Chloroplast sequence of treegourd (Crescentia cujete, Bignoniaceae) to study phylogeography and domestication

Comparative chloroplast genomics and insights into the molecular evolution of Tanaecium (Bignonieae, Bignoniaceae)

Species of Tanaecium (Bignonieae, Bignoniaceae) are lianas distributed in the Neotropics and centered in the Amazon. Members of the genus exhibit exceptionally diverse flower morphology and pollination systems. Here, we sequenced, assembled, and annotated 12 complete and four partial chloroplast genomes representing 15 Tanaecium species and more than 70% of the known diversity in the genus. Gene content and order were similar in all species of Tanaecium studied, with genome sizes ranging between 158,470 and 160,935 bp. Tanaecium chloroplast genomes have 137 genes, including 80-81 protein-coding genes, 37 tRNA genes, and four rRNA genes. No rearrangements were found in Tanaecium plastomes, but two different patterns of boundaries between regions were recovered. Tanaecium plastomes show nucleotide variability, although only rpoA was hypervariable. Multiple SSRs and repeat regions were detected, and eight genes were found to have signatures of positive selection. Phylogeny reconstruction using 15 Tanaecium plastomes resulted in a strongly supported topology, elucidating several relationships not recovered previously and bringing new insights into the evolution of the genus.

A Review of the Phytochemistry, Ethnobotany, Toxicology, and Pharmacological Potentials of Crescentia cujete L. (Bignoniaceae)

Crescentia cujete is an economical and medicinal plant of wide indigenous uses including hypertension, diarrhea, respiratory ailments, stomach troubles, infertility problems, cancer, and snakebite. Despite these attributes, C. cujete is largely underutilized, notwithstanding the few progresses made to date. Here, we reviewed the available findings on the ethnobotany, phytochemistry, toxicology, and pharmacology, as well as other economic benefits of the plant. The information on the review was gathered from major scientific databases (Google scholar, Scopus, Science Direct, Web of Science, PubMed, Springer, and BioMed Central) using journals, books, and/or chapters, dissertations, and conference proceedings. The review established the antidiabetic, antioxidant, acaricidal, antibacterial, anti-inflammatory, anthelmintic, antivenom, wound healing, neuroprotection, antiangiogenic, and cytotoxic properties from aqueous and organic (particularly ethanol) aerial parts attributed to several secondary metabolites such as flavonoids, alkaloids, saponins, tannins, phenols, cardiac glycosides, phytosterols, reducing sugar, and volatile oils. Economically, the fruit hard outer shell found applications as musical tools, tobacco pipes, bowls, food containers, and bioethanol production. While most of the current studies on C. cujete are mainly from Asia and South America (Philippines, Bangladesh, India, etc.), part of the persistence challenge is lack of comprehensive data on the plant from in vivo pharmacological studies of its already characterized compounds for probable clinical trials toward drug discovery. Consequently, upon this, modern and novel translational studies including the concept of '-omics' are suggested for studies aiming to outfit more comprehensive data on its therapeutic profiles against pathological markers of diseases and to fully explore its economic benefits.

Chloroplast genome assembly of Handroanthus impetiginosus: comparative analysis and molecular evolution in Bignoniaceae

Bignoniaceae species have conserved chloroplast structure, with hotspots of nucleotide diversity. Several genes are under positive selection, and can be targets for evolutionary studies. Bignoniaceae is one of the most species-rich family of woody plants in Neotropical seasonally dry forests. Here we report the assembly of Handroanthus impetiginosus chloroplast genome and evolutionary comparative analyses of ten Bignoniaceae species representing the genera for which whole-genome chloroplast sequences were available. The chloroplast genome of H. impetiginosus is 159,462 bp in size and has a similar structure compared to the other nine species. The total number of genes was slightly variable amongst the Bignoniaceae, ranging from 124 in H. impetiginosus to 144 in Anemopaegma acutifolium. The inverted repeat (IR) size was variable, ranging from 24,657 bp (Tecomaria capensis) to 40,481 bp (A. acutifolium), due to the contraction and retraction at its boundaries. However, gene boundaries were very similar among the ten species. We found 98 forward and palindromic dispersed repeats, and 85 simple sequence repeats (SSRs). In general, chloroplast sequences were highly conserved, with few nucleotide diversity hotspots in the genes accD, clpP, rpoA, ycf1, ycf2. The phylogenetic analysis based on 77 coding genes was highly consistent with Angiosperm Phylogeny Group (APG) IV. Our results also indicate that most genes are under negative selection or neutral evolution. We found no evidence of branch-site selection, implying that H. impetiginosus is not evolving faster than the other species analyzed, notwithstanding we found site positive selection signal in several genes. These genes can provide targets for evolutionary studies in Bignoniaceae and Lamiales species.

UPLC-MS/MS-based molecular networking and NMR structural determination for the untargeted phytochemical characterization of the fruit of Crescentia cujete (Bignoniaceae)

The fruit pulp of Crescentia cujete is traditionally used in folk medicine for the treatment of a variety of respiratory conditions and gastrointestinal disorders. Due to the lack of a comprehensive phytochemical description of the fruit of this plant, its active compounds and rational quality control parameters have not yet been described. An untargeted metabolomics approach combining UPLC-MS/MS-based molecular networking with conventional isolation and NMR methods was carried out for the phytochemical profiling of the fruit pulp of Crescentia cujete. Sixty-six metabolites, including nine n-alkyl glycosides, twenty-three phenolic acid derivatives (such as cinnamoyl and benzoyl derivatives), fifteen flavonoids, four phenylethanoid derivatives and fifteen iridoid glycosides were identified at different levels of confirmation: eighteen confirmed structures (Level 1), six probable structures (Level 2) and forty two tentative candidates (Level 3). Among these, all four phenylethanoid derivatives were described for the first time within this species. In addition, 8-epi-eranthemoside, crescentiol A and crescentiol B were reported as three undescribed iridoid glucosides. The use of molecular networking has resulted in a detailed phytochemical overview of this species. This work provides a useful tool for further development and validation of appropriate analytical methods for routine quality control assessment of commercially available products containing the fruit of this species and further interpretation of their related pharmacological effects.

Tropical Trees as Time Capsules of Anthropogenic Activity

After the ice caps, tropical forests are globally the most threatened terrestrial environments. Modern trees are not just witnesses to growing contemporary threats but also legacies of past human activity. Here, we review the use of dendrochronology, radiocarbon analysis, stable isotope analysis, and DNA analysis to examine ancient tree management. These methods exploit the fact that living trees record information on environmental and anthropogenic selective forces during their own and past generations of growth, making trees living archaeological 'sites'. The applicability of these methods across prehistoric, historic, and industrial periods means they have the potential to detect evolving anthropogenic threats and can be used to set conservation priorities in rapidly vanishing environments.

Comparative Chloroplast Genomics at Low Taxonomic Levels: A Case Study Using Amphilophium (Bignonieae, Bignoniaceae)

Chloroplast (cp) genome organization, gene order, and content have long been considered conserved among land plants. Despite that, the generation of thousands of complete plastomes through next-generation sequencing (NGS) has challenged their conserved nature. In this study, we analyze 11 new complete plastomes of Amphilophium (Bignonieae, Bignoniaceae), a diverse genus of Neotropical lianas, and that of Anemopaegma prostratum. We explored the structure and content of the assembled plastomes and performed comparative analyses within Amphilophium and among other plastomes available for Bignoniaceae. The overall gene content and orientation of plastomes is similar in all species studied. Plastomes are not conserved among Amphilophium, showing significant differences in length (155,262-164,786 bp), number of genes duplicated in the IRs (eight, 18, or 19), and location of the SC/IR boundaries (i.e., LSC/IRa junction between rps19 and rpl2 genes, within petD, or within petB). Length differences reflect expansions of the IRs and contractions of the LSC regions. The plastome of A. prostratum is 168,172 bp, includes 19 duplicated genes, and has the LSC/IRa boundary located within the petB gene. Amphilophium plastomes show high nucleotide diversity, with many hypervariable regions, and 16 genes with signatures of positive selection. Multiple SSRs and repeat regions were identified for Amphilophium and Anemopaegma prostratum. The differences in structure detected within Amphilophium plastomes in terms of LSC/IR and IR/SSC boundaries, number of duplicated genes, and genome sizes are mostly shared between taxa that belong to the same clade. Our results bring new insights into the evolution of plastomes at low taxonomic levels.

Human management and hybridization shape treegourd fruits in the Brazilian Amazon Basin

Local people's perceptions of cultivated and wild agrobiodiversity, as well as their management of hybridization are still understudied in Amazonia. Here we analyze domesticated treegourd (Crescentia cujete), whose versatile fruits have technological, symbolic, and medicinal uses. A wild relative (C. amazonica) of the cultivated species grows spontaneously in Amazonian flooded forests. We demonstrated, using whole chloroplast sequences and nuclear microsatellites, that the two species are strongly differentiated. Nonetheless, they hybridize readily throughout Amazonia and the proportions of admixture correlate with fruit size variation of cultivated trees. New morphotypes arise from hybridization, which are recognized by people and named as local varieties. Small hybrid fruits are used to make the important symbolic rattle (maracá), suggesting that management of hybrid trees is an ancient human practice in Amazonia. Effective conservation of Amazonian agrobiodiversity needs to incorporate this interaction between wild and cultivated populations that is managed by smallholder families. Beyond treegourd, our study clearly shows that hybridization plays an important role in tree crop phenotypic diversification and that the integration of molecular analyses and farmers’ perceptions of diversity help disentangle crop domestication history.

Plastome Rearrangements in the "Adenocalymma-Neojobertia" Clade (Bignonieae, Bignoniaceae) and Its Phylogenetic Implications

The chloroplast is one of the most important organelles of plants. This organelle has a circular DNA with approximately 130 genes. The use of plastid genomic data in phylogenetic and evolutionary studies became possible with high-throughput sequencing methods, which allowed us to rapidly obtain complete genomes at a reasonable cost. Here, we use high-throughput sequencing to study the "Adenocalymma-Neojobertia" clade (Bignonieae, Bignoniaceae). More specifically, we use Hi-Seq Illumina technology to sequence 10 complete plastid genomes. Plastomes were assembled using selected plastid reads and de novo approach with SPAdes. The 10 assembled genomes were analyzed in a phylogenetic context using five different partition schemes: (1) 91 protein-coding genes ("coding"); (2) 76 introns and spacers with alignment manually edited ("non-coding edited"); (3) 76 non-coding regions with poorly aligned regions removed using T-Coffee ("non-coding filtered"); (4) 91 coding regions plus 76 non-coding regions edited ("coding + non-coding edited"); and, (5) 91 protein-coding regions plus the 76 filtered non-coding regions ("coding + non-coding filtered"). Fragmented regions were aligned using Mafft. Phylogenetic analyses were conducted using Maximum Likelihood (ML) and Bayesian Criteria (BC). The analyses of the individual plastomes consistently recovered an expansion of the Inverted Repeated (IRs) regions and a compression of the Small Single Copy (SSC) region. Major genomic translocations were observed at the Large Single Copy (LSC) and IRs. ML phylogenetic analyses of the individual datasets led to the same topology, with the exception of the analysis of the "non-coding filtered" dataset. Overall, relationships were strongly supported, with the highest support values obtained through the analysis of the "coding + non-coding edited" dataset. Four regions at the LSC, SSC, and IR were selected for primer development. The "Adenocalymma-Neojobertia" clade shows an unusual pattern of plastid structure variation, including four major genomic translocations. These rearrangements challenge the current view of conserved plastid genome architecture in terms of gene order. It also complicates both genomic assemblies using reference genomes and sequence alignments using whole plastomes. Therefore, strategies that employ de novo assemblies and manual evaluation of sequence alignments are required to prevent assembly and alignment errors.