The soil fungal community of the Klang Gates quartz ridge in Malaysia was determined by ITS amplicon sequencing using the Illumina HiSeq platform. The community contained 2767 OTUs, 47% of which could not be assigned to a phylum, likely representing new lineages. Those that could be assigned were found within 5 phyla, 16 classes, 49 orders and 98 families with over 85% of these within the Ascomycota. Sequence data is available from the NCBI's Sequence Read Archive (PRJNA542066). This data illustrates the microbial diversity in a particularly nutrient poor tropical soil and can be used for broader-scale comparisons of microbial distributions.
Arthrobacter sp. EM1 is a cold-adapted bacterium isolated from the Antarctic region, which was known to exhibit mannan-degrading activity. Accordingly, this strain not only promises a cell factory for mannan-degrading enzymes, widely used in industry but also serves as a model organism to decipher its cold adaptation mechanism. Accordingly, whole genome sequencing of the EM1 strain was performed via Single Molecule Real Time sequencing under the PacBio platform, followed by genome HGAP de novo assembly and genome annotation through Rapid Annotation System Technology (RAST) server. The chromosome of this strain is 3,885,750 bp in size with a GC content of 65.8. The annotation predicted a total of 3607 protein-coding genes and 65 RNA genes, which were classified under 398 subsystems. The subsystem with the highest number of genes is carbohydrate metabolism (397 genes), which includes two genes encoding mannan-degrading enzymes (endoglucanase and α-mannosidase). This confirmed that the EM1 strain is able to produce cold-adapted mannan degrading enzymes. The complete genome sequence data have been submitted to the National Center for Biotechnology Information (NCBI) and have been deposited at GenBank (Bioproject ID Accession Number: PRJNA963062; Biosample ID Accession Number: SAMN34434776; GenBank: CP124836.1; https://www.ncbi.nlm.nih.gov/nuccore/CP124836).
In this article, nine complete genomes of viruses from the genus Alphanodavirus and Betanodavirus (Family Nodaviridae) were comparatively analyzed and the data of their evolutionary origins and relatedness are reported. The nucleotide sequence alignment of the complete genomes from all species and their deduced evolutionary relationships are presented. High sequence similarity within the genus Betanodavirus compared to the genus Alphanodavirus was revealed in multiple sequence alignment of the Nodaviridae genomes. The amino acid sequence similarity for both RNA1 and RNA2 ORF is more conserved in Betanodavirus, compared to Alphanodavirus. The conserved and variable regions within the virus genome that were defined based on the multiple sequence alignments are presented in this dataset.
Interest in harvesting potential benefits from microalgae renders it necessary to have the many ecological niches of a single species to be investigated. This dataset comprises de novo whole genome assembly of two mangrove-isolated microalgae (from division Chlorophyta); Chlorella vulgaris UMT-M1 and Messastrum gracile SE-MC4 from Universiti Malaysia Terengganu, Malaysia. Library runs were carried out with 2 × 150 base paired-ends reads, whereas sequencing was conducted using Illumina Novaseq 2500 platform. Sequencing yielded raw reads amounting to ∼11 Gb in total bases for both species and was further assembled de novo. Genome assembly resulted in a 50.15 Mbp and 60.83 Mbp genome size for UMT-M1 and SE-MC4, respectively. All filtered and assembled genomic data sequences have been submitted to National Centre for Biotechnology Information (NCBI) and can be located at DDBJ/ENA/GenBank under the accession of VJNP00000000 (UMT-M1) and VIYE00000000 (SE-MC4).
Messastrum gracile SE-MC4 is a non-model microalga exhibiting superior oil-accumulating abilities. However, biomass production in M. gracile SE-MC4 is limited due to low cell proliferation especially after prolonged cultivation under oil-inducing culture conditions. Present data consist of next generation RNA sequencing data of M. gracile SE-MC4 under exponential and stationary growth stages. RNA of six samples were extracted and sequenced with insert size of 100 bp paired-end strategy using BGISEQ-500 platform to produce a total of 59.64 Gb data with 314 million reads. Sequences were filtered and de novo assembled to form 53,307 number of gene sequences. Sequencing data were deposited in National Center for Biotechnology Information (NCBI) and can be accessed via BioProject ID PRJNA552165. This information can be used to enhance biomass production in M. gracile SE-MC4 and other microalgae aimed towards improving biodiesel development.
This dataset presents morphological features, elemental composition and functional groups of different pre- and post-gamma (γ)-irradiated chitosan (10kGy & 20kGy) prepared from shrimp waste. The γ-irradiated chitosan was characterized using Fourier transfer infrared (FTIR) spectroscopy and X-ray diffraction (XRD) analyses. Thermogravimetry/differential thermal analysis (TG/DTA) were performed using Perkin Elmer Pyris Diamond DSC with a heating rate of 10 °C/minute and dynamic synthetic atmospheric air set at flow rate of 100 ml/minute. We observed γ-irradiated chitosan to have shorter polymer size, small pores and compacted structure with active alkyl and hydroxyl groups when compared to non-irradiated chitosan. Our data provides baseline understanding for structure of shrimp chitosan after 60Co exposure which means, the biopolymer becomes more stable and is considered suitable for vast food industry applications.
Inactivation of smoothened protein (SMO) by the antagonists in SHH-driven cancer types is essential for inhibition of cancer progression. This article presents molecular dynamics (MD) trajectories of water solution of three protein-ligand complexes smoothened-β-sitosterol (SMO-BST), smoothened-sonidegib (SMO-SNG) and smoothened-cholesterol (SMO-CLR) using CHARMM36 and SPC/E water model combination. Additionally, the work presents the topologies and trajectories of GROMACS files that were employed to analyse the protein-ligand interaction types (PyContact) and binding energy calculation (g_mmpbsa). The data demonstrated that equilibrated models of SMO-SNG and SMO-CLR complexes showed crucial residues that almost similar for interaction and contribution energy as previously reported in laboratory setup (in vitro). Initial simulations confirmed the role of ARG451 and TRP535 in the dynamic regulation of SMO. These data then were used as a reference for understanding the molecular dynamics of SMO-BST complex and thus predicted its mechanism of action.
Barrientosiimonas humi gen. nov., sp. nov. 39T is a rare actinobacteria strain isolated from the less explored extreme environment of the Antarctic soil. Here, we present the whole genome sequencing and annotation data from the high-quality draft genome of B. humi from Antarctica. The extracted genomic deoxyribonucleic acid (DNA) was sequenced using the PacBio Sequel sequencing platform, followed by the Illumina HiSeq sequencing system. Subsequently, the assembly data from Canu 1.7 and Pilon were subjected to bioinformatics analysis for genome annotation to analyze the entire genomic information of the sequences. Different bioinformatics analysis approaches were used to disclose a high-quality draft genome basis for B. humi and provided a better understanding of its biological and molecular functions. Note that 83,639 reads were predicted from its 3.6Mb genome size, with a guanine-cytosine content (GC) content of 72.39%. The genome was assembled into two contigs, where the larger contig represents the chromosome and the smaller contig represents the plasmid. It is composed of 3,381 coding genes, with about 95% of them being functionally annotated. It consists of 3,318 coding sequences, one tmRNA gene, 57 tRNA genes, and five repeated regions. B. humi was evident, sharing a close sequence similarity with the species Demetria terragena and the family Dermacoccaceae. Gene Ontology (GO) functional classification indicated cell and cell parts were highly represented among the cellular component category; catalytic activity and binding were the most enriched processes within the molecular function category; metabolic and cellular processes were the most represented in the biological process category. Clusters of Orthologous Group (COG) functional classification revealed metabolism-related genes were highly enriched and mostly mapped to amino acid transport metabolism, transcription, energy production, and conversion. Moreover, the Kyoto Encyclopedia of Genes and Genomes (KEGG) functional classification reported that the metabolism process was the most represented KEGG pathway. There were 52 biosynthetic gene clusters involved in secondary metabolites biosynthesis, indicating B. humi has antibacterial, antifungal, cytotoxic, and inhibitor bioactivities. The dataset of the whole-genome sequence of B. humi has been deposited in the European Nucleotide Archive (ENA) repository under the accession number PRJEB44986 / ERP129097. The dataset of the genome annotation of B. humi had been deposited in Zenodo. The reported genomic sequence data for B. humi contributes comprehensive data to the current molecular information of the species, serving as a significant approach that facilitates the advancement of medicine.
Fission tracks are linear trails of intense radiation damage in the crystal structure of a mineral, produced by spontaneous fissioning of uranium-238 (238U) atoms. Detail information on the low-temperature thermal histories of rocks, below∼120 °C for tracks in apatite and below∼350 °C for zircon, can be provided by Fission-track (FT) analysis. The purpose of this article is to present apatite and zircon fission-track data, and U-Pb granite ages that provide information about the cooling histories of a rock which can be crucial in comprehending the exhumation episodes of the study area, in particular, and the region, in general. Granite samples were collected along the same vertical profile at different elevation, 178-944 m.a.s.l. These samples were used to determine Fission-Track and crystallization ages. HeFTy software was employed to interpret the cooling histories of the samples using forward and inverse models. The inverse model was an approach of reproducing the observed data, and it was carried out only for fission-track data from the apatite grains. And it was constructed after generating a number of forward models, where in each of these models the predicted apatite fission-track parameters were compared to the measured values. The apatite fission track (AFT) and zircon fission track (ZFT) data indicated expected age trends, i.e. the older ages at higher elevations and the younger ages at lower elevations. Similarly, the data shows that the apatite and zircon FT ages appear younger than the age of the rock crystallization. The U-Pb age in zircon consistently suggest the age of the granite is Late Triassic.
This data article provides macroeconomic data that can be used to generate macroeconomic volatility. The data cover a sample of seven selected countries in the Asia Pacific region for the period 2004-2014, including both developing and developed countries. This dataset was generated to enhance our understanding of the sources of macroeconomic volatility affecting the countries in this region. Although the Asia Pacific region continues to remain as the most dynamic part of the world's economy, it is not spared from various sources of macroeconomic volatility through the decades. The reported data cover 15 types of macroeconomic data series, representing three broad categories of indicators that can be used to proxy macroeconomic volatility. They are indicators that account for macroeconomic volatility (i.e. volatility as a macroeconomic outcome), domestic sources of macroeconomic volatility and external sources of macroeconomic volatility. In particular, the selected countries are Malaysia, Thailand, Indonesia and Philippines, which are regarded as developing countries, while Singapore, Japan and Australia are developed countries. Despite the differences in level of economic development, these countries were affected by similar sources of macroeconomic volatility such as the Asian Financial Crisis and the Global Financial Crisis. These countries were also affected by other similar external turbulence arising from factors such as the global economic slowdown, geopolitical risks in the Middle East and volatile commodity prices. Nonetheless, there were also sources of macroeconomic volatility which were peculiar to certain countries only. These were generally domestic sources of volatility such as political instability (for Thailand, Indonesia and Philippines), natural disasters and anomalous weather conditions (for Thailand, Indonesia, Philippines, Japan and Australia) and over-dependence on the electronic sector (for Singapore).
These datasets present a list of small RNAs from three drug-susceptible Mycobacterium tuberculosis strains isolated from Sabah, Malaysia. Sputum samples were obtained from three tuberculosis patients belonging to different districts. The bacteria were detected using GeneXpert MTB/RIF, isolated and cultured in BACTECTM MGITTM 320, and tested for their drug susceptibility. Total RNAs were extracted, sequenced, and analyzed using bioinformatic tools to filter out small RNA present in the Mycobacterium tuberculosis strains. Small RNA sequencing generated total raw reads of 63,252,209, 63,636,812, and 61,148,224 and total trimmed reads (15-30 nucleotides) of 51,533,188, 53,520,197, and 51,363,772 for Mycobacterium tuberculosis strain SBH49, SBH149, and SBH372, respectively. The raw data were submitted to the Sequence Read Archive (SRA) database of the National Center for Biotechnology Information (NCBI) under the accession numbers of SRX16744291 (SBH49), SRX16744292 (SBH149), and SRX16744293 (SBH372). Small RNAs play important roles in cellular processes such as cell differentiation, cell signaling, development of resistance to antibiotics and immune response, and metabolism regulation. The small RNAs determined here could provide further insights into various cellular processes crucial for Mycobacterium tuberculosis survivability and a better understanding of their gene regulation which ultimately opens a new pathway for combating tuberculosis infection.
Mangrovimonas sp. strain CR14 is a halophilic bacterium affiliated with family Flavobacteriaceae which was successfully isolated from mangrove soil samples obtained from Tanjung Piai National Park, Johor. The whole genome of strain CR14 was sequenced on an Illumina HiSeq 2500 platform (2 × 150 bp paired end). Herein, we report the genome sequence of Mangrovimonas sp. strain CR14 in which its assembled genome consisted 20 contigs with a total size of 3,590,195 bp, 3209 coding sequences, and an average 36.08% G + C content. Genome annotation and gene mining revealed that this bacterium demonstrated proteolytic activity which could be potentially applied in detergent industry. This whole-genome shotgun data of Mangrovimonas sp. strain CR14 has been deposited at DDBJ/ENA/GenBank under the accession JAAFZY000000000. The version described in this paper is version JAAFZY010000000.
The data presented in this article examine the relationship between the subcomponents of emotional intelligence (emotional perception and expression, emotional facilitation of thinking, emotional understanding and emotional management) and the stages of change (pre-contemplation, contemplation, action and maintenance). The final data were obtained from 429 Malaysian inmates (374 male and 55 female) recruited from eight Malaysian prisons in four different zones. The two instruments used were the Self-Rated Malaysian Emotional Intelligence Scale (SRMEIS) and the University Rhodes Island Change Assessment Scale (URICA). Both instruments underwent expert validation through construct and test-retest validity. The researcher randomly distributed a total of 550 questionnaires, of which 429 were accepted and 121 were rejected due to missing data and outliers, resulting in 78% of participants providing data that could be used in the analyses. All participants were informed of the confidentiality of their data, and their participation was voluntary. SPSS and Excel files are provided as supplementary material.
The oil palm industry, especially in Indonesia and Malaysia is being threatened by Basal Stem Rot (BSR) disease caused by Ganoderma boninense. There is no conclusive remedy in handling this disease effectively. In this study, metagenomics analysis of soil were analyzed for a better understanding of the microbial diversity in relation to BSR disease. Study was conducted in three plantation sites of Sabah, Malaysia which incorporated different disease management and agronomic practices. The estates are located at Sandakan (Kam Cheong Plantation), Lahad Datu (FGV Ladang Sahabat) and Tawau (Warisan Gagah). Soil samples were collected from disease free, high and low BSR incidence plots. Illumina MiSeq metagenomic analysis using V3-V4 region of 16S rRNA gene was employed to study the microbial diversity. Bacteria (97.4%) and Archaea (0.2%) were found majority in kingdom taxonomy level. The most abundant phyla were Proteobacteria, Acidobacteria, Actinobacteria, and Verrucomicrobia. Higher alpha diversity of all species was observed among all tested soil from each estates. Beta analysis was analyzed using non phylogenetic UnifRac matrix and visualized using Principal Coordinates Analysis (PCoA). The tested soil samples in Kam Cheong Plantation were found to have similar bacterial communities. The data provided is useful as an indicator in developing biology controls against Ganoderma boninense.
The data available in this repository were gathered from Balok, the only most productive spawning site for horseshoe crabs Tachypleus gigas and Carcinoscorpius rotundicauda in East Coast of Peninsular Malaysia. The mangrove horseshoe crab, C. rotundicauda population and spawning data are available in the first table. The horseshoe crabs were retrieved from Balok River using 11.43 cm mesh size gill nets installed at the river mouth, the confluence and last meander. The arthropods were inspected for damage, abnormality and growth before their release into Balok River, particularly at the site of capture. Sediment samples were retrieved at their spawning grounds to ascertain sediment composition and size classifications which were also processed using Logarithmic Method of Moments. Water parameters like temperature, pH and salinity were also investigated during year 2016. All these information are compiled into the second table and arranged according to the period of data availability. The horseshoe crab catch data of years 2012, 2013, 2014, 2015 and 2016 were made available by artisanal fisher and compiled in the third and fourth table for inter-species comparison.
We collected data on the trade of seven turtle and tortoise species endemic to Indonesia and Malaysia (Amyda cartilaginea, Batagur borneoensis, Cuora amboinensis, Carettochelys insculpta, Heosemys annandalii, Heosemys grandis, and Heosemys spinosa). The data on those species included: operations costs of three breeding farms and one export facility; species life-history traits; and species international legal trade and confiscation data. We collected data for the facilities (one in Malaysia and three in Indonesia) using site visits and a semi-structured questionnaire. We conducted a literature review to compile relevant information on species' life-history traits to estimate breeding viability. We downloaded species-specific data on international trade from the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) Trade Database for the exporting countries (Malaysia and Indonesia) for 2000-2015. We compared legal trade with confiscation data obtained from CITES. The data in this article can provide insights into the operations of turtle breeding farms in Southeast Asia. These data can be used as a reference for the inspection of breeding farms and for legislative bodies to determine whether captive breeding for select turtle species is feasible.
In this article we present a standardized dataset on 6659 songbirds (Passeriformes) highlighting information relevant to species conservation prioritization with a main focus to support the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). Data were collected from both scientific and grey literature as well as several online databases. The data are structured into six knowledge categories: Conventions and Treaties, Human Use, Extinction Risk, Management Opportunities, Biological Information, and Intrinsic Values. The Conventions and Treaties category includes the listings for two international conventions, CITES and the Convention on the Conservation of Migratory Species of Wild Animals (CMS), as well as EU listings for the EU Wildlife Trade Regulations and the EU Birds Directive. The Human Use category contains information on both regulated trade collected from the CITES Trade Database and the United States' Law Enforcement Management Information System (LEMIS), and highly aggregated data on seizures which we obtained from TRAFFIC, the United Nations Office on Drugs and Crime (UNODC) and two data sources on traditional medicine. We also present, for the first time, the complete Songbirds in Trade Database (SiTDB), a trade database curated by taxon expert S. Bruslund based on expert knowledge, literature review, market surveys and sale announcements. Data on the types of human use, including traditional medicine are also provided. The knowledge area on Extinction Risk contains data on the species' IUCN Red List status, the Alliance for Zero Extinction Trigger Species status, site and population at the site, the species' IUCN Climate Change Vulnerability Assessment, and the listing of priority species at the Asian Songbird Crisis Summit. In the Management Opportunities category, we gathered data on ex-situ management from Species360 zoo holdings as well as species management plans from the European and North American Zoo Associations (EAZA and AZA, respectively). Biological Information includes data on body mass, clutch size, diet, availability of data from the IUCN Red List on habitat systems, extent of occurrence, generation length, migration pattern, distribution, and biological data from the Demographic Species Knowledge Index, number of occurrences recorded by the Global Biodiversity Information Facility (GBIF) as well as genomic data from the Bird 10 000K Genomes (B10K) project, Vertebrate Genome Project (VGP) and GenBank. Information on invasive species is also part of this knowledge area. The Intrinsic Value category refers to two measures of the species' intrinsic value, namely Ecological and Evolutionary Distinctiveness. In order to make these knowledge areas comparable, we standardized data following the taxonomy of the Handbook of the Birds of the World and Birdlife (Version 4, 2019). The data enable a broad spectrum of analyses and will be useful to scientists for further research and to policymakers, zoos and other conservation stakeholders for future prioritization decisions.
The dataset contains tree height data collected in 200 mangrove and non-mangrove trees sampled in various sites in Malaysia. Different height measurement methods were performed, including visual measurements (stick, thumb rule) and precision field instruments (clinometer, laser rangefinder and altimeter), which were compared against benchmark values obtained using an unmanned aerial vehicle (UAV) and a Leica distometer. The core data have been analysed and interpreted in the paper by Saliu et al. ''An accuracy analysis of mangrove tree height mensuration using forestry techniques, hypsometers and UAVs '' [1], in which the accuracy of each method for tree height measurement was discussed.
This paper presents the results of mercury analysis on 786 abiotic (surface sediments) and biotic (plant and animal tissues) samples collected from 10 sites at Matang Mangrove Forest Reserve in Peninsular Malaysia. Sediment samples were collected at the surface level from both river bank and forest understory. Whereas plant tissues obtained from Rhizophora apiculata Blume and Rhizophora mucronata L. consisted of leaves (in four stages namely young, mature, senescent and decomposing), bark and roots (divided into xylem, cortex and epidermis), the animal samples were represented by muscle tissue of the gastropod Cassidula aurisfelis Bruguière and the cockle Tegillarca granosa L. The mercury concentration measurements were obtained through a cold vapor atomic absorption spectrometer. The core data have been analysed and interpreted in the paper "Distribution of mercury in sediments, plant and animal tissues in Matang Mangrove Forest Reserve, Malaysia" [1].
The present dataset provides information on the abundance of microplastics (MPs) in relation to different feeding habits of the four mangrove brachyuran crab species namely, Parasesarma eumolpe, Austruca annulipes, Metaplax elegans and Scylla olivacea at Setiu Wetlands in Peninsular Malaysia. Three sites namely, Pulau Layat (upstream, close to the core mangrove zone), Kampung Pengkalan Gelap (midstream, close to the settlements), and Pulau Sutung (downstream, close to the shifted river mouth) were chosen for the sample collection (through hand catch method and traps) in both the dry (Feb-Mar 2021) and the wet (Dec 2021 - Jan 2022) seasons. The cardiac stomach of each crab was dissected, digested in potassium hydroxide and then filtered through a 1.6 µm pore size glass fibre filter using the vacuum pump. The abundance, type and colour of MPs per crab individual were determined under a stereomicroscope (Carl Zeiss Stemi 508, China) attached to the digital camera (Axiocam 208 colour). The general abundance of MPs was found in the order of carnivorous S. olivacea > microphytobenthos feeder A. annulipes > herbivorous P. eumolpe > detritivorous M. elegans. The data also reveal morphometric measurements such as body weight, gut weight, carapace width and carapace length of the crab specimens. The information given in this article is useful for study replications and scientific comparisons, especially with brachyuran crabs and other organisms with similar feeding guilds, in the mangroves of Malaysia and elsewhere.