André S. Chanderbali

Ancestral polyploidy in seed plants and angiosperms

Whole-genome duplication (WGD), or polyploidy, followed by gene loss and diploidization has long been recognized as an important evolutionary force in animals, fungi and other organisms, especially plants. The success of angiosperms has been attributed, in part, to innovations associated with gene or whole-genome duplications, but evidence for proposed ancient genome duplications pre-dating the divergence of monocots and eudicots remains equivocal in analyses of conserved gene order. Here we use comprehensive phylogenomic analyses of sequenced plant genomes and more than 12.6 million new expressed-sequence-tag sequences from phylogenetically pivotal lineages to elucidate two groups of ancient gene duplications—one in the common ancestor of extant seed plants and the other in the common ancestor of extant angiosperms. Gene duplication events were intensely concentrated around 319 and 192 million years ago, implicating two WGDs in ancestral lineages shortly before the diversification of extant seed plants and extant angiosperms, respectively. Significantly, these ancestral WGDs resulted in the diversification of regulatory genes important to seed and flower development, suggesting that they were involved in major innovations that ultimately contributed to the rise and eventual dominance of seed plants and angiosperms.

A genome triplication associated with early diversification of the core eudicots.

BackgroundAlthough it is agreed that a major polyploidy event, gamma, occurred within the eudicots, the phylogenetic placement of the event remains unclear.ResultsTo 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.ConclusionsThe 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.

Assembly and Validation of the Genome of the Nonmodel Basal Angiosperm Amborella

Shaping Plant Evolution Amborella trichopoda is understood to be the most basal extant flowering plant and its genome is anticipated to provide insights into the evolution of plant life on Earth (see the Perspective by Adams). To validate and assemble the sequence, Chamala et al. (p. 1516) combined fluorescent in situ hybridization (FISH), genomic mapping, and next-generation sequencing. The Amborella Genome Project (p. 10.1126/science.1241089) was able to infer that a whole-genome duplication event preceded the evolution of this ancestral angiosperm, and Rice et al. (p. 1468) found that numerous genes in the mitochondrion were acquired by horizontal gene transfer from other plants, including almost four entire mitochondrial genomes from mosses and algae. Fluorescence in situ hybridization allows for next-generation sequencing of a large, difficult genome. [Also see Perspective by Adams; Research Articles by Amborella Genome Project and Rice et al.] Genome sequencing with next-generation sequence (NGS) technologies can now be applied to organisms pivotal to addressing fundamental biological questions, but with genomes previously considered intractable or too expensive to undertake. However, for species with large and complex genomes, extensive genetic and physical map resources have, until now, been required to direct the sequencing effort and sequence assembly. As these resources are unavailable for most species, assembling high-quality genome sequences from NGS data remains challenging. We describe a strategy that uses NGS, fluorescence in situ hybridization, and whole-genome mapping to assemble a high-quality genome sequence for Amborella trichopoda, a nonmodel species crucial to understanding flowering plant evolution. These methods are applicable to many other organisms with limited genomic resources.

What Is the Relationship among Hernandiaceae, Lauraceae, and Monimiaceae, and Why Is This Question So Difficult to Answer?

Molecular and morphological phylogenetic studies in the Laurales have found that Hernandiaceae, Lauraceae, and Monimiaceae sensu stricto form a monophyletic group. Because of the paucity of phylogenetically informative substitutions, however, relationships among families within this clade remain unclear. In general, molecular phylogenies may conflict because of a variety of factors, including substitution rate variation among sites and lineages, taxon sampling, outgroup choice, and base compositional biases. We analyzed a total of 2846 aligned nucleotides from a plastid intron, three spacers, and a portion of the nuclear 26S rRNA gene in a sample of Hernandiaceae, Lauraceae, and Monimiaceae; we used four outgroups with differing substitution rates. Despite obtaining single best topologies with maximum likelihood, minimum evolution, and parsimony approaches, family relationships remained as poorly supported as they were in the previous molecular studies. Exploration of the data indicates that varying substitution rates across lineages or sites, insufficient taxon sampling, fast‐evolving outgroups, or biased base composition are unlikely to explain the difficult reconstruction. Exclusion of some of the longest branched taxa (the hemiparasite Cassytha, selected Hernandiaceae, and two of the four outgroups) had no effect on topologies. To resolve relationships among the three families one could now complement existing five‐gene data sets by adding the basal genera of Lauraceae, Monimiaceae, and Hernandiaceae, which are newly sampled here, or, our preferred strategy, by sequencing low‐copy nuclear genes for the key genera to obtain different kinds of data.

Conservation and canalization of gene expression during angiosperm diversification accompany the origin and evolution of the flower.

The origin and rapid diversification of the angiosperms (Darwins “Abominable Mystery”) has engaged generations of researchers. Here, we examine the floral genetic programs of phylogenetically pivotal angiosperms (water lily, avocado, California poppy, and Arabidopsis) and a nonflowering seed plant (a cycad) to obtain insight into the origin and subsequent evolution of the flower. Transcriptional cascades with broadly overlapping spatial domains, resembling the hypothesized ancestral gymnosperm program, are deployed across morphologically intergrading organs in water lily and avocado flowers. In contrast, spatially discrete transcriptional programs in distinct floral organs characterize the more recently derived angiosperm lineages represented by California poppy and Arabidopsis. Deep evolutionary conservation in the genetic programs of putatively homologous floral organs traces to those operating in gymnosperm reproductive cones. Female gymnosperm cones and angiosperm carpels share conserved genetic features, which may be associated with the ovule developmental program common to both organs. However, male gymnosperm cones share genetic features with both perianth (sterile attractive and protective) organs and stamens, supporting the evolutionary origin of the floral perianth from the male genetic program of seed plants.

Genetic Footprints of Stamen Ancestors Guide Perianth Evolution in Persea (Lauraceae)

The perianth of Persea americana (Lauraceae) consists of two whorls of morphologically similar laminar organs, termed tepals. Closely related Persea borbonia, however, produces a dimorphic perianth with smaller outer tepals. To assess whether homologues of floral organ identity genes in Persea may play a role in shaping this dimorphic perianth, we compared their expression patterns in the two species. A homologue of AP1 (A‐function) is expressed at low levels in both perianth types but was not tepal specific. Homologues of AGL6, however, show the tepal‐specific expression pattern expected of A‐function genes. Homologues of AP3 and PI (B‐function) are expressed in tepals of both perianth types, indicating that perianth dimorphism in Persea is not regulated by these genes. Differential expression across the dimorphic perianth as absence late in outer tepal development was evident for homologues of AG (C‐function) and SEP3 (E‐function). Genetic studies in model systems indicate a conserved role for AG homologues in specifying stamen and carpel identity, but the expression pattern in Persea indicates a novel role in perianth development. On the basis of gene expression and the occasional presence of tepaloid organs in stamen whorls, we hypothesize that the tepals of Persea and perhaps other Lauraceae are derived from stamens.

Transcriptional signatures of ancient floral developmental genetics in avocado (Persea americana; Lauraceae)

The debate on the origin and evolution of flowers has recently entered the field of developmental genetics, with focus on the design of the ancestral floral regulatory program. Flowers can differ dramatically among angiosperm lineages, but in general, male and female reproductive organs surrounded by a sterile perianth of sepals and petals constitute the basic floral structure. However, the basal angiosperm lineages exhibit spectacular diversity in the number, arrangement, and structure of floral organs, whereas the evolutionarily derived monocot and eudicot lineages share a far more uniform floral ground plan. Here we show that broadly overlapping transcriptional programs characterize the floral transcriptome of the basal angiosperm Persea americana (avocado), whereas floral gene expression domains are considerably more organ specific in the model eudicot Arabidopsis thaliana. Our findings therefore support the “fading borders” model for organ identity determination in basal angiosperm flowers and extend it from the action of regulatory genes to downstream transcriptional programs. Furthermore, the declining expression of components of the staminal transcriptome in central and peripheral regions of Persea flowers concurs with elements of a previous hypothesis for developmental regulation in a gymnosperm “floral progenitor.” Accordingly, in contrast to the canalized organ-specific regulatory apparatus of Arabidopsis, floral development may have been originally regulated by overlapping transcriptional cascades with fading gradients of influence from focal to bordering organs.

Expression of Floral Regulators in Basal Angiosperms and the Origin and Evolution of ABC‐Function

Abstract The ABC‐model of floral organ identity explains the regular, sequential development of sepals, petals, stamens, and carpels in eudicot flowers. This general model, based on studies of the derived eudicots Arabidopsis and Antirrhinum, may apply to nearly all eudicots, most of which are characterized by discrete whorls of floral organs. However, floral morphology of basal angiosperms is typically characterized by variable numbers of floral parts and gradual transitions among floral organs, and it is unclear that the ABC‐model applies to such flowers. Here we explore the origin and evolution of ABC‐function through consideration of expression data for homologs of ABC‐genes for basal angiosperms and conclude that the ABC‐model represents an evolutionarily derived regulatory network that arose through spatial restriction of regulatory gene expression.

A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure

BackgroundRecent phylogenetic analyses have identified Amborella trichopoda, an understory tree species endemic to the forests of New Caledonia, as sister to a clade including all other known flowering plant species. The Amborella genome is a unique reference for understanding the evolution of angiosperm genomes because it can serve as an outgroup to root comparative analyses. A physical map, BAC end sequences and sample shotgun sequences provide a first view of the 870 Mbp Amborella genome.ResultsAnalysis of Amborella BAC ends sequenced from each contig suggests that the density of long terminal repeat retrotransposons is negatively correlated with that of protein coding genes. Syntenic, presumably ancestral, gene blocks were identified in comparisons of the Amborella BAC contigs and the sequenced Arabidopsis thaliana, Populus trichocarpa, Vitis vinifera and Oryza sativa genomes. Parsimony mapping of the loss of synteny corroborates previous analyses suggesting that the rate of structural change has been more rapid on lineages leading to Arabidopsis and Oryza compared with lineages leading to Populus and Vitis. The gamma paleohexiploidy event identified in the Arabidopsis, Populus and Vitis genomes is shown to have occurred after the divergence of all other known angiosperms from the lineage leading to Amborella.ConclusionsWhen placed in the context of a physical map, BAC end sequences representing just 5.4% of the Amborella genome have facilitated reconstruction of gene blocks that existed in the last common ancestor of all flowering plants. The Amborella genome is an invaluable reference for inferences concerning the ancestral angiosperm and subsequent genome evolution.

Evolving Ideas on the Origin and Evolution of Flowers: New Perspectives in the Genomic Era.

The origin of the flower was a key innovation in the history of complex organisms, dramatically altering Earth’s biota. Advances in phylogenetics, developmental genetics, and genomics during the past 25 years have substantially advanced our understanding of the evolution of flowers, yet crucial aspects of floral evolution remain, such as the series of genetic and morphological changes that gave rise to the first flowers; the factors enabling the origin of the pentamerous eudicot flower, which characterizes ∼70% of all extant angiosperm species; and the role of gene and genome duplications in facilitating floral innovations. A key early concept was the ABC model of floral organ specification, developed by Elliott Meyerowitz and Enrico Coen and based on two model systems, Arabidopsis thaliana and Antirrhinum majus. Yet it is now clear that these model systems are highly derived species, whose molecular genetic-developmental organization must be very different from that of ancestral, as well as early, angiosperms. In this article, we will discuss how new research approaches are illuminating the early events in floral evolution and the prospects for further progress. In particular, advancing the next generation of research in floral evolution will require the development of one or more functional model systems from among the basal angiosperms and basal eudicots. More broadly, we urge the development of “model clades” for genomic and evolutionary-developmental analyses, instead of the primary use of single “model organisms.” We predict that new evolutionary models will soon emerge as genetic/genomic models, providing unprecedented new insights into floral evolution.