Ahmad Sofiman Othman

Genetic relationship between Coptotermes gestroi and Coptotermes vastator (Isoptera: Rhinotermitidae).

Abstract The phylogenetic relationship of Coptotermes gestroi (Wasmann) and Coptotermes vastator Light (Isoptera: Rhinotermitidae) was determined using DNA sequence comparisons of mitochondrial genes. Partial sequences of the ribosomal RNA small subunit 12S, ribosomal RNA large subunit 16S, and mitochondrial COII were obtained from nine populations of C. gestroi from South East Asia (Malaysia, Singapore, Thailand, and Indonesia) and four populations of C. vastator from the Philippines and Hawaii. In addition, four populations of Coptotermes formosanus Shiraki and Globitermes sulphureus (Haviland) were used as the outgroups. Consensus sequences were obtained and aligned. C. vastator and C. gestroi are synonymous, based on high sequence homology across the 12S, 16S, and COII genes. The interspecific pairwise sequence divergence, based on Kimura 2-parameter model between C. gestroi and C. vastator, varied only up to 0.80%. Morphometric measurements of 16 characteristics revealed numerous overlaps between the examined individuals of both species. Based on the molecular phylogenetics and morphometric data, it is proposed that C. vastator is a junior synonym of C. gestroi.

The rubber tree genome shows expansion of gene family associated with rubber biosynthesis

Hevea brasiliensis Muell. Arg, a member of the family Euphorbiaceae, is the sole natural resource exploited for commercial production of high-quality natural rubber. The properties of natural rubber latex are almost irreplaceable by synthetic counterparts for many industrial applications. A paucity of knowledge on the molecular mechanisms of rubber biosynthesis in high yield traits still persists. Here we report the comprehensive genome-wide analysis of the widely planted H. brasiliensis clone, RRIM 600. The genome was assembled based on ~155-fold combined coverage with Illumina and PacBio sequence data and has a total length of 1.55 Gb with 72.5% comprising repetitive DNA sequences. A total of 84,440 high-confidence protein-coding genes were predicted. Comparative genomic analysis revealed strong synteny between H. brasiliensis and other Euphorbiaceae genomes. Our data suggest that H. brasiliensis’s capacity to produce high levels of latex can be attributed to the expansion of rubber biosynthesis-related genes in its genome and the high expression of these genes in latex. Using cap analysis gene expression data, we illustrate the tissue-specific transcription profiles of rubber biosynthesis-related genes, revealing alternative means of transcriptional regulation. Our study adds to the understanding of H. brasiliensis biology and provides valuable genomic resources for future agronomic-related improvement of the rubber tree.

Molecular Systematics of Coptotermes (Isoptera: Rhinotermitidae) from East Asia and Australia

ABSTRACT Analyses of mitochondrial DNA sequences (12S, 16S, and COII) were conducted to determine the phylogenetic relationships among the following 11 putative subterranean termites of Coptotermes: Coptotermes cochlearus Xia & He, Coptotermes curvignathus Holmgren, Coptotermes dimorphus Xia & He, Coptotermes formosanus Shiraki, Coptotermes gestroi (Wasmann), Coptotermes kalshoveni Kemner, Coptotermes sepangensis Krishna, and Coptotermes travians (Haviland) from East Asia, and Coptotermes acinaciformis Froggatt, Coptotermes frenchi Hill, and Coptotermes lacteus (Froggatt) from Australia. Available sequences for these species and those of Coptotermes guangzhouensis Ping from GenBank also were included in the analyses. Maximum parsimony and maximum likelihood of the combined nucleotide matrices of the 12S, 16S, and COII genes resulted in two major clades with six subclades: I (C. acinaciformis), II(C. lacteus and C. frenchi), III (C. curvignathus), IV (C. kalshoveni, C. sepangensis and C. travians), V (C. gestroi) and VI (C. formosanus, C. cochlearus, C. dimorphus and C. guangzhouensis). C. cochlearus and C. dimorphus are possibly junior synonyms of C. formosanus with nucleotide differences of up to 1.0%.

Phylogeny of Asian Homalomena (Araceae) based on the ITS Region Combined with Morphological and Chemical Data

Abstract A phylogenetic analysis of the genus Homalomena (Araceae: Homalomeneae) based on the nITS region is presented. Eighty-nine taxa are included; representing all Asian supergroups, several Neotropical species currently assigned to Homalomena, and selected species of Philodendron. Asian Homalomena is well supported as monophyletic and excludes Neotropical Homalomena. The Cyrtocladon supergroup is monophyletic after transferring the Insignis complex and Havilandii complex into the Punctulata supergroup. The Homalomena and Chamaecladon supergroups are well supported. A reduced phylogeny of 20 accessions representing 15 taxa was used for subsequent morphological and chemical marker optimization. A constricted spathe and four stamens per staminate flower are plesiomorphic for Homalomena. Staminodes among the pistillate zone are lost three times independently in Homalomena supergroup, Punctulata supergroup, and H. vivens. Chemical markers identified from liquid chromatography-mass spectroscopy profiling provided an independent set of markers that further support the separation of Neotropical species of Homalomena from the Asian taxon. Three chemical markers at Rt 2.55 min, 2.69 min, and 2.90 min are shared among the majority of taxa sampled for Asian Homalomena, and Neotropical species currently assigned to Homalomena show two unique peaks at Rt 3.25 min and 3.54 min. Five chemical markers support the Cyrtocladon supergroup with the exception of Homalomena vivens. A chemical marker at Rt 3.60 min is plesiomorphic for the Chamaecladon, Homalomena and Punctulata supergroups. A chemical marker at Rt 2.80 min is apomorphic for the Chamaecladon supergroup, with a separate gain in H. punctulata. This study supports removal of the Neotropical species from Homalomena, redefines the morphological boundaries of Homalomena sensu stricto (i.e. the Asian species), and supports and refines the grouping of Asian species into supergroups.

A nationwide biotechnology outreach and awareness program for Malaysian high schools

Biotechnology education in developing nations remains one of the rate limiting factors in achieving optimal human resource capacity to drive and tap the bio-resources of these nations. Many developing countries are situated within rich bio-diversity enclaves. Biotechnology offers the promise of tapping these bio resources towards due process of developing these nations. While there may be a steady stream of biology and biotechnology based graduates, from Malaysian as well as foreign universities contributing to the human resource base for these countries, the numbers and knowledge diversity produced, still lack the capacity to optimally power research and development as well as supply the industrial biotechnology sectors of these countries. Realizing the need to address these issues at the grassroots level of higher education, Malaysia has taken an active step of bringing biotechnology into the classrooms of high schools throughout the country. These future generations of Malaysians, are hoped to progress towards manning and driving Malaysias BioValley initiatives (a biotech based R&D and industry cluster), towards the national dream of developed nation status by the year 2020, using biotechnology as an economic growth vehicle. Here, we share our experiences in developing and proliferating a biotechnology awareness program for Malaysian high schools. It is hoped that similar programs will strive towards similar objectives in other developing countries.

Genetic analysis of population structure of Coptotermes gestroi (Isoptera: Rhinotermitidae) in native and introduced populations.

ABSTRACT We used microsatellite markers to characterize the population structure of Coptotermes gestroi (Wasmann), an economically important termite species in the tropics. Eighty-five colonies were sampled from seven countries (Malaysia, Thailand, Singapore, Indonesia, the Philippines, Taiwan, and the United States [Hawaii]). Ten to 20 workers per colony were genotyped using eight variable microsatellite loci. STRUCTURE analysis partitioned the 13 spatially separated populations into four clusters. Individuals in the Peninsular Malaysia and Singapore population groups displayed admixture clusters. There was low genetic differentiation (FST = 0.073) among the Peninsular Malaysia populations, suggesting moderate gene flow among them. Comparatively, there was moderate genetic differentiation (FST = 0.192) and positive correlation between genetic distance and geographic distance among all of the 13 putative populations studied, which suggests limited gene flow among them. There was no significant isolation by distance within the three largest populations (Penang, Kuala Lumpur, and Singapore), presumably because humans aid the dispersal and fragmentation of colonies in these cities. However, significant isolation by distance was found in introduced populations (Taiwan). Population structure analysis demonstrated that C. gestroi populations in Taiwan were likely introduced from the Philippines.

Identification of differentially expressed genes and signalling pathways in bark of Hevea brasiliensis seedlings associated with secondary laticifer differentiation using gene expression microarray

The natural rubber of Para rubber tree, Hevea brasiliensis, is the main crop involved in industrial rubber production due to its superior quality. The Hevea bark is commercially exploited to obtain latex, which is produced from the articulated secondary laticifer. The laticifer is well defined in the aspect of morphology; however, only some genes associated with its development have been reported. We successfully induced secondary laticifer in the jasmonic acid (JA)-treated and linolenic acid (LA)-treated Hevea bark but secondary laticifer is not observed in the ethephon (ET)-treated and untreated Hevea bark. In this study, we analysed 27,195 gene models using NimbleGen microarrays based on the Hevea draft genome. 491 filtered differentially expressed (FDE) transcripts that are common to both JA- and LA-treated bark samples but not ET-treated bark samples were identified. In the Eukaryotic Orthologous Group (KOG) analysis, 491 FDE transcripts belong to different functional categories that reflect the diverse processes and pathways involved in laticifer differentiation. In the Kyoto Encyclopedia of Genes and Genomes (KEGG) and KOG analysis, the profile of the FDE transcripts suggest that JA- and LA-treated bark samples have a sufficient molecular basis for secondary laticifer differentiation, especially regarding secondary metabolites metabolism. FDE genes in this category are from the cytochrome (CYP) P450 family, ATP-binding cassette (ABC) transporter family, short-chain dehydrogenase/reductase (SDR) family, or cinnamyl alcohol dehydrogenase (CAD) family. The data includes many genes involved in cell division, cell wall synthesis, and cell differentiation. The most abundant transcript in FDE list was SDR65C, reflecting its importance in laticifer differentiation. Using the Basic Local Alignment Search Tool (BLAST) as part of annotation and functional prediction, several characterised as well as uncharacterized transcription factors and genes were found in the dataset. Hence, the further characterization of these genes is necessary to unveil their role in laticifer differentiation. This study provides a platform for the further characterization and identification of the key genes involved in secondary laticifer differentiation.

Intracellular Delivery of Proteins via Fusion Peptides in Intact Plants

In current plant biotechnology, the introduction of exogenous DNA encoding desired traits is the most common approach used to modify plants. However, general plant transformation methods can cause random integration of exogenous DNA into the plant genome. To avoid these events, alternative methods, such as a direct protein delivery system, are needed to modify the plant. Although there have been reports of the delivery of proteins into cultured plant cells, there are currently no methods for the direct delivery of proteins into intact plants, owing to their hierarchical structures. Here, we demonstrate the efficient fusion-peptide-based delivery of proteins into intact Arabidopsis thaliana. Bovine serum albumin (BSA, 66 kDa) was selected as a model protein to optimize conditions for delivery into the cytosol. The general applicability of our method to large protein cargo was also demonstrated by the delivery of alcohol dehydrogenase (ADH, 150 kDa) into the cytosol. The compatibility of the fusion peptide system with the delivery of proteins to specific cellular organelles was also demonstrated using the fluorescent protein Citrine (27 kDa) conjugated to either a nuclear localization signal (NLS) or a peroxisomal targeting signal (PTS). In conclusion, our designed fusion peptide system can deliver proteins with a wide range of molecular weights (27 to 150 kDa) into the cells of intact A. thaliana without interfering with the organelle-targeting peptide conjugated to the protein. We expect that this efficient protein delivery system will be a powerful tool in plant biotechnology.

Physiological changes in major soldiers of Macrotermes gilvus (Isoptera: Termitidae) induced by the endoparasitoid Misotermes mindeni (Diptera: Phoridae)

The majority of true parasitoids manipulate their hosts physiology for their own benefit. In this study, we documented the physiological changes that occurred in major soldiers of the subterranean termite Macrotermes gilvus (Hagen) (Isoptera: Termitidae) parasitized by the koinobiont larval endoparasitoid Misotermes mindeni Disney and Neoh (Diptera: Phoridae). We compared the metabolic rate, body water content, body water loss rate, cuticular permeability, and desiccation tolerance between parasitized and unparasitized major soldiers. The metabolic rate of parasitized hosts was significantly higher than that of unparasitized termites. Mean total body water content of parasitized major soldiers (64.73±3.26%) was significantly lower than that of unparasitized termites (71.99±2.23%). Parasitized hosts also had significantly lower total body water loss rates (5.72±0.06%/h) and higher cuticular permeability (49.37±11.26 μg/cm/h/mmHg) than unparasitized major soldiers (6.75±0.16%/h and 60.76±24.98 μg/cm/h/mmHg, respectively). Parasitized major soldiers survived almost twice as long as unparasitized termites (LT(50)=6.66 h and LT(50)=3.40 h, respectively) and they had significantly higher tolerance to water loss compared to unparasitized termites (45.28±6.79% and 32.84±7.69%, respectively). Body lipid content in parasitized hosts (19.84±6.27%) was significantly higher than that of unparasitized termites (6.17±7.87%). Finally, parasitized hosts had a significantly lower percentage of cuticular water content than unparasitized major soldiers (10.97±1.84% and 13.17±2.21%, respectively). Based on these data, we conclude that the parasitism-induced physiological changes in the host are beneficial to the parasitoids as the alterations can clearly increase the parasites chances of survival when exposed to extreme environmental conditions and ensure that the parasitoids are able to complete their larval development successfully before the host dies.

Studies on Hanguana (Commelinales: Hanguanaceae) for Sunda IV: Hanguana major clarified, a new species from Sarawak, Malaysian Borneo, and description of male reproductive organs in H. bakoensis

SummaryHanguana major Airy Shaw, a highly distinctive but hitherto taxonomically confused species is re-delimited and shown to be restricted to a highland area centred on Gunung Kinabalu, Sabah, with a single collection from the highlands of Limbang, Sarawak. Airy Shaw’s original Latin description is amended to omit spurious morphological data, and is presented in English. One element of the plate accompanying the original publication, determined by Airy Shaw as Hanguana malayana (Jack) Merr., is described as a novel species: H. loi Mohd Fahmi, Sofiman Othman & P. C. Boyce, endemic to SW Sarawak. A key to the described Bornean Hanguana species is provided; H. major and H. loi are illustrated. Lastly, the hitherto unknown male inflorescences and flowers of H. bakoensis Siti Nurfazilah, Sofiman Othman & P. C. Boyce are described.