A field experiment was conducted from June to December, 2013 to study the genetic diversity of 15 modern T. Aman rice
varieties of Bangladesh (Oryza sativa L.) with a view to assess the superior genotype in future hybridization program
for developing new rice varieties that is suitable for the target environment. Analysis of variance for each trait showed
significant differences among the varieties. High heritability associated with high genetic advance in percent of mean
was observed for plant height and thousand seed weight which indicated that selection for these characters would be
effective. Hence, thrust has to be given for these characters in future breeding program to improve the yield trait in rice.
Multivariate analysis based on 10 agronomic characters indicated that the 15 varieties were grouped into four distant
clusters. The inter cluster distance was maximum between cluster II and cluster IV. The highest intra-cluster distance was
found in cluster IV. Based on positive value of vector 1 and vector 2, plant height and 1000-seed weight had maximum
contribution towards genetic divergence. From the results, it can be concluded that the varieties BRRI dhan40, BRRI
dhan44, BRRI dhan46, BRRI dhan49 and BINA dhan7 may be selected for future hybridization program.
The COVID-19 pandemic first emerged in Malaysia in Jan 2020. As of 12th Sept 2021, 1,979,698 COVID-19 cases that occurred over three major epidemic waves were confirmed. The virus contributing to the three epidemic waves has not been well-studied. We sequenced the genome of 22 SARS-CoV-2 strains detected in Malaysia during the second and the ongoing third wave of the COVID-19 epidemic. Detailed phylogenetic and genetic variation analyses of the SARS-CoV-2 isolate genomes were performed using these newly determined sequences and all other available sequences. Results from the analyses suggested multiple independent introductions of SARS-CoV-2 into Malaysia. A new B.1.524(G) lineage with S-D614G mutation was detected in Sabah, East Malaysia and Selangor, Peninsular Malaysia on 7th October 2020 and 14th October 2020, respectively. This new B.1.524(G) group was not the direct descendant of any of the previously detected lineages. The new B.1.524(G) carried a set of genetic variations, including A701V (position variant frequency = 0.0007) in Spike protein and a novel G114T mutation at the 5'UTR. The biological importance of the specific mutations remained unknown. The sequential appearance of the mutations, however, suggests that the spread of the new B.1.524(G) lineages likely begun in Sabah and then spread to Selangor. The findings presented here support the importance of SARS-CoV-2 full genome sequencing as a tool to establish an epidemiological link between cases or clusters of COVID-19 worldwide.
Leptospirosis is an endemic zoonoses of global proportions. Stray dogs have been postulated to play a role in disease transmission; however, supporting information are still limited. Roaming behavior may not only predispose the dogs to infection, but could also contribute to disease spread. In this study, the susceptibility of urban stray dogs in shedding Leptospira spp. was determined. Blood, urine, and tissue samples of kidney and liver were collected from 100 dogs from 2 animal control facilities. Serological testing using microscopic agglutination test (MAT) were performed on blood against 20 leptospiral serovars with a cut-off titre of ≥ 1:100. Samples were cultured onto semi-solid Ellinghausen and McCullough modified by Johnson and Harris (EMJH) media. Isolates were identified using molecular polymerase chain reaction (PCR) using 2 primers (16s rRNA and LipL32) and hyperimmune serum (HIS) MAT. The seroprevalence for the dogs positive for leptospirosis was 32% (n=32/100) with the following detected serovars: Javanica (n=13), Bataviae (n=10), Icterohaemorrhagiae (n=3), Autumnalis (n=2), Canicola (n=1), Pyrogenes (n=1), Copenhageni (n=1), and Australis (n=1). Six Leptospira spp. isolated were procured from urine (n=2), kidney (n=2) and liver (n=2). All 6 isolates belonged to L. interrogans, a pathogenic variant of Leptospira spp. Serotyping and phylogenetic analysis suggested serovar Bataviae (n=5) and serovar Canicola (n=1). Presence of vaccinal serovars (Icterohaemorrhagiae and Canicola) suggested potential post-vaccination antibodies but the predominance of non-vaccinal serovars (Javanica and Bataviae) indicate the possibility of current infection or post-exposure. Isolation of Leptospira spp. directly from urine sample not only suggested an active infection but highlighted the potential shedding capability among these stray dogs. These findings further strengthen speculations that urban stray dogs could play a role in transmission and dissemination of leptospirosis through their constant movement. The urine of infected dogs may contaminate the environment, posing a major public health threat.
Scedosporium spp. are the second most prevalent filamentous fungi after Aspergillus spp. recovered from cystic fibrosis (CF) patients in various regions of the world. Although invasive infection is uncommon prior to lung transplantation, fungal colonization may be a risk factor for invasive disease with attendant high mortality post-transplantation. Abundant in the environment, Scedosporium aurantiacum has emerged as an important fungal pathogen in a range of clinical settings. To investigate the population genetic structure of S. aurantiacum, a MultiLocus Sequence Typing (MLST) scheme was developed, screening 24 genetic loci for polymorphisms on a tester strain set. The six most polymorphic loci were selected to form the S. aurantiacum MLST scheme: actin (ACT), calmodulin (CAL), elongation factor-1α (EF1α), RNA polymerase subunit II (RPB2), manganese superoxide dismutase (SOD2), and β-tubulin (TUB). Among 188 global clinical, veterinary, and environmental strains, 5 to 18 variable sites per locus were revealed, resulting in 8 to 23 alleles per locus. MLST analysis observed a markedly high genetic diversity, reflected by 159 unique sequence types. Network analysis revealed a separation between Australian and non-Australian strains. Phylogenetic analysis showed two major clusters, indicating correlation with geographic origin. Linkage disequilibrium analysis revealed evidence of recombination. There was no clustering according to the source of the strains: clinical, veterinary, or environmental. The high diversity, especially amongst the Australian strains, suggests that S. aurantiacum may have originated within the Australian continent and was subsequently dispersed to other regions, as shown by the close phylogenetic relationships between some of the Australian sequence types and those found in other parts of the world. The MLST data are accessible at http://mlst.mycologylab.org. This is a joined publication of the ISHAM/ECMM working groups on "Scedosporium/Pseudallescheria Infections" and "Fungal Respiratory Infections in Cystic Fibrosis".
We report here the genome sequences of Salmonella enterica subsp. enterica serovar Typhimurium strains TT6675 and TT9097, which we utilize for genetic analyses of giant bacterial viruses. Our analyses identified several genetic variations between the two strains, most significantly confirming strain TT6675 as a serine suppressor and TT9097 as a nonsuppressor.
Genetic diversity represents the heritable variation both within and among populations of organisms, and in the context of this paper, among bamboo species. Bamboo is an economically important member of the grass family Poaceae, under the subfamily Bambusoideae. India has the second largest bamboo reserve in Asia after China. It is commonly known as "poor man's timber", keeping in mind the variety of its end use from cradle to coffin. There is a wide genetic diversity of bamboo around the globe and this pool of genetic variation serves as the base for selection as well as for plant improvement. Thus, the identification, characterization and documentation of genetic diversity of bamboo are essential for this purpose. During recent years, multiple endeavors have been undertaken for characterization of bamboo species with the aid of molecular markers for sustainable utilization of genetic diversity, its conservation and future studies. Genetic diversity assessments among the identified bamboo species, carried out based on the DNA fingerprinting profiles, either independently or in combination with morphological traits by several researchers, are documented in the present review. This review will pave the way to prepare the database of prevalent bamboo species based on their molecular characterization.
Accurate and consistent interpretation of sequence variants is integral to the delivery of safe and reliable diagnostic genetic services. To standardize the interpretation process, in 2015, the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) published a joint guideline based on a set of shared standards for the classification of variants in Mendelian diseases. The generality of these standards and their subjective interpretation between laboratories has prompted efforts to reduce discordance of variant classifications, with a focus on the expert specification of the ACMG/AMP guidelines for individual genes or diseases. Herein, we describe our experience as a ClinGen Variant Curation Expert Panel to adapt the ACMG/AMP criteria for the classification of variants in three globin genes (HBB, HBA2, and HBA1) related to recessively inherited hemoglobinopathies, including five evidence categories, as use cases demonstrating the process of specification and the underlying rationale.
The Plasmodium knowlesi secreted protein with an altered thrombospondin repeat (PkSPATR) is an important protein that helps in the parasite's invasion into the host cell. This protein has been regarded as one of the potential vaccine candidates against P. knowlesi infection. This study investigates the genetic diversity and natural selection of PkSPATR gene of P. knowlesi clinical isolates from Malaysia. PCR amplification of the full length PkSPATR gene was performed on 60 blood samples of infected P. knowlesi patients from Peninsular Malaysia and Malaysian Borneo. The amplified PCR products were cloned and sequenced. Sequence analysis of PkSPATR from Malaysia showed higher nucleotide diversity (CDS p: 0.01462) than previously reported Plasmodium vivax PvSPATR (p = 0.0003). PkSPATR from Peninsular Malaysia was observed to have slightly higher diversity (CDS p: 0.01307) than those from Malaysian Borneo (CDS p: 0.01212). Natural selection analysis on PkSPATR indicated significant purifying selection. Multiple amino acid sequence alignment revealed 69 polymorphic sites. The phylogenetic tree and haplotype network did not show any distinct clustering of PkSPATR. The low genetic diversity level, natural selection and absence of clustering implied functional constrains of the PkSPATR protein.
Knowledge on the population of genetic structure and ecological behaviour of Apis dorsata from Peninsular Malaysia is needed for effective management and conservation of this species since unsustainable whole solitary low nest cutting for product harvesting is the current common practice here. The analysis of 15 single locus DNA microsatellite markers on samples from 20 solitary nests of A. dorsata showed that while these markers were polymorphic, high intracolonial relatedness existed. Furthermore, in general, slightly negative values of intercolony relatedness (R) among the nests of A. dorsata were found. However, positive values of mean intercolony relatedness were observed between 54 pairs of nests out of 190 possible combinations. The R values among nest pairs 3-4 and 3-5 was higher than 0.50 showing that their queens were half siblings, whereas nest pair 19-20 showed relatedness of 0.95 indicating that the same queen was sampled. The results that we obtained could not conclusively support the hypothesis of this study that the honey hunters in Marang district of Malaysia repeatedly harvest the same nest located at a different site and at a different time during the same honey harvesting season. However, our finding of an appreciable level of intercolonial relatedness between several pairs of nests in this pioneer study indicated that a comprehensive study with a larger sample size of solitary nests found throughout the region would be necessary to provide concrete proof for this novel idea.
Microsatellites are the most popular markers for parentage assignment and population genetic studies. To meet the demand for international comparability for genetic studies of Asian seabass, a standard panel of 28 microsatellites has been selected and characterized using the DNA of 24 individuals from Thailand, Malaysia, Indonesia and Australia. The average allele number of these markers was 10.82 +/- 0.71 (range: 6-19), and the expected heterozygosity averaged 0.76 +/- 0.02 (range: 0.63-1.00). All microsatellites showed Mendelian inheritance. In addition, eight standard size controls have been developed by cloning a set of microsatellite alleles into a pGEM-T vector to calibrate allele sizes determined by different laboratories, and are available upon request. Seven multiplex PCRs, each amplifying 3-5 markers, were optimized to accurately and rapidly genotype microsatellites. Parentage assignment using 10 microsatellites in two crosses (10 x 10 and 20 x 20) demonstrated a high power of these markers for revealing parent-sibling connections. This standard set of microsatellites will standardize genetic diversity studies of Asian seabass, and the multiplex PCR sets will facilitate parentage assignment.
Ten polymorphic microsatellite markers have been developed for Gonystylus bancanus (Ramin), a protected tree species of peat swamp forests in Malaysia and Indonesia. Eight markers were also shown to be polymorphic in other Gonystylus species. The markers will enable assessing the amount of genetic variation within and among populations and the degree of population differentiation, such that donor populations can be selected for reforestation projects. They may be used for tracing and tracking of wood in the production chain, so that legal trade in this Convention on International Trade in Endangered Species of Wild Fauna and Flora-protected timber species, derived from specifically described origins, can be distinguished from illegally logged timber.
The authors have characterised the genetic diversity of the bluetongue virus (BTV) RNA segments 3 and 10 from Indonesia, Malaysia and Australia. Analysis of RNA segment 3, which codes for the core protein VP3, showed conserved sequences in the previously defined Australasian topotype, but which further divided into four distinct clades or genotypes. Certain genotypes appeared to be geographically restricted while others were distributed widely throughout South-East Asia. Ongoing surveillance programmes in Australia have identified the movement of Indonesian genotypes into northern Australia and possible reassortment among them. Similarly, analysis of RNA segment 10, which codes for the non-structural protein NS3/3A, showed they were also conserved and grouped into five clades or genotypes, three Asian and two North American/South African.
Biocatalyst should have sufficient and efficient activity for the intended
biotechnological application. In the quest for novel biocatalyst, there is a need to have a
genetic diversity either by finding it within the astronomically large number of possible
candidates or to obtain it by bioengineering an existing gene supported by various
bioinformatic and molecular engineering tools. Nowadays, it is well-known that a huge
number of microorganisms is unculturable and poses great challenges to access biocatalysts
from these microbes. Metagenomics is one of the methods widely applied to reach out
maximum possible variants to “bioprospect” biocatalysts. On the other hand, other approaches
are available to bioengineer enzymes by modifying the DNA sequence precisely based on the
structure and the function information of the protein in the case of rational design, or by a
brave creation of anarchic mutations of the DNA sequence with directed evolution method. In
this regard, both approaches, whether to bioprospect or to bioengineer biocatalysts have
advantages and disadvantages which will be discussed in this paper.KEY WORDS: Sugar
industry wastewater; aluminium sulphate; primary treatment, ferric chloride; polyaluminium
chloride
The trend of microsatellite marker discovery and development revolved as a result of the advancement of next generation sequencing (NGS) technology as it has developed numerous microsatellites within a short period of time at a low cost. This study generated microsatellite markers using RAD sequencing technologies for the understudied Nephelium lappaceum. A total of 1403 microsatellite markers were successfully designed, which consisted of 853 di-, 525 tri-, 17 tetra-, 5 penta-, and 3 hexanucleotide microsatellite markers. Subsequently, selection of 39 microsatellites was made for the evaluation of genetic diversity of the selected 22 rambutan varieties. Twelve microsatellites, which exhibited high call rates across the samples, were used to assess the diversity of the aforementioned rambutan varieties. The analysis of 12 microsatellites revealed the presence of 72 alleles and six alleles per locus in average. Furthermore, the polymorphic information content (PIC) value ranged from 0.326 (NlaSSR20) to 0.832 (NlaSSR32), which included an average of 0.629 per locus, while the generated Neighbour Joining dendrogram showed two major clusters. The pairwise genetic distance of shared alleles exhibited a range of values from 0.046 (R134↔R170) to 0.818 (R5↔R170), which suggested highest dissimilarity detected between R5 and R170. Notably, these research findings would useful for varietal identification, proper management and conservation of the genetic resources, and exploitation and utilization in future breeding programs.
Hanging Coffin is a unique and ancient burial custom that has been practiced in southern China, Southeast Asia, and near Oceania regions for more than 3,000 years. Here, we conducted mitochondrial whole-genome analyses of 41 human remains sampled from 13 Hanging Coffin sites in southern China and northern Thailand, which were dated between ∼2,500 and 660 years before present. We found that there were genetic connections between the Hanging Coffin people living in different geographic regions. Notably, the matrilineal genetic diversity of the Hanging Coffin people from southern China is much higher than those from northern Thailand, consistent with the hypothesized single origin of the Hanging Coffin custom in southern China about 3,600 years ago, followed by its dispersal in southern China through demic diffusion, whereas the major dispersal pattern in Southeast Asia is cultural assimilation in the past 2,000 years.
Population genetic structure of Varuna litterata living along the coast of Thailand were examined in this study. The samples were collected from 3 coastal regions: The Andaman sea (Satun, Trang, Phang Nga), the lower Gulf of Thailand (Pattani, Songkhla, Nakhon Si Thammarat) and the upper Gulf of Thailand (Petchburi, Samut Songkram, Rayong, Trat). Intraspecific variation was determined based on partial sequences of the cytochrome oxidase subunits I gene. A total of 182 samples were collected but only 32 haplotypes were obtained from these samples. An excess of rare haplotypes indicated that the female effective population size of V. litterata living along the coast of Thailand is large. Estimated values of haplotype diversity and nucleotide diversity were 0.790 and 0.003, respectively. The AMOVA (analysis of molecular variance) and phylogenetic analysis results showed that based on genetic variation, the population of this organism was found to have 2 genetically different populations: The Andaman sea population and the Gulf of Thailand population. Genetic exchange of V. litterata among populations inhabiting along the coast of Thailand could be described by the stepping stone model. The results of neutrality tests, both Tajima's D and Fu's Fs statistics, yielded negative values (-1.992 and -26.877, respectively) and statistically significant deviation from the neutrality, indicating that the V. litterata living along the Thailand coast had experienced population expansion. Mismatch distribution analysis indicated that a possible expansion occurred 211,428 years ago during the Pleistocene glaciations period.
Eighty-four specimens collected from 13 populations from Malaysia, Thailand, and Vietnam were analysed, revealing 21 putative haplotypes with overall estimated haplotype and nucleotide diversities of 0.79 and 0.0079, respectively. High levels of diversity and an absence of founder effects were observed among populations in peninsular Malaysia. In contrast, populations from Sarawak exhibited low genetic diversity, which is a typical sign of colonies introduced from a single source. Historical translocation of Trichopodus pectoralis from Thailand to Malaysia, as well as to the Philippines, Indonesia, and Myanmar was apparent. Historical introduction of T. pectoralis from Vietnam was also detected in peninsular Malaysia.