Vincent Okelo Wanga

The genus Zehneria (Cucurbitaceae) presents significant taxonomic challenges due to morphological similarities among species and a lack of resolution in molecular studies. In this study, we sequenced and assembled the chloroplast genomes of seven African Zehneria species collected from Kenya, complementing a previously published accession (Zehneria sp. MZ427944.1), to establish a comprehensive plastome-based framework for the genus. The plastomes ranged from 157,150 to 157,365 bp and exhibited a conserved quadripartite structure, with 130–132 annotated genes, including 86–87 protein-coding genes, 36–37 tRNAs, and 8 rRNAs. Structural variation, particularly in non-coding regions and inverted repeat boundaries, was observed, with eight hypervariable loci providing potential targets for molecular marker development. Simple sequence repeat (SSR) analysis revealed a predominance of A/T mononucleotides across species. Codon usage analysis revealed a strong AT-bias across all species, with codons ending in A or U accounting for 72.2% of synonymous codon preferences. Selective pressure analysis identified eight protein-coding genes with Ka/Ks ratios exceeding 1.0, including psaJ and rps8, proposed as candidate molecular barcodes pending further validation. Phylogenomic analysis of 79 protein-coding genes strongly supported the monophyly of Zehneria (ML bootstrap = 96–100%; PP = 1.0), with one node showing slightly reduced support (BS = 96%), and enhanced resolution of interspecific relationships compared to prior studies using fewer loci. This work offers novel insights into genomic diversity and evolutionary history of sampled Zehneria species, providing a critical molecular resource for future taxonomic and phylogenetic studies within Cucurbitaceae. Broader taxon sampling, particularly from Asian lineages, will be necessary to fully resolve interspecific relationships across the genus.

Ctenium has about 20 species distributed in Africa, Arabia, and the Neotropics, with no species occurring on more than one continent. Its relationship with the morphologically similar Kampochloa is still unclear and has not been investigated. In this study, we performed phylogenomic analyses using 71 protein‐coding genes of 24 newly sequenced plastomes, of 13 species of Ctenium and 1 species of Kampochloa to understand their biogeography and the phylogenetic and evolutionary relationships between these two genera and within Ctenium. Our results support two major clades of Ctenium: the Neotropics and Old‐World clades. Kampochloa is shown to be a close relative of the genus Ctenium, and their morphological similarities support this. Divergence time estimation analyses show that Kampochloa and Ctenium diverged around 7.99 Ma, and might have originated in the late Miocene during the rapid expansion of C₄ grasslands. With this evidence from morphology and phylogenomic data, we propose the inclusion of the previously unplaced Kampochloa into the subtribe Cteniinae.

Climate change poses a serious long-term threat to biodiversity. To effectively reduce biodiversity loss, conservationists need to have a thorough understanding of the preferred habitats of species and the variables that affect their distribution. Therefore, predicting the impact of climate change on species-appropriate habitats may help mitigate the potential threats to biodiversity distribution. Xerophyta, a monocotyledonous genus of the family Velloziaceae is native to mainland Africa, Madagascar, and the Arabian Peninsula. The key drivers of Xerophyta habitat distribution and preference are unknown. Using 308 species occurrence data and eight environmental variables, the MaxEnt model was used to determine the potential distribution of six Xerophyta species in Africa under past, current and future climate change scenarios. The results showed that the models had a good predictive ability (Area Under the Curve and True Skill Statistics values for all SDMs were more than 0.902), indicating high accuracy in forecasting the potential geographic distribution of Xerophyta species. The main bioclimatic variables that impacted potential distributions of most Xerophyta species were mean temperature of the driest quarter (Bio9) and precipitation of the warmest quarter (Bio18). According to our models, tropical Africa has zones of moderate and high suitability for Xerophyta taxa, which is consistent with the majority of documented species localities. The habitat suitability of the existing range of the Xerophyta species varied based on the climate scenario, with most species experiencing a range loss greater than the range gain regardless of the climate scenario. The projected spatiotemporal patterns of Xerophyta species help guide recommendations for conservation efforts.

Polygonatum Miller belongs to the tribe Polygonateae of Asparagaceae. The horizontal creeping fleshy roots of several species in this genus serve as traditional Chinese medicine. Previous studies have mainly reported the size and gene contents of the plastomes, with little information on the comparative analysis of the plastid genomes of this genus. Additionally, there are still some species whose chloroplast genome information has not been reported. In this study, the complete plastomes of six Polygonatum were sequenced and assembled, among them, the chloroplast genome of P. campanulatum was reported for the first time. Comparative and phylogenetic analyses were then conducted with the published plastomes of three related species. Results indicated that the whole plastome length of the Polygonatum species ranged from 154,564 bp (P. multiflorum) to 156,028 bp (P. stenophyllum) having a quadripartite structure of LSC and SSC separated by two IR regions. A total of 113 unique genes were detected in each of the species. Comparative analysis revealed that gene content and total GC content in these species were highly identical. No significant contraction or expansion was observed in the IR boundaries among all the species except P. sibiricum1, in which the rps19 gene was pseudogenized owing to incomplete duplication. Abundant long dispersed repeats and SSRs were detected in each genome. There were five remarkably variable regions and 14 positively selected genes were identified among Polygonatum and Heteropolygonatum. Phylogenetic results based on chloroplast genome strongly supported the placement of P. campanulatum with alternate leaves in sect. Verticillata, a group characterized by whorled leaves. Moreover, P. verticillatum and P. cyrtonema were displayed as paraphyletic. This study revealed that the characters of plastomes in Polygonatum and Heteropolygonatum maintained a high degree of similarity. Five highly variable regions were found to be potential specific DNA barcodes in Polygonatum. Phylogenetic results suggested that leaf arrangement was not suitable as a basis for delimitation of subgeneric groups in Polygonatum and the definitions of P. cyrtonema and P. verticillatum require further study.

Justicia tanalensis (Acanthaceae) was rediscovered from the central highland of Madagascar since the last collection in 1895. Its morphological characters are reported and amended with photographs in this paper. The species is characterized by a prostrate herbaceous habit and a simple spike with one flower per node. It has a distribution range in the central-eastern Madagascar. The conservation assessment of the species is provided. Because no holotype was indicated in the protologue and the type specimens cited by the original author were collected in two different times, they should be considered as two gatherings and they are syntypes. The lectotype specimen of the name is designated here as well.

Background: Calanthe(Epidendroideae, Orchidaceae) is a pantropical genus distributed in Asia and Africa. Its species are of great importance in terms of economic, ornamental and medicinal values. However, due to limited and confusing delimitation characters, the taxonomy of theCalanthealliance (Calanthe,Cephalantheropsis, andPhaius) has not been sufficiently resolved. Additionally, the limited genomic information has shown incongruences in its systematics and phylogeny. In this study, we used illumina platform sequencing, performed ade novoassembly, and did a comparative analysis of 8Calanthegroup species' plastomes: 6Calantheand 2Phaiusspecies. Phylogenetic analyses were used to reconstruct the relationships of the species as well as with other species of the family Orchidaceae.Results: The complete plastomes of theCalanthegroup species have a quadripartite structure with varied sizes ranging between 150,105bp-158,714bp, including a large single-copy region (LSC; 83,364bp- 87,450bp), a small single-copy region (SSC; 16,297bp -18,586bp), and a pair of inverted repeat regions (IRs; 25,222bp - 26,430bp). The overall GC content of these plastomes ranged between 36.6-36.9%. These plastomes encoded 131-134 differential genes, which included 85-88 protein-coding genes, 37-38 tRNA genes, and 8 rRNA genes. Comparative analysis showed no significant variations in terms of their sequences, gene content, gene order, sequence repeats and the GC content hence highly conserved. However, some genes were lost inC.delavayi(P. delavayi), includingndhC,ndhF, andndhKgenes. Compared to the coding regions, the non-coding regions had more sequence repeats hence important for species DNA barcoding. Phylogenetic analysis revealed a paraphyletic relationship in theCalanthegroup, and confirmed the position ofPhaius delavayiin the genusCalantheas opposed to its previous placement inPhaius.Conclusion: This study provides a report on the complete plastomes of 6Calantheand 2Phaiusspecies and elucidates the structural characteristics of the plastomes. It also highlights the power of plastome data to resolve phylogenetic relationships and clarifies taxonomic disputes among closely related species to improve our understanding of their systematics and evolution. Furthermore, it also provides valuable genetic resources and a basis for studying evolutionary relationships and population genetics among orchid species.

Fortunella venosa (Rutaceae) is an endangered species endemic to China and its taxonomic status has been controversial. The genus Fortunella contains a variety of important economic plants with high value in food, medicine, and ornamental. However, the placement of Genus Fortunella into Genus Citrus has led to controversy on its taxonomy and Systematics. In this present research, the Chloroplast genome of F. venosa was sequenced using the second-generation sequencing, and its structure and phylogenetic relationship analyzed. The results showed that the Chloroplast genome size of F. venosa was 160,265 bp, with a typical angiosperm four-part ring structure containing a large single copy region (LSC) (87,597 bp), a small single copy region (SSC) (18,732 bp), and a pair of inverted repeat regions (IRa\IRb) (26,968 bp each). There are 134 predicted genes in Chloroplast genome, including 89 protein-coding genes, 8 rRNAs, and 37 tRNAs. The GC-content of the whole Chloroplast genome was 43%, with the IR regions having a higher GC content than the LSC and the SSC regions. There were no rearrangements present in the Chloroplast genome; however, the IR regions showed obvious contraction and expansion. A total of 108 simple sequence repeats (SSRs) were present in the entire chloroplast genome and the nucleotide polymorphism was high in LSC and SSC. In addition, there is a preference for codon usage with the non-coding regions being more conserved than the coding regions. Phylogenetic analysis showed that species of Fortunella are nested in the genus of Citrus and the independent species status of F. venosa is supported robustly, which is significantly different from F. japonica. These findings will help in the development of DNA barcodes that can be useful in the study of the systematics and evolution of the genus Fortunella and the family Rutaceae.

Madagascar shelters over 14,000 plant species, of which 90% are endemic. Some of the plants are very important for the socio-cultural and economic potential. Tampolo forest, located in the northeastern part of Madagascar, is one of the remnant littoral forests hinged on by the adjacent local communities for their daily livelihood. However, it has considerably shrunk due to anthropogenic activities forming forest patches. Thus, documenting the useful plants in and around the forest is important for understanding the ethnobotany in this area. Methods: In this study we (1) collected and identified useful plants utilized by local communities. Voucher specimens were collected following the information given by interviewees, (2) recorded the collection activities and the consumption methods through semi-structured interviews of the local inhabitants, and (3) performed a phytochemical screening to identify the active compounds and the potential healing metabolites of the medicinal plants. Results: A total of 65 people between 25 and 75 years old were interviewed. Surveys recorded 123 species used as timber, food, or medicine. Among them, 92 were forest species and 31 were ruderal species. Medicinal plants were mostly used to cure stomach ailments (71%), fever (33.3%), and fatigue (25%) with leaves (68%) being the most used plant part. Phytochemical analyses of 20 endemic medicinal species showed the presence of compounds that could be responsible for the therapeutic effects of the plants. Conclusions: Tampolo forest proves to be an important littoral forest highly utilized by the adjacent local communities due to the presence of a high number of useful plants which are mostly endemic to the region. Hence, our investigation assessed the importance of these species in the locality and this can be used for further study on ecology, conservation, and valorization of these species.