From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales

The link between ancient whole-genome duplications and cold adaptations in the Caryophyllaceae

PREMISE

The Caryophyllaceae (the carnation family) have undergone multiple transitions into colder climates and convergence on cushion plant adaptation, indicating that they may provide a natural system for cold adaptation research. Previous research has suggested that putative ancient whole-genome duplications (WGDs) are correlated with niche shifts into colder climates across the Caryophyllales. Here, we explored the genomic changes potentially involved in one of these discovered shifts in the Caryophyllaceae.

METHODS

We constructed a data set combining 26 newly generated transcriptomes with 45 published transcriptomes, including 11 cushion plant species across seven genera. With this data set, we inferred a dated phylogeny for the Caryophyllaceae and mapped ancient WGDs and gene duplications onto the phylogeny. We also examined functional groups enriched for gene duplications related to the climatic shift.

RESULTS

The ASTRAL topology was mostly congruent with the current consensus of relationships within the family. We inferred 15 putative ancient WGDs in the family, including eight that have not been previously published. The oldest ancient WGD (ca. 64.4-56.7 million years ago), WGD1, was found to be associated with a shift into colder climates by previous research. Gene regions associated with ubiquitination were overrepresented in gene duplications retained after WGD1 and those convergently retained by cushion plants in Colobanthus and Eremogone, along with other functional annotations.

CONCLUSIONS

Gene family expansions induced by ancient WGDs may have contributed to the shifts to cold climatic niches in the Caryophyllaceae. Transcriptomic data are crucial resources that help unravel heterogeneity in deep-time evolutionary patterns in plants.

An updated phylogeny and adaptive evolution within Amaranthaceae s.l. inferred from multiple phylogenomic datasets

Amaranthaceae s.l. is a widely distributed family consisting of over 170 genera and 2000 species. Previous molecular phylogenetic studies have shown that Amaranthaceae s.s. and traditional Chenopodiaceae form a monophyletic group (Amaranthaceae s.l.), however, the relationships within this evolutionary branch have yet to be fully resolved. In this study, we assembled the complete plastomes and full-length ITS of 21 Amaranthaceae s.l. individuals and compared them with 38 species of Amaranthaceae s.l. Through plastome structure and sequence alignment analysis, we identified a reverse complementary region approximately 5200 bp long in the genera Atriplex and Chenopodium. Adaptive evolution analysis revealed significant positive selection in eight genes, which likely played a driving role in the evolution of Amaranthaceae s.l., as demonstrated by partitioned evolutionary analysis. Furthermore, we found that about two-thirds of the examined species lack the ycf15 gene, potentially associated with natural selection pressures from their adapted habitats. The phylogenetic tree indicated that some genera (Chenopodium, Halogeton, and Subtr. Salsolinae) are paraphyletic lineages. Our results strongly support the clustering of Amaranthaceae s.l. with monophyletic traditional Chenopodiaceae (Clades I and II) and Amaranthaceae s.s. After a comprehensive analysis, we determined that cytonuclear conflict, gene selection by adapted habitats, and incomplete lineage sorting (ILS) events were the primary reasons for the inconsistent phylogeny of Amaranthaceae s.l. During the last glacial period, certain species within Amaranthaceae s.l. underwent adaptations to different environments and began to differentiate rapidly. Since then, these species may have experienced morphological and genetic changes distinct from those of other genera due to intense selection pressure.

Probing of plant transcriptomes reveals the hidden genetic diversity of the family Secoviridae

Secoviruses are single-stranded RNA viruses that infect plants. In the present study, we identified 61 putative novel secoviral genomes in various plant species by mining publicly available plant transcriptome data. These viral sequences represent the genomes of 13 monopartite and 48 bipartite secovirids. The genome sequences of 52 secovirids were coding-complete, and nine were partial. Except for small open reading frames (ORFs) determined in waikaviral genomes and RNA2 of torradoviruses, all of the recovered genomes/genome segments contained a large ORF encoding a polyprotein. Based on genome organization and phylogeny, all but three of the novel secoviruses were assigned to different genera. The genome organization of two identified waika-like viruses resembled that of the recently identified waika-like virus Triticum aestivum secovirus. Phylogenetic analysis revealed a pattern of host-virus co-evolution in a few waika- and waika-like viruses and increased phylogenetic diversity of nepoviruses. The study provides a basis for further investigation of the biological properties of these novel secoviruses.

Comparative analysis of floral transition and floral organ formation in two contrasting species: Disocactus speciosus and D. eichlamii (Cactaceae)

KEY MESSAGE

Contrasting morphologies in Disocactus are the result of differential development of the vegetative and floral tissue where intercalary growth is involved, resulting in a complex structure, the floral axis. Species from the Cactaceae bear adaptations related with their growth in environments under hydric stress. These adaptations have translated into the reduction and modification of various structures such as leaves, stems, lateral branches, roots and the structuring of flowers in a so-called flower-shoot. While cacti flowers and fruits have a consistent structure with showy hermaphrodite or unisexual flowers that produce a fruit called cactidium, the developmental dynamics of vegetative and reproductive tissues comprising the reproductive unit have only been inferred through the analysis of pre-anthetic buds. Here we present a comparative analysis of two developmental series covering the early stages of flower formation and organ differentiation in Disocactus speciosus and Disocactus eichlamii, which have contrasting floral morphologies. We observe that within the areole, a shoot apical meristem commences to grow upward, producing lateral leaves with a spiral arrangement, rapidly transitioning to a floral meristem. The floral meristem produces tepal primordia and a staminal ring meristem from which numerous or few stamens develop in a centrifugal manner in D. speciosus and D. eichlamii, respectively. Also, the inferior ovary derives from the floral meristem flattening and an upward growth of the surrounding tissue of the underlying stem, producing the pericarpel. This structure is novel to cacti and lacks a clear anatomical delimitation with the carpel wall. Here, we present a first study that documents the early processes taking place during initial meristem determination related to pericarpel development and early floral organ formation in cacti until the establishment of mature floral organs.

Phylogenomics and the rise of the angiosperms

Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods1,2. A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome3,4. Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins5-7. However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications. Here, we build the tree of life for almost 8,000 (about 60%) angiosperm genera using a standardized set of 353 nuclear genes8. This 15-fold increase in genus-level sampling relative to comparable nuclear studies9 provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade.

Medullary bundles in Caryophyllales: form, function, and evolution

The occurrence of conducting vascular tissue in the pith (CVTP) of tracheophytes is noteworthy. Medullary bundles, one of the remarkable examples of CVTP, evolved multiple times across angiosperms, notably in the Caryophyllales. Yet, information on the occurrence of medullary bundles is fragmented, hampering our understanding of their structure-function relationships, and evolutionary implications. Using three plastid molecular markers (matK, rbcL, and rps16 intron), a phylogeny is constructed for 561 species of Caryophyllales, and anatomical data are assembled for 856 species across 40 families to investigate the diversity of medullary bundles, their function, evolution, and diversification dynamics. Additionally, correlated evolution between medullary bundles and successive cambia was tested. Medullary bundles are ancestrally absent in Caryophyllales and evolved in core and noncore families. They are structurally diverse (e.g. number, arrangement, and types of bundles) and functionally active throughout the plant's lifespan, providing increased hydraulic conductivity, especially in herbaceous plants. Acquisition of medullary bundles does not explain diversification rate heterogeneity but is correlated to a higher diversification rate. Disparate developmental pathways were found leading to rampant convergent evolution of CVTP in Caryophyllales. These findings indicate the diversification of medullary bundles and vascular tissues as another central theme for functional and comparative molecular studies in Caryophyllales.

Multiple mechanisms explain loss of anthocyanins from betalain-pigmented Caryophyllales, including repeated wholesale loss of a key anthocyanidin synthesis enzyme

In this study, we investigate the genetic mechanisms responsible for the loss of anthocyanins in betalain-pigmented Caryophyllales, considering our hypothesis of multiple transitions to betalain pigmentation. Utilizing transcriptomic and genomic datasets across 357 species and 31 families, we scrutinize 18 flavonoid pathway genes and six regulatory genes spanning four transitions to betalain pigmentation. We examined evidence for hypotheses of wholesale gene loss, modified gene function, altered gene expression, and degeneration of the MBW (MYB-bHLH-WD40) trasnscription factor complex, within betalain-pigmented lineages. Our analyses reveal that most flavonoid synthesis genes remain conserved in betalain-pigmented lineages, with the notable exception of TT19 orthologs, essential for the final step in anthocyanidin synthesis, which appear to have been repeatedly and entirely lost. Additional late-stage flavonoid pathway genes upstream of TT19 also manifest strikingly reduced expression in betalain-pigmented species. Additionally, we find repeated loss and alteration in the MBW transcription complex essential for canonical anthocyanin synthesis. Consequently, the loss and exclusion of anthocyanins in betalain-pigmented species appear to be orchestrated through several mechanisms: loss of a key enzyme, downregulation of synthesis genes, and degeneration of regulatory complexes. These changes have occurred iteratively in Caryophyllales, often coinciding with evolutionary transitions to betalain pigmentation.

Genomic exploration of Sesuvium sesuvioides: comparative study and phylogenetic analysis within the order Caryophyllales from Cholistan desert, Pakistan

BACKGROUND

The Aizoaceae family's Sesuvium sesuvioides (Fenzl) Verdc is a medicinal species of the Cholistan desert, Pakistan. The purpose of this study was to determine the genomic features and phylogenetic position of the Sesuvium genus in the Aizoaceae family. We used the Illumina HiSeq2500 and paired-end sequencing to publish the complete chloroplast sequence of S. sesuvioides.

RESULTS

The 155,849 bp length cp genome sequence of S. sesuvioides has a 36.8% GC content. The Leucine codon has the greatest codon use (10.6%), 81 simple sequence repetitions of 19 kinds, and 79 oligonucleotide repeats. We investigated the phylogeny of the order Caryophyllales' 27 species from 23 families and 25 distinct genera. The maximum likelihood tree indicated Sesuvium as a monophyletic genus, and sister to Tetragonia. A comparison of S. sesuvioides, with Sesuvium portulacastrum, Mesembryanthemum crystallinum, Mesembryanthemum cordifolium, and Tetragonia tetragonoides was performed using the NCBI platform. In the comparative investigation of genomes, all five genera revealed comparable cp genome structure, gene number and composition. All five species lacked the rps15 gene and the rpl2 intron. In most comparisons with S. sesuvioides, transition substitutions (Ts) were more frequent than transversion substitutions (Tv), producing Ts/Tv ratios larger than one, and the Ka/Ks ratio was lower than one. We determined ten highly polymorphic regions, comprising rpl22, rpl32-trnL-UAG, trnD-GUC-trnY-GUA, trnE-UUC-trnT-GGU, trnK-UUU-rps16, trnM-CAU-atpE, trnH-GUG-psbA, psaJ-rpl33, rps4-trnT-UGU, and trnF-GAA-ndhJ.

CONCLUSION

The whole S. sesuvioides chloroplast will be examined as a resource for in-depth taxonomic research of the genus when more Sesuvium and Aizoaceae species are sequenced in the future. The chloroplast genomes of the Aizoaceae family are well preserved, with little alterations, indicating the family's monophyletic origin. This study's highly polymorphic regions could be utilized to build realistic and low-cost molecular markers for resolving taxonomic discrepancies, new species identification, and finding evolutionary links among Aizoaceae species. To properly comprehend the evolution of the Aizoaceae family, further species need to be sequenced.

Unravelling phylogenetic relationships of the tribe Cereeae using target enrichment sequencing

BACKGROUND AND AIMS

Cactaceae are succulent plants, quasi-endemic to the American continent, and one of the most endangered plant groups in the world. Molecular phylogenies have been key to unravelling phylogenetic relationships among major cactus groups, previously hampered by high levels of morphological convergence. Phylogenetic studies using plastid markers have not provided adequate resolution for determining generic relationships within cactus groups. This is the case for the tribe Cereeae s.l., a highly diverse group from tropical America. Here we aimed to reconstruct a well-resolved phylogenetic tree of tribe Cereeae and update the circumscription of suprageneric and generic groups in this tribe.

METHODS

We integrated sequence data from public gene and genomic databases with new target sequences (generated using the customized Cactaceae591 probe set) across representatives of this tribe, with a denser taxon sampling of the subtribe Cereinae. We inferred concatenated and coalescent phylogenetic trees and compared the performance of both approaches.

KEY RESULTS

Six well-supported suprageneric clades were identified using different datasets. However, only genomic datasets, especially the Cactaceae591, were able to resolve the contentious relationships within the subtribe Cereinae.

CONCLUSIONS

We propose a new taxonomic classification within Cereeae based on well-resolved clades, including new subtribes (Aylosterinae subtr. nov., Uebelmanniinae subtr. nov. and Gymnocalyciinae subtr. nov.) and revised subtribes (Trichocereinae, Rebutiinae and Cereinae). We emphasize the importance of using genomic datasets allied with coalescent inference to investigate evolutionary patterns within the tribe Cereeae.

More than a spiny morphology: plastome variation in the prickly pear cacti (Opuntieae)

BACKGROUND

Plastid genomes (plastomes) have long been recognized as highly conserved in their overall structure, size, gene arrangement and content among land plants. However, recent studies have shown that some lineages present unusual variations in some of these features. Members of the cactus family are one of these lineages, with distinct plastome structures reported across disparate lineages, including gene losses, inversions, boundary movements or loss of the canonical inverted repeat (IR) region. However, only a small fraction of cactus diversity has been analysed so far.

METHODS

Here, we investigated plastome features of the tribe Opuntieae, the remarkable prickly pear cacti, which represent one of the most diverse and important lineages of Cactaceae. We assembled de novo the plastome of 43 species, representing a comprehensive sampling of the tribe, including all seven genera, and analysed their evolution in a phylogenetic comparative framework. Phylogenomic analyses with different datasets (full plastome sequences and genes only) were performed, followed by congruence analyses to assess signals underlying contentious nodes.

KEY RESULTS

Plastomes varied considerably in length, from 121 to 162 kbp, with striking differences in the content and size of the IR region (contraction and expansion events), including a lack of the canonical IR in some lineages and the pseudogenization or loss of some genes. Overall, nine different types of plastomes were reported, deviating in the presence of the IR region or the genes contained in the IR. Overall, plastome sequences resolved phylogenetic relationships within major clades of Opuntieae with high bootstrap values but presented some contentious nodes depending on the dataset analysed (e.g. whole plastome vs. genes only). Congruence analyses revealed that most plastidial regions lack phylogenetic resolution, while few markers are supporting the most likely topology. Likewise, alternative topologies are driven by a handful of plastome markers, suggesting recalcitrant nodes in the phylogeny.

CONCLUSIONS

Our study reveals a dynamic nature of plastome evolution across closely related lineages, shedding light on peculiar features of plastomes. Variation of plastome types across Opuntieae is remarkable in size, structure and content and can be important for the recognition of species in some major clades. Unravelling connections between the causes of plastome variation and the consequences for species biology, physiology, ecology, diversification and adaptation is a promising and ambitious endeavour in cactus research. Although plastome data resolved major phylogenetic relationships, the generation of nuclear genomic data is necessary to confront these hypotheses and assess the recalcitrant nodes further.

Plant physiology: The overturning of assumed functional relevance of 'salt' bladders

For decades, the function of epidermal bladder cells in quinoa and iceplant was thought to be physiological because of their function in a related species. Exciting new research carefully demolishes that assumption, suggesting that these structures serve primarily biotic defense roles, setting up a great many interesting, important questions.

The genome of the glasshouse plant noble rhubarb (Rheum nobile) provides a window into alpine adaptation

Glasshouse plants are species that trap warmth via specialized morphology and physiology, mimicking a human glasshouse. In the Himalayan alpine region, the highly specialized glasshouse morphology has independently evolved in distinct lineages to adapt to intensive UV radiation and low temperature. Here we demonstrate that the glasshouse structure - specialized cauline leaves - is highly effective in absorbing UV light but transmitting visible and infrared light, creating an optimal microclimate for the development of reproductive organs. We reveal that this glasshouse syndrome has evolved at least three times independently in the rhubarb genus Rheum. We report the genome sequence of the flagship glasshouse plant Rheum nobile and identify key genetic network modules in association with the morphological transition to specialized glasshouse leaves, including active secondary cell wall biogenesis, upregulated cuticular cutin biosynthesis, and suppression of photosynthesis and terpenoid biosynthesis. The distinct cell wall organization and cuticle development might be important for the specialized optical property of glasshouse leaves. We also find that the expansion of LTRs has likely played an important role in noble rhubarb adaptation to high elevation environments. Our study will enable additional comparative analyses to identify the genetic basis underlying the convergent occurrence of glasshouse syndrome.

Deep reticulation: the long legacy of hybridization in vascular plant evolution

Hybridization has long been recognized as a fundamental evolutionary process in plants but, until recently, our understanding of its phylogenetic distribution and biological significance across deep evolutionary scales has been largely obscure. Over the past decade, genomic and phylogenomic datasets have revealed, perhaps not surprisingly, that hybridization, often associated with polyploidy, has been common throughout the evolutionary history of plants, particularly in various lineages of flowering plants. However, phylogenomic studies have also highlighted the challenges of disentangling signals of ancient hybridization from other sources of genomic conflict (in particular, incomplete lineage sorting). Here, we provide a critical review of ancient hybridization in vascular plants, outlining well-documented cases of ancient hybridization across plant phylogeny, as well as the challenges unique to documenting ancient versus recent hybridization. We provide a definition for ancient hybridization, which, to our knowledge, has not been explicitly attempted before. Further documenting the extent of deep reticulation in plants should remain an important research focus, especially because published examples likely represent the tip of the iceberg in terms of the total extent of ancient hybridization. However, future research should increasingly explore the macroevolutionary significance of this process, in terms of its impact on evolutionary trajectories (e.g. how does hybridization influence trait evolution or the generation of biodiversity over long time scales?), as well as how life history and ecological factors shape, or have shaped, the frequency of hybridization across geologic time and plant phylogeny. Finally, we consider the implications of ubiquitous ancient hybridization for how we conceptualize, analyze, and classify plant phylogeny. Networks, as opposed to bifurcating trees, represent more accurate representations of evolutionary history in many cases, although our ability to infer, visualize, and use networks for comparative analyses is highly limited. Developing improved methods for the generation, visualization, and use of networks represents a critical future direction for plant biology. Current classification systems also do not generally allow for the recognition of reticulate lineages, and our classifications themselves are largely based on evidence from the chloroplast genome. Updating plant classification to better reflect nuclear phylogenies, as well as considering whether and how to recognize hybridization in classification systems, will represent an important challenge for the plant systematics community.

Phylogenomics and Biogeography of the Mammilloid Clade Revealed an Intricate Evolutionary History Arose in the Mexican Plateau

Mexico harbors ~45% of world’s cacti species richness. Their biogeography and phylogenomics were integrated to elucidate the evolutionary history of the genera Coryphantha, Escobaria, Mammillaria, Mammilloydia, Neolloydia, Ortegocactus, and Pelecyphora (Mammilloid Clade). We analyzed 52 orthologous loci from 142 complete genomes of chloroplast (103 taxa) to generate a cladogram and a chronogram; in the latter, the ancestral distribution was reconstructed with the Dispersal-Extinction-Cladogenesis model. The ancestor of these genera arose ~7 Mya on the Mexican Plateau, from which nine evolutionary lineages evolved. This region was the site of 52% of all the biogeographical processes. The lineages 2, 3 and 6 were responsible for the colonization of the arid southern territories. In the last 4 Mya, the Baja California Peninsula has been a region of prolific evolution, particularly for lineages 8 and 9. Dispersal was the most frequent process and vicariance had relevance in the isolation of cacti distributed in the south of Mexico. The 70 taxa sampled as Mammillaria were distributed in six distinct lineages; one of these presumably corresponded to this genus, which likely had its center of origin in the southern part of the Mexican Plateau. We recommend detailed studies to further determine the taxonomic circumscription of the seven genera.

A plastid phylogenomic framework for the palm family (Arecaceae)

BACKGROUND

Over the past decade, phylogenomics has greatly advanced our knowledge of angiosperm evolution. However, phylogenomic studies of large angiosperm families with complete species or genus-level sampling are still lacking. The palms, Arecaceae, are a large family with ca. 181 genera and 2600 species and are important components of tropical rainforests bearing great cultural and economic significance. Taxonomy and phylogeny of the family have been extensively investigated by a series of molecular phylogenetic studies in the last two decades. Nevertheless, some phylogenetic relationships within the family are not yet well-resolved, especially at the tribal and generic levels, with consequent impacts for downstream research.

RESULTS

Plastomes of 182 palm species representing 111 genera were newly sequenced. Combining these with previously published plastid DNA data, we were able to sample 98% of palm genera and conduct a plastid phylogenomic investigation of the family. Maximum likelihood analyses yielded a robustly supported phylogenetic hypothesis. Phylogenetic relationships among all five palm subfamilies and 28 tribes were well-resolved, and most inter-generic phylogenetic relationships were also resolved with strong support.

CONCLUSIONS

The inclusion of nearly complete generic-level sampling coupled with nearly complete plastid genomes strengthened our understanding of plastid-based relationships of the palms. This comprehensive plastid genome dataset complements a growing body of nuclear genomic data. Together, these datasets form a novel phylogenomic baseline for the palms and an increasingly robust framework for future comparative biological studies of this exceptionally important plant family.

The molecular phylogenetic position of Harpagocarpus (Polygonaceae) sheds new light on the infrageneric classification of Fagopyrum

In the context of the molecular phylogeny of Polygonaceae, the phylogenetic positions of most genera and their relationships have been resolved. However, the monotypic genus Harpagocarpus has never been included in any published molecular phylogenetic studies. In the present study, we adopt a two-step approach to confirm the phylogenetic placement of Harpagocarpus using two datasets: (1) a concatenated dataset of three chloroplast DNA (cpDNA) regions (matK, rbcL and trnL-F) for Polygonaceae and (2) a combined cpDNA dataset of five sequences (accD, matK, psbA-trnH, rbcL and trnL-F) for Fagopyrum. Our analyses confirm the previous hypothesis based on morphological, anatomical and palynological investigations that Harpagocarpus is congeneric with Fagopyrum and further reveal that H.snowdenii (≡ F.snowdenii) is sister to the woody buckwheat F.tibeticum. Within Fagopyrum, three highly supported clades were discovered and the first sectional classification was proposed to accommodate them: sect. Fagopyrum comprises the two domesticated common buckwheat (F.esculentum and F.tataricum) and their wild relatives (F.esculentumsubsp.ancestrale, F.homotropicum and F.dibotrys) which are characterised by having large corymbose inflorescences and achenes greatly exceeding the perianth; sect. Tibeticum, including F.snowdenii and F.tibeticum, is characterised by the achene having appurtenances along the ribs, greatly exceeding the perianth and the perianth accrescent in fruit; sect. Urophyllum contains all other species of which the achenes were completely enclosed in the perianth. This study is very helpful to understand the phylogeny of the Fagopyrum and sheds light on the future study of taxonomy, biogeography, diversification and character evolution of the genus.

A target Capture Probe Set Useful for Deep- and Shallow-Level Phylogenetic Studies in Cactaceae

The molecular phylogenies of Cactaceae have enabled us to better understand their systematics, biogeography, and diversification ages. However, most of the phylogenetic relationships within Cactaceae major groups remain unclear, largely due to the lack of an appropriate set of molecular markers to resolve its contentious relationships. Here, we explored the genome and transcriptome assemblies available for Cactaceae and identified putative orthologous regions shared among lineages of the subfamily Cactoideae. Then we developed a probe set, named Cactaceae591, targeting both coding and noncoding nuclear regions for representatives from the subfamilies Pereskioideae, Opuntioideae, and Cactoideae. We also sampled inter- and intraspecific variation to evaluate the potential of this panel to be used in phylogeographic studies. We retrieved on average of 547 orthologous regions per sample. Targeting noncoding nuclear regions showed to be crucial to resolving inter- and intraspecific relationships. Cactaceae591 covers 13 orthologous genes shared with the Angiosperms353 kit and two plastid regions largely used in Cactaceae studies, enabling the phylogenies generated by our panel to be integrated with angiosperm and Cactaceae phylogenies, using these sequences. We highlighted the importance of using coalescent-based species tree approaches on the Cactaceae591 dataset to infer accurate phylogenetic trees in the presence of extensive incomplete lineage sorting in this family.

Effectiveness of Two Universal Angiosperm Probe Sets Tested In Silico for Caryophyllids Taxa with Emphasis on Cacti Species

In angiosperms, huge advances in massive DNA sequencing technologies have impacted phylogenetic studies. Probe sets have been developed with the purpose of recovering hundreds of orthologous loci of targeted DNA sequences (TDS) across different plant lineages. We tested in silico the effectiveness of two universal probe sets in the whole available genomes of Caryophyllids, emphasizing phylogenetic issues in cacti species. A total of 870 TDS (517 TDS from Angiosperm v.1 and 353 from Angiosperms353) were individually tested in nine cacti species and Amaranthus hypochondriacus (external group) with ≥17 Gbp of available DNA data. The effectiveness was measured by the total number of orthologous loci recovered and their length, the percentage of loci discarded by paralogy, and the proportion of informative sites (PIS) in the alignments. The results showed that, on average, Angiosperms353 was better than Angiosperm v.1 for cacti species, since the former obtained an average of 275.6 loci that represent 123,687 bp, 2.48% of paralogous loci, and 4.32% of PIS in alignments, whereas the latter recovered 148.4 loci (37,683 bp), 10.38% of paralogous loci, and 3.49% of PIS. We recommend the use of predesigned universal probe sets for Caryophyllids, since these recover a high number of orthologous loci that resolve phylogenetic relationships.

Evolutionary Genetics of Cacti: Research Biases, Advances and Prospects

Here, we present a review of the studies of evolutionary genetics (phylogenetics, population genetics, and phylogeography) using genetic data as well as genome scale assemblies in Cactaceae (Caryophyllales, Angiosperms), a major lineage of succulent plants with astonishing diversity on the American continent. To this end, we performed a literature survey (1992-2021) to obtain detailed information regarding key aspects of studies investigating cactus evolution. Specifically, we summarize the advances in the following aspects: molecular markers, species delimitation, phylogenetics, hybridization, biogeography, and genome assemblies. In brief, we observed substantial growth in the studies conducted with molecular markers in the past two decades. However, we found biases in taxonomic/geographic sampling and the use of traditional markers and statistical approaches. We discuss some methodological and social challenges for engaging the cactus community in genomic research. We also stressed the importance of integrative approaches, coalescent methods, and international collaboration to advance the understanding of cactus evolution.

A New Approach Using Targeted Sequence Capture for Phylogenomic Studies across Cactaceae

Relationships within the major clades of Cactaceae are relatively well known based on DNA sequence data mostly from the chloroplast genome. Nevertheless, some nodes along the backbone of the phylogeny, and especially generic and species-level relationships, remain poorly resolved and are in need of more informative genetic markers. In this study, we propose a new approach to solve the relationships within Cactaceae, applying a targeted sequence capture pipeline. We designed a custom probe set for Cactaceae using MarkerMiner and complemented it with the Angiosperms353 probe set. We then tested both probe sets against 36 different transcriptomes using Hybpiper preferentially retaining phylogenetically informative loci and reconstructed the relationships using RAxML-NG and Astral. Finally, we tested each probe set through sequencing 96 accessions, representing 88 species across Cactaceae. Our preliminary analyses recovered a well-supported phylogeny across Cactaceae with a near identical topology among major clade relationships as that recovered with plastome data. As expected, however, we found incongruences in relationships when comparing our nuclear probe set results to plastome datasets, especially at the generic level. Our results reveal great potential for the combination of Cactaceae-specific and Angiosperm353 probe set application to improve phylogenetic resolution for Cactaceae and for other studies.

Two independently evolved natural mutations additively deregulate TyrA enzymes and boost tyrosine production in planta

l-Tyrosine is an essential amino acid for protein synthesis and is also used in plants to synthesize diverse natural products. Plants primarily synthesize tyrosine via TyrA arogenate dehydrogenase (TyrA_a or ADH), which are typically strongly feedback inhibited by tyrosine. However, two plant lineages, Fabaceae (legumes) and Caryophyllales, have TyrA enzymes that exhibit relaxed sensitivity to tyrosine inhibition and are associated with elevated production of tyrosine-derived compounds, such as betalain pigments uniquely produced in core Caryophyllales. Although we previously showed that a single D222N substitution is primarily responsible for the deregulation of legume TyrAs, it is unknown when and how the deregulated Caryophyllales TyrA emerged. Here, through phylogeny-guided TyrA structure-function analysis, we found that functionally deregulated TyrAs evolved early in the core Caryophyllales before the origin of betalains, where the E208D amino acid substitution in the active site, which is at a different and opposite location from D222N found in legume TyrAs, played a key role in the TyrA functionalization. Unlike legumes, however, additional substitutions on non-active site residues further contributed to the deregulation of TyrAs in Caryophyllales. The introduction of a mutation analogous to E208D partially deregulated tyrosine-sensitive TyrAs, such as Arabidopsis TyrA2 (AtTyrA2). Moreover, the combined introduction of D222N and E208D additively deregulated AtTyrA2, for which the expression in Nicotiana benthamiana led to highly elevated accumulation of tyrosine in planta. The present study demonstrates that phylogeny-guided characterization of key residues underlying primary metabolic innovations can provide powerful tools to boost the production of essential plant natural products.

Gene duplications and phylogenomic conflict underlie major pulses of phenotypic evolution in gymnosperms

Inferring the intrinsic and extrinsic drivers of species diversification and phenotypic disparity across the tree of life is a major challenge in evolutionary biology. In green plants, polyploidy (or whole-genome duplication, WGD) is known to play a major role in microevolution and speciation, but the extent to which WGD has shaped macroevolutionary patterns of diversification and phenotypic innovation across plant phylogeny remains an open question. Here, we examine the relationship of various facets of genomic evolution-including gene and genome duplication, genome size, and chromosome number-with macroevolutionary patterns of phenotypic innovation, species diversification, and climatic occupancy in gymnosperms. We show that genomic changes, such as WGD and genome-size shifts, underlie the origins of most major extant gymnosperm clades, and notably, our results support an ancestral WGD in the gymnosperm lineage. Spikes of gene duplication typically coincide with major spikes of phenotypic innovation, while increased rates of phenotypic evolution are typically found at nodes with high gene-tree conflict, representing historic population-level dynamics during speciation. Most shifts in gymnosperm diversification since the rise of angiosperms are decoupled from putative WGDs and instead are associated with increased rates of climatic occupancy evolution, particularly in cooler and/or more arid climatic conditions, suggesting that ecological opportunity, especially in the later Cenozoic, and environmental heterogeneity have driven a resurgence of gymnosperm diversification. Our study provides critical insight on the processes underlying diversification and phenotypic evolution in gymnosperms, with important broader implications for the major drivers of both micro- and macroevolution in plants.

Concordance-based approaches for the inference of relationships and molecular rates with phylogenomic datasets

Gene tree conflict is common and finding methods to analyze and alleviate the negative effects that conflict has on species tree analysis is a crucial part of phylogenomics. This study aims to expand the discussion of inferring species trees and molecular branch lengths when conflict is present. Conflict is typically examined in two ways: inferring its prevalence, and inferring the influence of the individual genes (how strongly one gene supports any given topology compared to an alternative topology). Here, we examine a procedure for incorporating both conflict and the influence of genes in order to infer evolutionary relationships. All supported relationships in the gene trees are analyzed and the likelihood of the genes constrained to these relationships is summed to provide a likelihood for the relationship. Consensus tree assembly is conducted based on the sum of likelihoods for a given relationship and choosing relationships based on the most likely relationship assuming it does not conflict with a relationship that has a higher likelihood score. If it is not possible for all most likely relationships to be combined into a single bifurcating tree then multiple trees are produced and a consensus tree with a polytomy is created. This procedure allows for more influential genes to have greater influence on an inferred relationship, does not assume conflict has arisen from any one source, and does not force the dataset to produce a single bifurcating tree. Using this approach on three empirical datasets, we examine and discuss the relationship between influence and prevalence of gene tree conflict. We find that in one of the datasets, assembling a bifurcating consensus tree solely composed of the most likely relationships is impossible. To account for conflict in molecular rate analysis we also introduce a concordance-based approach to the summary and estimation of branch lengths suitable for downstream comparative analyses. We demonstrate through simulation that even under high levels of stochastic conflict, the mean and median of the concordant rates recapitulate the true molecular rate better than using a supermatrix approach. Using a large phylogenomic dataset, we examine rate heterogeneity across concordant genes with a focus on the branch subtending crown angiosperms. Notably, we find highly variable rates of evolution along the branch subtending crown angiosperms. The approaches outlined here have several limitations, but they also represent some alternative methods for harnessing the complexity of phylogenomic datasets and enrich our inferences of both species' relationships and evolutionary processes.

Blurring the Boundaries between a Branch and a Flower: Potential Developmental Venues in CACTACEAE

Flowers are defined as short shoots that carry reproductive organs. In Cactaceae, this term acquires another meaning, since the flower is interpreted as a branch with a perianth at the tip, with all reproductive organs embedded within the branch, thus giving way to a structure that has been called a "flower shoot". These organs have long attracted the attention of botanists and cactologists; however, the understanding of the morphogenetic processes during the development of these structures is far from clear. In this review, we present and discuss some classic flower concepts used to define floral structures in Cactaceae in the context of current advances in flower developmental genetics and evolution. Finally, we propose several hypotheses to explain the origin of these floral shoot structures in cacti, and we suggest future research approaches and methods that could be used to fill the gaps in our knowledge regarding the ontogenetic origin of the "flower" in the cactus family.

Evolution and ecology of seed internal morphology in relation to germination characteristics in Amaranthaceae

BACKGROUND AND AIMS

Internal seed morphological traits such as embryo characteristics and nutritive tissue can vary considerably within a plant lineage. These traits play a prominent role in germination processes and the success of seedling establishment, and are therefore under high selective pressure, especially in environments hostile to seedlings, such as arid, saline or highly dynamic habitats. We investigated the relationships of seed internal morphology and germination characteristics of 84 species of Amaranthaceae s.l., a family with numerous lineages that have adapted to stressful growing conditions.

METHODS

We used seed cross-sections to assess embryo type and the ratios of embryo to seed surface and radicle to cotyledon length. Furthermore, seed mass, mean time to germination, habitat preferences and further plant traits such as C3 or C4 photosynthesis and life form were compiled for each species. Data were analysed using phylogenetic comparative methods.

KEY RESULTS

We found embryo type (λ = 1), log seed mass (λ = 0.86) and the ratio of embryo to seed size (λ = 0.78) to be evolutionarily stable, with an annular embryo as ancestral in the family. Linked to shifts to the three derived embryos types (spiral, horseshoe-shaped and curved) is an increase in the ratio of root to cotyledon length and a reduction of nutritive tissue. We observed stabilizing selection towards seeds with relatively large embryos with longer radicles and less nutritive tissue that are able to germinate faster, especially in lineages with C4 photosynthesis and/or salt tolerance.

CONCLUSIONS

We conclude that the evolutionary shift of nutrient storage from perisperm to embryo provides an ecological advantage in extreme environments, because it enables faster germination and seedling establishment. Furthermore, the evolutionary shift towards a higher ratio of root to cotyledon length especially in small-seeded Amaranthaceae growing in saline habitats can provide an ecological advantage for fast seedling establishment.

Plastome analysis unveils Inverted Repeat (IR) expansion and positive selection in Sea Lavenders (Limonium, Plumbaginaceae, Limonioideae, Limonieae)

The genus Limonium, commonly known as Sea Lavenders, is one of the most species-rich genera of the family Plumbaginaceae. In this study, two new plastomes for the genus Limonium, viz. L. tetragonum and L. bicolor, were sequenced and compared to available Limonium plastomes, viz. L. aureum and L. tenellum, to understand the gene content and structural variations within the family. The loss of the rpl16 intron and pseudogenisation of rpl23 was observed. This study reports, for the first time, expansion of the IRs to include the ycf1 gene in Limonium plastomes, incongruent with previous studies. Two positively selected genes, viz. ndhF and ycf2, were identified. Furthermore, putative barcodes are proposed for the genus, based on the nucleotide diversity of four Limonium plastomes.

Secretory structures in plants: Lessons from the Plumbaginaceae on their origin, evolution and roles in stress tolerance

The Plumbaginaceae (non-core Caryophyllales) is a family well known for species adapted to a wide range of arid and saline habitats. Of its salt-tolerant species, at least 45 are in the genus Limonium; two in each of Aegialitis, Limoniastrum and Myriolimon, and one each in Psylliostachys, Armeria, Ceratostigma, Goniolimon and Plumbago. All the halophytic members of the family have salt glands and salt glands are also common in the closely related Tamaricaceae and Frankeniaceae. The halophytic species of the three families can secrete a range of ions (Na⁺ , K⁺ , Ca²⁺ , Mg²⁺ , Cl^- , HCO₃^- , SO₄^2- ) and other elements (As, Cd, Cr, Cu, Fe, Mn, Ni, Pb and Zn). Salt glands are, however, absent in salt-tolerant members of the sister family Polygonaceae. We describe the structure of the salt glands in the three families and consider whether glands might have arisen as a means to avoid the toxicity of Na⁺ and/or Cl^- or to regulate Ca²⁺ concentrations with the leaves. We conclude that the establishment of lineages with salt glands took place after the split between the Polygonaceae and its sister group the Plumbaginaceae.

A Review of C4 Plants in Southwest Asia: An Ecological, Geographical and Taxonomical Analysis of a Region With High Diversity of C4 Eudicots

Southwest Asia is climatically and topographically a highly diverse region in the xeric belt of the Old World. Its diversity of arid habitats and climatic conditions acted as an important area for the evolution and diversification of up to 20 (of 38 known) independent Eudicot C4 origins. Some of these lineages present unique evolutionary strategies like single-cell functioning C4 and C3-C4 switching mechanisms. The high diversity of C4 taxa in Southwest (SW) Asia is also related to the presence of seven phytogeographic zones including the Irano-Turanian region as a center of diversification of many Caryophyllales lineages and the Somali-Masai region (Southern Oman and Yemen) as a center of diversification for C4 Monocots. Nevertheless, the C4 flora of SW Asia has not received detailed attention. This paper presents a comprehensive review of all known C4 species in the area based on a literature survey, own floristic observations, as well as taxonomic, phylogenetic and herbarium data, and δ13C-isotope ratio analysis. The resulting checklist includes a total number of 923 (861 native, of which 141 endemic, and 62 introduced) C4 species, composed of 350 Eudicots and 509 Monocots, most of which are therophytic and hemicryptophytic xerophytes with pluriregional and Irano-Turanian distribution. Two hundred thirty-nine new δ13C-isotope ratios of C4 and C3 plants, as well as some taxonomic changes are presented. An analysis of the distribution of the three main C4 plant families (Chenopodiaceae, Poaceae, and Cyperaceae) in the region in relation to climatic variables indicates that the increase of C4 species follows more or less a latitudinal gradient similar to global patterns, while separate taxonomic groups seem to depend on specific factors as continentality (Chenopodiaceae), average annual temperature (Cyperaceae), and the presence of summer precipitation (Poaceae). An increase of C4 Eudicots in W-E direction even in similar longitudinal belts is explained by a combination of edaphic and climatic conditions. The provided data should encourage a deeper interest in the evolution of C4 lineages in SW Asia and their adaptation to ecological and climatical conditions and awaken interest in the importance of local C4 crops, the conservation of threatened C4 taxa, and awareness of human impacts on the rapid environmental changes in the region.

Evolution of l-DOPA 4,5-dioxygenase activity allows for recurrent specialisation to betalain pigmentation in Caryophyllales

The evolution of l-DOPA 4,5-dioxygenase activity, encoded by the gene DODA, was a key step in the origin of betalain biosynthesis in Caryophyllales. We previously proposed that l-DOPA 4,5-dioxygenase activity evolved via a single Caryophyllales-specific neofunctionalisation event within the DODA gene lineage. However, this neofunctionalisation event has not been confirmed and the DODA gene lineage exhibits numerous gene duplication events, whose evolutionary significance is unclear. To address this, we functionally characterised 23 distinct DODA proteins for l-DOPA 4,5-dioxygenase activity, from four betalain-pigmented and five anthocyanin-pigmented species, representing key evolutionary transitions across Caryophyllales. By mapping these functional data to an updated DODA phylogeny, we then explored the evolution of l-DOPA 4,5-dioxygenase activity. We find that low l-DOPA 4,5-dioxygenase activity is distributed across the DODA gene lineage. In this context, repeated gene duplication events within the DODA gene lineage give rise to polyphyletic occurrences of elevated l-DOPA 4,5-dioxygenase activity, accompanied by convergent shifts in key functional residues and distinct genomic patterns of micro-synteny. In the context of an updated organismal phylogeny and newly inferred pigment reconstructions, we argue that repeated convergent acquisition of elevated l-DOPA 4,5-dioxygenase activity is consistent with recurrent specialisation to betalain synthesis in Caryophyllales.

Exploration of Plastid Phylogenomic Conflict Yields New Insights into the Deep Relationships of Leguminosae

Phylogenomic analyses have helped resolve many recalcitrant relationships in the angiosperm tree of life, yet phylogenetic resolution of the backbone of the Leguminosae, one of the largest and most economically and ecologically important families, remains poor due to generally limited molecular data and incomplete taxon sampling of previous studies. Here, we resolve many of the Leguminosae's thorniest nodes through comprehensive analysis of plastome-scale data using multiple modified coding and noncoding data sets of 187 species representing almost all major clades of the family. Additionally, we thoroughly characterize conflicting phylogenomic signal across the plastome in light of the family's complex history of plastome evolution. Most analyses produced largely congruent topologies with strong statistical support and provided strong support for resolution of some long-controversial deep relationships among the early diverging lineages of the subfamilies Caesalpinioideae and Papilionoideae. The robust phylogenetic backbone reconstructed in this study establishes a framework for future studies on legume classification, evolution, and diversification. However, conflicting phylogenetic signal was detected and quantified at several key nodes that prevent the confident resolution of these nodes using plastome data alone. [Leguminosae; maximum likelihood; phylogenetic conflict; plastome; recalcitrant relationships; stochasticity; systematic error.].

Insights Into Chloroplast Genome Evolution Across Opuntioideae (Cactaceae) Reveals Robust Yet Sometimes Conflicting Phylogenetic Topologies

Chloroplast genomes (plastomes) are frequently treated as highly conserved among land plants. However, many lineages of vascular plants have experienced extensive structural rearrangements, including inversions and modifications to the size and content of genes. Cacti are one of these lineages, containing the smallest plastome known for an obligately photosynthetic angiosperm, including the loss of one copy of the inverted repeat (∼25 kb) and the ndh gene suite, but only a few cacti from the subfamily Cactoideae have been sufficiently characterized. Here, we investigated the variation of plastome sequences across the second-major lineage of the Cactaceae, the subfamily Opuntioideae, to address (1) how variable is the content and arrangement of chloroplast genome sequences across the subfamily, and (2) how phylogenetically informative are the plastome sequences for resolving major relationships among the clades of Opuntioideae. Our de novo assembly of the Opuntia quimilo plastome recovered an organelle of 150,347 bp in length with both copies of the inverted repeat and the presence of all the ndh gene suite. An expansion of the large single copy unit and a reduction of the small single copy unit was observed, including translocations and inversion of genes, as well as the putative pseudogenization of some loci. Comparative analyses among all clades within Opuntioideae suggested that plastome structure and content vary across taxa of this subfamily, with putative independent losses of the ndh gene suite and pseudogenization of genes across disparate lineages, further demonstrating the dynamic nature of plastomes in Cactaceae. Our plastome dataset was robust in resolving three tribes with high support within Opuntioideae: Cylindropuntieae, Tephrocacteae and Opuntieae. However, conflicting topologies were recovered among major clades when exploring different assemblies of markers. A plastome-wide survey for highly informative phylogenetic markers revealed previously unused regions for future use in Sanger-based studies, presenting a valuable dataset with primers designed for continued evolutionary studies across Cactaceae. These results bring new insights into the evolution of plastomes in cacti, suggesting that further analyses should be carried out to address how ecological drivers, physiological constraints and morphological traits of cacti may be related with the common rearrangements in plastomes that have been reported across the family.

Disentangling Sources of Gene Tree Discordance in Phylogenomic Data Sets: Testing Ancient Hybridizations in Amaranthaceae s.l

Gene tree discordance in large genomic data sets can be caused by evolutionary processes such as incomplete lineage sorting and hybridization, as well as model violation, and errors in data processing, orthology inference, and gene tree estimation. Species tree methods that identify and accommodate all sources of conflict are not available, but a combination of multiple approaches can help tease apart alternative sources of conflict. Here, using a phylotranscriptomic analysis in combination with reference genomes, we test a hypothesis of ancient hybridization events within the plant family Amaranthaceae s.l. that was previously supported by morphological, ecological, and Sanger-based molecular data. The data set included seven genomes and 88 transcriptomes, 17 generated for this study. We examined gene-tree discordance using coalescent-based species trees and network inference, gene tree discordance analyses, site pattern tests of introgression, topology tests, synteny analyses, and simulations. We found that a combination of processes might have generated the high levels of gene tree discordance in the backbone of Amaranthaceae s.l. Furthermore, we found evidence that three consecutive short internal branches produce anomalous trees contributing to the discordance. Overall, our results suggest that Amaranthaceae s.l. might be a product of an ancient and rapid lineage diversification, and remains, and probably will remain, unresolved. This work highlights the potential problems of identifiability associated with the sources of gene tree discordance including, in particular, phylogenetic network methods. Our results also demonstrate the importance of thoroughly testing for multiple sources of conflict in phylogenomic analyses, especially in the context of ancient, rapid radiations. We provide several recommendations for exploring conflicting signals in such situations. [Amaranthaceae; gene tree discordance; hybridization; incomplete lineage sorting; phylogenomics; species network; species tree; transcriptomics.]

Diversity, distribution, development, and evolution of medullary bundles in Nyctaginaceae

PREMISE

Medullary bundles, i.e., vascular units in the pith, have evolved multiple times in vascular plants. However, no study has ever explored their anatomical diversity and evolution within a phylogenetic framework. Here, we investigated the development of the primary vascular system within Nyctaginaceae showing how medullary bundles diversified within the family.

METHODS

Development of 62 species from 25 of the 31 genera of Nyctaginaceae in stem samples was thoroughly studied with light microscopy and micro-computed tomography. Ancestral states were reconstructed using a maximum likelihood approach.

RESULTS

Two subtypes of eusteles were found, the regular eustele, lacking medullary bundles, observed exclusively in representatives of Leucastereae, and the polycyclic eustele, containing medullary bundles, found in all the remaining taxa. Medullary bundles had the same origin and development, but the organization was variable and independent of phyllotaxy. Within the polycyclic eustele, medullary bundles developed first, followed by the formation of a continuous concentric procambium, which forms a ring of vascular bundles enclosing the initially formed medullary bundles. The regular eustele emerged as a synapomorphy of Leucastereae, while the medullary bundles were shown to be a symplesiomorphy for Nyctaginaceae.

CONCLUSIONS

Medullary bundles in Nyctaginaceae developed by a single shared pathway, that involved the departure of vascular traces from lateral organs toward the pith. These medullary bundles were encircled by a continuous concentric procambium that also constituted the polycyclic eustele, which was likely a symplesiomorphy for Nyctaginaceae with one single reversion to the regular eustele.

A consensus phylogenomic approach highlights paleopolyploid and rapid radiation in the history of Ericales

PREMISE

Large genomic data sets offer the promise of resolving historically recalcitrant species relationships. However, different methodologies can yield conflicting results, especially when clades have experienced ancient, rapid diversification. Here, we analyzed the ancient radiation of Ericales and explored sources of uncertainty related to species tree inference, conflicting gene tree signal, and the inferred placement of gene and genome duplications.

METHODS

We used a hierarchical clustering approach, with tree-based homology and orthology detection, to generate six filtered phylogenomic matrices consisting of data from 97 transcriptomes and genomes. Support for species relationships was inferred from multiple lines of evidence including shared gene duplications, gene tree conflict, gene-wise edge-based analyses, concatenation, and coalescent-based methods, and is summarized in a consensus framework.

RESULTS

Our consensus approach supported a topology largely concordant with previous studies, but suggests that the data are not capable of resolving several ancient relationships because of lack of informative characters, sensitivity to methodology, and extensive gene tree conflict correlated with paleopolyploidy. We found evidence of a whole-genome duplication before the radiation of all or most ericalean families, and demonstrate that tree topology and heterogeneous evolutionary rates affect the inferred placement of genome duplications.

CONCLUSIONS

We provide several hypotheses regarding the history of Ericales, and confidently resolve most nodes, but demonstrate that a series of ancient divergences are unresolvable with these data. Whether paleopolyploidy is a major source of the observed phylogenetic conflict warrants further investigation.

A Novel Divergent Geminivirus Identified in Asymptomatic New World Cactaceae Plants

Cactaceae comprise a diverse and iconic group of flowering plants which are almost exclusively indigenous to the New World. The wide variety of growth forms found amongst the cacti have led to the trafficking of many species throughout the world as ornamentals. Despite the evolution and physiological properties of these plants having been extensively studied, little research has focused on cactus-associated viral communities. While only single-stranded RNA viruses had ever been reported in cacti, here we report the discovery of cactus-infecting single-stranded DNA viruses. These viruses all apparently belong to a single divergent species of the family Geminiviridae and have been tentatively named Opuntia virus 1 (OpV1). A total of 79 apparently complete OpV1 genomes were recovered from 31 different cactus plants (belonging to 20 different cactus species from both the Cactoideae and Opuntioideae clades) and from nine cactus-feeding cochineal insects (Dactylopius sp.) sampled in the USA and Mexico. These 79 OpV1 genomes all share > 78.4% nucleotide identity with one another and < 64.9% identity with previously characterized geminiviruses. Collectively, the OpV1 genomes display evidence of frequent recombination, with some genomes displaying up to five recombinant regions. In one case, recombinant regions span ~40% of the genome. We demonstrate that an infectious clone of an OpV1 genome can replicate in Nicotiana benthamiana and Opuntia microdasys. In addition to expanding the inventory of viruses that are known to infect cacti, the OpV1 group is so distantly related to other known geminiviruses that it likely represents a new geminivirus genus. It remains to be determined whether, like its cactus hosts, its geographical distribution spans the globe.

Phylogenetic Relationships and Evolutionary Trends in the Cactus Family

Members of the cactus family are keystone species of arid and semiarid biomes in the Americas, as they provide shelter and resources to support other members of ecosystems. Extraordinary examples are the several species of flies of the genus Drosophila that lay eggs and feed in their rotting stems, which provide a model system for studying evolutionary processes. Although there is significant progress in understanding the evolution of Drosophila species, there are gaps in our knowledge about the cactus lineages hosting them. Here, we review the current knowledge about the evolution of Cactaceae, focusing on phylogenetic relationships and trends revealed by the study of DNA sequence data. During the last several decades, the availability of molecular phylogenies has considerably increased our understanding of the relationships, biogeography, and evolution of traits in the family. Remarkably, although succulent cacti have very low growth rates and long generation times, they underwent some of the fastest diversifications observed in the plant kingdom, possibly fostered by strong ecological interactions. We have a better understanding of the reproductive biology, population structure and speciation mechanisms in different clades. The recent publication of complete genomes for some species has revealed the importance of phenomena such as incomplete lineage sorting. Hybridization and polyploidization are common in the family, and have been studied using a variety of phylogenetic methods. We discuss potential future avenues for research in Cactaceae, emphasizing the need of a concerted effort among scientists in the Americas, together with the analyses of data from novel sequencing techniques.

Phylogenetic Conflicts, Combinability, and Deep Phylogenomics in Plants

Studies have demonstrated that pervasive gene tree conflict underlies several important phylogenetic relationships where different species tree methods produce conflicting results. Here, we present a means of dissecting the phylogenetic signal for alternative resolutions within a data set in order to resolve recalcitrant relationships and, importantly, identify what the data set is unable to resolve. These procedures extend upon methods for isolating conflict and concordance involving specific candidate relationships and can be used to identify systematic error and disambiguate sources of conflict among species tree inference methods. We demonstrate these on a large phylogenomic plant data set. Our results support the placement of Amborella as sister to the remaining extant angiosperms, Gnetales as sister to pines, and the monophyly of extant gymnosperms. Several other contentious relationships, including the resolution of relationships within the bryophytes and the eudicots, remain uncertain given the low number of supporting gene trees. To address whether concatenation of filtered genes amplified phylogenetic signal for relationships, we implemented a combinatorial heuristic to test combinability of genes. We found that nested conflicts limited the ability of data filtering methods to fully ameliorate conflicting signal amongst gene trees. These analyses confirmed that the underlying conflicting signal does not support broad concatenation of genes. Our approach provides a means of dissecting a specific data set to address deep phylogenetic relationships while also identifying the inferential boundaries of the data set. [Angiosperms; coalescent; gene-tree conflict; genomics; phylogenetics; phylogenomics.]

Phylogenomics in Cactaceae: A case study using the chollas sensu lato (Cylindropuntieae, Opuntioideae) reveals a common pattern out of the Chihuahuan and Sonoran deserts

PREMISE

Although numerous phylogenetic studies have been conducted in Cactaceae, whole-plastome datasets have not been employed. We used the chollas to develop a plastome dataset for phylogeny reconstruction to test species relationships, biogeography, clade age, and morphological evolution.

METHODS

We developed a plastome dataset for most known diploid members of the chollas (42 taxa) as well as for other members of Cylindropuntieae. Paired-end, raw reads from genome skimming were reference-mapped onto a de novo plastome assembly of one species of cholla, Cylindropuntia bigelovii, and were used to build our plastome dataset, which was analyzed using various methods.

RESULTS

Our plastome dataset resolved the phylogeny of the chollas, including most interspecific and intraspecific relationships. Tribe Cylindropuntieae arose ~18 mya, during the early Miocene in southern South America, and is supported as sister to the South American clade Tephrocacteae. The (Micropuntia (Cylindropuntia + Grusonia)) clade most likely originated in the Chihuahuan Desert region around 16 mya and then migrated into other North American desert regions. Key morphological characters for recognizing traditional taxonomic series in Cylindropuntia (e.g., spiny fruit) are mostly homoplasious.

CONCLUSIONS

This study provides the first comprehensive plastome phylogeny for any clade within Cactaceae. Although the chollas s.l. are widespread throughout western North American deserts, their most recent common ancestor likely arose in the Chihuahuan Desert region during the mid-Miocene, with much of their species diversity arising in the early to mid-Pliocene, a pattern strikingly similar to those found in other western North American desert groups.

Research Progress of Betalain in Response to Adverse Stresses and Evolutionary Relationship Compared with Anthocyanin

Betalains are applicable to many aspects of life, and their properties, characteristics, extraction and biosynthesis process have been thoroughly studied. Although betalains are functionally similar to anthocyanins and can substitute for them to provide pigments for plant color, it is rare to study the roles of betalains in plant responses to adverse environmental conditions. Owing to their antioxidant capability to remove excess reactive oxygen species (ROS) in plants and humans, betalains have attracted much attention due to their bioactivity. In addition, betalains can also act as osmotic substances to regulate osmotic pressure in plants and play important roles in plant responses to adverse environmental conditions. The study of the physiological evolution of betalains is almost complete but remains complicated because the evolutionary relationship between betalains and anthocyanins is still uncertain. In this review, to provide a reference for the in-depth study of betalains compared with anthocyanins, the biochemical properties, biosynthesis process and roles of betalains in response to environmental stress are reviewed, and the relationship between betalains and anthocyanins is discussed.

A Universal Probe Set for Targeted Sequencing of 353 Nuclear Genes from Any Flowering Plant Designed Using k-Medoids Clustering

Sequencing of target-enriched libraries is an efficient and cost-effective method for obtaining DNA sequence data from hundreds of nuclear loci for phylogeny reconstruction. Much of the cost of developing targeted sequencing approaches is associated with the generation of preliminary data needed for the identification of orthologous loci for probe design. In plants, identifying orthologous loci has proven difficult due to a large number of whole-genome duplication events, especially in the angiosperms (flowering plants). We used multiple sequence alignments from over 600 angiosperms for 353 putatively single-copy protein-coding genes identified by the One Thousand Plant Transcriptomes Initiative to design a set of targeted sequencing probes for phylogenetic studies of any angiosperm group. To maximize the phylogenetic potential of the probes, while minimizing the cost of production, we introduce a k-medoids clustering approach to identify the minimum number of sequences necessary to represent each coding sequence in the final probe set. Using this method, 5-15 representative sequences were selected per orthologous locus, representing the sequence diversity of angiosperms more efficiently than if probes were designed using available sequenced genomes alone. To test our approximately 80,000 probes, we hybridized libraries from 42 species spanning all higher-order groups of angiosperms, with a focus on taxa not present in the sequence alignments used to design the probes. Out of a possible 353 coding sequences, we recovered an average of 283 per species and at least 100 in all species. Differences among taxa in sequence recovery could not be explained by relatedness to the representative taxa selected for probe design, suggesting that there is no phylogenetic bias in the probe set. Our probe set, which targeted 260 kbp of coding sequence, achieved a median recovery of 137 kbp per taxon in coding regions, a maximum recovery of 250 kbp, and an additional median of 212 kbp per taxon in flanking non-coding regions across all species. These results suggest that the Angiosperms353 probe set described here is effective for any group of flowering plants and would be useful for phylogenetic studies from the species level to higher-order groups, including the entire angiosperm clade itself.

Evolution of Portulacineae Marked by Gene Tree Conflict and Gene Family Expansion Associated with Adaptation to Harsh Environments

Several plant lineages have evolved adaptations that allow survival in extreme and harsh environments including many families within the plant clade Portulacineae (Caryophyllales) such as the Cactaceae, Didiereaceae, and Montiaceae. Here, using newly generated transcriptomic data, we reconstructed the phylogeny of Portulacineae and examined potential correlates between molecular evolution and adaptation to harsh environments. Our phylogenetic results were largely congruent with previous analyses, but we identified several early diverging nodes characterized by extensive gene tree conflict. For particularly contentious nodes, we present detailed information about the phylogenetic signal for alternative relationships. We also analyzed the frequency of gene duplications, confirmed previously identified whole genome duplications (WGD), and proposed a previously unidentified WGD event within the Didiereaceae. We found that the WGD events were typically associated with shifts in climatic niche but did not find a direct association with WGDs and diversification rate shifts. Diversification shifts occurred within the Portulacaceae, Cactaceae, and Anacampserotaceae, and whereas these did not experience WGDs, the Cactaceae experienced extensive gene duplications. We examined gene family expansion and molecular evolutionary patterns with a focus on genes associated with environmental stress responses and found evidence for significant gene family expansion in genes with stress adaptation and clades found in extreme environments. These results provide important directions for further and deeper examination of the potential links between molecular evolutionary patterns and adaptation to harsh environments.

Biogeography of the xerophytic genus Anabasis L. (Chenopodiaceae)

AIM

Using the extremophile genus Anabasis, which includes c. 28 succulent, xerophytic C4 species, and is widely distributed in arid regions of Northern Africa, Arabia, and Asia, we investigate biogeographical relationships between the Irano-Turanian floristic region (ITfr) and its neighboring regions. We test whether the spread of arid and semi-arid biomes in Eurasia coincides with the biogeography of this drought-adapted genus, and whether the ITfr acted as source area of floristic elements for adjacent regions.

LOCATION

Deserts and semi-deserts of Northern Africa, Mediterranean, Arabia, West and Central Asia.

METHODS

Four cpDNA markers (rpL16 intron, atpB-rbcL, trnQ-rps16, and ndhF-rpL32 spacers) were sequenced for 58 accessions representing 21 Anabasis species. Phylogenetic relationships and divergence times were inferred using maximum likelihood and a time-calibrated Bayesian approach. To document the extant distribution of Anabasis, material from 23 herbaria was surveyed resulting in 441 well-documented collections used for the coding of eight floristic regions. Using this coded data, ancestral range was estimated using "BioGeoBEARS" under the DEC model.

RESULTS

Anabasis originated during the Late Miocene and the ancestral range was probably widespread and disjunct between Western Mediterranean and the Irano-Turanian regions. Diversification started with two divergence events at the Miocene/Pliocene boundary (5.1 and 4.5 mya) leading to Asian clade I with ITfr origin which is sister to a slightly younger Asian clade II, which originated in the Western ITfr, and a Mediterranean/North African clade with an origin in the Western Mediterranean.

MAIN CONCLUSIONS

Anabasis did not follow aridification and continuously expanded its distribution area, in fact its probably wide ancestral distribution area seems to have been fragmented during the very Late Miocene and the remnant lineages then expanded into neighboring arid regions. This genus supports the role of the ITfr as source area for xerophytic elements in the Mediterranean and Central Asia.

A roadmap for global synthesis of the plant tree of life

Providing science and society with an integrated, up-to-date, high quality, open, reproducible and sustainable plant tree of life would be a huge service that is now coming within reach. However, synthesizing the growing body of DNA sequence data in the public domain and disseminating the trees to a diverse audience are often not straightforward due to numerous informatics barriers. While big synthetic plant phylogenies are being built, they remain static and become quickly outdated as new data are published and tree-building methods improve. Moreover, the body of existing phylogenetic evidence is hard to navigate and access for non-experts. We propose that our community of botanists, tree builders, and informaticians should converge on a modular framework for data integration and phylogenetic analysis, allowing easy collaboration, updating, data sourcing and flexible analyses. With support from major institutions, this pipeline should be re-run at regular intervals, storing trees and their metadata long-term. Providing the trees to a diverse global audience through user-friendly front ends and application development interfaces should also be a priority. Interactive interfaces could be used to solicit user feedback and thus improve data quality and to coordinate the generation of new data. We conclude by outlining a number of steps that we suggest the scientific community should take to achieve global phylogenetic synthesis.