Typhonium flagelliforme, an Indonesian endemic medicinal species from the Araceae family, has attracted growing scientific interest due to its notable anticancer potential. Recognized as a valuable genetic resource, this species offers promising prospects for future breeding and biotechnological applications. In this study, we report the first complete chloroplast (cp.) genome of T. flagelliforme. The chloroplast genome spans 167,120 bp and displays the canonical quadripartite organization, comprising a large single-copy (LSC) region of 89,453 bp, a small single-copy (SSC) region of 14,524 bp, and two inverted repeats (IRs) of 31,573 bp each. Genome annotation recovered 130 genes, including 87 protein-coding genes, 8 rRNA genes, and 35 tRNA genes. We identified 102 simple sequence repeats (SSRs), with mononucleotide repeats representing the majority (86

Typhonium flagelliforme , an Araceae species recognized for its anticancer metabolites distributed throughout its roots, tubers, stems, and leaves, remains underexplored at the molecular level. In this study, we developed expressed sequence tag–simple sequence repeat (EST-SSR) markers from the T. flagelliforme transcriptome and evaluated their utility in assessing the genetic diversity of Indonesian germplasm as well as their transferability to other Araceae species. Transcriptome assembly yielded 41,392 unigenes, of which 9,868 were successfully annotated. Mining of 18,225 unigenes identified 24,404 potential EST-SSRs, with an overall frequency of one SSR per 4.36 kb and di-nucleotide repeats (45.83%) being the most abundant motif. From these, 38 primer pairs were randomly selected, and 32 produced clear amplicons, of which 23 (60.5%) were polymorphic across 14 accessions. A total of 15 alleles were detected, with an average of 2.87 alleles per locus. The mean observed and expected heterozygosity were 0.238 and 0.620, respectively, while the polymorphism information content (PIC) ranged from 0.416 to 0.580, with an average of 0.515, indicating a moderate level of polymorphism. Genetic structure analysis and principal coordinate analysis (PCoA) consistently grouped the accessions into three distinct genetic clusters, underscoring the effectiveness of the developed markers in resolving population structure. To our knowledge, this represents the first genetic diversity analysis of Indonesian T. flagelliforme germplasm using EST-SSR markers. The newly developed resources provide a valuable foundation for molecular characterization, germplasm conservation, and breeding applications in T. flagelliforme and potentially related Araceae species.

Typhonium flagelliforme, a medicinal plant endemic to Indonesia and belonging to the Araceae family, has garnered significant attention due to its potential anticancer properties. Given its therapeutic relevance, this species represents a promising genetic resource for future plant breeding initiatives. In the present study, whole genome sequencing (WGS) of T. flagelliforme was performed using the Illumina NextSeq 2000 platform. Sequencing was conducted with a paired-end 150 bp (PE150) approach, yielding approximately 112 GB of raw data. The estimated genome size was 714.70 Mb, with an assembly contig N50 of 3,971 bp and a Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness score of 76.08

Glucomannan is a non-starch carbohydrate predominantly found in tubers, serving as a significant resource for food and health industries. Despite the widely recognized glucomannan content in taro tubers, there is limited understanding regarding the gene level. Therefore, this research aimed to identify putative Cellulose Synthase-like A (CslA) gene sequences associated with glucomannan biosynthesis in eddoe taro plant. Genome isolation was carried out on six genotypes of eddoe taro, each showing different glucomannan content. A pair of primers designed from the mannan synthase encoding gene sequences obtained from the NCBI. Subsequently, sequences of the PCR product were analyzed for identification and in-silico analysis. The result of in-silico RFLP analysis showed that six genotypes had polymorphic allelic fragments. The DNA sequences showed a high similarity to CslA gene, among representative taro tubers compared to the reference plants. A total of three nucleotide sequences fragments from the S7 and S34 genotypes as well as two from S15, S28, S30, and S36, corresponded to CslA gene of Amorphophallus konjac. Phylogenetic analysis based on nucleotide sequences showed that S7 and S34 had distinctive characteristics, indicating specific and wide adaptation, respectively. Despite the presence of single nucleotide polymorphism, the in-silico transcription-translation showed that the protein constructed had a highly similar consensus motif. These results suggested the identified sequences as a potential CslA-encoding gene that had functioned in the biosynthesis of mannan synthase to produce glucomannan in taro plants.

Typhonium flagelliforme, a distinctive medicinal plant belonging to the Araceae family, is native Indonesian herb renowned for its anticancer properties. Despite of significant potential medicinal value, the availability of molecular markers for studying its genetic diversity and evolutionary background were limited. In this study, we performed the first transcriptome of T. flagelliforme leaf using paired-end Illumina NovaSeq 6000 PE150 which generated 10.79 GB of raw data. De novo assembly using rnaSpades resulted in a total of 11,521 transcripts with contigs length and longest contigs respectively 123,909,948 bp and 28,917,662 bp. The analysis succesfully identified 20,960 genic SSR loci from the transcriptome sequencing data using the Microsatellite (MISA) tool. The perfect motifs showed the following distribution of motif types: mononucleotides (32.1%), dinucleotides (40.8%), trinucleotides (24.9%), tetranucleotides (1.5%), pentanucleotides (0.2%), and hexanucleotides (0.4%). From these, 161 primer pairs were designed and 40 selected primers were validated. To the best of our knowledge, this is the first study to identify and characterize EST- SSR markers in T. flagelliforme. These markers are potential for genetic diversity assessment, marker-assisted selection (MAS), cultivar identification, kinship analysis, and genetic mapping.

Sago plant (Metroxylon sagu Rottb.) is one of the most carbohydrate-producing plants in the world. Microsatellites or simple sequence repeats (SSRs) play an important role in the genome and are used extensively compared to other molecular markers. For the first time, we are exploiting data expressed sequence tags (EST) of sago plants to identify and characterise markers in this species. EST data about sago plants are obtained through the EST database on the National Center for Biotechnology Information (NCBI) website. We obtained data of 458 Kb (412 contig) with a maximum and minimum length of 1,138 and 124 nucleotides, respectively. We successfully identified 820 perfectly patterned SSR using Phobos 3.3.12 software. The type characterisation of EST-SSR was dominated by tri-nucleotides 36% (294), followed by hexa-nucleotides 24% (202), tetra-nucleotides 15% (120), penta-nucleotides 13% (108) and di-nucleotides 12% (96). The most frequency of SSR motifs in each type is AG, AAG and AAAG. Analysis of synteny on the EST sequence with the online application Phytozome found that sequences were distributed on 12 Oryza sativa chromosomes with a likeness percentage between 63% to 100% and e-value between 0 to 0.094. We developed the primer and generated 19 primers. Furthermore, we validated 7 primers that all generated polymorphic alleles. To our knowledge, this report is the first identification and characterisation of EST-SSR for sago species and these markers can be used for genetic diversity analysis, marker assisted selection (MAS), cultivar identification, kinship analysis and genetic mapping analysis.

Ganoderma boninense, the causative agent behind basal stem rot (BSR) disease in oil palm, instigated a pressing need for innovative and ecologically sustainable strategies to counter its impact. Biological control strategies, particularly employing bio-fungicides, have emerged as environmentally friendly alternatives for managing oil palm plant diseases. This study delved into harnessing the biocontrol potential of Indigenous bacterial isolate by investigating and evaluating its bioactive compounds of ethyl acetate extract with the capacity to suppress G. boninense growth in oil palm plants. Molecular identification was utilized to identify of bacterial isolate using 16S rRNA primers (5′- AGA GTT TGA TCC TGG CTC AG– 3′) and (5′- GGA TAC CTT GTT ACG ACT T– 3′). The agar well diffusion technique and scanning electron microscopy (SEM) were utilized to assess the inhibitory effects of bacterial ethyl acetate extract against G. boninense. A comprehensive analysis of the bacterial ethyl acetate extracts was conducted by gas chromatography - mass spectrometry (GC–MS). Molecular identification confirmed that the bacterial isolate was Bacterium strain BS1727. By employing SEM, the ethyl acetate extracts had influenced on G. boninense mycelial architecture. The exposure to the bacterial ethyl acetate extracts induced degradation and morphological distortion of the mycelial structure, serving as an indicator of its impact on the mycelium's structural modulation. Noteworthy, the spectrum of bioactive compounds was a subset of aromatic hydrocarbons, encompassing volatile organic compounds (VOCs). Based on GC–MS analysis, among the VOCs, acetic acid butyl ester and toluene showed the highest relative peak areas, 46.34

Curcuma longa is a medicinal plant renowned for its therapeutic properties and potential treatment of cancer. This study focused on the biosynthesis of diterpenoids in the rhizome and leaves of C. longa. The genes responsible for producing these medicinal compounds were analyzed using BLASTx, Gene Ontology (GO) annotation, differential expression, and homology. The substantial dataset was obtained from the National Center for Biotechnology Information (NCBI), comprising 151,730,334 clean reads and 167,264 transcripts for the analysis. The results of the BLASTx analysis were as follows: NR yielded 65.93%, Swiss-Prot yielded 44.52%, and COG yielded 17.35%. Subsequently, GO annotation was performed using Blast2GO, resulting in an annotation rate of 56.79%. Differential expression analysis revealed a total of 636 genes that were significantly differentiated between the rhizome and leaves. The homology analysis resulted in 11 proteins associated with diterpenoid biosynthesis and nine proteins related to CYP450. Approximately three class I proteins were highly expressed in the rhizome. Additionally, seven CYP450 enzymes from the CYP71D and CYP726 subfamilies were identified; three were highly expressed in the rhizome. The expression patterns of these enzymes were similar to the aforementioned three class I diTPSs, indicating their potential involvement in macroditerpenoid biosynthesis in C. longa. These findings provide valuable genomic resources for future functional genomics research on C. longa, facilitating targeted efforts to enhance the production of bioactive compounds.

Recalcitrancy is the main problem in rice anther culture, especially in an Indica subspecies. It is well known that recalcitrancy is genotype dependent, and the effort to tackle this problem is mostly in the manipulations of media. Uncovering the genes responsible for recalcitrancy will benefit to enhance the success of this technique to accelerate the breeding process of Indonesian rice varieties which mostly belong to the indica subspecies. RNA-Seq is considered one of the best approaches to finding candidate genes responsible for specific traits including recalcitrant in anther culture. The aim of this study was to obtain the high concentration and good quality of RNA extracted methods using various extraction kits. The RNA extraction was carried out using Tripure, Promega, and RibospinTM Plant (Geneall) kit methods. Quality of RNA provided by the Promega kit showed good quality of RNA in all three genotypes tested ranging from 2.06±0.01-2.11±0.00 for A260/280 and 1.86±0.14-1.95±0.10 for A260/230.

Sago palm ( Metroxylon sagu Rottb.) is a carbohydrate-producing plant. It produces a starchy, edible pith or core within its trunk, which is the primary portion used for human consumption. To date, little has been investigated about the diversity of sago palm plants in Bengkulu, Indonesia. In this study, DNA was extracted from young leaves collected from nine locations in Bengkulu and amplified using 10 simple sequence repeat (SSR) primers. Data analysis was conducted using NTSYs and POPGEN32 software. This study shows that the Sentot (B5), Damri (B7), and Merapi (B9) accessions had the highest expected heterozygosity (He), thereby indicating high genetic diversity. The largest genetic distances were observed for Lagan (B2) and Makmur Swamp (B4) compared with Dendam Lake (B3), while the smallest genetic distances were between the Sentot (B5) and Damri (B7) areas. We found two groups using phylogenetic analysis, GenAlEx and STRUCTURE. This result is consistent with two types of habitats and leaf morphologies among sago palm plants; i.e., plants in permanent swampy areas with a soil pH of 5.0–5.3 showing spines in the middle of the midrib extending up to the leaf tip and plants in wet peat areas with a soil pH of 5.3–6.0 showing spines only on the edge of the leaf. The results of our research provide information on genetic similarities between populations to assist in plant breeding.

Breeding is one method to develop better varieties. This method can be accelerated by using haploid technology. The availability of haploid inducer lines in maize makes in-vivo techniques preferred, especially for temperate maize. Developing in-vitro through anther culture in haploid breeding is still needed since haploid inducer lines are still limited in tropical maize. Like many other crops facing recalcitrancy problems, maize also experiences the same, so cracking recalcitrant traits using transcriptomic approaches is necessary. In order to enhance the success of the sequencing, obtaining a high quantity and quality of RNA product is needed since it will affect the data. This study aimed to determine the best RNA extraction methods using three different kits of maize explant for anther culture with high purity and concentrations. RNA extraction in this study was performed using Tripure, RibospinTM, Promega, and Tripure kits. The results showed that all All the kits were able to produce high concetration of RNA, where the Ribospin (Geneall) performed the best (both for the concentration and purity). Meanwhile Tripure kit were only able to produced highest concentration of RNA, but lowest purity.

Curcuma aeruginosa Roxb. is an Indonesian traditional medicinal plant of the Zingiberaceae family. C. aeruginosa is known to have anticancer activity, especially in the rhizomes. Despite many studies on the phytochemical content of this plant with antioxidant and anticancer activity, transcriptomic studies are still limited in terms of genetic information. We ran transcriptome of Curcuma aeruginosa using a paired-end Illumina NextSeq 550 with PE150 mode and generating 12.8 GB of raw data. Raw reads have been filed with NCBI under project number PRJNA918644. This dataset allowed us to identify genes associated with biosynthetic pathways of anticancer drugs. Transcriptome data can also be used to develop new EST-SSR and SNP markers for use in plant breeding programs.

Background and Objective: Sago palm (Metroxylon sagu Rottb.) is one of the largest carbohydrate-producing plants in the world.SSR has an essential role in the genome and is widely used to determine plant diversity compared to other molecular markers.This research focused on identifying the diversity of sago palms in the West Kalimantan region using SSR markers.The benefit of this research is to obtain EST-SSR information on sago palms that can be used to design SSR primers so that it can be used to study the diversity of sago populations in the West Kalimantan Region.Materials and Methods: DNA isolation was obtained by extracting young leaves of sago palms originating from West Kalimantan.The DNA concentration and quality were measured using Nanodrop.SSR amplification using PCR was carried out on sago palm accessions with polymorphic primers from sago accession selection.Results: DNA concentration measurements were 33.8-1380.3ng µLG 1 and DNA purity was 1.8.The results of the SSR analysis using seven primers on 27 sago accessions produced an average number of alleles and the percentage of polymorphic primers 3.57 and 0.538, respectively.The highest number of alleles and PICs produced by sV2006 primers are 5 and 0.721.Analysis of the diversity of 27 accessions of sago with seven primers in the form of phylogenetic trees forming three different groups.Conclusion: There was a high diversity of 37 accessions of sago Kalimantan in our study with 7 primers and the phylogenetic trees formed three groups.The sago accession from West Kalimantan has different variations between Pontianak and the accession from Mempawah, while the accession from Sambas has several similarities with Mempawah and Singkawang.

Oil palm empty fruit bunches (OPEFB) are the lignocellulosic complex organic waste material from palm oil mills that is cheap, environmentally friendly, and abundant in Indonesia. Slow degradation of OPEFB becomes a problem for oil palm plantations. OPEFB which has decayed naturally for 6 months, 1 year, and 2 years were obtained from the Oil Palm Plantation, PTPN VIII Cikasungka, Bogor, Indonesia. In this study, fungal and bacterial diversity in naturally decaying OPEFB in plantations was identified using Illumina MiSeq sequencing of the ITS2 for fungal, the V3 region of the 16S rRNA gene, and the V4 region of the 18S rRNA gene for bacterial. Bacterial diversity in decaying OPEFB was dominated by the phylum Planctomycetes (40-60%), whereas most of the fungal sequences taken belonged to Ascomycota (60-90%). Biodiversity profile resulting from metagenomic analysis is useful for increasing knowledge about microbial composition in the natural degradation process of OPEFB. The resulting data can be used to compare the diversity of bacteria at different weathering times and depths. In-depth observation of the diversity of lignin-degrading microbes from the natural decomposition of OPEFB has the potential to discover novel enzymes and ligninolytic activities that are useful for the fast degradation of OPEFB, production of biofuels based on enzymatic technology, and the development of high value-added biomass products.

The assembly of dihaploid rice plants through anther culture was constrained due to the recalcitrant properties. A comprehensive investigation of gene expression patterns among rice varieties with recalcitrant and non-recalcitrant anthers will help to understand the cellular mechanisms and biological processes of recalcitrant properties in rice anther cultures. Therefore, we performed RNA sequencing and analysis on the anthers of three selected Indonesian rice varieties with opposite recalcitrant properties. The varieties are Fatmawati with non-recalcitrant properties, IR64 recalcitrant and Tarabas unknown. The Illumina NextSeq PE150 sequencer was used to generate a total crude nucleotide of approximately 41.21 Gb in size. From 272,239,682 total paired final raw reads, 137,343,391 total net reads were obtained and uploaded to NCBI's Sequence Read Archive (SRA) repository under BioProject accession number PRJNA856048. This dataset allowed us to identify and profile all expressed genes with functions associated with recalcitrant and non-recalcitrant properties. In addition, the transcriptome data obtained will be valuable for the discovery of potential gene markers and functional SNPs associated with functional traits to assist rice breeding programs through the development of Marker Assisted Selection (MAS).

Sago palm (Metroxylon sagu Rottb.) is one of the most productive carbohydrate-producing crops. Unfortunately, only limited information regarding sago palm genetics is available. This study aimed to develop simple sequence repeat (SSR) markers using sago palm NGS genomic data and use these markers to evaluate the genetic diversity of sago palm from Indonesia. De novo assembly of partial sago palm genomic data and subsequent SSR mining identified 29,953 contigs containing 31,659 perfect SSR loci and 31,578 contigs with 33,576 imperfect SSR loci. The perfect SSR loci density was 132.57/Mb, and AG, AAG and AAAT were the most frequent SSR motifs. Five hundred perfect SSR loci were randomly selected and used for designing SSR primers; 93 SSR primer pairs were identified. After synteny analysis using rice genome sequences, 20 primer pairs were validated using 11 sago palm accessions, and seven primers generated polymorphic alleles. Genetic diversity analysis of 41 sago palm accessions from across Indonesia using polymorphic SSR loci indicated the presence of three clusters. These results demonstrated the success of SSR identification and marker development for sago palm based on NGS genome data, which can be further used for assisting sago palm breeding in the future.

Sago genome sequencing analysis is still very limited. This study is a preliminary study of sago sequence analysis obtained from NGS technology to understand and identify new genetic sequences that have homology to genes in the NCBI database. Sequences were analyzed using Blast2Go to determine the genetic function annotation, putative gene identification was performed on the Arabidopsis database using the BLASTx program with a 10 -3 e-value limit on The Arabidopsis Information Resource (TAIR) (http://www.arabidopsis.org/index.jsp). Gene interactions were analyzed using DAVID and GeneMania programs. Based on sequence analysis with Blast2Go, 33 sequences with Blastx hit consisting of: 29 sequences had a high homology. The sago sequences with a similarity of ≥ 90% are glutamate decarboxylase and HT1-like serine threonine kinase with hit number 10. The distribution of interactions between genes from GeneMania analysis is known to be mostly interconnected in the 65.13% protein domain, predicted 19.83%, genes with 14.47% shared expression and the remaining 0.57% had localization together.