The complete mitochondrial genome of the Bass yabby Trypaea australiensis was obtained from a partial genome scan using the MiSeq sequencing system. The T. australiensis mitogenome is 16,821 bp in length (70.25% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a putative 1977 bp non-coding AT-rich region. This Trypaea mitogenome sequence is the 5th for the family Callianassidae and represents a new gene order for the Decapoda involving protein-coding, rRNA and tRNA genes and the control region.
The mitochondrial genome of the rock pool prawn (Palaemon serenus), is sequenced, making it the third for genera of the family Palaemonidae and the first for the genus Palaemon. The mitogenome is 15,967 base pairs in length and comprises 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The P. serenus mitogenome has an AT bias of 58.97% and a base composition of 29.79% for T, 24.14% for C, 29.18% for A, and 16.89% for G. The mitogenome gene order of P. serenus is identical to Exopalaemon carinicauda.
The mitochondrial genome sequence of the Australian freshwater shrimp, Paratya australiensis, is presented, which is the fourth for genera of the superfamily Atyoidea and the first atyid from the southern hemisphere. The base composition of the P. australiensis, mitogenome is 33.55% for T, 18.24% for C, 35.16% for A, and 13.06% for G, with an AT bias of 71.58%. It has a mitogenome of 15,990 base pairs comprised of 13 protein-coding, 2 ribosomal subunit and 22 transfer RNAs genes and a non-coding AT-rich region. The mitogenome gene order for the species is typical for atyid shrimps, which conform to the primitive pan crustacean model.
The complete mitochondrial genome of the hermit crab Clibanarius infraspinatus was recovered by genome skimming using Next-Gen sequencing. The Clibanarius infraspinatus mitogenome has 16,504 base pairs (67.94% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a putative 1500 bp non-coding AT-rich region. The Clibanarius infraspinatus mitogenome sequence is the first for the family Diogenidae and the second for the superfamily Paguroidea and exhibits a translocation of the ND3 gene not previously reported for the Decapoda.
A Gram-negative, filamentous aerobic bacterium designated as strain Mgbs1T was isolated on 12 April 2017 from the subsurface soil and leaf litter substrate at the base of a Koompassia malaccensis tree in a tropical peat swamp forest in the northern regions of the state of Selangor, Malaysia (3° 39' 04.7' N 101° 17' 43.7'' E). Phylogenetic analyses based on the full 16S rRNA sequence revealed that strain Mgbs1T belongs to the genus Chitinophaga with the greatest sequence similarity to Chitinophaga terrae KP01T (97.65 %), Chitinophaga jiangningensis DSM27406T (97.58 %), and Chitinophaga dinghuensis DHOC24T (97.17 %). The major fatty acids of strain Mgbs1T (>10 %) are iso-C15 : 0, C16 : 1 ω5c and iso-C17 : 0 3-OH while the predominant respiratory quinone is menaquinone-7. Strain Mgbs1T has a complete genome size of 8.03 Mb, with a G+C content of 48.5 mol%. The DNA-DNA hybridization (DDH) score between strain Mgbs1T and C. jiangningensis DSM27406T was 15.9 %, while in silico DDH values of strain Mgbs1T against C. dinghuensis DHOC24T and C. terrae KP01T were 20.0 and 19.10% respectively. Concurrently, Average Nucleotide Identity (ANI) scores between strain Mgbs1T against all three reference strains are 73.2 %. Based on the phenotypic, chemotaxonomic, and phylogenetic consensus, strain Mgbs1T represents a novel species of the genus Chitinophaga, for which the name Chitinophaga extrema sp. nov. is proposed (=DSM 108835T=JCM 33276T).
Jeotgalibacillus spp. are halophilic bacteria within the family Planococcaceae. No genomes of Jeotgalibacillus spp. have been reported to date, and their metabolic pathways are unknown. How the bacteria survive in hypertonic conditions such as seawater is yet to be discovered. As only few studies have been conducted on Jeotgalibacillus spp., potential applications of these bacteria are unknown. Here, we present the complete genome of J. malaysiensis D5(T) (=DSM 28777(T) =KCTC 33350(T)), which is invaluable in identifying interesting applications for this genus.
The genome data of Streptomyces sp. FH025 comprised of 8,381,474 bp with a high GC content of 72.51%. The genome contains 7035 coding sequences spanning 1261 contigs. Streptomyces sp. FH025 contains 57 secondary metabolite gene clusters including polyketide synthase, nonribosomal polyketide synthase and other biosynthetic pathways such as amglyccycl, butyrolactone, terpenes, siderophores, lanthipeptide-class-iv, and ladderane. 16S rRNA analysis of Streptomyces sp. FH025 is similar to the Streptomyces genus. This whole genome project has been deposited at NCBI under the accession JAFLNG000000000.
The Austropotamobius pallipes complete mitogenome has been recovered using Next-Gen sequencing. Our sample of A. pallipes has a mitogenome of 15,679 base pairs (68.44% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a 877 bp non-coding AT-rich region. This is the first mitogenome sequenced for a crayfish from the family Astacidae and the 4(th) for northern hemisphere genera.
Aquilaria tree species are naturally distributed in the Indomalesian region and are protected against over-exploitation. They produce a fragrant non-timber product of high economic value, agarwood. Ambiguous species delimitation and limited genetic information within Aquilaria are among the impediments to conservation efforts. In this study, we conducted comparative analysis on eight Aquilaria species complete chloroplast (cp) genomes, of which seven were newly sequenced using Illumina HiSeq X Ten platform followed by de novo assembly. Aquilaria cp genomes possess a typical quadripartite structure including gene order and genomic structure. The length of each of the cp genome is about 174 kbp and encoded between 89 and 92 proteins, 38 tRNAs, and 8 rRNAs, with 27 duplicated in the IR (inverted repeat) region. Besides, 832 repeats (forward, reverse, palindrome and complement repeats) and nine highly variable regions were also identified. The phylogenetic analysis suggests that the topology structure of Aquilaria cp genomes were well presented with strong support values based on the cp genomes data set and matches their geographic distribution pattern. In summary, the complete cp genomes will facilitate development of species-specific molecular tools to discriminate Aquilaria species and resolve the evolutionary relationships of members of the Thymelaeaceae family.
Periodontal disease represents a group of oral inflammatory infections initiated by oral pathogens which exist as a complex biofilms on the tooth surface and cause destruction to tooth supporting tissues. The severity of this disease ranges from mild and reversible inflammation of the gingiva (gingivitis) to chronic destruction of connective tissues, the formation of periodontal pocket and ultimately result in loss of teeth. While human subgingival plaque harbors more than 500 bacterial species, considerable research has shown that Porphyromonas gingivalis, a Gram-negative anaerobic bacterium, is the major etiologic agent which contributes to chronic periodontitis. This black-pigmented bacterium produces a myriad of virulence factors that cause destruction to periodontal tissues either directly or indirectly by modulating the host inflammatory response. Here, this review provides an overview of P. gingivalis and how its virulence factors contribute to the pathogenesis with other microbiome consortium in oral cavity.
A Gram-negative bacterium, Pantoea stewartii subspecies stewartii (P. stewartii subsp. stewartii) has been recognized as the causative agent for jackfruit bronzing disease in Malaysia. Here, we report the whole genome sequencing dataset of P. stewartii subsp. stewartii strain SQT1 isolated from local infected jackfruit. The paired-end libraries with an insert size of 350 bp was subjected to the Illumina Hiseq 4000, generating a genome size of 4,783,993 bp with a G+C content of 53.7%. A total protein of 4,671 was identified including virulence factors, resistance factors and secretion systems. Pantoea stewartii subsp. stewartii strain DC283 (NCBI accession no. CP017581.1) was used as a reference genome, where the query hit 72% coverage and average sequencing depth of 68. In total, 28,717 nucleotide polymorphisms, 520 small insertion/deletions and 142 structure variants were identified. The complete genome was deposited at the European Nucleotide Archive under the sample accession number ERP119356 and study accession number PRJEB36196.
The taxonomic position of a novel Amycolatopsis strain isolated from a high altitude Atacama Desert subsurface soil was established using a polyphasic approach. The strain, isolate H5T, was shown to have chemical properties typical of members of the genus Amycolatopsis such as meso-diaminopimelic acid as the diamino acid in the cell wall peptidoglycan, arabinose and galactose as diagnostic sugars and MK-9(H4) as the predominant isoprenologue. It also has cultural and morphological properties consistent with its classification in the genus, notably the formation of branching substrate hyphae which fragment into rod-like elements. 16S rRNA gene sequence analyses showed that the strain is closely related to the type strain of Amycolatopsis mediterranei but could be distinguished from this and other related Amycolatopsis strains using a broad range of phenotypic properties. It was separated readily from the type strain of Amycolatopsis balhymycina, its near phylogenetic neighbour, based on multi-locus sequence data, by low average nucleotide identity (92.9%) and in silico DNA/DNA relatedness values (51.3%) calculated from draft genome assemblies. Consequently, the strain is considered to represent a novel species of Amycolatopsis for which the name Amycolatopsis vastitatis sp. nov. is proposed. The type strain is H5T (= NCIMB 14970T = NRRL B-65279T).
Here we report the complete mitochondrial genome of the Bornean banteng Bos javanicus lowi (Cetartiodactyla, Bovidae), which was determined using next-generation sequencing. The mitochondrial genome is 16,344 bp in length containing 13 protein-coding genes, 21 tRNAs and 2 rRNAs. It shows the typical pattern of bovine mitochondrial arrangement. Phylogenetic tree analysis of complete mtDNA sequences showed that Bornean banteng is more closely related to gaur than to other banteng subspecies. Divergence dating indicated that Bornean banteng and gaur diverged from their common ancestor approximately 5.03 million years ago. These results suggest that Bornean banteng might be a distinct species in need of conservation.
Discovery of species-specific interaction between the host and virus has drawn the interest of many researchers to study the evolution of the newly emerged virus. Comparative genome analysis provides insights of the virus functional genome evolution and the underlying mechanisms of virus-host interactions. The analysis of nucleotide composition signified the evolution of nodavirus towards host specialization in a host-specific mutation manner. GC-rich genome of betanodavirus was significantly deficient in UpA and UpU dinucleotides composition, whilst the AU-rich genome of gammanodavirus was deficient in CpG dinucleotide. The capsid of MrNV and PvNV of gammanodavirus retains the highest abundance of adenine and uracil at the second codon position, respectively, which were found to be very distinctive from the other genera. ENC-GC3 plot inferred the influence of natural selection and mutational pressure in shaping the evolution of MrNV RdRp and capsid, respectively. Furthermore, CAI/eCAI analysis predicts a comparable adaptability of MrNV in squid, Sepia officinalis than its natural host, Macrobrachium rosenbergii. Thus, further study is warranted to investigate the capacity of MrNV replication in S. officinalis owing to its high codon adaptation index.
The increasing interest in understanding the evolutionary relationship between members of the Pteropodidae family has been greatly aided by genomic data from the Old World fruit bats. Here we present the complete mitogenome of Geoffroy's rousette, Rousettus amplexicaudatus found in Peninsular Malaysia . The mitogenome constructed is 16,511bp in length containing 37 genes; 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a D-loop region. The overall base composition is estimated to be 32.28% for A, 25.64% for T, 14.09% for G and 27.98% for C, indicating a slightly AT rich feature (57.93%). A phylogenetic and BLASTn analysis against other available mitogenomes showed Malaysian R. amplexicaudatus matched 98% similarity to the same species in Cambodia and Vietnam. However, it differed considerably (92.53% similarity) with the same species in the Philippines. This suggests flexibility in Rousettus sp. with regards to adapting to mesic and dry habitats, ability for long-distance dispersal and remarkably precise lingual echolocation thus supporting its wide-range distribution and colonization. Further taxonomical and mitogenomic comparatives are required in resolving the evolutionary relationship between Rousettus spp.
In 2019, 10 million new cases of tuberculosis have been reported worldwide. Our data reports genetic analyses of a Mycobacterium tuberculosis strain SBH321 isolated from a 31-year-old female with pulmonary tuberculosis. The genomic DNA of the strain was extracted from pure culture and subjected to sequencing using Illumina platform. M. tuberculosis strain SBH321 consists of 4,374,895 bp with G+C content of 65.59%. The comparative analysis by SNP-based phylogenetic analysis using maximum-likelihood method showed that our strain belonging to sublineage of the Ural family of Europe-America-Africa lineage (Lineage 4) and clustered with M. tuberculosis strain OFXR-4 from Taiwan. The whole genome sequence is deposited at DDBJ/ENA/GenBank under the accession WCJH00000000 (SRR10230353).
A Mycobacterium tuberculosis strain SBH162 was isolated from a 49-year-old male with pulmonary tuberculosis. GeneXpert MDR/RIF identified the strain as rifampicin-resistant M. tuberculosis. The whole genome sequencing was performed using Illumina HiSeq 4000 system to further investigate and verify the mutation sites of the strain through genetic analyses namely variant calling using bioinformatics tools. The de novo assembly of genome generated 100 contigs with N50 of 156,381bp. The whole genome size was 4,343,911 bp with G + C content of 65.58% and consisted of 4,306 predicted genes. The mutation site, S450L, for rifampicin resistance was detected in the rpoB gene. Based on the phylogenetic analysis using the Maximum Likelihood method, the strain was identified as belonging to the Europe America Africa lineage (Lineage 4). The genome dataset has been deposited at DDBJ/ENA/GenBank under the accession number SMOE00000000.
Salmonella is a gram-negative rod-shape bacterium from the family of Enterobacteriaceae that can cause a wide range of human disease such as enteric fever, gastroenteritis and bacteremia. Here we sequenced two genomes of Salmonella bacteria isolated from the Gallus gallus domesticus host. Genomic DNA of the two Salmonella isolates were extracted and subjected to whole genome sequencing using Illumina platform. The draft genome size of the two Salmonella isolates was determined to be 4,902,295 bp (S18) and 4,847,310 bp (S20) respectively. The percentage of GC content for both draft genomes is the same which is 52.1%. Both the whole genome shotgun project (S18 and S20) has been deposited in National Center for Biotechnology Information Sequence Read Archive under the accession number of SRR7503041 (S18) and SRR7503040 (S20). The sequenced genome (S18 and S20) were aligned with the reference genome and three other Salmonella genomes from serogroup B, D and E. The data obtained show the presence of unique DNA sequences in S18 and S20 genomes. This unique DNA sequences are from the fimbrial gene group.
The taxonomic position of an actinobacterium strain, C296001T, isolated from a soil sample collected in Sarawak, Malaysia, was established using a polyphasic approach. Phylogenetically, strain C296001T was closely associated with the genus Luteipulveratus and formed a distinct monophyletic clade with the only described species, Luteipulveratus mongoliensis NBRC 105296T. The 16S rRNA gene sequence similarity between strain C296001T and L. mongoliensis was 98.7 %. DNA-DNA hybridization results showed that the relatedness of strain C296001T to L. mongoliensis was only 21.5 %. The DNA G+C content of strain C296001T was 71.7 mol%. Using a PacBio RS II system, whole genome sequences for strains C296001T and NBRC 105296T were obtained. The genome sizes of 4.5 Mbp and 5.4 Mbp determined were similar to those of other members of the family Dermacoccaceae. The cell-wall peptidoglycan contained lysine, alanine, aspartic acid, glutamic acid and serine, representing the peptidoglycan type A4α l-Lys-l-Ser-d-Asp. The major menaquinones were MK-8(H4), MK-8 and MK-8(H2). Phosphatidylglycerol, phosphatidylinositol, diphosphatidylglycerol and phosphoglycolipid were the polar lipids, while the whole-cell sugars were glucose, fucose and lesser amounts of ribose and galactose. The major fatty acids were iso-C16 : 0, anteiso-C17 : 0, iso-C16 : 1 H, anteiso-C17 : 1ω9c, iso-C18 : 0 and 10-methyl C17 : 0. Chemotaxonomic analyses showed that C296001T had typical characteristics of members of the genus Luteipulveratus, with the main differences occurring in phenotypic characteristics. On the basis of the phenotypic and chemotaxonomic evidence, it is proposed that strain C296001T be classified as a representative of a novel species in the genus Luteipulveratus, for which the name Luteipulveratus halotolerans sp. nov. is recommended. The type strain is C296001T ( = ATCC TSD-4T = JCM 30660T).
Copepoda is one of the most ecologically important animal groups on Earth, yet very few genetic resources are available for this Subclass. Here, we present the first whole genome sequence (WGS, acc. UYDY01) and the first mRNA transcriptome assembly (TSA, Acc. GHAJ01) for the tropical cyclopoid copepod species Apocyclops royi Until now, only the 18S small subunit of ribosomal RNA gene and the COI gene has been available from A. royi, and WGS resources was only available from one other cyclopoid copepod species. Overall, the provided resources are the 8th copepod species to have WGS resources available and the 19th copepod species with TSA information available. We analyze the length and GC content of the provided WGS scaffolds as well as the coverage and gene content of both the WGS and the TSA assembly. Finally, we place the resources within the copepod order Cyclopoida as a member of the Apocyclops genus. We estimate the total genome size of A. royi to 450 Mb, with 181 Mb assembled nonrepetitive sequence, 76 Mb assembled repeats and 193 Mb unassembled sequence. The TSA assembly consists of 29,737 genes and an additional 45,756 isoforms. In the WGS and TSA assemblies, >80% and >95% of core genes can be found, though many in fragmented versions. The provided resources will allow researchers to conduct physiological experiments on A. royi, and also increase the possibilities for copepod gene set analysis, as it adds substantially to the copepod datasets available.