Dr. Isna Arofatun Nikmah, S.Si, M.Si.

New bent-toed gecko (Squamata: Gekkonidae) from Simeulue Island, Indonesia

Complete chloroplast genome of the underutilized legume jack bean (Canavalia ensiformis, Fabaceae) reveals genetic makeup, mutational hotspots, and phylogenetic relationships

New bent-toed gecko (Squamata: Gekkonidae) from Simeulue Island, Indonesia

We describe a new species of Cyrtodactylus Gray that belongs to the C. quadrivirgatus complex within the C. sworderi group from Simeulue, an adjacent island to Sumatra. It is a medium-sized (SVL) species with adult males reaching 57.2 mm and females 59.9 mm; tubercles present on both dorsal of brachium; ventrolateral fold present; 2022 irregular dorsal tubercle rows at midbody; 3435 paravertebral tubercle series; 3842 ventral scale rows across belly; precloacal groove absent; 2 precloacal pores present in males, absent in females; enlarged precloacofemoral scales present; abrupt transition between the enlarged femorals and the adjacent scales on the posterior margin of the thigh; 21 subdigital lamellae on the fourth toe; and subequal median subcaudal scales not transversely enlarged. The new species is genetically divergent from the other congeners of the C. sworderi group, with genetic divergences (p-distances) ranging from 12.420.1% for the mitochondrial ND2 gene.

Comparative analysis of the complete chloroplast genome of jack bean (Canavalia ensiformis, Fabaceae) revealed mutational hotspots and phylogenetic relationships

Abstract In recent years, the study of chloroplast genomes has gained increasing attention due to its significance in understanding plant evolution, phylogenetics, and genetic engineering. Canavalia ensiformis, commonly known as jack bean, is a leguminous plant of agricultural and ecological importance, with its chloroplast genome offering potential insights into adaptive mechanisms, species divergence, and biotechnological applications. This study focuses on the structure, organization, and gene content of the C. ensiformis chloroplast genome and its comparative analysis with other members of Phaseoleae (Fabaceae). We assembled and annotated the complete chloroplast genome of C. ensiformis using a combination of Illumina short-reads and Oxford Nanopore long-reads available on GenBank. The C. ensiformis chloroplast genome was organized as a single circular structure of 157,809 bp in length and divided into four main regions: a large single-copy (77,529 bp), a small single-copy (18,934 bp), and a pair of inverted repeat regions (30,673 bp). The genome encoded 95 protein-coding genes, 8 rRNA, and 37 tRNA genes. To explore evolutionary relationships, we conducted a comparative analysis of plastid genomes across Phaseoleae species. Structural variations, gene rearrangements, and divergence in non-coding regions were assessed, revealing conserved synteny and lineage-specific differences within the tribe. The phylogenomic analysis based on plastid genome sequences further clarified the evolutionary placement of C. ensiformis within Phaseoleae. The results contribute to a broader understanding of plastid genome evolution in legumes, one of the most species-rich plant families, and provide valuable genomic resources for future research in molecular phylogenetics and crop improvement.

Integrating Differential Expression and Weighted Correlation Network Analysis for Identifying Genes Controlling Shoot Development in Sorghum Bicolor

Pengendalian Kapang Patogen Tanaman Kakao (Theobroma cacao L.) Menggunakan Konsorsium Kapang Tanah (Trichoderma spp. dan Aspergillu ssp.)

Kakao (Theobroma cacao L.) merupakan salah satu komoditas yang memiliki peranan penting bagi perekonomian nasional, terutama sebagai sumber devisa negara melalui ekspor. Namun perkembangan dan produksi kakao di beberapa daerah terhambat oleh adanya penyakit busuk buah yang disebabkan oleh Phytophthora palmivora (P. palmivora). Penelitian ini bertujuan untuk mengevaluasi efektivitas konsorsium Trichoderma spp. dan Aspergillus sp. terhadap P. palmivora. Penelitian ini terdiri dari empat pekerjaan utama: isolasi kapang patogen; isolasi Trichoderma spp. dan Aspergillus sp.; identifikasi jamur patogen dan antagonis; Uji antagonisme in vitro, terdiri dari (1) Trichoderma spp (2) Aspergillus spp., (3) Trichoderma spp. dan Aspergillus sp.consortium terhadap jamur patogen. Hasil penelitian menunjukkan bahwa konsorsium kultur ganda Trichoderma spp. dan Aspergillus sp. efektif menghambat pertumbuhan jamur patogen sekitar 73,08%. Ketika konsorsium diinokulasi terlebih dahulu, persentase penghambatannya adalah 100%. Hal ini menunjukkan bahwa waktu inokulasi sangat mempengaruhi efektivitas konsorsium Trichoderma spp. dan Aspergillus sp.Kata kunci: Jamur Antagonis, Kakao, Konsorsium, Patogen

A complete chloroplast and mitochondrial genome for velvet bean (Mucuna pruriens, Fabaceae), with genome structure and intergenomic sequence transfers analyses

Abstract Mucuna pruriens , commonly known as the velvet bean, holds considerable economic and cultural importance as a member of the Fabaceae family. The economic value of this plant is derived from its high protein content, medicinal properties, and potential applications in agriculture and industry. Although the entire nuclear genome consisting of 11 chromosomes of M. pruriens has been published, the comprehensive assembly of the organelle genome, specifically the mitochondria, has not been previously accomplished. The evaluation of sequence transfer from both the chloroplast and mitochondrial genomes to the nuclear genome has not been conducted. The complete chloroplast and mitochondrial genome of M. pruriens var. utilis was assembled and annotated through the utilization of a hybrid approach involving Illumina short-reads and Oxford Nanopore long-reads. The genome of chloroplasts was found to be arranged in a singular circular structure measuring 155,617 bp in length. This structure encompassed a total of 75 genes responsible for encoding proteins, along with 4 genes for ribosomal RNA and 28 genes for transfer RNA. The organization of the mitochondrial genome consisted of a singular circular structure measuring 410,745 bp in length, encompassing a total of 39 protein-coding genes, 4 ribosomal RNA genes, and 16 transfer RNA genes. Through the analysis of sequence transfer, it has been determined that a total of 154,498 bp and 158,285 bp of DNA, derived from the chloroplast and mitochondrial genome respectively, have been incorporated into the nuclear genome. These transfer events predominantly occurred in a relatively recent timeframe. The frequency of transfers of chloroplast to nuclear genome sequences was found to be similar to that of transfers of mitochondrial to nuclear genome sequences. This study presents the initial assembly of the entire organelle, specifically the mitochondrial genome of M. pruriens , which serves as a valuable tool for comprehending the genomic evolution within the diverse Fabaceae family.

Construction of an ultra-high-density consensus genetic map and analysis of recombination rate variation in Sorghum bicolor

Abstract. Satrio RD, Nikmah IA, Fendiyanto MH, Pratami MP, Awwanah M, Sari NIP, Farah N, Nurhadiyanta. 2022. Construction of an ultra-high-density consensus genetic map and analysis of recombination rate variation in Sorghum bicolor. Asian J Agric 6: 47-54. Sorghum is one of the most widely grown cereal crops on a global scale. A consensus map is a method for combining genetic information from multiple populations, and it is an effective way to increase genome coverage and marker density. This study constructed a consensus map by combining publicly available marker data from four mapping populations. A total of 3449 non-redundant polymorphic markers at the nucleotide level were used to construct a single consensus map on 10 sorghum chromosomes. This study generated an ultra-high-density sorghum consensus map consisting of a large number of markers spanning 1571.68 cM and averaging one marker per 0.46 cM. Due to the high density of the markers, it is only 0.06% of the markers had an interval greater than 5 cM. The rates of local recombination were estimated using a set of all markers genetic and physical positions along each of the 10 chromosomes. The analysis of the recombination rate on 10 sorghum chromosomes revealed that it decreased as the centromere position was getting closer. The consensus map generated in this study can be used to integrate information related to sorghum genetic resources and QTLs to the genome sequence, thereby accelerating the discovery of novel potential genes in sorghum.

Potential of invasive alien species Clidemia hirta as antibacterial against Salmonella typhi and Staphylococcus aureus

Abstract. Pratami MP, Fendiyanto MH, Satrio RD, Widana IDKK, Nikmah IA, Sari NIP, Awwanah M, Farah N, Darmadi D. 2021. Potential of invasive alien species Clidemia hirta as antibacterial against Salmonella typhi and Staphylococcus aureus. Biodiversitas 22: 3363-3369. Clidemia hirta D. Don is an invasive alien species (IAS) that is a threat to biodiversity in tropical country particularly Indonesia, and remains underutilized to date. Conversely, prevalence of typhus in Indonesia is generally higher every year. Thus, the aim of this study was to detect phytochemicals in ethanolic and aqueous extracts of C. hirta and their antibacterial activity against Salmonella typhi and Staphylococcus aureus. The research methods included sample identification, generating the simplicia, determination of water content, extraction, phytochemical screening tests, and antibacterial activity tests. Identification was made based on morphological characteristics. The water content in the dried powder of simplicia was 12.26 ± 0.39%. Phytochemical results showed that 70% ethanol extract of C. hirta contained flavonoids, saponins, tannins, and triterpenoids compounds. In addition, aqueous extract of C. hirta showed positive results on flavonoids, saponins, tannins, and steroids tests. Antibacterial activity results showed that ethanolic extracts of C. hirta inhibited S. typhi and S. aureus at all concentrations, while aqueous extract inhibited bacterial growth in only 12.5% ??and 25% concentrations. These findings indicate that C. hirta has antibacterial activity that inhibits S. typhi and S. aureus. This information can be used for adding preliminary data to metabolite interest researchers, i.e., biologists and biotechnologists in the future.

Short Communication: Identification of spoilage fungi in Myristica fragrans using DG18 and CYA Media

Abstract. Fendiyanto MH, Satrio RD, Pratami MP, Nikmah IA. 2021. Short Communication: Identification of spoilage fungi in Myristica fragrans using DG18 and CYA Media. Asian J Trop Biotechnol 18: 51-54. To date, very few studies have been conducted on the identification of spoilage fungi in Myristica fragrans. Therefore, this study aimed to identify the spoilage fungi in Myristica fragrans growing on DG18 media and CYA Identification Media. Isolation of the fungus was carried out by the dilution plating method using a dilution range of 10-1 to 10-5. The isolation results at 10-2 and 10-3 dilutions on nutmeg (Myristica fragrans) seed samples indicated the presence of Aspergillus niger and A. flavus. The fungal species that could be found and identified using the direct plating method were A. niger, A. flavus, Penicillium citrinum, and Fusarium sp. The results of fungal isolation showed that the species of spoilage fungi on postharvest of M. fragrans seeds, including Aspergillus flavus, A. niger, A. tamarii, Endomyces fibuliger, Eurotium chevalieri, E. repens, and Penicillium citrinum, Trichoderma sp. The highest population of spoilage fungi isolated from Myristica fragrans seeds was Aspergillus niger. This finding indicates that A.niger can be identified as spoilage fungi isolated from Myristica fragrans.

Differential hierarchical metabolites expression of red/white Salacca sumatrana arillus and its molecular docking studies

Abstract. Fendiyanto MH, Satrio RD, Widana IDKK, Pratami MP, Nikmah IA, Darmadi D. 2021. Differential hierarchical metabolites expression of red/white Salacca sumatrana Arillus and its molecular docking studies. Biodiversitas 22: 1014-1024. Salak Sidempuan (Salacca sumatrana) is one of the medicinal plants originating from tropical countries. However, there is very little research on the study of finding bioactive compounds in S. sumatrana using the metabolomic approach. Here, we use two population types of S. sumatrana, e.g., fruit with red and white arillus. We extracted the compounds from the two tissues using the GC-MS technique and further analyzed their antiviral potential using an in-silico molecular docking technique. Fold change analysis showed that in white arillus there were 21 upregulated compounds and 25 downregulated compounds. Metabolites that have high expression in white arillus tissue are ranxinic acid, nicotinic alcohol, stearic acid, 2-furan carboxaldehyde, and others. Six accessions from S. sumatrana based on PCA analysis and separate dendrogram according to the type of arillus, i.e., red and white arillus. Two compounds that act as antivirals found in this study are stearic acid and palmitic acid based on preliminary molecular docking studies. These two compounds could be used for further studies as a preventive measure against SARS-Cov-2 in the future, however, it needs further comprehensive and clinical analysis the future. In conclusion, metabolites in white arillus were distinctly different from red arillus of Snake fruits. In addition, studies on differential metabolite expression on two types of arillus (red/white) can be used as markers in identifying arillus color early by plant breeders.

Analysis of Superoxide Dismutase (OsSOD) Gene Expression using qRT- PCR, its Morphophysiological Characters and Path Analysis in Rice Variety IR64 Under Aluminum Stress

Rice treated with aluminum (Al) can produce active oxygen species (AOS). The existence of AOS can cause the rice plants to become morpho-physiologically damaged and eventually cause a decrease in productivity. The AOS reductive compounds are physiologically responded by plants using antioxidant compounds, one of which is the superoxide dismutase enzyme (SOD). Therefore, this research aimed to analyze FeSOD, MnSOD and CuZnSOD gene expressions in IR64 rice variety as information for selection and genetic improvement of rice to overcome national food security. We tested the root architecture, analyzed SOD gene expression and performed path analysis tests. The results showed that rice treated with aluminum (Al) showed dramatically increased CuZnSOD and FeSOD gene expression, while MnSOD gene expression was relatively the same under Al stress or normal conditions. The level of expression of the two genes positively correlated with physiological characteristics such as chlorophyll and root length. Thus, these two genes can be used as markers in studying Al tolerance in Indica cv. rice. IR64.

Morphological and genetic variation in populations of Desmos chinensis Lour. (Annonaceae)

Abstract. Nikmah IA, Rugayah R, Chikmawati T. 2021. Morphological and genetic variation in populations of Desmos chinensis Lour. (Annonaceae). Biodiversitas 22: 811-822. Desmos chinensis is a woody climber or scandent shrub genus in Annonaceae that has moniliform fruits. Desmos chinensis Lour. can be found throughout Southeast Asia. This species is widely used as a traditional medicine in several countries in Asia, however, the information on its morphological and genetic variation has never been reported. The objective of this study was to reveal the genetic variation of Desmos chinensis on Java island (Indonesia) based on the morphological characters and Inter-Simple Sequence Repeats (ISSR) markers. Leaf samples were collected by exploring seven regions in Java island. Variation in morphological characteristics were described and discussed in detail. Genetic variation was assessed using the ISSR marker. The morphological characteristics of D. chinensis in Java varies in habit; leaf shape, leaf size, leaf color; flower position, flower reflexity, pedicel bract position, number of petals, petal color, petal shape, petal apex, undulation of petal; and number of monocarp per fruit. A total of 53 samples collected from seven populations were screened by 25 ISSR primers, wherein 11 primers produced 47 clear and reproducible bands covering 85.1% of polymorphic bands. Desmos chinensis in Java were divided into five natural populations. Furthermore, the mean value of the Shannon index and genetic diversity index were 0.223 and 0.151, respectively. Moreover, the variations within and among populations examined using AMOVA showed the occurrence of 38% of total genetic variations among the different populations, therefore, the remaining 62% was due to variations within the population. Morphological and genetic variations are important preliminary information for determining the conservation strategy of Desmos chinensis.

Leaf anatomical variation in Desmos Lour. and Dasymaschalon (Hook. f. & Thomson) Dalla Torre & Harms species (Annonaceae)

Abstract. Nikmah IA, Rugayah R, Chikmawati T. 2020. Leaf anatomical variation in Desmos Lour. and Dasymaschalon (Hook. f. & Thomson) Dalla Torre & Harms species (Annonaceae). Biodiversitas 21: 3317-3330. The relationships between Desmos and Dasymaschalon are debated for along time. Those two genera have high morphological similarities, especially in their generative character (moniliform monocarps). Therefore, sterile specimens of Desmos are difficult to be distinguished from Dasymaschalon. Leaf anatomy in paradermal section of 20 taxa (12 species of Desmos, eight species of Dasymaschalon) have been carried out. The data were used to support the interspecific and intergeneric delimitation of Desmos and Dasymaschalon. Desmos and Dasymaschalon are two distinct genera mainly distinguished based on the anticlinal wall undulation of epidermal cells and supported by variation of the crystal type, and size. The anticlinal wall undulation of Desmos is almost straight to slightly wavy, and never sinuous, meanwhile, Dasymaschalon varies from almost straight to deeply sinusoid. The crystals of Desmos consist of rhombohedric, druse type A, and druse type B crystals, whereas Dasymaschalon has prism, druse type A, druse type B, and drue type C crystals.

Reinstatement of Desmos subbiglandulosus (Annonaceae) in Borneo

Desmos subbiglandulosus (Miq.) Merr., previously placed as a synonym of Desmos dumosus (Roxb.) Saff., is reinstated based on the examination of herbarium specimens and type material of D. subbiglandulosus from Borneo deposited in Herbarium Bogoriense. The specimens of D. subbiglandulosus and D. dumosus are morphologically distinct. All the specimens Desmos from Borneo previously identified as D. dumosus should belong to D. subbiglandulosus.

Genetic Diversity of Porang Populations (Amorphophallus Muelleri Blume) In Central Java and West Java Based on LEAFY Second Intron Marker

Porang (Amorphophallus muelleri Blume) dispersed and grows well in Java island. This research aimed to determine the genetic diversity of porang populations in Central Java and West Java based on LEAFY second intron (nuclear genome encoding flower development). DNA samples of porang were from previous study, which are obtained from Central Java (Pamedaran, Grobogan, Wonogiri, Karangtengah) and West Java (Cisompet) as ingroup. A. variabilis from Pamedaran Brebes, A. ochroleucus, A. longituberosus, A. sumawongii, and A. tinekeae from genbank were treated as outgroup. LEAFY second intron was amplified using primers FLint2 F1 5’-CTTCCACCTCTACGACCAGTG-3’ and FLint2 R1 5’-TCTTGGGCTTGTTGATGTAGC-3’. Analysis using dnasp5 showed that 23 samples had 89 invariable sites and 139 variable sites that consisted of 12 singleton two variants sites, 118 parsimony-informative two variants sites and 9 Parsimony-informative three variants sites. The total of haplotype were 7 haplotypes where 16 ingroup samples clumped on haplotype 1 whereas 2 samples of Grobogan (Grobogan I and Grobogan III) clumped on haplotype 2 and outgroup samples occupied at their own haplotype. Genetic distance of all ingroup samples were 0-0,004 showing no differences among individuals. Analysis of phylogenetic tree using Maximum Parsimony, Neighbor Joining and Maximum Likelihood resulting a polytomy branch of ingroup samples except Grobogan which forms a separated sub clad. Key words: Genetic diversity, haplotype, Java, LEAFY, Porang.