The bacterium strain SE31, a member of the genus Sciscionella, was isolated from intertidal sediments collected from Cape Rachado, Malaysia. The high quality draft genome sequence of Sciscionella strain SE31 with a genome size of approximately 7.4 Mbp is reported. Preliminary analysis revealed 46 putative gene clusters involved in the biosynthesis of secondary metabolites and 113 putative genes that are associated with bacterial virulence, disease and defense. Availability of the genome sequence of Sciscionella SE31 will contribute to a better understanding of the genus Sciscionella.
Anew hydrophilid genus Chimaerocyon gen. nov. containing two species, C. shimadai sp. nov. (Malaysia: Pahang) and C. sumatranus sp. nov. (Indonesia: Sumatra), is described. Specimens of C. shimadai were collected from brood cells in anest of Pheidole singaporensis Özdikmen, 2010. The biology of C. sumatranus remains unknown. A molecular phylogeny based on four genes (cox1, cox2, 18S and 28S) supports the placement of the genus as deeply nested within the Cercyon-group of the tribe Megasternini. This position is supported by the subdistal position of the median spur in the hind wing (unique to Megasternini) and the presence of sucking disc on male maxilla (unique for Megastemini+Sphaeridiini). The remaining external morphology differs substantially from other representatives of Megasternini. The hypothesis that the aberrant morphology of Chimaerocyon gen. nov. is a consequence of myrmecophily is discussed.
Burkholderia sp. strain GG4, isolated from the ginger rhizosphere, possesses a unique N-acylhomoserine lactone (AHL)-modifying activity that reduces 3-oxo-AHLs to 3-hydroxy-AHLs. To the best of our knowledge, this is the first sequenced genome from a bacterium of the genus Burkholderia that shows both quorum-sensing and signaling confusion activities.
Cupriavidus sp. strain BIS7 is a Malaysian tropical soil bacterium that exhibits broad heavy-metal resistance [Co(II), Zn(II), Ni(II), Se(IV), Cu(II), chromate, Co(III), Fe(II), and Fe(III)]. It is particularly resistant to Fe(II), Fe(III), and Zn(II). Here we present the assembly and annotation of its genome.
The Malayan gaur (Bos gaurus hubbacki) is one of the three subspecies of gaurs that can be found in Malaysia. We examined the phylogenetic relationships of this subspecies with other species of the genus Bos (B. javanicus, B. indicus, B. taurus, and B. grunniens). The sequence of a key gene, cytochrome b, was compared among 20 Bos species and the bongo antelope, used as an outgroup. Phylogenetic reconstruction was employed using neighbor joining and maximum parsimony in PAUP and Bayesian inference in MrBayes 3.1. All tree topologies indicated that the Malayan gaur is in its own monophyletic clade, distinct from other species of the genus Bos. We also found significant branching differences in the tree topologies between wild and domestic cattle.
A study of about 500 expressed sequence tags (ESTs), derived from a merozoite cDNA library, was initiated as an approach to generate a larger pool of gene information on Eimeria tenella. Of the ESTs, 47.7% had matches with entries in the databases, including ribosomal proteins, metabolic enzymes and proteins with other functions, of which 14.3% represented previously known E. tenella genes. Thus over 50% of the ESTs had no significant database matches. The E. tenella EST dataset contained a range of highly abundant genes comparable with that found in the EST dataset of T. gondii and may thus reflect the importance of such molecules in the biology of the apicomplexan organisms. However, comparison of the two datasets revealed very few homologies between sequences of apical organelle molecules, and provides evidence for sequence divergence between these closely-related parasites. The data presented underpin the potential value of the EST strategy for the discovery of novel genes and may allow for a more rapid increase in the knowledge and understanding of gene expression in the merozoite life cycle stage of Eimeria spp.
Since the inception of deep sequencing, isomiRs are consistently observed to be produced by most miRNA genes in a variety of cell types. IsomiRs appear as a variation in length from the canonical sequence annotated in miRBase, due to an addition or deletion of one or more nucleotides at the 5(') or 3(') ends or both. As the seed sequence is located at the 5(') end of the microRNA, the target mRNA will be theoretically different. Therefore, 5(')isomiRs might potentially target a new set mRNA compared to their canonical counterpart. This article gives an overview of investigations that explored the functional potential of isomiRs such as their ability to incorporate into Argonaute protein, the differential expression of isomiRs in various tissue types and cell lines, and the differences of mRNA targets between isomiR and its canonical microRNA. In addition, this article provides a brief introduction of RNA sponges as a potential way to inhibit isomiRs.
Vanadium-dependent haloperoxidases belong to a class of vanadium enzymes that may have potential industrial and pharmaceutical applications due to their high stability. In this study, the 5'-flanking genomic sequence and complete reading frame encoding vanadium-dependent bromoperoxidase (GcVBPO1) was cloned from the red seaweed, Fracilaria changii, and the recombinant protein was biochemically characterized. The deduced amino acid sequence of GcVBPO1 is 1818 nucleotides in length, sharing 49% identity with the vanadium-dependent bromoperoxidases from Corralina officinalis and Cor. pilulifera, respectively. The amino acid residues associated with the binding site of vanadate cofactor were found to be conserved. The Km value of recombinant GcVBPO1 for Br(-) was 4.69 mM, while its Vmax was 10.61 μkat mg(-1) at pH 7. Substitution of Arg(379) with His(379) in the recombinant protein caused a lower affinity for Br(-), while substitution of Arg(379) with Phe(379) not only increased its affinity for Br(-) but also enabled the mutant enzyme to oxidize Cl(-). The mutant Arg(379)Phe was also found to have a lower affinity for I(-), as compared to the wild-type GcVBPO1 and mutant Arg(379)His. In addition, the Arg(379)Phe mutant has a slightly higher affinity for H2O2 compared to the wild-type GcVBPO1. Multiple cis-acting regulatory elements associated with light response, hormone signaling, and meristem expression were detected at the 5'-flanking genomic sequence of GcVBPO1. The transcript abundance of GcVBPO1 was relatively higher in seaweed samples treated with 50 parts per thousand (ppt) artificial seawater (ASW) compared to those treated in 10 and 30 ppt ASW, in support of its role in the abiotic stress response of seaweed.
A 246-nt variant of Coconut cadang-cadang viroid (CCCVd) has been identified and described from oil palms with orange spotting symptoms in Malaysia. Compared with the 246-nt form of CCCVd from coconut, the oil palm variant substituted C(31)→U in the pathogenicity domain and G(70)→C in the central conserved domain. This is the first sequence reported for a 246-nt variant of CCCVd in oil palms expressing orange spotting symptoms.
Molecular and morphological analyses indicate that a new upland species of the Cyrtodactylus sworderi complex, C. tebuensis sp. nov. from Gunung Tebu, Terengganu, Malaysia is most closely related to C. sworderi and together they form the sister lineage to C. quadrivirgatus. Cyrtodactylus tebuensis sp. nov. is differentiated from all other species of Sundaland Cyrtodactylus on the basis of having the unique combination of large, conical, keeled body tubercles; tubercles present on top of head, occiput, nape, and limbs, and extending posteriorly beyond base of tail; 43-51 ventral scales; no transversely enlarged, median subcaudal scales; proximal, subdigital lamellae transversely expanded; 17-21 subdigital lamellae on fourth toe; an abrupt transition between posterior and ventral femoral scales; enlarged femoral scales; no femoral or precloacal pores; no precloacal groove; body bearing four wide, bold, dark brown stripes (lateral stripe on each flank and a pair of paravertebral stripes); and a pairwise sequence divergence of 13.0% from its closest relative C. sworderi based on the mitochondrial gene ND2. Cyrtodactylus tebuensis sp. nov. is the first endemic upland species of gekkonid from northeastern Peninsular Malaysia and underscores the necessity for additional field work in all upland systems.
A new species of karst-adapted gekkonid lizard of the genus Cnemaspis Strauch is described from Gua Gunting and Gua Goyang in a karst region of Merapoh, Pahang, Peninsular Malaysia whose unique limestone formations are in immediate danger of being quarried. The new species differs from all other species of Cnemaspis based on its unique suite of morphological and color pattern characters. Its discovery underscores the unique biodiversity endemic to karst regions and adds to a growing list of karst-adapted reptiles from Peninsular Malaysia. We posit that new karst-adapted species endemic to limestone forests will continue to be discovered and these regions will harbor a significant percentage of Peninsular Malaysia's biodiversity and thusly should be conserved rather than quarried.
Acinetobacter sp. strain GG2 is a quorum-sensing and quorum-quenching bacterium isolated from the ginger rhizosphere. It degrades a broad range of N-acylhomoserine lactone molecules via lactonase. The genome sequence of strain GG2 may provide insights on the regulation of quorum-sensing and quorum-quenching mechanisms in this bacterium.
Aeromonas is a pathogenic organism that is often found to infect humans. Here we report the draft genome of a clinical isolate in Malaysia, Aeromonas sp. strain 159, which shows N-acylhomoserine lactone production. In the draft genome of strain 159, luxI and luxR homologue genes were found to be located at contig 47, and these genes are believed to be important for the quorum-sensing system present in this pathogen.
A draft genome sequence of Pichia kudriavzevii M12 is presented here. The genome reveals the presence of genes encoding enzymes involved in xylose utilization and the pentose phosphate pathway for bioethanol production. Strain M12 is also a potential producer of phytases, enzymes useful in food processing and agriculture.
Recent work has suggested that in temperate and subtropical trees, leaf surface bacterial communities are distinctive to each individual tree species and dominated by Alpha- and Gammaproteobacteria. In order to understand how general this pattern is, we studied the phyllosphere bacterial community on leaves of six species of tropical trees at a rainforest arboretum in Malaysia. This represents the first detailed study of 'true' tropical lowland tree phyllosphere communities. Leaf surface DNA was extracted and pyrosequenced targeting the V1-V3 region of 16S rRNA gene. As was previously found in temperate and subtropical trees, each tree species had a distinctive bacterial community on its leaves, clustering separately from other tree species in an ordination analysis. Bacterial communities in the phyllosphere were unique to plant leaves in that very few operational taxonomic units (0.5%) co-occurred in the surrounding soil environment. A novel and distinctive aspect of tropical phyllosphere communities is that Acidobacteria were one of the most abundant phyla across all samples (on average, 17%), a pattern not previously recognized. Sequences belonging to Acidobacteria were classified into subgroups 1-6 among known 24 subdivisions, and subgroup 1 (84%) was the most abundant group, followed by subgroup 3 (15%). The high abundance of Acidobacteria on leaves of tropical trees indicates that there is a strong relationship between host plants and Acidobacteria in tropical rain forest, which needs to be investigated further. The similarity of phyllosphere bacterial communities amongst the tree species sampled shows a significant tendency to follow host plant phylogeny, with more similar communities on more closely related hosts.