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Aristolochia , a genus in the magnoliid order Piperales, has been famous for centuries for its highly specialized flowers and wide medicinal applications. Here, we present a new, high-quality genome sequence of Aristolochia fimbriata , a species that, similar to Amborella trichopoda , lacks further whole-genome duplications since the origin of extant angiosperms. As such, the A. fimbriata genome is an excellent reference for inferences of angiosperm genome evolution, enabling detection of two novel whole-genome duplications in Piperales and dating of previously reported whole-genome duplications in other magnoliids. Genomic comparisons between A. fimbriata and other angiosperms facilitated the identification of ancient genomic rearrangements suggesting the placement of magnoliids as sister to monocots, whereas phylogenetic inferences based on sequence data we compiled yielded ambiguous relationships. By identifying associated homologues and investigating their evolutionary histories and expression patterns, we revealed highly conserved floral developmental genes and their distinct downstream regulatory network that may contribute to the complex flower morphology in A. fimbriata . Finally, we elucidated the genetic basis underlying the biosynthesis of terpenoids and aristolochic acids in A. fimbriata . A high-quality genome of Aristolochia fimbriata illuminates its unique history of whole-genome duplication similar to Amborella , the genomic basis of its complex flower morphology and chemical biosynthesis, and the phylogenetic placement of magnoliids.

Phylogenetic relationships within the magnoliid order Piperales have been studied extensively, yet the relationships of the monotypic family Lactoridaceae and the holoparasitic Hydnoraceae to the remainder of the order remain a matter of debate. Since the first confident molecular phylogenetic placement of Hydnoraceae among Piperales, different studies have recovered various contradictory topologies. Most phylogenetic hypotheses were inferred using only a few loci and have had incomplete taxon sampling at the genus level. Based on these results and an online survey of taxonomic opinion, the Angiosperm Phylogeny Group lumped both Hydnoraceae and Lactoridaceae in Aristolochiaceae; however, the latter family continues to have unclear relationships to the aforementioned taxa. Here we present extensive phylogenomic tree reconstructions based on up to 137 loci from all three subcellular genomes for all genera of Piperales. We infer relationships based on a variety of phylogenetic methods, explore instances of phylogenomic discordance between the subcellular genomes, and test alternative topologies. Consistent with these phylogenomic results and a consideration of the principles of phylogenetic classification, we propose to exclude Hydnoraceae and Lactoridaceae from the broad circumscription of Aristolochiaceae, and instead favor recognition of four monophyletic and morphologically well circumscribed families in the perianth-bearing Piperales: Aristolochiaceae, Asaraceae, Hydnoraceae, and Lactoridaceae, with a total of six families in the order.

The pollen and orbicule morphology of the Korean Piperales ( Aristolochia , Asarum , Houttuynia , Piper , and Saururus ) were investigated via scanning electron microscopy. Piperales pollen is a monad, its size ranging from very small to large ( P  = 7.78–51.4 μm, E  = 6.68–43.1 μm), and having a mainly circular to sub-circular shape. The aperture type is constant in the genus [inaperturate ( Aristolochia ), tri to pentaporate ( Asarum ), and monosulcate ( Houttuynia , Piper , and Saururus )]. There are four distinct types of exine ornamentation: Fossulate with perforate, microreticulate with gemmae, microperforate with granula, and microechinate. The orbicules (minute sporopollenin granules) were observed in all studied taxa and thus, may be a possible symplesiomorphic characteristic of Piperales. Further, the observed orbicule surface ornamentation was similar to pollen exine patterns, for example muri, gemmae, or granula. This resemblance between orbicule and pollen exine ornamentation may imply a similar biosynthesis pattern of sporopollenin of pollen exine and orbicules. The phenogram resulting from a cluster analysis using palynological characters was generally consistent with the known molecular phylogeny of Piperales. This initial study will help understand the palynological diversity and provide detailed information of pollen and orbicule characteristics in Piperales.

Premise of research. Discoveries of fossil flowers in Cretaceous rocks offer improved evidence for relationships with living clades, but for more secure inferences formal phylogenetic analyses are desirable. We extend previous analyses of magnoliids, monocots, and basal eudicots to Aptian, Albian, and Cenomanian fossils related to the basal “ANITA” lines and Chloranthaceae. Methodology. We performed parsimony analyses of a morphological data set of Recent angiosperms and published fossils, with the arrangement of Recent taxa constrained to backbone trees based primarily on molecular data. Pivotal results. Not onlyMonetianthus(as previously inferred) but alsoCarpestellais nested within Nymphaeaceae, whilePluricarpellatiamay be a stem relative of Cabombaceae or Nymphaeaceae.Anacostia(withSimilipollispollen) is nested within Austrobaileyales. The position ofCouperites(withClavatipollenitespollen) is ambiguous: it may be on the stem lineage of Chloranthaceae (andCeratophyllum, if this extant aquatic is related to Chloranthaceae), nested in Chloranthaceae, or more basal. Plants withAsteropollispollen and reduced tepals are related to the chloranthaceous genusHedyosmum.Zlatkocarpus, which also has a reduced perianth, may be either a stem relative or a crown group member of Chloranthaceae. Plants that produced loosely reticulatePennipollispollen are more likely related to Chloranthaceae and/orCeratophyllumthan to monocots. We confirm thatCanrightia, with bisexual flowers and a reduced perianth, is a stem relative of Chloranthaceae. Despite similarities to Piperales,Appomattoxia(withTucanopollispollen) is more likely near the base of the ANITA grade or related to Chloranthaceae and/orCeratophyllum. Conclusions. The Cretaceous rise of angiosperms involved the radiation not only of magnoliids, eudicots, and monocots but also of basal ANITA lines, including both aquatic Nymphaeales and woody groups. Our results reaffirm the early diversity of Chloranthaceae and clarify their floral evolution, in which a shift to unisexual flowers preceded loss of the perianth.

Background Saururaceae are an ancient family within Piperales, comprising seven perennial herbs grouped into four relict genera: Anemopsis , Gymnotheca , Houttuynia , and Saururus ; distributed primarily in East Asia ( Gymnotheca , Houttuynia , and S. chinensis ) and North America ( Anemopsis and S. cernuus ). Despite the limited number of species, phylogenetic relationships remain inconsistent across non-molecular data, nuclear genes, and chloroplast genes. Results Here, we report for the first time the plastid genomes of G. involucrata and H. emeiensis and provide an additional plastid genome of S. chinensis, enabling a comprehensive analysis of the plastid genome evolution in Saururaceae. All seven plastomes exhibit the typical Quadripartite structure, ranging from 160,226 to 161,556 bp, and contain 131 genes. (114 unique), including 85 protein-coding genes (80 unique), 37 transfer RNAs (tRNAs), eight ribosomal RNAs (rRNAs), and one pseudogene ( ycf1 ). The plastomes are highly conserved in gene order, repeat composition, and codon usage patterns, particularly between H. cordata and H. emeiensis . Mutation hotspots were identified in both coding regions ( ycf1 , ndhD , ndhF , ccsA , matK ; Pi > 0.03) and non-coding regions ( rpl32_trnL , rps16_trnQ , ccsA_ndhD , psbM_trnD , psbZ_trnG , ndhE_ndhG , rps15_ycf1 , and petA_psbJ ; Pi > 0.06), and may serve as molecular markers for species delimitation and population-level studies. Phylogenetic analysis results based on whole plastomes, coding sequences (CDS), and intergenic spacers (IGS) resolve two major clades that correspond to the presence or absence of a flower bract stalk: Anemopsis – Houttuynia (lacking a bract stalk) and Gymnotheca – Saururus (with a bract stalk). Conclusion This study presents the plastid genomes of G. involucrata and H. emeiensis , revealing structural variations in the plastid genomes of Saururaceae and their implications for internal phylogeny. The findings presented herein provide a novel perspective on the adaptive evolution of Saururaceae, thus offering valuable data for a more in-depth exploration of the phylogeny of Piperales within Magnoliids.

Controlled spatiotemporal cell division and expansion are responsible for floral bilateral symmetry. Genetic studies have pointed to class II TCP genes as major regulators of cell division and floral patterning in model core eudicots. Here we study their evolution in perianth-bearing Piperales and their expression in Aristolochia, a rare occurrence of bilateral perianth outside eudicots and monocots. The evolution of class II TCP genes reveals single-copy CYCLOIDEA-like genes and three paralogs of CINCINNATA (CIN) in early diverging angiosperms. All class II TCP genes have independently duplicated in Aristolochia subgenus Siphisia. Also CIN2 genes duplicated before the diversification of Saruma and Asarum. Sequence analysis shows that CIN1 and CIN3 share motifs with Cyclin proteins and CIN2 genes have lost the miRNA319a binding site. Expression analyses of all paralogs of class II TCP genes in Aristolochia fimbriata point to a role of CYC and CIN genes in maintaining differential perianth expansion during mid- and late flower developmental stages by promoting cell division in the distal and ventral portion of the limb. It is likely that class II TCP genes also contribute to cell division in the leaf, the gynoecium and the ovules in A. fimbriata.

Extreme haustorial parasites have long captured the interest of naturalists and scientists with their greatly reduced and highly specialized morphology. Along with the reduction or loss of photosynthesis, the plastid genome often decays as photosynthetic genes are released from selective constraint. This makes it challenging to use traditional plastid genes for parasitic plant phylogenetics, and has driven the search for alternative phylogenetic and molecular evolutionary markers. Thus, evolutionary studies, such as molecular clock-based age estimates, are not yet available for all parasitic lineages. In the present study, we extracted 14 nuclear single copy genes (nSCG) from Illumina transcriptome data from one of the \"strangest plants in the world\", Hydnora visseri (Hydnoraceae). A ~15,000 character molecular dataset, based on all three genomic compartments, shows the utility of nSCG for reconstructing phylogenetic relationships in parasitic lineages. A relaxed molecular clock approach with the same multi-locus dataset, revealed an ancient age of ~91 MYA for Hydnoraceae. We then estimated the stem ages of all independently originated parasitic angiosperm lineages using a published dataset, which also revealed a Cretaceous origin for Balanophoraceae, Cynomoriaceae and Apodanthaceae. With the exception of Santalales, older parasite lineages tend to be more specialized with respect to trophic level and have lower species diversity. We thus propose the \"temporal specialization hypothesis\" (TSH) implementing multiple independent specialization processes over time during parasitic angiosperm evolution.

The classification of species-rich genera is one of the most challenging tasks in systematics. In this paper we present an updated infrageneric classification of the genus Peperomia (Piperaceae), one of the most species-rich genera of plants. The classification is based on a molecular phylogeny of 190 accessions and the placement of 1340 of the 1606 currently accepted taxa within this classification. We provide the most comprehensive circumscriptions of Peperomia subgenera since the work of Dahlstedt in 1900, with five newly described subgenera. Fourteen monophyletic groups were revealed by phylogenetic reconstructions, including two newly discovered clades. Extensive field work, monitoring of representative living collections in our botanical gardens, and herbarium studies were the basis for morphological assignment of 80% of Peperomia species to the subgenera recognized and described herein. This work, in combination with the detailed descriptions of these subgenera, will aid field botanists, taxonomists, and ecologists to properly collect and identify species. Although parallel evolution of characters makes identification of species within Peperomia difficult, especially in species-rich clades, the key to subgenera will provide a useful framework for anyone interested in this genus and will be a reference for further studies in Peperomia.

Aristolochia bahiensis F. González and Aristolochia hypoglauca Kuhlm. are reported as new records to the flora of Rio de Janeiro state, Brazil, and additionally we provide a discussion about morphological differences between Aristolochia tamnifolia (Klotzsch) Duch. and A. bahiensis. We present photographs, a geographic distribution map, and morphological observations for these three species. Aristolochia bahiensis F. González, Aristolochia hypoglauca Kuhlm. são reportadas como novas ocorrências para o estado do Rio de Janeiro, Brasil e são discutidas diferenças morfológicas de Aristolochia tamnifolia (Klotzsch) Duch. e A. bahiensis. São fornecidas fotografias, distribuição geográfica e comentários morfológicos para as três espécies.

Piper motuoense X.W.Qin, F.Su & C.Y.Hao, a new species of Piperaceae from Xizang, China, is described and illustrated in this paper. The new species resembles P. yinkiangense and P. anisotis , but it can be readily distinguished from the compared species by several characteristics. Gonophyll leaves are chartaceous and the leaf secondary vein count is 7–9, with the outermost pair being very weak when there are nine veins. Additionally, the apical pair arises 2–4 cm above the base and the leaf base is asymmetrical, with bilateral petioles that cling and heal together. Pistillate floral bracts are sessile, with 3, 4 or 5 stigmas. The description of the new species includes photographs, detailed descriptions, notes on etymology, distribution and habitat, as well as comparisons with morphologically similar species.