Displaying publications 21 - 40 of 746 in total

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  1. Understanding the genetic relationships between Indonesian bambara groundnut landraces and investigating their origins
    Redjeki ES, Ho WK, Shah N, Molosiwa OO, Ardiarini NR, Kuswanto, et al.
    Genome, 2020 Jun;63(6):319-327.
    PMID: 32097026 DOI: 10.1139/gen-2019-0137
    A total of 170 bambara groundnut (Vigna subterranea) accessions were evaluated using both simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers generated using genotyping-by-sequencing (GbS), of which 56 accessions were collected from West and East Java. Principal coordinate analysis (PCoA), population structure, and cluster analysis suggest that the East Java accessions could be a result of the introduction of selected West Java accessions. In addition, the current Indonesian accessions were likely introduced from Southern Africa, which would have produced a very marked founding effect such that these accessions present only a fraction of the genetic variability that exists within this species.
    Matched MeSH terms: Genetic Variation/genetics*
  2. Population Genetic Structure and Breeding Pattern of Cimex hemipterus (F.) (Hemiptera: Cimicidae) in Malaysia
    Seri Masran SNA, Ab Majid AH
    J Med Entomol, 2019 06 27;56(4):942-952.
    PMID: 30882146 DOI: 10.1093/jme/tjz024
    The surge in tropical bed bug Cimex hemipterus (Fabricius) (Hemiptera: Cimicidae) infestations has led to an increase in genomic studies. In this study, the population genetics and breeding patterns of 22 Malaysian populations were analyzed, including genetic differentiation and genetic distance. For seven microsatellite loci, the number of alleles varied from 6 to 14. The allelels per loci contrasted sharply between the overall population and within the populations. The average observed and expected heterozygosity was 0.280 and 0.828 for the overall population and 0.281 and 0.657 among the populations, respectively. Based on polymorphic information criteria, the markers with a value >0.5 were highly polymorphic. In the Hardy-Weinberg equilibrium, the loci of Ch 09ttn, Ch 01dn, and Ch 13dn of the overall population showed signs of a null allele. The stutter peaks caused no scoring errors; large allele dropouts were not detected for any loci; and a correlation imbalance was not indicated. The genetic differentiation among populations was moderate, with a coefficient of genetic differentiation (FST) of 0.144. The bed bug populations showed strong inbreeding, with highly positive coefficients of inbreeding (FIS). The molecular variation attributed to inbreeding was 83% within the populations, compared with 17% among the populations. The admixture individuals in STRUCTURE and neighbor-joining phylogenetic trees also indicated weak genetic structure in the geographical populations, suggesting moderate gene flows between populations. Thus, moderately active dispersion and human-mediated transport shaped the genetic structure of C. hemipterus populations in Malaysia.
    Matched MeSH terms: Genetic Variation*
  3. New insights into the haplotype diversity of the cosmopolitan cat flea Ctenocephalides felis (Siphonaptera: Pulicidae)
    Azrizal-Wahid N, Sofian-Azirun M, Low VL
    Vet Parasitol, 2020 May;281:109102.
    PMID: 32289653 DOI: 10.1016/j.vetpar.2020.109102
    The present study investigated the genetic profile of the cosmopolitan cat flea, Ctenocephalides felis (Siphonaptera: Pulicidae) from Malaysia and the reference data available in the National Center for Biotechnology Information (NCBI) GenBank. A set of sequences of 100 Malaysian samples aligned as 550 characters of the cytochrome c oxidase subunit I (cox1) and 706 characters of the II (cox2) genes revealed ten haplotypes (A1-A10) and eight haplotypes (B1-B8), respectively. The concatenated sequences of cox1 and cox2 genes with a total of 1256 characters revealed 15 haplotypes (AB1-AB15). Analyses indicated that haplotype AB1 was the most frequent and the most widespread haplotype in Malaysia. Overall haplotype and nucleotide diversities of the concatenated sequences were 0.52909 and 0.00424, respectively, with moderate genetic differentiation (FST = 0.17522) and high gene flow (Nm = 1.18). The western population presented the highest genetic diversity (Hd = 0.78333, Pi = 0.01269, Nh = 9), whereas the southern population demonstrated the lowest diversity (Hd = 0.15667, Pi = 0.00019, Nh = 3). The concatenated sequences showed genetic distances ranged from 0.08 % to 4.39 %. There were three aberrant haplotypes in cox2 sequences that highly divergent, suggesting the presence of cryptic species or occurrence of introgression. In the global point of view, the aligned sequences of C. felis revealed 65 haplotypes (AA1-AA65) by the cox1 gene (n = 586), and 27 haplotypes (BB1-BB27) by the cox2 gene (n = 204). Mapping of the haplotype network showed that Malaysian C. felis possesses seven unique haplotypes in both genes with the common haplotypes demonstrated genetic affinity with C. felis from Southeast Asia for cox1 and South America for cox2. The topologies of cox1 and cox2 phylogenetic trees were concordant with relevant grouping pattern of haplotypes in the network but revealed two major lineages by which Malaysian haplotypes were closely related with haplotypes from the tropical region.
    Matched MeSH terms: Genetic Variation*
  4. Fulltext Genetic Diversity and Clustering of the Rhoptry Associated Protein-1 of Plasmodium knowlesi from Peninsular Malaysia and Malaysian Borneo
    Azlan UW, Lau YL, Fong MY
    Korean J Parasitol, 2022 Dec;60(6):393-400.
    PMID: 36588415 DOI: 10.3347/kjp.2022.60.6.393
    Human infection with simian malaria Plasmodium knowlesi is a cause for concern in Southeast Asian countries, especially in Malaysia. A previous study on Peninsular Malaysia P. knowlesi rhoptry associated protein-1 (PkRAP1) gene has discovered the existence of dimorphism. In this study, genetic analysis of PkRAP1 in a larger number of P. knowlesi samples from Malaysian Borneo was conducted. The PkRAP1 of these P. knowlesi isolates was PCR-amplified and sequenced. The newly obtained PkRAP1 gene sequences (n = 34) were combined with those from the previous study (n = 26) and analysed for polymorphism and natural selection. Sequence analysis revealed a higher genetic diversity of PkRAP1 compared to the previous study. Exon II of the gene had higher diversity (π = 0.0172) than exon I (π = 0.0128). The diversity of the total coding region (π = 0.0167) was much higher than those of RAP1 orthologues such as PfRAP-1 (π = 0.0041) and PvRAP1 (π = 0.00088). Z-test results indicated that the gene was under purifying selection. Phylogenetic tree and haplotype network showed distinct clustering of Peninsular Malaysia and Malaysian Borneo PkRAP1 haplotypes. This geographical-based clustering of PkRAP1 haplotypes provides further evidence of the dimorphism of the gene and possible existence of 2 distinct P. knowlesi lineages in Malaysia.
    Matched MeSH terms: Genetic Variation*
  5. Fulltext Studies on the genetic variation of the green unicellular alga Haematococcus pluvialis (Chlorophyceae) obtained from different geographical locations using ISSR and RAPD molecular marker
    Mostafa N, Omar H, Tan SG, Napis S
    Molecules, 2011 Mar 22;16(3):2599-608.
    PMID: 21441863 DOI: 10.3390/molecules16032599
    Haematococcus pluvialis (Flotow) is a unicellular green alga, which is considered to be the best astaxanthin-producing organism. Molecular markers are suitable tools for the purpose of finding out genetic variations in organisms; however there have been no studies conducted on ISSR or RAPD molecular markers for this organism. The DNA of 10 different strains of H. pluvialis (four strains from Iran, two strains from Finland, one strain from Switzerland and three strains from the USA) was extracted. A genetic similarity study was carried out using 14 ISSR and 12 RAPD primers. Moreover, the molecular weights of the bands produced ranged from 0.14 to 3.4 Kb. The PCA and dendrogram clustered the H. pluvialis strains into various groups according to their geographical origin. The lowest genetic similarity was between the Iran2 and USA2 strains (0.08) and the highest genetic similarity was between Finland1 and Finland2 (0.64). The maximum numbers of bands produced by the ISSR and RAPD primers were 35 and 6 bands, respectively. The results showed that ISSR and RAPD markers are useful for genetic diversity studies of Haematococcus as they showed geographical discrimination.
    Matched MeSH terms: Genetic Variation*
  6. Fulltext Analysis of rDNA reveals a high genetic diversity of Halophila major in the Wallacea region
    Nguyen XV, Nguyen-Nhat NT, Nguyen XT, Dao VH, M Liao L, Papenbrock J
    PLoS One, 2021;16(10):e0258956.
    PMID: 34679102 DOI: 10.1371/journal.pone.0258956
    The genus Halophila shows the highest species diversity within the seagrass genera. Southeast Asian countries where several boundary lines exist were considered as the origin of seagrasses. We hypothesize that the boundary lines, such as Wallace's and Lydekker's Lines, may act as marine geographic barriers to the population structure of Halophila major. Seagrass samples were collected at three islands in Vietnamese waters and analyzed by the molecular maker ITS. These sequences were compared with published ITS sequences from seagrasses collected in the whole region of interest. In this study, we reveal the haplotype and nucleotide diversity, linking population genetics, phylogeography, phylogenetics and estimation of relative divergence times of H. major and other members of the Halophila genus. The morphological characters show variation. The results of the ITS marker analysis reveal smaller groups of H. major from Myanmar, Shoalwater Bay (Australia) and Okinawa (Japan) with high supporting values. The remaining groups including Sri Lanka, Viet Nam, the Philippines, Thailand, Malaysia, Indonesia, Two Peoples Bay (Australia) and Tokushima (Japan) showed low supporting values. The Wallacea region shows the highest haplotype and also nucleotide diversity. Non-significant differences were found among regions, but significant differences were presented among populations. The relative divergence times between some members of section Halophila were estimated 2.15-6.64 Mya.
    Matched MeSH terms: Genetic Variation*
  7. Fulltext Porous borders at the wild-crop interface promote weed adaptation in Southeast Asia
    Li LF, Pusadee T, Wedger MJ, Li YL, Li MR, Lau YL, et al.
    Nat Commun, 2024 Feb 21;15(1):1182.
    PMID: 38383554 DOI: 10.1038/s41467-024-45447-0
    High reproductive compatibility between crops and their wild relatives can provide benefits for crop breeding but also poses risks for agricultural weed evolution. Weedy rice is a feral relative of rice that infests paddies and causes severe crop losses worldwide. In regions of tropical Asia where the wild progenitor of rice occurs, weedy rice could be influenced by hybridization with the wild species. Genomic analysis of this phenomenon has been very limited. Here we use whole genome sequence analyses of 217 wild, weedy and cultivated rice samples to show that wild rice hybridization has contributed substantially to the evolution of Southeast Asian weedy rice, with some strains acquiring weed-adaptive traits through introgression from the wild progenitor. Our study highlights how adaptive introgression from wild species can contribute to agricultural weed evolution, and it provides a case study of parallel evolution of weediness in independently-evolved strains of a weedy crop relative.
    Matched MeSH terms: Genetic Variation*
  8. Fulltext Studies of Myxidium giardi Cépède, 1906 infections in Icelandic eels identifies a genetically diverse clade of myxosporeans that represents the Paramyxidium n. g. (Myxosporea: Myxidiidae)
    Freeman MA, Kristmundsson Á
    Parasit Vectors, 2018 Oct 22;11(1):551.
    PMID: 30348210 DOI: 10.1186/s13071-018-3087-y
    BACKGROUND: The myxosporean Myxidium giardi Cépède, 1906 was described infecting the kidney of the European eel, Anguilla anguilla (L.), having spindle-shaped myxospores and terminal sub-spherical polar capsules. Since then, numerous anguillid eels globally have been documented to have similar Myxidium infections. Many of these have been identified using the morphological features of myxospores or by the location of infection in the host, and some have been subsequently synonymised with M. giardi. Therefore, it is not clear whether M. giardi is a widely distributed parasite, infecting numerous species of eels, in multiple organs, or whether some infections represent other, morphologically similar but different species of myxosporeans. The aim of the present study was to assess the status of M. giardi infections in Icelandic eels, and related fish hosts in Malaysia and to use spore morphology and molecular techniques to evaluate the diversity of myxosporeans present.

    RESULTS: The morphologies of the myxospores from Icelandic eels were very similar but the overall dimensions were significantly different from the various tissue locations. Myxospores from the kidney of the Malaysian tarpon, Megalops cyprinoides (Broussonet), were noticeably smaller. However, the SSU rDNA sequences from the different tissues locations in eels, were all very distinct, with percentage similarities ranging from 92.93% to as low as 89.8%, with the sequence from Malaysia being even more dissimilar. Molecular phylogenies consistently placed these sequences together in a clade that we refer to as the Paramyxidium clade that is strongly associated with the Myxidium clade (sensu stricto). We erect the genus Paramyxidium n. g. (Myxidiidae) to accommodate these histozoic taxa, and transfer Myxidium giardi as Paramyxidium giardi Cépède, 1906 n. comb. as the type-species.

    CONCLUSIONS: There is not a single species of Myxidium (M. giardi) causing systemic infections in eels in Iceland. There are three species, confirmed with a robust phylogeny, one of which represents Paramyxidium giardi n. comb. Additional species probably exist that infect different tissues in the eel and the site of infection in the host fish is an important diagnostic feature for this group (Paramyxidium n. g. clade). Myxospore morphology is generally conserved in the Paramyxidium clade, although actual spore dimensions can vary between some species. Paramyxidium spp. are currently only known to infect fishes from the Elopomorpha.

    Matched MeSH terms: Genetic Variation*
  9. Molecular insight into genetic differentiation, population structure and banding pattern analysis of Bambara groundnut (Vigna subterranea [L.] Verdc.) linked with inter simple sequence repeats (ISSR)
    Khan MMH, Rafii MY, Ramlee SI, Jusoh M, Al Mamun M, Kundu BC
    Mol Biol Rep, 2023 Sep;50(9):7619-7637.
    PMID: 37531035 DOI: 10.1007/s11033-023-08693-x
    BACKGROUND: A set of 44 selected Bambara groundnut (Vigna subterranea [L.] Verdc.) accessions was sampled from 11 distinct populations of four geographical zones to assess the genetic drift, population structure, phylogenetic relationship, and genetic differentiation linked with ISSR primers.

    METHODS AND RESULTS: The amplification of genomic DNA with 32 ISSR markers detected an average of 97.64% polymorphism while 35.15% and 51.08% polymorphism per population and geographical zone, respectively. Analysis of molecular variance revealed significant variation within population 75% and between population 25% whereas within region 84% and between region 16%. The Bidillali exposed greater number of locally common band i.e., NLCB (≤ 25%) = 25 and NLCB (≤ 50%) = 115 were shown by Cancaraki while the lowest was recorded as NLCB (≤ 25%) = 6 and NLCB (≤ 50%) = 72 for Roko and Maibergo, accordingly. The highest PhiPT value was noted between Roko and Katawa (0.405*) whereas Nei's genetic distance was maximum between Roko and Karu (0.124). Based on Nei's genetic distance, a radial phylogenetic tree was constructed that assembled the entire accessions into 3 major clusters for further confirmation unrooted NJ vs NNet split tree analysis based on uncorrected P distance exposed the similar result. Principal coordinate analysis showed variation as PC1 (15.04%) > PC2 (5.81%).

    CONCLUSIONS: The current study leads to prompting the genetic improvement and future breeding program by maximum utilization and better conservation of existing accessions. The accessions under Cancaraki and Jatau are population documented for future breeding program due to their higher genetic divergence and homozygosity.

    Matched MeSH terms: Genetic Variation/genetics
  10. Fulltext Genetic Diversity and Phylogeography of Thottapalayam thottimvirus (Hantaviridae) in Asian House Shrew (Suncus murinus) in Eurasia
    Kikuchi F, Aoki K, Ohdachi SD, Tsuchiya K, Motokawa M, Jogahara T, et al.
    Front Cell Infect Microbiol, 2020;10:438.
    PMID: 32974220 DOI: 10.3389/fcimb.2020.00438
    Murid and cricetid rodents were previously believed to be the principal reservoir hosts of hantaviruses. Recently, however, multiple newfound hantaviruses have been discovered in shrews, moles, and bats, suggesting a complex evolutionary history. Little is known about the genetic diversity and geographic distribution of the prototype shrew-borne hantavirus, Thottapalayam thottimvirus (TPMV), carried by the Asian house shrew (Suncus murinus), which is widespread in Asia, Africa, and the Middle East. Comparison of TPMV genomic sequences from two Asian house shrews captured in Myanmar and Pakistan with TPMV strains in GenBank revealed that the Myanmar TPMV strain (H2763) was closely related to the prototype TPMV strain (VRC66412) from India. In the L-segment tree, on the other hand, the Pakistan TPMV strain (PK3629) appeared to be the most divergent, followed by TPMV strains from Nepal, then the Indian-Myanmar strains, and finally TPMV strains from China. The Myanmar strain of TPMV showed sequence similarity of 79.3-96.1% at the nucleotide level, but the deduced amino acid sequences showed a high degree of conservation of more than 94% with TPMV strains from Nepal, India, Pakistan, and China. Cophylogenetic analysis of host cytochrome b and TPMV strains suggested that the Pakistan TPMV strain was mismatched. Phylogenetic trees, based on host cytochrome b and cytochrome c oxidase subunit I genes of mitochondrial DNA, and on host recombination activating gene 1 of nuclear DNA, suggested that the Asian house shrew and Asian highland shrew (Suncus montanus) comprised a species complex. Overall, the geographic-specific clustering of TPMV strains in Asian countries suggested local host-specific adaptation. Additional in-depth studies are warranted to ascertain if TPMV originated in Asian house shrews on the Indian subcontinent.
    Matched MeSH terms: Genetic Variation*
  11. Mitochondrial genomics identifies major haplogroups in Aboriginal Australians
    van Holst Pellekaan SM, Ingman M, Roberts-Thomson J, Harding RM
    Am J Phys Anthropol, 2006 Oct;131(2):282-94.
    PMID: 16596590
    We classified diversity in eight new complete mitochondrial genome sequences and 41 partial sequences from living Aboriginal Australians into five haplogroups. Haplogroup AuB belongs to global lineage M, and AuA, AuC, AuD, and AuE to N. Within N, we recognize subdivisions, assigning AuA to haplogroup S, AuD to haplogroup O, AuC to P4, and AuE to P8. On available evidence, (S)AuA and (M)AuB are widespread in Australia. (P4)AuC is found in the Riverine region of western New South Wales, and was identified by others in northern Australia. (O)AuD and (P8)AuE were clearly identified only from central Australia. Our eight Australian full mt genome sequences, combined with 20 others (Ingman and Gyllensten 2003 Genome Res. 13:1600-1606) and compared with full mt genome sequences from regions to the north that include Papua New Guinea, Malaya, and Andaman and Nicobar Islands, show that ancestral connections between regions are deep and limited to clustering at the level of the N and M macrohaplogroups. The Australian-specific distribution of the five haplogroups identified indicates genetic isolation over a long period. Ancestral connections within Australia are deeper than those reflected by known linguistic or culturally based affinities. Applying a coalescence analysis to a gene tree for the coding regions of the eight genomic sequences, we made estimates of time depth that support a continuity of presence for the descendants of a founding population already established by 40,000 years ago.
    Matched MeSH terms: Genetic Variation*
  12. Intraspecific genetic diversity with unrestricted gene flow in the domoic acid-producing diatom Nitzschia navis-varingica (Bacillariophyceae) from the Western Pacific
    Tan SN, Kotaki Y, Teng ST, Lim HC, Gao C, Lundholm N, et al.
    Harmful Algae, 2025 Jan;141:102769.
    PMID: 39645396 DOI: 10.1016/j.hal.2024.102769
    The benthic pennate diatom Nitzschia navis-varingica, known for producing domoic acid (DA) and its isomers, is widely distributed in the Western Pacific (WP) region. To investigate the genetic differentiation and gene flow patterns among the populations in the WP, the genetic diversity of 354 strains of N. navis-varingica was analysed using two nuclear-encoded rDNA loci: the large subunit rDNA (LSU rDNA) and the internal transcribed spacer 2 (ITS2). Frustule morphology of each strain was examined by TEM. The LSU rDNA phylogeny revealed a monophyletic lineage encompassing all strains, with sequence divergences of <0.9 %. Phylogenetic and population genetic analyses of ITS2 identified eight distinct clades (designated as Groups A to H) with moderate to high genetic heterogeneity (0.5-19.7 %). The low genetic differentiations between the geographically separated populations (pairwise FST of <0.03) suggested high gene flow and lack of spatial genetic structuring. Molecular clock analysis of the ITS2 phylogeny traced the evolutionary history of N. navis-varingica to the Eocene Epoch, and the split between clades likely occurred from the mid-Miocene to Pleistocene Epochs (10.8-1.2 Ma). The population dispersal in the WP were likely influenced by historical events like the Quarternary glacial cycles during the period, contributing to its homogenous distributions in the region.
    Matched MeSH terms: Genetic Variation*
  13. Fulltext A taxonomic study on the genus Ettchellsia Cameron, with descriptions of three new species (Hymenoptera, Megalyridae, Dinapsini)
    Mita T, Shaw SR
    Zookeys, 2012.
    PMID: 23378818 DOI: 10.3897/zookeys.254.4182
    Three new species of Ettchellsia Cameron, namely, Ettchellsia ignitasp. n. from Peninsular Malaysia and Borneo, Ettchellsia nigripessp. n. from Sulawesi and Ettchellsia reidisp. n. from Borneo are described and illustrated. A key to the species of Ettchellsia is provided based on females.
    Matched MeSH terms: Genetic Variation
  14. Inheritance of seed protein content and other agronomic characters in long bean (Vigna sesquipedalis Fruw.)
    Mak C, Yap TC
    Theor Appl Genet, 1980 Sep;56(5):233-9.
    PMID: 24305859 DOI: 10.1007/BF00295454
    Seven varieties of long bean, which included three local and four exotic, were crossed in a complete diallel. This was an attempt to study the inheritance of crude protein content, protein yield, flowering date, pod yield and yield components.Both additive and non-additive gene effects were responsible for the genetic variation in the diallel population. However, dominance variance was more important than additive variance in crude protein content, number of pods per plant and number of seeds per pod. For seed weight and pod length, additive variance was more important.The crude protein content, protein yield and number of pods per plant appeared to be controlled by overdominance effects. Partial dominance seemed to be the case for flowering date, pod length and seed weight; complete to overdominance for pod yield. High protein appeared to be associated with recessive genes whereas there was a general trend of high yielding parents carrying more dominant genes.
    Matched MeSH terms: Genetic Variation
  15. Fulltext A glance at molecular identification of bamboo (poaceae: bambusoideae)
    Nabilah Mohamad Khairi, Wilson Thau Lym Yong, Julius Kulip, Kenneth Francis Rodrigues
    Borneo International Journal of Biotechnology, 2020;1(1):19-33.
    MyJurnal
    Conservation of plant species plays a vital role in preventing the loss of valuable plant resources. The success of conservation depends on the correct identification and characterization of plant species. Bamboo is one of the most important plants with multiple uses that have contributed to the economy and socio-economy of many people in rural areas. It is under the subfamily of Bambusoideae that includes both woody and herbaceous bamboo. Conventionally, like other plants, bamboo has been classified dependently based on morphological characteristics. However, morphological identification leads to difficulties and misclassification of bamboo species due to their infrequent flowering behaviour and peculiar reproductive biology. Since then, molecular markers have been introduced to overcome the problems associated with bamboo taxonomy and phylogeny. This paper provides an overview of the diverse, predominantly molecular techniques used to assess and determine the genetic diversity of bamboo species.
    Matched MeSH terms: Genetic Variation
  16. Fulltext Phenotypic and genotypic identification of hard ticks of the genus Haemaphysalis (Acari: Ixodidae) in Peninsular Malaysia
    Ernieenor FCL, Ernna G, Mariana A
    Exp Appl Acarol, 2017 Apr;71(4):387-400.
    PMID: 28409404 DOI: 10.1007/s10493-017-0120-3
    Morphotaxonomy based on phenotypic traits of immature hard ticks (Acari: Ixodidae) is a skill challenge and has prompted many inexperienced acarologists to adopt DNA-based methods for identifying and discriminating the species. The aim of this study is therefore to utilize COI gene for verifying the morphological status of Haemaphysalis ticks in Peninsular Malaysia. A total of 19 on-host ticks collected from four localities were first identified using specific illustrated taxonomic keys that lead to the genus of Haemaphysalis. Genotypic traits of tick species were then verified molecularly based on cytochrome oxidase subunit I (COI) gene using polymerase chain reaction and direct sequencing. Clustering analysis was carried out by constructing a phylogenetic tree to determine the genetic variation and diversity of local Haemaphysalis ticks. Based on external morphological characterizations, all immature ticks were successfully identified down to the genus level only. Molecular analysis of the genotypic using COI gene revealed 16 individuals (84%) as Haemaphysalis hystricis, and three individuals as H. humerosa with sequence homology of 97-99 and 86-87%, respectively. Haemaphysalis hystricis were clustered in their respective monophyletic group in the phylogeny trees with a bootstrap of 100%. Furthermore, a low intraspecific variation (<0.3%) was observed among Malaysian H. hystricis but high interspecific value (>15%) recorded. This study morphologically and molecularly confirms the presence of H. hystricis in Malaysia and the findings will add value to the existing knowledge in identification of ticks in this country.
    Matched MeSH terms: Genetic Variation
  17. Fulltext An Overview of the Genetic Variations of the SARS-CoV-2 Genomes Isolated in Southeast Asian Countries
    Yap PSX, Tan TS, Chan YF, Tee KK, Kamarulzaman A, Teh CSJ
    J Microbiol Biotechnol, 2020 Jul 28;30(7):962-966.
    PMID: 32627759 DOI: 10.4014/jmb.2006.06009
    Monitoring the mutation dynamics of human severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical in understanding its infectivity, virulence and pathogenicity for development of a vaccine. In an "age of mobility," the pandemic highlights the importance and vulnerability of regionalization and labor market interdependence in Southeast Asia. We intend to characterize the genetic variability of viral populations within the region to provide preliminary information for regional surveillance in the future. By analyzing 142 complete genomes from South East Asian (SEA) countries, we identified three central variants distinguished by nucleotide and amino acid changes.
    Matched MeSH terms: Genetic Variation
  18. Geographic structure of genetic variation in the Parachute Gecko Ptychozoon lionotum Annandale, 1905 across Indochina and Sundaland with descriptions of three new species
    Grismer LL, Wood PLJ, Grismer JL, Quah ESH, Thy N, Phimmachak S, et al.
    Zootaxa, 2019 Jul 16;4638(2):zootaxa.4638.2.1.
    PMID: 31712473 DOI: 10.11646/zootaxa.4638.2.1
    An integrative taxonomic analysis of the Ptychozoon lionotum group across its range in Indochina and Sundaland recovers P. lionotum sensu lato Annandale, 1905 as paraphyletic with respect to P. popaense Grismer, Wood, Thura, Grismer, Brown, Stuart, 2018a and composed of four allopatric, genetically divergent, ND2 mitochondrial lineages. Multivariate and univariate analyses of continuous and discrete morphological and color pattern characters statistically and discretely diagnose each lineage from one another and together, with maximum likelihood and Bayesian inference analyses, provide the foundation for the recognition of each lineage as a new species-hypotheses corroborated with a Generalized Mixed Yule Coalescent species delimitation analysis. Ptychozoon cicakterbang sp. nov. ranges throughout Peninsular Malaysia to Pulau Natuna Besar, Indonesia; P. kabkaebin sp. nov. is endemic to northern and central Laos; and P. tokehos sp. nov. ranges from southern Thailand south of the Isthmus of Kra northward to Chiang Mai, fringing the Chao Phraya Basin and ranging southward through Cambodia to southern Vietnam. Ptychozoon lionotum sensu stricto ranges from northwestern Laos through southern Myanmar to eastern India. The phylogeographic structure within each species varies considerably with P. lionotum s.s. showing no genetic divergence across its 1,100 km range compared to P. cicakterbang sp. nov. showing upwards of 8.2% sequence divergence between syntopic individuals. Significant phylogeographic structure exists within P. tokehos sp. nov. and increased sampling throughout Thailand may require additional taxonomic changes within this species.
    Matched MeSH terms: Genetic Variation
  19. Genetic Diversity of Bemisia tabaci (Hemiptera: Aleyrodidae) Species Complex Across Malaysia
    Shadmany M, Boykin LM, Muhamad R, Omar D
    J Econ Entomol, 2019 02 12;112(1):75-84.
    PMID: 30272175 DOI: 10.1093/jee/toy273
    The tobacco whitefly Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) is a cryptic species complex with members capable of inducing huge economic losses. Precise identification of members of this complex proves essential in managing existing populations and preventing new incursions. Despite records of serious outbreaks of this pest in Malaysia little is known about species status of B. tabaci in this region. To address this, a comprehensive sampling of B. tabaci from different host plants was conducted in 10 states of Malaysia from 2010 to 2012. Members of the complex were identified by sequencing partial mitochondrial cytochrome oxidase subunit I (mtCOI) gene and constructing a Bayesian phylogenetic tree. Seven putative species were identified including Asia I, Mediterranean (MED), China 1, China 2, Asia II 6, Asia II 7, and Asia II 10. The most important finding of the study is the identification of the invasive MED species from locations without previous records of this species. All putative species except Asia I and MED are recorded from Malaysia for the first time. This study provided the first introductory map of B. tabaci species composition in Malaysia and emphasizes the urgent need for further studies to assess the status of MED invasion in this country.
    Matched MeSH terms: Genetic Variation
  20. Molecular Identification and Genetic Variation of Rattus Species From Oil Palm Plantations of Malaysia Based on Mitochondrial Cytochrome Oxidase Subunit I (COI) Gene Sequences
    Nasir MH, Bhassu S, Mispan MS, Bakar SA, Jing KJ, Omar H
    Zoolog Sci, 2022 Dec;39(6):554-561.
    PMID: 36495490 DOI: 10.2108/zs210093
    Rats (Rattus species) are the most notorious vertebrate pests in Malaysian oil palm plantations. Although many studies have been conducted on Asian rats, little attention has been paid to their species composition and phylogenetic relationships in oil palm plantations in Peninsular Malaysia. We determined the mitochondrial cytochrome oxidase subunit I (COI) gene sequence (708 bp) for 216 individual rats collected from five oil palm plantations in Peninsular Malaysia. Phylogenetic analysis in conjunction with comparison with sequences from the nucleotide sequence database revealed five distinct lineages in the Malaysian oil plantations: Rattus tiomanicus, Rattus argentiventer, Rattus exulans, Rattus tanezumi, and a taxon corresponding to the Malayan house rat, which was most frequently observed (∼50%). The last taxon has traditionally been classified as a synonym of Rattus rattus (Rattus rattus diardii) or Rattus tanezumi, but our phylogenetic analysis placed it as an independent lineage, which is not particularly closely related to R. rattus or R. tanezumi, and which we refer to as Rattus diardii. The construction of the network showed that there is considerable genetic variation within the lineages of R. diardii and R tiomanicus, suggesting that these two species are native to the Malay Peninsula.
    Matched MeSH terms: Genetic Variation
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