In this paper, the H. brasiliensis COBRA gene family, alleged to be involved in laticifer differentiation, was identified from the public rubber tree genome of Reyan 7-33-97 clone. A comparative analysis was carried out against A. thaliana genomic database. This analysis has resulted to the in silico validation of thirteen putative genes encoding glycophosphatidylinositol anchors (GPI) proteins harbored by nine Hevea genomic scaffolds. The sequence’s similarity of HbCOBL against AtCOBL genes were ranged from the threshold 50 to 81.58% covering 151 to 458 amino acid residues, respectively. Three partial and ten full-length protein sequences of HbCOBL genes were annotated. The partial protein sequences ranged from 89 to 184 amino acid residues as opposed to the full-length proteins ranging from 160 to 471 amino acid residues. Two types of COBRA domains (pfam04833 and cl04787) were found among HbCOBL genes. Phylogenetic analysis has clustered two subfamilies. Nine HbCOBL genes (HbCOBL-B, HbCOBL-J, HbCOBL-C, HbCOBL-H, HbCOBL-F, HbCOBL-I, HbCOBL-M, HBCOBL-A, and HbCOBL-N) were clustered as COBRA gene subfamily-I. By contrast, four genes (HbCOBL-O, HbCOBL-P, HbCOBL-E, and HbCOBL-L) were clustered as COBRA gene subfamily-II. The HbCOB subfamily-II was marked by the addition of 203 residues in C-terminal which is different with Arabidopsis. The gene HbCOBL-C was the putative ortholog to AtCOB carrying the unique COBRA domain cl04787 with 74 amino acid residues. Taken together, these results showed that Hevea and Arabidopsis COBRA genes might share similar functions while differ in gene structure.
Ficus spp. belongs to the tribe Ficeae in the Moraceae family. Many members of this genus have been collected and grown in Bogor Botanic Gardens. There are 519 living collections of Ficus conserved since 1817, and 13 of them have not been identified until the species level. This research aimed to identify the Ficus sp. originated from Kaur Selatan (Bengkulu) using morphological and molecular approaches. Morphological characterization and herbarium specimen observation have been carried out to identify the Ficus sp. The molecular approach was conducted through DNA barcoding using ITS primer. The molecular identification using ITS sequence showed that Ficus sp. is Ficus crassiramea with 99.87% similarity to the sequence in NCBI. Morphological observation through herbarium specimen showed that there are 9 vegetative characters specific to Ficus crassiramea.
Recent studies have identified Sugars Will Eventually be Exported Transporters (SWEET), a novel type of sugar transporters in diverse plant species. This gene family selectively transports different kinds of sugar substrates, including sucrose, fructose and glucose. In this paper, three Metroxylon sagu SWEET genes (MsSWEET-X, MsSWEET-Y and MsSWEET-Z), predicted to be involved in starch accumulation, were identified from the NCBI EST database. A comparative analysis was carried out against Arabidopsis thaliana TAIR and Elaeis guineensis NCBI genome databases resulting in amino acid residues similarity of three MsSWEET genes of 21.32 to 76.25 %. One full-length coding sequence (CDS) of 229 amino acids from MsSWEET-X has been annotated as opposed to the partial CDSs from the other two. Three types of putative protein domains (Calreticulin, Glycosyl hydrolases and Triose-phosphate transporter) were predicted for MsSWEET-X, MsSWEET-Y and MsSWEET-Z, respectively. Multiple Alignment sing Fast Fourier Transform (MAFFT) has identified three conserved amino acid motifs (Motif-A, Motif-B and Motif-C) among three compared species. Phylogenetic analysis using Maximum-Likelihood Estimation has revealed two genes AtCRT3 and MsSWEET-X at the upstream of initial tree branches (0.17 and 0.12 length) showing their early evolutionary orthology. By contrast, MsSWEET-Y gene was predicted to be the latest homolog of SWEET16 and SWEET17 undergoing speciation events from both Arabidopsis and oil palm. Taken together, these results showed that even though the oil palm and sago palm shared the common ancestry of monocotyledonous family, their SWEET genes were divergent. The gene MsSWEET-X was highly close to its homolog in Arabidopsis.
Bogor Botanic Gardens (BBG) is an ex-situ plant conservation area with thousands of plant collections. The trees of the Lauraceae in BBG experienced the highest number of deaths among other families. However most of them were categorized as young planting years (0-15 years). A tree health monitoring in the Lauraceae needs to be conducted to provide an overview, trend, and value of the level of damage. Forest Health Monitoring (FHM) method was carried out on two plots consisting of 149 trees. FHM can identify the types and levels of damage through monitoring and recording a series of tree damage. The results showed that among 149 trees, with 103 healthy, 9 lightly damaged, 10 moderately damaged, 15 heavily damaged, and 12 dead. The damage was primarily found in the stem (63 trees), the crown branch (51 trees), and the roots (13 trees). The severity of the damage was mainly at a mild level (0-19%). The cause of the damage is discussed. Further observations and frequent monitoring of the health of the Lauraceae need to be conducted by management to reduce the number of dead collections of the family. Keywords: botanic gardens, Forest Health Monitoring, lauraceae, tree health
Protease inhibitors (PIs) are small proteins that form complexes with proteases and inhibits their proteolytic activity. Its potential application as an antimicrobial agent has been studied. Most of PIs' molecule size is around 8-22 kDa depending on their protein families.To date, on the basis of sequence homologies of inhibitor domains, PIs have been classified into 48 families in all organisms. In plant, more than 13 families of PIs have been identified but they were not widely identified in the rubber tree (Hevea brasiliensis Muell.Arg). In the present study, 40 putative HbPI genes, designated as HbPI01 to HbPI36, were identified from whole-genome sequence of rubber tree clone Reyan 7-33-97 using 7453 scaffolds available online in NCBI with the accession code: LVXX01000000. Multiple sequence alignment using MUSCLE algorithm discovered seven conserved motifs (Motifs I-VII) among HbPIs. Phylogenetic analysis of 50 and 36 PI amino acid residues of 32 scaffolds containing putative PI genes from Arabidopsis thaliana and H. brasiliensis showed three clusters (families): LTP-I, SERPIN and LTP-II. LTP-I has 23 putative HbPI genes (HbPI05 to HbPI27) and 12 AtPI genes. SERPIN, a family member of serine protease inhibitor group, has 11 putative HbPI genes (HbPI01 to HbPI04 and HbPI28 to HbPI34) and 22 AtPI genes. LTP-II has 2 putative HbPI genes (HbPI35 to HbPI36) and 16 AtPI genes. In conclusion, this work provides valuable information for further functional characterization of HbPI genes in H. brasiliensis.[Key words: protease inhibitor, genome-wide, scaffold, in silico, Hevea brasiliensis]. AbstrakProtease inhibitor (PI) merupakan protein yang membentuk kompleks dengan protease dan menghambat aktivitas proteolitik dari enzim tersebut. Potensi penggunaan protease inhibitor sebagai agensia antimikroba telah diketahui. Kebanyakan PI memiliki ukuran molekul sekitar 8-22 kDa bergantung pada familinya. Saat ini, PI dapat diklasifikasikan menjadi 48 famili di seluruh organisme berdasarkan kemiripan sekuen dari domain inhibitornya. Pada tanaman, lebih dari 13 famili PI telah diketahui tetapi pada tanaman karet (Hevea brasiliensis Muell.Arg) belum diidentifikasi. Pada penelitian ini, sebanyak 40 gen putatif penyandi PI (HbPI01 hingga HbPI36) telah berhasil diidentifikasi dari 7453 scaffold genom utuh tanaman karet klon Reyan 7-33-97 yang tersedia secara daring dengan kode aksesi LVXX01000000. Penjajaran sekuen menggunakan algoritma MUSCLE memper-lihatkan tujuh konservasi motif (Motif I-VIII) pada famili gen putatif HbPIs. Analisis pohon filogenetik dari tanaman Arabidopsis thaliana dan H. brasiliensis sebanyak 50 dan 36 sekuen residu asam amino dari 32 scaffold yang mengandung gen putatif PI menunjukkan adanya tiga klaster besar, yaitu famili LTP-I, SERPIN dan LTP-II. LTP-I terdiri dari 23 gen putatif HbPI (HbPI05 hingga HbPI27) dan 12 gen AtPI. SERPIN yang merupakan anggota kelas protease inhibitor serin terdiri dari 11 gen putatif HbPI (HbPI01hingga HbPI04 dan HbPI28 hingga HbPI34) dan 22 gen AtPI. LTP-II terdiri dari 2 gen putatif HbPI (HbPI35 hingga HbPI36) dan 16 gen AtPIs. Penelitian ini menghasilkan informasi penting untuk melakukan karakterisasi fungsional lebih mendalam pada gen HbPI tanaman karet ke depannya.[Kata kunci: protease inhibitor, genome-wide,scaffold, in silico, Hevea brasiliensis].
An increasing number of explants is necessary toobtain plantlets in large quantities, for mass propagationof rubber plants. However, high level of contamination atthe primary culture stage is still a major constraint in invitro microcutting of rubber. The aim of this study was tooptimize surface sterilization procedures to reduce micro-bial contamination at the primary culture. Sterilizationexperiment was conducted in two step., The first step wasto determine the effect of washing the explants withrunning water prior to sterilization and then using Deso-germe, ethanol or H 2 O 2 , while the second step was toidentify the suitable sterilization process on reducing thelevel of contamination. The results showed that the surfacesterilization with only one type of sterilization agent couldnot reduce contamination level caused either by bacteriaor fungi, while sterilization with three types of sterilizingagents increased the number of dead explants. The besttreatment for surface sterilization was the directsterilization of explants using 70% ethanol for one minuteand 17.6% H 2 O 2 for 20 minutes without washing with tapwater (A-CD treatment). The percentage of viable andaseptic explantsof this treatment was 76.7%, which wassignificantly higher than those of other treatments. Thistreatment reduced contamination level to 21.7%.AbstrakPeningkatan jumlah eksplan sangat diperlukan untukmemperoleh planlet dalam jumlah besar pada perbanyakanmassal tanaman karet secara in vitro. Namun, tingginyatingkat kontaminasi pada tahap kultur primer masih me-rupakan kendala utama dalam kultur stek mikro tanamankaret. Tujuan penelitian adalah mengoptimasi prosedursterilisasi permukaan eksplan untuk mengurangi jumlaheksplan yang terkontaminasi mikroba pada tahap kulturprimer. Percobaan sterilisasi dilaksanakan dalam duatahap, tahap pertama untuk mengetahui pengaruh pen-cucian eksplan dengan air mengalir pada awal sterilisasiserta penggunaan Desogerme, etanol dan H 2 O 2 , sedang-kan tahap kedua untuk mendapatkan proses sterilisasi yangpaling sesuai dalam menurunkan tingkat kontaminasi.Hasil penelitian menunjukkan bahwa perlakuan sterilisasipermukaan yang menggunakan satu jenis bahan sterilantidak dapat mengurangi kontaminasi, baik oleh bakterimaupun cendawan. Perlakuan sterilisasi eksplan dengantiga jenis bahan sterilan meningkatkan kematian eksplan.Perlakuan sterilisasi permukaan terbaik adalah sterilisasilangsung eksplan menggunakan etanol 70% selama satu menit dan H 2 O 2 17,6% selama 20 menit, tanpa pencuciandengan air mengalir (perlakuan A-CD). Persentase eksplansteril yang hidup sebesar 76,7%, berbeda nyata dibanding-kan dengan perlakuan lainnya. Perlakuan tersebut dapatmengurangi kontaminasi menjadi sebesar 21,7%.
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