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Based on observations of living plants of in the field, together with examination of herbarium specimens and descriptions of both and (including type material), we demonstrated that is a synonym of . The species was previously compared with ; our phylogenetic analysis revealed that and belong to different lineages, the former being closely related to the larger-leaved clade.

Celery (Apium graveolens L. 2n = 2x = 22), a member of the Apiaceae family, is among the most important and globally grown vegetables. Here, we report a high-quality genome sequence assembly, anchored to 11 chromosomes, with total length of 3.33 Gb and N50 scaffold length of 289.78 Mb. Most (92.91%) of the genome is composed of repetitive sequences, with 62.12% of 31 326 annotated genes confined to the terminal 20% of chromosomes. Simultaneous bursts of shared long-terminal repeats (LTRs) in different Apiaceae plants suggest inter-specific exchanges. Two ancestral polyploidizations were inferred, one shared by Apiales taxa and the other confined to Apiaceae. We reconstructed 8 Apiales proto-chromosomes, inferring their evolutionary trajectories from the eudicot common ancestor to extant plants. Transcriptome sequencing in three tissues (roots, leaves and petioles), and varieties with different-coloured petioles, revealed 4 and 2 key genes in pathways regulating anthocyanin and coumarin biosynthesis, respectively. A remarkable paucity of NBS disease-resistant genes in celery (62) and other Apiales was explained by extensive loss and limited production of these genes during the last ~10 million years, raising questions about their biotic defence mechanisms and motivating research into effects of chemicals, for example coumarins, that give off distinctive odours. Celery genome sequencing and annotation facilitates further research into important gene functions and breeding, and comparative genomic analyses in Apiales.

Two new species of (Apiaceae), and , from Gangwon Province, South Korea, are described. Both species are most similar to and because of their linear ultimate leaf segments. was found on crevices of rocks in mountain summits and can be distinguished by its pubescent ovary, purple anthers, oblong schizocarp, and 1 or (2) vittae per vallecula and 4 on the commissural face. was found in open areas on rocky cliffs along the Donggang River and can be distinguished by its glabrous ovary, whitish-yellow anthers, narrowly ellipsoid schizocarp, and 3 vittae per vallecula and 4 on the commissural face. Distinguishing characteristics, full descriptions, illustrations, photographs, taxonomic notes on geographical distribution, ecology, and phenology of the two species are presented. An identification key for all Korean species of is also provided. In addition, the mericarp surface of two new species and their close relatives are compared using micromorphological analysis.

The WRKY transcription factors family, which participates in many physiological processes in plants, constitutes one of the largest transcription factor families. The Asterales and the Apiales are two orders of flowering plants in the superorder Asteranae. Among the members of the Asterales, globe artichoke (Cynara cardunculus var. scolymus L.), sunflower (Helianthus annuus L.), and lettuce (Lactuca sativa L.) are important economic crops worldwide. Within the Apiales, ginseng (Panax ginseng C. A. Meyer) and Panax notoginseng (Burk.) F.H. Chen are important medicinal plants, while carrot (Daucus carota subsp. carota L.) has significant economic value. Research involving genome-wide identification of WRKY transcription factors in the Asterales and the Apiales has been limited. In this study, 490 WRKY genes, 244 from three species of the Apiales and 246 from three species of the Asterales, were identified and categorized into three groups. Within each group, WRKY motif characteristics and gene structures were similar. WRKY gene promoter sequences contained light responsive elements, core regulatory elements, and 12 abiotic stress cis-acting elements. WRKY genes were evenly distributed on each chromosome. Evidence of segmental and tandem duplication events was found in all six species in the Asterales and the Apiales, with segmental duplication inferred to play a major role in WRKY gene evolution. Among the six species, we uncovered 54 syntenic gene pairs between globe artichoke and lettuce. The six species are thus relatively closely related, consistent with their traditional taxonomic placement in the Asterales. This study, based on traditional species classifications, was the first to identify WRKY transcription factors in six species from the Asteranae. Our results lay a foundation for further understanding of the role of WRKY transcription factors in species evolution and functional differentiation.

Main conclusionMembers of Apiales are monophyletic and radiated in the Late Cretaceous. Fruit morphologies are critical for Apiales evolution and negative selection and mutation pressure play important roles in environmental adaptation.Apiales include many foods, spices, medicinal, and ornamental plants, but the phylogenetic relationships, origin and divergence, and adaptive evolution remain poorly understood. Here, we reconstructed Apiales phylogeny based on 72 plastid genes from 280 species plastid genomes representing six of seven families of this order. Highly supported phylogenetic relationships were detected, which revealed that each family of Apiales is monophyletic and confirmed that Pennanticeae is a member of Apiales. Genera Centella and Dickinsia are members of Apiaceae, and the genus Hydrocotyle previously classified into Apiaceae is confirmed to belong to Araliaceae. Besides, coalescent phylogenetic analysis and gene trees cluster revealed ten genes that can be used for distinguishing species among families of Apiales. Molecular dating suggested that the Apiales originated during the mid-Cretaceous (109.51 Ma), with the families’ radiation occurring in the Late Cretaceous. Apiaceae species exhibit higher differentiation compared to other families. Ancestral trait reconstruction suggested that fruit morphological evolution may be related to shifts in plant types (herbaceous or woody), which in turn is related to the distribution areas and species numbers. Codon bias and positive selection analyses suggest that negative selection and mutation pressure may play important roles in environmental adaptation of Apiales members. Our results improve the phylogenetic framework of Apiales and provide insights into the origin, divergence, and adaptive evolution of this order and its members.

Two new species of Dendropanax (Araliaceae) endemic to Costa Rica are described. Dendropanax aberrans J.F. Morales resembles D. grandiflorus but differs by the inflorescence structure (panicle of umbels vs. single umbel), and the smaller sizes of both the hypanthium and the petals. Dendropanax zarratu J.F. Morales is unique among Central America and West Indian taxa. It is recognized by its panicle of umbels, with the peduncles agglomerate, flowers 8-9-merous, hypanthium 7-8 mm long, and fruits 1.2-1.4 cm long. Illustrations of the new species and a key to the four Dendropanax having elongated hypanthia (≥ 4 mm long) in Mexico, Central America, the West Indies, and Colombia are provided. Se describen dos nuevas especies de Dendropanax (Araliaceae) endémicas de Costa Rica. Dendropanax aberrans J.F. Morales se parece a D. grandiflorus pero difiere por la estructura de la inflorescencia (panícula de umbelas vs. umbela simple), hipantio y pétalos más pequeños. Dendropanax zarratu J.F. Morales se reconoce por sus panículas de umbelas, con los pedúnculos aglomerados, flores 8-9-meras, hipantio 7-8 mm de largo y frutos de 1,2-1,4 cm de largo. Se proveen ilustraciones y una clave parta las cuatro especies de Dendropanax con hipantio elongado (≥ 4 mm long) en México, Centro América, el Caribe y Colombia.

Background The genus Hydrocotyle Tourn. ex L. is a key group for further study on the evolution of Apiales, comprising around 170 species globally. Previous studies mainly focused on separate sections and provided much information about this genus, but its infrageneric relationships are still confusing. In addition, the genetic basis of its adaptive evolution remains poorly understood. To investigate the phylogeny and evolution of the genus, we selected ten representative species covering two of three diversity distribution centers and exhibiting rich morphology diversity. Comparative plastome analysis was conducted to clarify the structural character of Hydrocotyle plastomes. Positive selection analyses were implemented to assess the evolution of the genus. Phylogenetic inferences with protein-coding sequences (CDS) of Hydrocotyle and 17 related species were also performed. Results Plastomes within Hydrocotyle were generally conservative in structure, gene order, and size. A total of 14 regions ( rps16-trnK , trnQ-rps16 , atpI-atpH , trnC-petN-psbM , ycf3-trnS , accD-psaI-ycf4 , petA-psbJ , rps12-rpl20 , rpl16 intron, rps3-rpl16 intron, rps9-rpl22 , ndhF-rpl32 , ndhA intron, and ycf1a) were recognized as hotspot regions within the genus, which suggested to be promising DNA barcodes for global phylogenetic analysis of Hydrocotyle . The ycf15 gene was suggested to be a protein-coding gene for Hydrocotyle species, and it could be used as a DNA barcode to identify Hydrocotyle . In phylogenetic analysis, three monophyletic clades (Clade I, II, III) were identified with evidence of rapid radiation speciation within Clade I. The selective pressure analysis detected that six CDS genes ( ycf1b , matK , atpF , accD , rps14 , and psbB ) of Hydrocotyle species were under positive selection. Within the genus, the last four genes were conservative, suggesting a relation to the unique evolution of the genus in Apiales. Seven genes ( atpE , matK , psbH , ycf1a , ycf1b , rpoA , and ycf2 ) were detected to be under some degree of positive selection in different taxa within the genus Hydrocotyle , indicating their role in the adaptive evolution of species. Conclusions Our study offers new insights into the phylogeny and adaptive evolution of Hydrocotyle . The plastome sequences could significantly enhance phylogenetic resolution and provide genomic resources and potential DNA markers useful for future studies of the genus.

Background HOPZ-ACTIVATED RESISTANCE 1 (ZAR1) is a nucleotide-binding leucine-rich repeat (NLR) protein functioning as a recognition hub to initiate effector-triggered immunity against bacterial pathogens. To initiate defense, ZAR1 associates with different HOPZ-ETI-DEFICIENT 1 (ZED1)-Related Kinases (ZRKs) to form resistosomes to indirectly perceive effector-induced perturbations. Few studies have focused on the phylogenomic characteristics of ZAR1 and ZRK immune gene families and their evolutionary relationships. To trace the origin and divergence of ZAR1 and ZRK immune gene families across the plant kingdom, we performed phylogenomic analyses using an extended set of plant genomes. Results Genome-wide identification of ZAR1 and ZRK immune gene families by blast similarity searches combined with phylogenetic analysis showed that these two gene families have experienced frequent gene losses in massive lineages. Gene distribution patterns across the plant kingdom revealed that ZAR1 and ZRK emerged after the divergence of most angiosperms from Amborella and before the split of magnoliids, monocots, and eudicots. Co-occurrence of ZAR1-A and ZRKs was found in various plant species belonging to different angiosperm orders, but both genes were found to be absent in chlorophyta, bryophytes, lycophytes, ferns, and gymnosperms. We also detected a large number of concerted gene losses in angiosperms, especially within the orders Fabales, Cucurbitales, Asterales, and Apiales. All analysed monocot genomes thus far examined, except for the aroid Colocasia esculenta , were previously reported to lack both ZAR1-A and ZRKs. Here we now report other exceptions on the concerted ZAR1-A – ZRKs presence-absence pattern within several early diverging monocot lineages, including the genome of Acorus tatarinowii —a species representing the first branching monocot lineage. We also revealed strong variation in ZAR1-A – ZRKs co-occurrence within the asterid order Ericales, suggesting patterns of de-coevolution in angiosperms. Our research further shows that both gene families experienced significant diversification through various duplication events. Additionally, their evolutionary paths have been shaped by frequent gene losses and lineage-specific transposition. Conclusion This study provides novel findings on the evolution of ZAR1 and ZRK immune gene families across a wide range of plant species, suggesting that more potential exceptions can be expected when expanding the list of sequenced genomes from distinct orders. Our results provide new hypotheses about the origin and diversification of these critical immune genes for future functional studies.

Premise of research. Permineralized fruits of Pantocarpon Kapgate, Patil, Ilamkar & Ramteke have been reinvestigated to better understand this abundant component of the Deccan Maastrichtian–Paleocene flora of central India. Methodology. Peels and X-ray microcomputed tomography (μ-CT) were used to compare the morphology and anatomy of the silicified fruits with that of possible extant relatives. Pivotal results. We show, for the first time, the surface morphology of these fruits, which are encased within opaque chert, and clarify additional characters of morphology and anatomy. By varying the orientation of digital sectioning planes through the fruit using μ-CT data, we show that five different generic names (Pantocarpon and the junior synonyms Bicarpelarocarpon, Plectroniocarpon, Loganiocarpon, and Verbenaceocarpon) were previously applied to the same entity, each based on holotypes studied in different physical planes of section. Several distinctive characters, including tricarpellate syncarpous fruits, paired apical apertures, empty sterile locules, single-seeded fertile locules, and longitudinal germination valves, are shared with the extant eudicot family, Torricelliaceae (Apiales). The pair of endocarp apertures resembles that in Aralidium and Torricellia. There are some obvious differences, however, from fruits of the three living genera. In Torricellia, Melanophylla, and Aralidium, there are two sterile locules (lateral) and a single fertile one (median), whereas in Pantocarpon, there are two fertile locules (lateral) and a single sterile one (median). Conclusions. Recognition of Pantocarpon as a potential member of Torricelliaceae is interesting because it would be the most ancient record known for the family (next youngest being middle Eocene, ca. 47 Ma) and provides additional biogeographic information. The occurrence of this taxon in India at about 66 Ma, when the subcontinent was still isolated from other major landmasses, indicates that this region may have played a role in early evolution of the family, which is now disjunct between Madagascar, China, and Malesia.

Background Carrot ( Daucus carota subsp. carota L.) is an important root crop with an available high-quality genome. The carrot genome is thought to have undergone recursive paleo-polyploidization, but the extent, occurrences, and nature of these events are not clearly defined. Results Using a previously published comparative genomics pipeline, we reanalysed the carrot genome and characterized genomic fractionation, as well as gene loss and retention, after each of the two tetraploidization events and inferred a dominant and sensitive subgenome for each event. In particular, we found strong evidence of two sequential tetraploidization events, with one (Dc-α) approximately 46–52 million years ago (Mya) and the other (Dc-β) approximately 77–87 Mya, both likely allotetraploidization in nature. The Dc-β event was likely common to all Apiales plants, occurring around the divergence of Apiales-Bruniales and after the divergence of Apiales-Asterales, likely playing an important role in the derivation and divergence of Apiales species. Furthermore, we found that rounds of polyploidy events contributed to the expansion of gene families responsible for plastidial methylerythritol phosphate (MEP), the precursor of carotenoid accumulation, and shaped underlying regulatory pathways. The alignment of orthologous and paralogous genes related to different events of polyploidization and speciation constitutes a comparative genomics platform for studying Apiales, Asterales, and many other related species. Conclusions Hierarchical inference of homology revealed two tetraploidization events that shaped the carrot genome, which likely contributed to the successful establishment of Apiales plants and the expansion of MEP, upstream of the carotenoid accumulation pathway.