Displaying publications 181 - 200 of 742 in total

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  1. Genetic variability and evolutionary analyses of the coat protein gene of Tomato mosaic virus
    Rangel EA, Alfaro-Fernández A, Font-San-Ambrosio MI, Luis-Arteaga M, Rubio L
    Virus Genes, 2011 Dec;43(3):435-8.
    PMID: 21881940 DOI: 10.1007/s11262-011-0651-3
    Tomato mosaic virus (ToMV), a member of the genus Tobamovirus, infects several ornamental and horticultural crops worldwide. In this study, the nucleotide sequences of the coat protein gene of worldwide ToMV isolates were analyzed to estimate the genetic structure and diversity of this virus and the involved evolutionary forces. The phylogenetic analysis showed three clades with high bootstrap support: Clade I contained three ToMV isolates from Brazil collected from pepper, Clade II comprised one Brazilian ToMV isolate from pepper, and Clade III was composed of ToMV isolates collected from different plant hosts (pepper, tomato, eggplant, lilac, camellia, dogwood, red spruce, etc.) and water (from melting ice, lakes and streams) from different countries: USA, Brazil, Korea, Germany, Spain, Denmark (Greenland), China, Taiwan, Malaysia, Iran, and Kazakhstan. With the exception of Brazil, nucleotide diversity within and between different geographic regions was very low, although statistical analyses suggested some gene flow between most of these regions. Our analyses also suggested a strong negative selection which could have contributed to the genetic stability of ToMV.
    Matched MeSH terms: Genetic Variation*
  2. Fulltext Is there a genetic variation association in the IL-10 and TNF alpha promoter gene with gestational diabetes mellitus?
    Montazeri S, Nalliah S, Radhakrishnan AK
    Hereditas, 2010 Apr;147(2):94-102.
    PMID: 20536548 DOI: 10.1111/j.1601-5223.2009.02134.x
    Gestational diabetes mellitus (GDM), defined as carbohydrate intolerance diagnosed for the first time during pregnancy, affects both maternal and fetal health. Possession of a specific genetic polymorphism can be a predisposing factor for susceptibility to some diseases. The aim of this study was to investigate the association between single nucleotide polymorphisms (SNP) in the promoter gene of interleukin-10 (IL-10) as well as tumor necrosis factor-alpha (TNF alpha) with the development of GDM. Two hundred and twelve consecutive series of eligible normal pregnant women (controls) and gestational diabetes mellitus women were selected based on the study's inclusion and exclusion criteria. DNA was extracted from blood and genotyped for IL-10 at three positions and TNF alpha for gene polymorphism using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Plasma levels of IL-10 and TNF alpha at different gestational periods as well as postpartum were quantified using enzyme linked immunosorbent assay (ELISA). The results of the study showed that the difference in the frequency of SNP at position -597 in the promoter of the human IL-10 gene between the control and GDM groups was statistically significant (p < 0.05). In contrast, there was no significant difference in the frequency of SNP at the other two sites in the promoter region of the human IL-10 gene (-824 and -1082) as well as position -308 in the promoter of the human TNF-alpha (p > 0.05). In addition, there was no significant difference between the two groups in terms of plasma levels of IL-10 as well as TNF alpha in different stages of pregnancy. SNP at position -597 was significantly associated with the development of GDM and shows potential for use as a predictive marker for GDM.
    Matched MeSH terms: Genetic Variation*
  3. Fulltext Genetic structure of Phytophthora infestans populations in China indicates multiple migration events
    Guo L, Zhu XQ, Hu CH, Ristaino JB
    Phytopathology, 2010 Oct;100(10):997-1006.
    PMID: 20839935 DOI: 10.1094/PHYTO-05-09-0126
    One hundred isolates of Phytophthora infestans collected from 10 provinces in China between 1998 and 2004 were analyzed for mating type, metalaxyl resistance, mitochondrial DNA (mtDNA) haplotype, allozyme genotype, and restriction fragment length polymorphism (RFLP) with the RG-57 probe. In addition, herbarium samples collected in China, Russia, Australia, and other Asian countries were also typed for mtDNA haplotype. The Ia haplotype was found during the first outbreaks of the disease in China (1938 and 1940), Japan (1901, 1930, and 1931), India (1913), Peninsular Malaysia (1950), Nepal (1954), The Philippines (1910), Australia (1917), Russia (1917), and Latvia (1935). In contrast, the Ib haplotype was found after 1950 in China on both potato and tomato (1952, 1954, 1956, and 1982) and in India (1968 and 1974). Another migration of a genotype found in Siberia called SIB-1 (Glucose-6-phosphate isomerase [Gpi] 100/100, Peptidase [Pep] 100/100, IIa mtDNA haplotype) was identified using RFLP fingerprints among 72% of the isolates and was widely distributed in the north and south of China and has also been reported in Japan. A new genotype named CN-11 (Gpi 100/111, Pep 100/100, IIb mtDNA haplotype), found only in the south of China, and two additional genotypes (Gpi 100/100, Pep 100/100, Ia mtDNA haplotype) named CN-9 and CN-10 were identified. There were more diverse genotypes among isolates from Yunnan province than elsewhere. The SIB-1 (IIa) genotype is identical to those from Siberia, suggesting later migration of this genotype from either Russia or Japan into China. The widespread predominance of SIB-1 suggests that this genotype has enhanced fitness compared with other genotypes found. Movement of the pathogen into China via infected seed from several sources most likely accounts for the distribution of pathogen genotypes observed. MtDNA haplotype evidence and RFLP data suggest multiple migrations of the pathogen into China after the initial introduction of the Ia haplotype in the 1930s.
    Matched MeSH terms: Genetic Variation*
  4. Fulltext Mitochondrial and Y-chromosome diversity of the Tharus (Nepal): a reservoir of genetic variation
    Fornarino S, Pala M, Battaglia V, Maranta R, Achilli A, Modiano G, et al.
    BMC Evol. Biol., 2009;9:154.
    PMID: 19573232 DOI: 10.1186/1471-2148-9-154
    Central Asia and the Indian subcontinent represent an area considered as a source and a reservoir for human genetic diversity, with many markers taking root here, most of which are the ancestral state of eastern and western haplogroups, while others are local. Between these two regions, Terai (Nepal) is a pivotal passageway allowing, in different times, multiple population interactions, although because of its highly malarial environment, it was scarcely inhabited until a few decades ago, when malaria was eradicated. One of the oldest and the largest indigenous people of Terai is represented by the malaria resistant Tharus, whose gene pool could still retain traces of ancient complex interactions. Until now, however, investigations on their genetic structure have been scarce mainly identifying East Asian signatures.
    Matched MeSH terms: Genetic Variation*
  5. Patterns of rapd markers and heavy metal concentrations in Perna viridis (L.), collected from metal-contaminated and uncontaminated coastal waters: are they correlated with each other?
    Yap CK, Chua BH, Teh CH, Tan SG, Ismail A
    Genetika, 2007 May;43(5):668-74.
    PMID: 17633561
    Genetic variation due to heavy metal contamination has always been an interesting topic of study. Because of the numerous contaminants being found in coastal and intertidal waters, there is always much discussion and argument as to which contaminant(s) caused the variations in the genetic structures of biomonitors. This study used a Single Primer Amplification Reaction (SPAR) technique namely Random Amplified Polymorphic DNA (RAPD) to determine the genetic diversity of the populations of the green-lipped mussel Perna viridis collected from a metal-contaminated site at Kg. Pasir Puteh and those from four relatively' uncontaminated sites (reference sites). Heavy metal levels (Cd, Cu, Pb and Zn) were also measured in the soft tissues and byssus of the mussels from all the sites. Cluster analyses employing UPGMA done based on the RAPD makers grouped the populations into two major clusters; the Bagan Tiang, Pantai Lido, Pontian and Kg. Pasir Puteh populations were in one cluster, while the Sg. Belungkor population clustered by itself. This indicated that the genetic diversity based on bands resulting from the use of all four RAPD primers on P. viridis did not indicate its potential use as a biomarker of heavy metal pollution in coastal waters. However, based on a correlation analysis between a particular metal and a band resulting from a specific RAPD primer revealed some significant (P < 0.01) correlations between the primers and the heavy metal concentrations in the byssus and soft tissues. Thus, the correlation between a particular metal and the bands resulting from the use of a specific RAPD primer on P. viridis could be used as biomonitoring tool of heavy metal pollution.
    Matched MeSH terms: Genetic Variation*
  6. Allozyme variation in the camaenid tree snails Amphidromus atricallosus (Gould, 1843) and A. inversus (Müller, 1774)
    Prasankok P, Ota H, Toda M, Panha S
    Zoolog Sci, 2007 Feb;24(2):189-97.
    PMID: 17409732
    We examined allozyme variation in two camaenid tree snails, Amphidromus atricallosus and A. inversus, across two principal regions of Thailand and from Singapore, plus for A. inversus, one site in peninsular Malaysia. Using horizontal starch gel electrophoresis, 13 allozyme loci (11 polymorphic) were screened for A. atricallosus and 18 (5 polymorphic) for A. inversus. Heterozygosity was higher in A. atricallosus (Hexp=0.018-0.201, mean=0.085) than in A. inversus (Hexp=0-0.023, mean= 0.002). Genetic heterogeneity among samples was higher in A. inversus (Fst=0.965) than in A. atricallosus (Fst=0.781). Within A. atricallosus, populations were more differentiated in southern Thailand (Fst=0.551) than in eastern Thailand (Fst=0.144). The high Fst and low Hexp in populations of A. inversus suggest that this species is likely to have experienced a series of strong bottlenecks, perhaps occurring chiefly on offshore continental-shelf islands. The low Fst values of A. atricallosus in eastern Thailand suggest frequent gene flows among populations in this region. The southern and eastern samples of A. atricallosus exhibited fixed allele differences at four loci and great genetic distance (Nei's D=0.485-0.946), suggesting that these two samples may actually represent, or else be evolving into, separate species.
    Matched MeSH terms: Genetic Variation*
  7. Mitochondrial DNA variation within and among regional populations of longtail macaques (Macaca fascicularis) in relation to other species of the fascicularis group of macaques
    Smith DG, McDonough JW, George DA
    Am J Primatol, 2007 Feb;69(2):182-98.
    PMID: 17177314
    An 835 base pair (bp) fragment of mitochondrial DNA (mtDNA) was sequenced to characterize genetic variation within and among 1,053 samples comprising five regional populations each of longtail macaques (Macaca fascicularis) and rhesus macaques (Macaca mulatta), and one sample each of Japanese (M. fuscata) and Taiwanese (M. cyclopis) macaques. The mtDNA haplotypes of longtail macaques clustered in two large highly structured clades (Fas1 and Fas2) of a neighbor-joining tree that were reciprocally monophyletic with respect to those representing rhesus macaques, Japanese macaques, and Taiwanese macaques. Both clades exhibited haplotypes of Indonesian and Malaysian longtail macaques widely dispersed throughout them; however, longtail macaques from Indochina, Philippines, and Mauritius each clustered in a separate well-defined clade together with one or a few Malaysian and/or Indonesian longtail macaques, suggesting origins on the Sunda shelf. Longtail macaques from Malaysia and Indonesia were far more genetically diverse, and those from Mauritius were far less diverse than any other population studied. Nucleotide diversity between mtDNA sequences of longtail macaques from different geographic regions is, in some cases, greater than that between Indian and Chinese rhesus macaques. Approximately equal amounts of genetic diversity are due to differences among animals in the same regional population, different regional populations, and different species. A greater proportion of genetic variance was explained by interspecies differences when Japanese and Taiwanese macaques were regarded as regional populations of rhesus macaques than when they were treated as separate species. Rhesus macaques from China were more closely related to both Taiwanese and Japanese macaques than to their own conspecifics from India.
    Matched MeSH terms: Genetic Variation*
  8. Population structure and intraspecific aggression in the invasive ant species Anoplolepis gracilipes in Malaysian Borneo
    Drescher J, Blüthgen N, Feldhaar H
    Mol Ecol, 2007 Apr;16(7):1453-65.
    PMID: 17391269
    Invasive species are one of the main sources of the ongoing global loss of biodiversity. Invasive ants are known as particularly damaging invaders and their introductions are often accompanied by population-level behavioural and genetic changes that may contribute to their success. Anoplolepis gracilipes is an invasive ant that has just recently received increased attention due to its negative impact on native ecosystems. We examined the behaviour and population structure of A. gracilipes in Sabah, Malaysia. A total of 475 individuals from 24 colonies were genotyped with eight microsatellite markers. Intracolonial relatedness was high, ranging from 0.37 to 1 (mean +/- SD: 0.82 +/- 0.04), while intercolonial relatedness was low (0.0 +/- 0.02, range -0.5-0.76). We compared five distinct sampling regions in Sabah and Brunei. A three-level hierarchical F-analysis revealed high genetic differentiation among colonies within the same region, but low genetic differentiation within colonies or across regions. Overall levels of heterozygosity were unusually high (mean H(O) = 0.95, mean H(E) = 0.71) with two loci being entirely heterozygous, indicating an unusual reproductive system in this species. Bioassays revealed a negative correlation between relatedness and aggression, suggesting kinship as one factor facilitating supercolony formation in this species. Furthermore, we genotyped one individual per nest from Sabah (22 nests), Sarawak (one nest), Brunei (three nests) and the Philippines (two nests) using two mitochondrial DNA markers. We found six haplotypes, two of which included 82.1% of all sequences. Our study shows that the sampled area in Sabah consists of a mosaic of differently interrelated nests in different stages of colony establishment. While some of the sampled colonies may belong to large supercolonies, others are more likely to represent recently introduced or dispersed propagules that are just beginning to expand.
    Matched MeSH terms: Genetic Variation*
  9. Genetic diversity and molecular identification of mosquito species in the Anopheles maculatus group using the ITS2 region of rDNA
    Walton C, Somboon P, O'Loughlin SM, Zhang S, Harbach RE, Linton YM, et al.
    Infect Genet Evol, 2007 Jan;7(1):93-102.
    PMID: 16782411
    The species diversity and genetic structure of mosquitoes belonging to the Anopheles maculatus group in Southeast Asia were investigated using the internal transcribed spacer 2 (ITS2) of ribosomal DNA (rDNA). A molecular phylogeny indicates the presence of at least one hitherto unrecognised species. Mosquitoes of chromosomal form K from eastern Thailand have a unique ITS2 sequence that is 3.7% divergent from the next most closely related taxon (An. sawadwongporni) in the group. In the context of negligible intraspecific variation at ITS2, this suggests that chromosomal form K is most probably a distinct species. Although An. maculatus sensu stricto from northern Thailand and southern Thailand/peninsular Malaysia differ from each other in chromosomal banding pattern and vectorial capacity, no intraspecific variation was observed in the ITS2 sequences of this species over this entire geographic area despite an extensive survey. A PCR-based identification method was developed to distinguish five species of the group (An. maculatus, An. dravidicus, An. pseudowillmori, An. sawadwongporni and chromosomal form K) to assist field-based studies in northwestern Thailand. Sequences from 187 mosquitoes (mostly An. maculatus and An. sawadwongporni) revealed no intraspecific variation in specimens from Thailand, Cambodia, mainland China, Malaysia, Taiwan and Vietnam, suggesting that this identification method will be widely applicable in Southeast Asia. The lack of detectable genetic structure also suggests that populations of these species are either connected by gene flow and/or share a recent common history.
    Matched MeSH terms: Genetic Variation*
  10. Patterns of genetic diversity and migration in increasingly fragmented and declining orang-utan (Pongo pygmaeus) populations from Sabah, Malaysia
    Goossens B, Chikhi L, Jalil MF, Ancrenaz M, Lackman-Ancrenaz I, Mohamed M, et al.
    Mol Ecol, 2005 Feb;14(2):441-56.
    PMID: 15660936
    We investigated the genetic structure within and among Bornean orang-utans (Pongo pygmaeus) in forest fragments of the Lower Kinabatangan flood plain in Sabah, Malaysia. DNA was extracted from hair and faecal samples for 200 wild individuals collected during boat surveys on the Kinabatangan River. Fourteen microsatellite loci were used to characterize patterns of genetic diversity. We found that genetic diversity was high in the set of samples (mean H(E) = 0.74) and that genetic differentiation was significant between the samples (average F(ST) = 0.04, P < 0.001) with F(ST) values ranging from low (0.01) to moderately large (0.12) values. Pairwise F(ST) values were significantly higher across the Kinabatangan River than between samples from the same river side, thereby confirming the role of the river as a natural barrier to gene flow. The correlation between genetic and geographical distance was tested by means of a series of Mantel tests based on different measures of geographical distance. We used a Bayesian method to estimate immigration rates. The results indicate that migration is unlikely across the river but cannot be completely ruled out because of the limited F(ST) values. Assignment tests confirm the overall picture that gene flow is limited across the river. We found that migration between samples from the same side of the river had a high probability indicating that orang-utans used to move relatively freely between neighbouring areas. This strongly suggests that there is a need to maintain migration between isolated forest fragments. This could be done by restoring forest corridors alongside the river banks and between patches.
    Matched MeSH terms: Genetic Variation*
  11. Molecular variation of Spiranthes sinensis (Orchidaceae) in Japan, with special reference to systematic treatment of seasonally differentiated groups and a dwarf form, f. gracilis, from Yakushima Island
    Tsukaya H
    J Plant Res, 2005 Feb;118(1):13-8.
    PMID: 15654504
    Molecular variations of Spiranthes sinensis Ames var. australis (R.Br.) H. Hara et Kitam. ex Kitam. in Japan were examined to evaluate the validity of the seasonally differentiated groups and a dwarf form of the species, which is endemic to Yakushima Island, Japan. Sequence differences in the plastid trnL-F locus clearly distinguished Japanese S. sinensis var. australis from S. sinensis var. sinensis collected from Ryukyu. In contrast, the trnL-F sequence of S. sinensis var. australis from Sabah, Malaysia, clearly differed from that of Japanese S. sinensis var. australis, suggesting genetic heterogeneity of Spiranthes sinensis var. australis in Asia. Moreover, a molecular analysis based on the sequences of nuclear ITS1 regions indicated that there are two major groups of S. sinensis var. australis in Japan, with a geographic distribution boundary on Kyushu Island. However, the trnL-F and ITS1 sequences did not support the genetic differentiation of the seasonally differentiated groups or the dwarf form from the other Japanese individuals. Based on these molecular data, the systematic treatment of physiological and morphological variations in the Japanese population of S. sinensis. var. australis is discussed.
    Matched MeSH terms: Genetic Variation*
  12. 3'-UTR variations and G6PD deficiency
    Amini F, Ismail E
    J Hum Genet, 2013 Apr;58(4):189-94.
    PMID: 23389243 DOI: 10.1038/jhg.2012.155
    The combination of two silent mutations, c.1311C>T in exon 11 and IVS11 T93C (glucose-6-phosphate dehydrogenase (G6PD) 1311T/93C), with unknown mechanism, have been reported in G6PD-deficient individuals in Asian populations including Malaysian aboriginal group, Negrito. Here, we report the screening of G6PD gene in 103 Negrito volunteers using denaturing high-performance liquid chromatography (dHPLC) and direct sequencing. A total of 48 individuals (46.6%) were G6PD deficient, 83.3% of these carried G6PD 1311T/93C with enzyme activity ranging from 1.8 to 4.8 U gHb(-1). Three novel single-nucleotide polymorphisms (SNPs), rs112950723, rs111485003 and rs1050757, were found in the G6PD 3'-untranslated region (UTR). Strong association was observed between haplotype 1311T/93C and rs1050757G, which is located inside the 35 bp AG-rich region. In silico analysis revealed that the transition of A to G at position rs1050757 makes significant changes in the G6PD mRNA secondary structure. Moreover, putative micro (mi)RNA target sites were identified in 3'-UTR of G6PD gene, two of these in the region encompassing rs1050757. It could be speculated that rs1050757 have a potential functional effect on the downregulation of mRNA and consequently G6PD deficiency either by affecting mRNA stability and translation or mirRNA regulation process. This is the first report of biochemical association of an SNP in 3'-UTR of G6PD gene and the possible role of mRNA secondary structure.
    Matched MeSH terms: Genetic Variation*
  13. Fulltext Deep whole-genome sequencing of 100 southeast Asian Malays
    Wong LP, Ong RT, Poh WT, Liu X, Chen P, Li R, et al.
    Am J Hum Genet, 2013 Jan 10;92(1):52-66.
    PMID: 23290073 DOI: 10.1016/j.ajhg.2012.12.005
    Whole-genome sequencing across multiple samples in a population provides an unprecedented opportunity for comprehensively characterizing the polymorphic variants in the population. Although the 1000 Genomes Project (1KGP) has offered brief insights into the value of population-level sequencing, the low coverage has compromised the ability to confidently detect rare and low-frequency variants. In addition, the composition of populations in the 1KGP is not complete, despite the fact that the study design has been extended to more than 2,500 samples from more than 20 population groups. The Malays are one of the Austronesian groups predominantly present in Southeast Asia and Oceania, and the Singapore Sequencing Malay Project (SSMP) aims to perform deep whole-genome sequencing of 100 healthy Malays. By sequencing at a minimum of 30× coverage, we have illustrated the higher sensitivity at detecting low-frequency and rare variants and the ability to investigate the presence of hotspots of functional mutations. Compared to the low-pass sequencing in the 1KGP, the deeper coverage allows more functional variants to be identified for each person. A comparison of the fidelity of genotype imputation of Malays indicated that a population-specific reference panel, such as the SSMP, outperforms a cosmopolitan panel with larger number of individuals for common SNPs. For lower-frequency (<5%) markers, a larger number of individuals might have to be whole-genome sequenced so that the accuracy currently afforded by the 1KGP can be achieved. The SSMP data are expected to be the benchmark for evaluating the value of deep population-level sequencing versus low-pass sequencing, especially in populations that are poorly represented in population-genetics studies.
    Matched MeSH terms: Genetic Variation*
  14. Comparative analysis of viral genomes from acute and chronic hepatitis B reveals novel variants associated with a lower rate of chronicity
    Chook JB, Ngeow YF, Khang TF, Ng KP, Tiang YP, Mohamed R
    J Med Virol, 2013 Mar;85(3):419-24.
    PMID: 23297244 DOI: 10.1002/jmv.23500
    Infection with the hepatitis B virus (HBV) may lead to an acute or chronic infection. It is generally accepted that the clinical outcome of infection depends on the balance between host immunity and viral survival strategies. In order to persist, the virus needs to have a high rate of replication and some immune-escape capabilities. Hence, HBVs lacking these properties are likely to be eliminated more rapidly by the host, leading to a lower rate of chronicity. To test this hypothesis, 177 HBV genomes from acute non-fulminant cases and 1,149 from chronic cases were retrieved from GenBank for comparative analysis. Selection of candidate nucleotides associated with the disease state was done using random guess cut-off and the Bonferroni correction. Five significant nucleotides were detected using this filtering step. Their predictive values were assessed using the support vector machine classification with five-fold cross-validation. The average prediction accuracy was 61% ± 1%, with a sensitivity of 24% ± 1%, specificity of 98% ± 1%, positive predictive value of 92% ± 4% and negative predictive value of 56% ± 1%. BCP/X, enhancer I and surface/polymerase variants were found to be associated almost exclusively with acute hepatitis. These HBV variants are novel potential markers for non-progression to chronic hepatitis.
    Matched MeSH terms: Genetic Variation*
  15. Fulltext Population expansion and gene flow in Giardia duodenalis as revealed by triosephosphate isomerase gene
    Choy SH, Mahdy MA, Al-Mekhlafi HM, Low VL, Surin J
    Parasit Vectors, 2015;8:454.
    PMID: 26373536 DOI: 10.1186/s13071-015-1084-y
    Giardia duodenalis is a protozoan parasite that can cause significant diarrhoeal diseases. Knowledge of population genetics is a prerequisite for ascertaining the invasion patterns of this parasite. In order to infer evolutionary patterns that could not be uncovered based on the morphological features, a population genetic study with the incorporation of molecular marker was carried out to access the genetic structure of G. duodenalis isolated from the Malaysian population and the global populations.
    Matched MeSH terms: Genetic Variation*
  16. Complete mitochondrial genome reveals genetic diversity of Angiostrongylus cantonensis (Nematoda: Angiostrongylidae)
    Yong HS, Song SL, Eamsobhana P, Goh SY, Lim PE
    Acta Trop, 2015 Dec;152:157-164.
    PMID: 26348256 DOI: 10.1016/j.actatropica.2015.09.001
    Angiostrongylus cantonensis is a zoonotic parasite that causes eosinophilic meningitis in humans. Earlier work on its mitochondrial genome was based on long polymerase chain reaction method. To date, only the mitogenome of the isolates from China has been studied. We report here the complete mitogenome of the Thailand isolate based on next generation sequencing and compare the genetic diversity with other isolates. The mitogenome of the Thailand isolate (13,519bp) is longer than those of the China isolates (13,497-13,502bp). Five protein-coding genes (atp6, cox1, cox2, cob, nad2) show variations in length among the isolates. The stop codon of the Thailand isolate differs from the China and Taiwan isolates in 4 genes (atp6, cob, nad2, nad6). Additionally, the Thailand isolate has 4 incomplete T stop codon compared to 3 in the China and Taiwan isolates. The control region is longer in the Thailand isolate (258bp) than the China (230-236bp) and Taiwan (237bp) isolates. The intergenic sequence between nad4 and cox1 genes in the Thailand isolate lacks 2bp (indels) at the 5'-end of the sequence as well as differs at 7 other sites compared to the China and Taiwan isolates. In the Thailand isolate, 18 tRNAs lack the entire TΨC-arm, compared to 17 in the China isolate and 16 in the Taiwan isolate. Phylogenetic analyses based on 36 mt-genes, 12 PCGs, 2 rRNA genes, 22 tRNA genes and control region all indicate closer genetic affinity between the China and Taiwan isolates compared to the Thailand isolate. Based on 36 mt-genes, the inter-isolate genetic distance varies from p=3.2% between China and Taiwan isolates to p=11.6% between Thailand and China isolates. The mitogenome will be useful for population, phylogenetics and phylogeography studies.
    Matched MeSH terms: Genetic Variation*
  17. Cytogenetic and Molecular Evidence of Additional Cryptic Diversity in High Elevation Black fly Simulium feuerborni (Diptera: Simuliidae) Populations in Southeast Asia
    Pramual P, Thaijarern J, Sofian-Azirun M, Ya'cob Z, Hadi UK, Takaoka H
    J Med Entomol, 2015 Sep;52(5):829-36.
    PMID: 26336220 DOI: 10.1093/jme/tjv080
    Simulium feuerborni Edwards is geographically widespread in Southeast Asia. Previous cytogenetic study in Thailand revealed that this species is a species complex composed of two cytoforms (A and B). In this study, we cytologically examined specimens obtained from the Cameron Highlands, Malaysia, and Puncak, Java, Indonesia. The results revealed two additional cytoforms (C and D) of S. feuerborni. Specimens from Malaysia represent cytoform C, differentiated from other cytoforms by a fixed chromosome inversion on the long arm of chromosome III (IIIL-5). High frequencies of the B chromosome (33-83%) were also observed in this cytoform. Specimens from Indonesia represent the cytoform D. This cytoform is differentiated from others by a fixed chromosome inversion difference on the long arm of chromosome II (IIL-4). Mitochondrial DNA sequences support genetic differentiation among cytoforms A, B, and C. The pairwise F(ST) values among these cytoforms were highly significantly consistent with the divergent lineages of the cytoforms in a median-joining haplotype network. However, a lack of the sympatric populations prevented us from testing the species status of the cytoforms.
    Matched MeSH terms: Genetic Variation*
  18. Fulltext Characterizing the genetic diversity of the monkey malaria parasite Plasmodium cynomolgi
    Sutton PL, Luo Z, Divis PCS, Friedrich VK, Conway DJ, Singh B, et al.
    Infect Genet Evol, 2016 06;40:243-252.
    PMID: 26980604 DOI: 10.1016/j.meegid.2016.03.009
    Plasmodium cynomolgi is a malaria parasite that typically infects Asian macaque monkeys, and humans on rare occasions. P. cynomolgi serves as a model system for the human malaria parasite Plasmodium vivax, with which it shares such important biological characteristics as formation of a dormant liver stage and a preference to invade reticulocytes. While genomes of three P. cynomolgi strains have been sequenced, genetic diversity of P. cynomolgi has not been widely investigated. To address this we developed the first panel of P. cynomolgi microsatellite markers to genotype eleven P. cynomolgi laboratory strains and 18 field isolates from Sarawak, Malaysian Borneo. We found diverse genotypes among most of the laboratory strains, though two nominally different strains were found to be genetically identical. We also investigated sequence polymorphism in two erythrocyte invasion gene families, the reticulocyte binding protein and Duffy binding protein genes, in these strains. We also observed copy number variation in rbp genes.
    Matched MeSH terms: Genetic Variation*
  19. Molecular genetic variation and structure of Southeast Asian crocodile (Tomistoma schlegelii): Comparative potentials of SSRs versus ISSRs
    Shafiei-Astani B, Ong AH, Valdiani A, Tan SG, Yien CY, Ahmady F, et al.
    Gene, 2015 Oct 15;571(1):107-16.
    PMID: 26112832 DOI: 10.1016/j.gene.2015.06.053
    Tomistoma schlegelii, also referred to as the "false gharial", is one of the most exclusive and least known of the world's fresh water crocodilians, limited to Southeast Asia. Indeed, lack of economic value for its skin has led to neglect the biodiversity of the species. The current study aimed to investigate the mentioned case using 40 simple sequence repeat (SSR) primer pairs and 45 inter-simple sequence repeat (ISSR) primers. DNA analysis of 17 T. schlegelii samples using the SSR and ISSR markers resulted in producing a total of 49 and 108 polymorphic bands, respectively. Furthermore, the SSR- and ISSR-based cluster analyses both generated two main clusters. However, the SSR based results were found to be more in line with the geographical distributions of the crocodile samples collected across the country as compared with the ISSR-based results. The observed heterozygosity (HO) and expected heterozygosity (HE) of the polymorphic SSRs ranged between 0.588-1 and 0.470-0.891, respectively. The present results suggest that the Malaysian T. schlegelii populations had originated from a core population of crocodiles. In cooperation with the SSR markers, the ISSRs showed high potential for studying the genetic variation of T. schlegelii, and these markers are suitable to be employed in conservation genetic programs of this endangered species. Both SSR- and ISSR-based STRUCTURE analyses suggested that all the individuals of T. schlegelii are genetically similar with each other.
    Matched MeSH terms: Genetic Variation*
  20. Fulltext Tests of conspecificity for allopatric vectors: Simulium nodosum and Simulium shirakii (Diptera: Simuliidae) in Asia
    Low VL, Adler PH, Sofian-Azirun M, Srisuka W, Saeung A, Huang YT, et al.
    Parasit Vectors, 2015 May 29;8:297.
    PMID: 26022092 DOI: 10.1186/s13071-015-0911-5
    BACKGROUND: Allopatric populations present challenges for biologists working with vectors. We suggest that conspecificity can be concluded in these cases when data from four character sets-chromosomal, ecological, molecular, and morphological-express variation no greater between the allopatric populations than between corresponding sympatric populations. We use this approach to test the conspecificity of Simulium nodosum Puri on the mainland of Southeast Asia and Simulium shirakii Kono & Takahasi in Taiwan. The validity of these two putative species has long been disputed given that they are morphologically indistinguishable.

    FINDINGS: The mitochondria-encoded cytochrome c oxidase subunit I (COI), 12S rRNA, and 16S rRNA genes and the nuclear-encoded 28S rRNA gene support the conspecific status of S. nodosum from Myanmar, Thailand, and Vietnam and S. shirakii from Taiwan; 0 to 0.19 % genetic differences between the two taxa suggest intraspecific polymorphism. The banding patterns of the polytene chromosomes of the insular Taiwanese population of S. shirakii and mainland populations of S. nodosum are congruent. The overlapping ranges of habitat characteristics and hosts of S. nodosum and S. shirakii corroborate the chromosomal, molecular, and morphological data.

    CONCLUSIONS: Four independent sources of evidence (chromosomes, DNA, ecology, and morphology) support the conspecificity of S. nodosum and S. shirakii. We, therefore, synonymize S. shirakii with S. nodosum. This study provides a guide for applying the procedure of testing conspecificity to other sets of allopatric vectors.

    Matched MeSH terms: Genetic Variation*
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