionally used to define major taxonomic splits within <it>Cuscuta </it>are homoplastic and are of limited use in defining true evolutionary groups. Chloroplast genome evolution seems to have evolved in a punctuated fashion, with episodes of loss involving suites of genes or tRNAs followed by stabilization of gene content in major clades. Nearly all species of <it>Cuscuta </it>retain some photosynthetic ability, most likely for nutrient apportionment to their seeds, while complete loss of photosynthesis and possible loss of the entire chloroplast genome is limited to a single small clade of outcrossing species found primarily in western South America.</p

Phylogeny and Origins of Holoparasitism in Orobanchaceae

• Premise: Orobanchaceae are a family of angiosperms that range from fully autotrophic and free-living to completely heterotrophic and dependent on their hosts (holoparasites). Most of the ca. 2060 species are hemiparasites that photosynthesize throughout all or part of their life cycles. Certain family members are ecologically important due to direct impacts on community biomass and diversity, plant–herbivore interactions, and nutrient cycling. Other members are among the most economically damaging weeds in the world. Multiple trophic transitions within this family make it ideal for studying molecular evolutionary and physiological changes that accompany the evolution of parasitism. • Methods: To establish a phylogenetic framework for such work, we substantially increased taxonomic sampling at loci for which a significant amount of data already existed (nuclear ITS and PHYA, plastid matK and rps2) and added data from the low-copy nuclear locus, PHYB. • Key results: The data provide strong support for relationships among six major clades and for the position of Brandisia hancei Hook. f. The positions ofBoschniakia himalaica Hook. f. & Thomson, Centranthera cochinchinensis(Lour.) Merr., Mannagettaea hummelii Harry Sm., and Pterygiella nigrescensOliv. are confirmed or suggested for the first time. • Conclusions: There is a single origin of parasitism, and from within the hemiparasites, holoparasitism has originated three times. Moving from the base to the tips of the Orobanchaceae tree, the successive major splits within the parasitic clade are: Cymbarieae + the rest; Orobancheae + the rest;Brandisia + the rest; Rhinantheae + the rest; and Pedicularideae + Buchnereae

Timing of Rapid Diversification and Convergent Origins of Active Pollination within Agavoideae (Asparagaceae)

PREMISE OF THE STUDY: Yucca species are ideal candidates for the study of coevolution due to the obligate mutualism they form with yucca moth pollinators (genera Tegeticula and Parategeticula). Yuccas are not the only species to exhibit a mutualism with yucca moths; the genus Hesperoyucca is pollinated by the California yucca moth (Tegeticula maculata). Relationships among yuccas, Hesperoyucca, and other members of subfamily Agavoideae are necessary to understand the evolution of this unique pollination syndrome. Here, we investigate evolutionary relationships of yuccas and closely related genera looking at the timing and origin of yucca moth pollination. METHODS: In this study, we sequenced the chloroplast genomes of 20 species in the subfamily Agavoideae (Asparagaceae) and three confamilial outgroup taxa to resolve intergeneric phylogenetic relationships of Agavoideae. We estimated divergence times using protein-coding genes from 67 chloroplast genomes sampled across monocots to determine the timing of the yucca moth pollination origin. KEY RESULTS: We confidently resolved intergeneric relationships in Agavoideae, demonstrating the origin of the yucca–yucca moth mutualism on two distinct lineages that diverged 27 million years ago. Comparisons of Yucca and Hesperoyucca divergence time to those of yucca moths (Tegeticula and Parategeticula, Prodoxidae) indicate overlapping ages for the origin of pollinating behavior in the moths and pollination by yucca moths in the two plant lineages. CONCLUSION: Whereas pollinating yucca moths have been shown to have a single origin within the Prodoxidae, there were independent acquisitions of active pollination on lineages leading to Yucca and Hesperoyucca within the Agavoideae