Tatiana Arias

Well-resolved phylogenetic relationships within the diverse Neotropical orchid genus Lepanthes are presented based on a genome skimming approach that yielded nine newly sequenced chloroplast genomes. We complemented this with 17–86 plastome coding genes for 26 species retrieved from GenBank, alongside amplified matK and rITS regions. The Lepanthes plastomes (157,185—158,260 bp, 37.15% GC content) contained 136 annotated genes, including 86 protein-coding, 42 tRNA, and 8 rRNA genes. We identified six hypervariable regions, including parts of the ycf1 gene, as potential DNA barcodes. Phylogenetic analyses revealed that Carl Luer’s subgeneric classifications are non-monophyletic, a finding confirmed by PCA of continuous morphological traits, reflecting significant morphological homoplasy. Six major clades were identified, though resolution for the phylogenetic backbone remains unresolved at two nodes. Subgenus Marsipanthes is not monophyletic as currently circumscribed, with two subclades recovered in distinct positions within the phylogeny. An early-diverging lineage, comprising species restricted to the eastern Andean slopes from southern Colombia to Peru, includes members of both Marsipanthes and Lepanthes. A derived clade, consisting of species from both subgenera, confined to the Chocó biogeographic region, forms an unresolved polytomy. Although only a subset of Lepanthes diversity was sampled, this study captures significant taxonomic, geographic, and morphological variation. It provides foundational insights into the genu's evolutionary history, along with tools and hypotheses that can be expanded upon in future research to further refine our understanding of its biogeographic history.

Field exploration across five Andean regions of Colombia resulted in the identification of 102 species in Lepanthes, documented through herbarium specimens, including spirit collections, and DNA voucher samples. Subsequent taxonomic analysis and further exploration allowed us to identify six new species, which are formally described here. We report an unprecedented case of flower polymorphism, where individuals at two distinct sites exhibited both flower morphologies previously recognized as separate species, Lepanthes silverstonei and L. licrophora. Based on these observations, we propose the synonymization of L. licrophora under the older name, L. silverstonei. This study significantly contributes to the understanding of Colombian Lepanthes diversity and establishes a foundation for future taxonomic, ecological, and conservation efforts.

Orchidaceae is one of the most species-rich families of flowering plants, with most current diversity having evolved within the last 5 My. Patterns associated with species richness and rapid diversification have been identified but have not often been associated with evolutionary processes. We review the most frequently identified correlates of diversity and suggest that the processes and rate by which they occur vary geographically and are largely dependent on persistent pulses of habitat instabilities, especially for epiphytes. Aggressive orogenesis creates fragmented habitats while global climatic cycles exacerbate the ecological instabilities. The need for repeated cycles of dispersal results in frequent founder events, which sets the stage for allopatric diversification via bouts of genetic drift and natural selection. The allopatry requirement can be bypassed by pollination systems involving flowers attracting pollinators through the production of sex signaling semiochemicals. The drift–selection model of diversification, coupled with persistent habitat instability throughout ecological and geological time scales, and sex signaling are the likely components of a multifactorial process leading to the rapid, recent diversification in this family.

Alternaria brassicicola is a seed-borne pathogen that causes black spot disease in Brassica crops, yet the seed defense mechanisms against this fungus remain poorly understood. Building upon recent reports that highlighted the involvement of indole pathways in seeds infected by Alternaria, this study provides transcriptomic resources to further elucidate the role of these metabolic pathways during the interaction between seeds and fungal pathogens. Using RNA sequencing, we examined the gene expression of glucosinolate-deficient mutant lines (cyp79B2/cyp79B3 and qko) and a camalexin-deficient line (pad3), generating a dataset from 14 samples. These samples were inoculated with Alternaria or water, and collected at 3, 6, and 10 days after sowing to extract total RNA. Sequencing was performed using DNBseq™ technology, followed by bioinformatics analyses with tools such as FastQC (version 0.11.9), multiQC (version 1.13), Venny (version 2.0), Salmon software (version 0.14.1), and R packages DESeq2 (version 1.36.0), ClusterProfiler (version 4.12.6) and ggplot2 (version 3.4.0). By providing this valuable dataset, we aim to contribute to a deeper understanding of seed defense mechanisms against Alternaria, leveraging RNA-seq for various analyses, including differential gene expression and co-expression correlation. This work serves as a foundation for a more comprehensive grasp of the interactions during seed infection and highlights potential targets for enhancing crop protection and management.

Seeds play a vital role in the perpetuation of plant species, both in natural environments and agriculture. However, they often face challenges from biotic stresses, such as seed-borne pathogenic fungi. The transgenerational transmission of these seed-borne fungi, along with their dissemination during seed commercialization, can contribute to the emergence of global epidemic diseases, resulting in substantial economic losses. Despite the recognized impact of seed-borne pathogens on agriculture, our understanding of seed–pathogen interactions remains limited. This review establishes parallels between the current state of knowledge regarding seed responses to pathogen interactions and well-established plant defense models, primarily derived from typical physiological conditions observed during leaf infections. Examining fragmented results from various pathosystems, this review seeks to offer a comprehensive overview of our current understanding of interactions during seed development and germination. The necrotrophic interactions in Brassicaceae are described using recent transcriptomic and genetic studies focused on the Arabidopsis/Alternaria pathosystem, which illustrates original response pathways in germinating seeds that markedly differ from the general concept of plant–pathogen interactions. The co-existence of regulatory mechanisms affecting both seed resistance and susceptibility, potentially promoting fungal colonization, is examined. The vulnerable response during germination emerges as a crucial consideration in the context of sustainable plant health management in agriculture.

Seeds play a vital role in the perpetuation of plant species, both in natural environments and agriculture. However, they often face challenges from biotic stresses, such as seedborne pathogenic fungi. The transgenerational transmission of these seedborne fungi, along with their dissemination during seed commercialization, can contribute to the emergence of global epidemic diseases, resulting in substantial economic losses. One such pathogenic fungus is Alternaria brassicicola, responsible for causing black spot disease in Brassicaceae. This necrotrophic seedborne fungus negatively impacts plant development, consequently affecting crop production and seed quality. To gain a deeper understanding of the interaction between seeds and necrotrophic fungi, the Arabidopsis thaliana/Alternaria brassicicola model pathosystem has been extensively studied. Recent transcriptomic and genetic studies revealed a distinctive immune response of seeds against this pathogen, divergent from the immune response described in the plant vegetative phase. In germinating seeds and seedlings, the necrotrophic fungus seems to induce susceptible response [1]. It was observed at the RNA level that to the detriment of jasmonic acid pathway, Alternaria induced the salicylic acid and glucosinolate (GSL) pathways. Genetic evidence identified that seedling necrosis, potentially beneficial to the growth of the necrotrophic agent, is hypersensitive response mediated by GSL pathway. Transmission of necrotrophic fungal from seed to seedling unveils novel regulations of the immune response, that would illustrate a trade-off between seedling establishment and fungal infection. This knowledge is promising to sustainably ensure the sanitary quality of crops.

Phylogenetic relationships for the genus Calliandra section Androcallis (Fabaceae) were reconstructed, including previously sequenced species from Central and South America and unexamined species from Colombia, one of Calliandra main diversity centers. Here, we generated novel DNA sequences of Calliandra species from Colombia for the nuclear Internal Transcribed Spacer (ITS) and the chloroplast trnL and trnL-F intergenic spacer. By incorporating a broader taxonomic sampling, the relationships among main clades in Androcallis were clarified, providing a systematics framework in which to test evolutionary hypotheses. Phylogenetic analysis recovered five well-supported clades within Androcallis. Most species within each clade had similar geographical distributions and relationships between the five major clades are strongly supported for the first time. However, core Androcallis relationships, including most species from Colombia sequenced here, remain unclear. A second goal of this study was to determine the taxonomic status of Calliandra medellinensis. This enigmatic taxon emblematic of Medellín, Colombia, is found in limited numbers within the Aburrá Valley and has been proposed to be a hybrid taxon. Here, C. medellinensis, C. magdalenae and C. haematocephala were not monophyletic within the core Androcallis clade. This suggests that C. medellinensis could potentially be an interspecific hybrid between C. magdalenae and C. haematocephala, thus challenging the taxonomic status of this species; however, more informative molecular markers should be used in future studies. Specifically, genomic studies should assess interspecific hybridization demographic models. Such insights can illuminate the C. medellinensis origin, guiding conservation strategies and providing valuable evolutionary overviews.

Phylogenetic relationships for the genus Calliandra section Androcallis (Fabaceae) were reconstructed, including previously sequenced species from Central and South America and unexamined species from Colombia, one of Calliandra main diversity centers. Here, we generated novel DNA sequences of Calliandra species from Colombia for the nuclear Internal Transcribed Spacer ( ITS) and the chloroplast trnL and trnL-F intergenic spacer. By incorporating a broader taxonomic sampling, the relationships among main clades in Androcallis were clarified, providing a systematics framework in which to test evolutionary hypotheses. Phylogenetic analysis recovered five well-supported clades within Androcallis . Most species within each clade had similar geographical distributions and relationships between the five major clades are strongly supported for the first time. However, core Androcallis relationships, including most species from Colombia sequenced here, remain unclear. A second goal of this study was to determine the taxonomic status of Calliandra medellinensis . This enigmatic taxon emblematic of Medellín, Colombia, is found in limited numbers within the Aburrá Valley and has been proposed to be a hybrid taxon. Here, C. medellinensis , C. magdalenae and C. haematocephala were not monophyletic within the core Androcallis clade. This suggests that C. medellinensis could potentially be an interspecific hybrid between C. magdalenae and C. haematocephala , thus challenging the taxonomic status of this species; however, more informative molecular markers should be used in future studies. Specifically, genomic studies should assess interspecific hybridization demographic models. Such insights can illuminate the C. medellinensis origin, guiding conservation strategies and providing valuable evolutionary overviews.

A checklist of Orchidaceae from Caquetá, Colombia is presented here. We recorded 98 genera and 418 species, exceeding a previous inventory by 276 species. The checklist is conservative in the number of genera and species by including only taxa that were fully and reliably identified and that are either linked to a corresponding herbarium voucher, a living collection specimen or a photo taken in the field and published in iNaturalist by one of the authors or a collaborator. The documented species diversity in the region could dramatically increase in the next few years with additional collecting efforts in the eastern slopes of the Andes nested in Caquetá. About 9% (418/4600) of all Orchidaceae species recorded for Colombia are reported for this area, showing the important contribution to orchid diversity of Andean-Amazonian foothills of Caquetá.