Sequence-Structure Comparative and Network-Based Prediction of Drought Gene Candidate Regulator in Elaeis guineensis

Drought poses a significant threat to global food security, particularly impacting crops like oil palm. Selecting genes for genome editing to enhance drought tolerance presents formidable challenges. To ensure that the target gene is chosen correctly and results in the desired character, a pilot study is necessary to determine the target gene for knockout. Two genes drought-related, AtBRL3 and AtOST2, were scrutinized in this context. Aligned with the Elaeis guineensis genome, their neighbouring proteins and gene ontology were analysed to identify potential targets for genome editing. AtBRL3, identified as BRL1 (XP_010913986.1) in E. guineensis, exhibited 58.48% identity and 100% coverage. It interacts with 12 nodes, including BIR1, BRI1, and AT2G20050, crucial for signalling pathways and cellular responses. Molecular function analysis revealed kinase activity. AtOST2 showed high similarity to plasma membrane ATPase/HA1 (XP_010913679.1) in E. guineensis, with 87.46% identity and 100% query cover. It correlated with 14 genes associated with ABA stimulus, stomatal movement, and hormone response. EgBRL1 and EgHA1, resembling AtBRL3 and AtOST2, respectively, emerge as promising targets for developing drought-tolerant oil palm cultivars through gene editing. Nonetheless, further validation through in vitro gRNA target selection and in vivo conversion of OST2/BRL3-containing plasmids in oil palm calluses is indispensable to demonstrate their efficacy in conferring novel drought resistance traits.

The Complete Chloroplast Genome of Medinilla tapete-magicum (Melastomataceae) from Sulawesi, Indonesia

In this study, the genome of an endemic Sulawesi’s plant, Medinilla tapete-magicum was sequenced using Illumina NextSeq 500 and assembled the whole chloroplast genome. Results showed that the cpGenome is 155,602 bp in size with typical quadripartite structure of a large single copy (LSC) region (85,409 bp), a short single copy (SSC) region (16,629 bp), and a pair of inverted repeats (IRs) regions (26,782 bp). The cpGenome is composed of 132 genes, which consists of 87 protein coding genes, 37 tRNAs, and 8 rRNAs. The sliding window analyses showed that psbB-psbH and ndhF-rpl32 can potentially be used as markers. Microsatellite motifs of mononucleotide A and T dominated in the cpGenome. The phylogenetic trees from the concatenated 76 shared protein coding gene sequences showed the Medinilla clade was monophyletic and M. tapete-magicum is a sister species in the SE Asian clade which contain M. magnifica and M. speciosa.

Plant Growth Promoting Endophytic Microorganisms from Orchids for A Sustainable Agriculture

Conventional agriculture practice has heavily relied on chemical fertilizers to increase crop yield. However, long-term application of chemical fertilizers carries tremendous negative impact on the environment and is unsustainable. Hence, the search for an alternative source of fertilizers is required. Orchids are flowers and can be found in tropical countries. The growth and development of orchids are closely tied to the presence of plant growth promoting endophytic microorganisms (PGPM). PGPM harbours various beneficial traits such as potassium and phosphorus solubilization and indole acetic acid and siderophore production which enhance and support plant growth and development. This review article showed that PGPM isolated from orchids could be utilized in conventional agriculture to reduce dependency on chemical fertilizer.

Hesperitin Synergistically Promotes the Senescence Induction of Pentagamavunone-1 in Luminal Breast Cancer Cells, T47D

Pentagamavunone-1 (PGV-1), a curcumin analog, is a promising anticancer candidate for several cancers that have been proven in vitro and in vivo. However, the efficacy of PGV-1 against breast cancer is subject to improvement to achieve a more suitable application. Here we propose hesperitin, a citrus flavonoid, to increase the anticancer potency of PGV-1 in luminal breast cancer cells. We use the T47D cell as the model to investigate the effect of co-administration of PGV-1 and hesperitin on cell cycle block, apoptosis modulation, and senescence phenomena. PGV-1 and hesperitin showed strong and weak cytotoxicity with an IC50 value of 2 µM and 100 µM, respectively. The co-treatment of PGV-1 and hesperitin resulted in strong synergistic effects with combination index (CI) value of ≤ 0.2. This combination caused apoptosis in correlation with cell cycle disruption in G2/M phase at 48 h. In particular, PGV-1 and hesperitin combination increased the incidence of cellular senescence significantly higher than the single treatment. Despite its senescence potentiation, hesperitin did not induce senescence in normal cells. Taken together, hesperitin may increase the anticancer potency of PGV-1 by modulating cell cycle arrest and apoptosis via the senescence mechanism.

First Report of Cladosporium dominicanum Zalar, de Hoog & Gunde-Cim. Infecting Whitefly on Ornamental Plants in Bali, Indonesia

As natural enemies, entomopathogenic fungi are essential for controlling certain plant pests, such as whitefly. Many types of entomopathogenic fungi can infect whiteflies, including those from the genera Aschersonia, Metarhizium, Beauveria, and Cladosporium. Currently, there is great interest in using entomopathogenic fungi as an environmentally friendly pest control in organic and sustainable agricultural systems. This study aimed to identify entomopathogenic fungus associated with whiteflies. Identification of entomopathogenic fungus was performed morphologically and molecularly using DNA barcoding with ITS-1 and ITS-4 as primers, in addition to sequencing and phylogenetic tree analysis. Whiteflies infected with entomopathogenic fungus were discovered on ornamental plants (Premna serratifolia, Ficus religiosa, and Ficus rumphii) in Denpasar, Bali, Indonesia from January to March 2023. We found that samples from the field had mycelium that was unbranched or sparingly branched with solitary conidiophores arising terminally from ascending hyphae or laterally from plagiotropous hyphae. Samples from PDA media had ramoconidia with darkened septa, straight and conidia in long branched chains, branching in all directions, conidia were obovoid, ovoid to limoniform. The fungal colonies had the characteristics of being grey-olivaceous, olivaceous-black, and the margins were grey-livaceous to white, gray olivaceous in colony center due to abundant sporulation. In addition, based on the BLAST nucleotide sequence from NCBI GenBank, the insect pathogen phylogenetic tree found in Denpasar, Bali, is in the same clade as Cladosporium dominicanum strain SCAU014, accession number KY827344.1. Based on morphological and molecular analysis the fungus that infects whiteflies on ornamental plants is C. dominicanum

Fern Species-Area Relationship in Urban Anthropogenic Islands in Slawi, Tegal, Central Java

In anthropogenic islands as urban parks, the fern species richness and composition may be determined ecologically by the quality of habitat, including area greenness, or biogeographically by area size. As the development of the theory of island biogeography also includes man-made parks, it is feasible to test whether area-species relationship applies in these urban parks, and is more pronouncedly evident compared to another ecological factor, such as NDVI. Total species number and composition of 8 urban parks in a kecamatan in Tegal Regency were collected and arranged in clustering methods to understand the similarity between parks. The similarity analysis result is important for the management of the parks in Slawi. The species richness data is subsequently tested using Pearson correlation and regression against NDVI and area sizes. The relation between NDVI and species richness is non-significant (p=0.058), while area size and species richness is significant (p=0.003). This signifies that the urban fern species richness is determined by area as biogeographical factor, compared to NDVI as ecological factor. This result is important for the purpose of designing and managing urban parks as evidently size is important in the effort of attracting native biodiversity into urban parks and in turn enhancing the well-being of urban population.

Lessons from the Mass Production of Wolbachia-infected Aedes aegypti for Egg Release in the Sleman and Bantul Districts of Yogyakarta

An efficacy study on wMel Wolbachia-infected Aedes aegypti technology conducted by the World Mosquito Program (WMP) Yogyakarta showed the reducing of dengue incidence in Yogyakarta City. Following this successful result, the intervention was scaled up into two neighbouring districts: Sleman and Bantul. This paper describes our experience in mass production for providing release material for a larger area to reach the deployment target, which includes insectary requirements, mass production protocols, and diagnostic screening. This review may serve as a reference guidance for national mass production for wMel Wolbachia-infected Ae. aegypti. 

Intraspecific Variability and Phenetic Relationships of Centella Asiatica (L.) Urb. Accessions from Central Java Based on Morphological Characters’

Centella asiatica (L.) Urb. is a plant species native to Java and one of the main basic materials in traditional and modern medicine. This study is the first to report the intraspecific variation and taxonomic relationships of C. asiatica accession from natural populations in Central Java.  The purpose of this study was to reveal phenotypic variations of C. asiatica populations and to asses phenetic relationships based on morphological characters. Thirty-two accessions of C. asiatica were collected from natural populations from eight mountains in Central Java. Observation on vegetative organs resulted in 25 morphological characters as a basis for assessing phenetic relationships using cluster analysis and principal component analysis. Result of cluster analysis showed that the grouping of accessions was not correlated to the localities from where the samples were collected, although there was a tendency that accessions from the same localities grouped in one cluster. The results of this study confirmed the existence of intraspecies morphological variability in C. asiatica which was not affected by geographical aspects. Results of principal component analysis indicated that the grouping of accessions was mainly determined by similarities in petiole color, stolon color, leaf margin, petiole length, stolon length, and leaf color. Given that the characters contributing to the grouping of accessions were mainly qualitative characters, the results indicated a genetic basis underlying phenotypic variations of C. asiatica accession. 

In Vitro Seed Germination and Shoot Growth of Nepenthes jamban Chi. C. Lee, Hernawati & Akhriadi, A Unique Pitcher Plant from Indonesia

The study to optimize in vitro propagation of the Indonesian native and critically endangered species, Nepenthes jamban, in order to support the ex-situ conservation efforts has been done.  Using Murashige and Skoog (MS) as a basal media, disinfected seeds of N. jamban were germinated on five types of germination media, viz. ¼ MS, ½ MS, MS, ¼ MS+benzyl adenine (BA)+Biotin and MS+BA+Biotin. Afterwards, in vitro shoots with 6-7 leaves were inoculated on growing media, i.e., ¼ MS, ¼ MS 60 (3:1) (MS modification with a higher concentration of nitrogen), and ¼ MS+naphtalene acetic acid (NAA)+BA. The results showed that the germination of N. jamban seeds was slow, indicated by the percentage of germination being less than 20% after 6 months of being planted on germination media. The highest percentage of germination was after the 6th month and the greatest pitcher development at the 10th month were obtained on ¼ MS medium. Furthermore, shoot growth and pitchers development consistently increased for 12 months in ¼ MS 60 (3:1) medium while other media resulted in a decrease in pitcher formation. It seemed that low concentrations of nutrient in the medium proved to be more effective to induce in vitro seed germination and enhance shoot growth which was also supported by higher nitrogen (nitrate) concentration in the medium. This study provides information that supports ex situ conservation action of native and critically endangered Nepenthes species from Indonesia.

Mining GATA Transcription Factor Encoding Genes in The Cocoa Tree (Theobroma cacao L.) Suggests Their Potential Roles in Embryo Development and Biotic Stress Response

GATA transcription factors (TFs) are widely recognized as significant regulators, characterized by a DNA-binding domain that consists of a type IV zinc finger motif. This TF family has been widely investigated in numerous higher plant species. The purpose of the present work was to comprehensively analyze the GATA TF in cocoa plant (Theobroma cacao L.) by using various bioinformatics tools. As a result, a total of 24 members of the GATA TFs have been identified and annotated in the assembly of the cocoa plant. According to phylogenetic analysis, these TcGATA proteins were classified into four distinct groups, including groups I (10 members), II (seven members), III (five members), and IV (two members). Next, our investigation indicated that the TcGATA proteins in different groups exhibited a high variation in their physic-chemical features due to their different protein lengths, gene structures, and conserved motif distributions, whereas the TcGATA proteins in the same clade might share the common conserved motifs. Additionally, the gene duplication of the TcGATA genes in the cocoa plant was also investigated. Of our interest, the relative expression levels of the TcGATA genes were investigated according to available transcriptome databases. The results exhibited differential expression patterns of all TcGATA genes in various developmental stages of zygotic and somatic embryogenesis, indicating that these TcGATA genes divergently function during various developmental stages of the zygotic and somatic embryos. Moreover, TcGATA genes were differently expressed under Phytophthora megakarya treatment across different points of treatment and cocoa varieties. To sum up, our findings could provide a basis for a further deep understanding of the GATAs in the cocoa plant.