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Who is biting you? DNA barcodes reveal cryptic diversity in human-biting black flies (Diptera: Simuliidae)

Jomkumsing P, Tangkawanit U, Wongpakam K, Pramual P

Acta Trop, 2019 Aug;196:22-29.
PMID: 31059708 DOI: 10.1016/j.actatropica.2019.05.001

Black flies (Simuliidae) are important biting insects and vectors of diseases agents of humans and livestock. Thus, understanding the taxonomy and biodiversity of these insects is crucial for control and management of these diseases. In this study, we used mitochondrial cytochrome c oxidase I sequences to examine genetic diversity of three human-biting and possible vector black fly taxa; the Simulium asakoae species-complex, S. chamlongi and S. nigrogilvum. High levels of genetic diversity (>3.5% intraspecific genetic divergence) were found in all three taxa. Phylogenetic analyses indicated that the S. asakoae complex can be divided into seven groups with the largest group consisting of specimens from Thailand, Malaysia and Myanmar. This group most likely represents true S. asakoae. The remaining haplotypes formed groups with conspecific haplotypes or with other closely related species. Among these groups, one including S. monglaense and another including S. myanmarense suggest that certain specimens identified as S. asakoae most likely belong to those species. Therefore, they constitute new locality records for Thailand and also represent new records of anthropophily. Members of S. chamlongi are not monophyletic as its clade also included S. hackeri. A median joining network revealed strong geographic associations of the haplotypes of S. nigrogilvum suggesting limitation of gene flow. Because this species occurs mainly in high elevation habitats, low land areas could present a barrier to gene flow.

Matched MeSH terms: Haplotypes
Fulltext The CHEK2 Variant C.349A>G Is Associated with Prostate Cancer Risk and Carriers Share a Common Ancestor

Brandão A, Paulo P, Maia S, Pinheiro M, Peixoto A, Cardoso M, et al.

Cancers (Basel), 2020 Nov 04;12(11).
PMID: 33158149 DOI: 10.3390/cancers12113254

The identification of recurrent founder variants in cancer predisposing genes may have important implications for implementing cost-effective targeted genetic screening strategies. In this study, we evaluated the prevalence and relative risk of the CHEK2 recurrent variant c.349A>G in a series of 462 Portuguese patients with early-onset and/or familial/hereditary prostate cancer (PrCa), as well as in the large multicentre PRACTICAL case-control study comprising 55,162 prostate cancer cases and 36,147 controls. Additionally, we investigated the potential shared ancestry of the carriers by performing identity-by-descent, haplotype and age estimation analyses using high-density SNP data from 70 variant carriers belonging to 11 different populations included in the PRACTICAL consortium. The CHEK2 missense variant c.349A>G was found significantly associated with an increased risk for PrCa (OR 1.9; 95% CI: 1.1-3.2). A shared haplotype flanking the variant in all carriers was identified, strongly suggesting a common founder of European origin. Additionally, using two independent statistical algorithms, implemented by DMLE+2.3 and ESTIAGE, we were able to estimate the age of the variant between 2300 and 3125 years. By extending the haplotype analysis to 14 additional carrier families, a shared core haplotype was revealed among all carriers matching the conserved region previously identified in the high-density SNP analysis. These findings are consistent with CHEK2 c.349A>G being a founder variant associated with increased PrCa risk, suggesting its potential usefulness for cost-effective targeted genetic screening in PrCa families.

Matched MeSH terms: Haplotypes
Mitochondrial Genetic Diversity of the Freshwater Snail Melanoides tuberculata

Chiu YW, Gan YC, Kuo PH, Hsu KC, Tan MS, Ju YM, et al.

Biochem Genet, 2018 Oct 26.
PMID: 30367289 DOI: 10.1007/s10528-018-9892-3

According to geological history, Peninsular Malaysia and Borneo formed at different times and were once connected during Quaternary glaciations. To determine how this history has influenced phylogeography, our study examined the population genetic structure of the tropical freshwater gastropod Melanoides tuberculata across Peninsular Malaysia and Borneo using the sequences from mitochondrial DNA 16S rRNA and cytochrome oxidase subunit I genes (1168 bp). In total, 104 specimens were collected from seventeen populations. All mtDNA haplotypes were identified as belonging to two highly divergent lineages, and these lineages were almost allopatric in their distributions. Our study found that the freshwater fauna in Malaysia might be divided into four regions: northeast Peninsular Malaysia, northwest Peninsular Malaysia, south Peninsular Malaysia, and Borneo. The phylogeography of M. tuberculata in Malaysia was shaped by the landforms of Peninsular Malaysia and by the paleo-river systems in the Sunda continental shelf. In addition, our study found that these two lineages in Malaysia have invaded the globe. These results suggest that Malaysia is located in important shipping lanes throughout the world, and the populations of M. tuberculate might be widely distributed throughout the world by shipping.

Matched MeSH terms: Haplotypes
POPULATION GENETICS OF LONGTAIL TUNA (Thunnus tonggol) (BLEEKER, 1851) FROM EAST MALAYSIA BASED ON MITOCHONDRIAL DNA D-LOOP MARKER

NURUL AZLIANA MOHD YASIN, NOORHANI SYAHIDA KASIM, TUN NURUL AIMI MAT JAAFAR, RUMEAIDA MAT PIAH, WAHIDAH MOHD ARSHAAD, SITI AZIZAH MOHD NOR, et al.

UMT Journal of Undergraduate Research, 2020;2(2):49-56.
MyJurnal

Present study investigates the genetic diversity and genetic distribution of the longtail tuna Thunnus tonggol collected from east Malaysia (Borneo states of Sabah and Sarawak) based on mitochondrial DNA D-loop sequence analysis. 58 fish samples were obtained, specifically from Kota Kinabalu, KK (n = 22), Miri, MR (n=20) and Bintulu, BT (n = 17). DNA template was isolated using the salt extraction method. Final length of 404 base pair (bp) D-loop sequences revealed 52 haplotypes that comprise of 77 variable sites (38 of parsimony informative and 39 singleton). A total of 20 haplotypes were found in KK, 19 haplotypes in MR and 16 haplotypes in BT. Molecular diversity indices revealed high haplotype diversity and low nucleotide diversity in all populations; KK (h = 0.9913 ± 0.0165, π = 0.00239 ± 0.0127), MR (h = 0.9942 ± 0.0193, π = 0.0226 ± 0.0121) and BT (h = 0.9926 ± 0.0230, π = 0.0196 ± 0.0171). Population comparison pairwise FST show that KK and BT were significantly genetically differentiated. The result from this study will be beneficial for fisheries management and also to provide information on the population genetics of T. tonggol in East Malaysian waters.

Matched MeSH terms: Haplotypes
Fulltext Population Genetic Structure of Ornate Threadfin Bream (Nemipterus hexodon) in Thailand

Supmee V, Songrak A, Suppapan J, Sangthong P

Trop Life Sci Res, 2021 Mar;32(1):63-82.
PMID: 33936551 DOI: 10.21315/tlsr2021.32.1.4

Ornate threadfin bream (Nemipterus hexodon) is an economically important fishery species in Southeast Asia. In Thailand, N. hexodon decreased dramatically due to overexploitation for commercial purposes. To construct an effective sustainable management plan, genetic information is necessary. Thus, in our study, the population genetic structure and demographic history of N. hexodon were investigated using 419 bp of the mitochondrial DNA sequence in cytochrome oxidase subunit I gene (mtDNA COI). A total of 142 samples was collected from nine localities in the Gulf of Thailand (Chonburi, Samut Songkhram, Surat Thani, Nakhon Si Thammarat, Songkhla), and the Andaman Sea (Satun, Trang, Krabi, Phang Nga). Fourteen polymorphic sites defined 18 haplotypes, revealing a high haplotype diversity and low nucleotide diversity among nine localities. The analysis of molecular variance (AMOVA) analysis, pairwise F
ST
, and minimum spanning network result revealed that the genetic structure of N. hexodon was separated into two populations: the Gulf of Thailand and the Andaman Sea population. The genetic structure of N. hexodon can be explained by a disruption of gene flow from the geographic barrier and the Pleistocene isolation of the marine basin hypothesis. Neutrality tests, Bayesian skyline analysis, mismatch distribution, and the estimated values of population growth suggested that N. hexodon had experienced a population expansion. The genetic information would certainly help us gain insight into the population genetic structure of N. hexodon living on the coast of Thailand.

Matched MeSH terms: Haplotypes
Episodic positive selection in the Cam734 haplotype and low prevalence of the A144F mutation in Plasmodium falciparum chloroquine resistance transporter gene among Thai isolates

Buppan P, Seethamchai S, Kuamsab N, Jongwutiwes S, Putaporntip C

Trop Biomed, 2018 Dec 01;35(4):861-871.
PMID: 33601836

Chloroquine resistance transporter of Plasmodium falciparum (PfCRT) is a food vacuolar transmembrane protein that mediates susceptibility of the parasite to chloroquine. A mutation at K76T of the Pfcrt gene is a key determinant for chloroquine resistance phenotype. In the absence of drug pressure, in vitro growth rate of chloroquine-resistance parasites was outcompeted by wild-type parasites unless intragenic compensatory mutations occurred. Chloroquine-resistant P. falciparum bearing the Cam734 haplotype known to circulate in endemic areas of Cambodia bordering Thailand contains 9 mutations in Pfcrt and exhibits both chloroquine resistance and comparable growth rate to the chloroquine-sensitive 3D7 strain. To analyze the evolution of the Cam734 haplotype, codon-based analysis was performed by using the mixed effects model of evolution (MEME), branch-site random effects likelihood (BR-REL) and other related methods. Results revealed that the Cam734 haplotype has evolved distinctively from other known mutant haplotypes including the most common Dd2 haplotype in Southeast Asia. Evidence of episodic positive selection was detected at codon 144, characterized by c.[430G>T; 431C>T] (p.A144F), known to be indispensable for both chloroquine resistance and restoration of growth rate of the parasites. To survey the prevalence of mutations at codons 76 and 144 in Pfcrt among Thai isolates, restriction fragment analysis of 548 P. falciparum isolates collected from six endemic provinces of Thailand during 1991 and 2016 was performed. The 144F Pfcrt mutant was detected in 7 (1.28%) isolates. All Thai isolates analyzed herein harbored a mutation at codon 76 whilst the wild-type parasite was not found. The low prevalence of isolates bearing the mutation 144F in PfCRT could imply little or lack of survival advantage of this mutant in endemic areas of Thailand where the wild-type parasites seem to be absent or extremely rare.

Matched MeSH terms: Haplotypes
Different patterns of pfcrt and pfmdr1 polymorphism in Plasmodium falciparum isolates from Tehama region, Yemen

Atroosh WM, Al-Mekhlafi HM, Al-Jasari A, Sady H, Dawaki SS, Elyana FN, et al.

PeerJ, 2016;4:e2191.
PMID: 27478699 DOI: 10.7717/peerj.2191

Introduction. Despite the efforts of the malaria control programme, malaria morbidity is still a common health problem in Yemen, with 60% of the population at risk. Plasmodium falciparum is responsible for 99% of malaria cases. The emergence in Yemen of parasite resistance to chloroquine (CQ) prompted the adoption of artemisinin combination therapy (ACT) in 2009, which involves the use of artesunate plus sulphadoxine-pyrimethamine (AS + SP). However, CQ was retained as the drug of choice for vivax malaria. To assess the impact of the change in the malaria treatment policy five years after its introduction, the present study investigated the mutations in the CQ resistance transporter (pfcrt) and multidrug resistance 1 (pfmdr1) genes. Method. A molecular investigation of 10 codons of pfcrt (72-76, 220, 271, 326, 356, and 371) and five codons of pfmdr1 (86, 184, 1034, 1042, and 1246) was conducted on P. falciparum isolates from districts with the highest malaria endemicity in the Hodeidah and Al-Mahwit governorates in Tehama region, Yemen. A total of 86 positive cases of falciparum monoinfection were investigated for the presence of mutations related to CQ and other antimalarials using a PCR-RFLP assay. Results. There was a wide prevalence of pfcrt gene mutations with the pfcrt 76T CQ resistance marker being predominant (97.7%). The prevalence of other pfcrt mutations varied from high (75E: 88%) to moderate (74I: 79.1%, 220S: 69.8%, 271E and 371I: 53.5%) or low (326S: 36%, 72S: 10.5%). Mutated pfcrt 72-76 amino acids haplotypes were highly prevalent (98.8%). Among these, the CVIET classic, old-world African/Southeast Asian haplotype was the most predominant, and was mostly found in the isolates from the Khamis Bani Saad district of Al-Mahwit (93.1%) and the AdDahi district of Hodeidah (88.9%). However, it was only found in 26.3% of the isolates from the Bajil district of Hodeidah. Surprisingly, the SVMNT new-world South American haplotype was exclusively detected in 9.3% of the isolates from the Bajil district of Hodeidah. Mutations at Y184F of pfmdr1 were found in all isolates (100%) from all districts. The mutation for codons 1034C and 86Y were found only in the isolates from the AdDahi and Khamis Bani Saad districts. Overall, the AdDahi and Khamis Bani Saad districts were similar in terms of carrying most of the mutations in the pfcrt and pfmdr1 genes, while there was a lower prevalence of mutation in the isolates from the Bajil district. Conclusion. The high prevalence of mutations in pfcrt 5 years after the official cessation of CQ use against P. falciparum suggests that there is sustained CQ pressure on P. falciparum isolates in the study area. Moreover, the low prevalence of mutations in the pfmdr1 gene could be a good indicator of the high susceptibility of P. falciparum isolates to antimalarials other than CQ. A new strategy to ensure the complete nationwide withdrawal of CQ from the private drug market is recommended.

Matched MeSH terms: Haplotypes
Fulltext MinION: A Novel Tool for Predicting Drug Hypersensitivity?

Chua EW, Ng PY

Front Pharmacol, 2016;7:156.
PMID: 27378921 DOI: 10.3389/fphar.2016.00156

The launch of the MinION Access Program has caused much activity within the scientific community. MinION represents a keenly anticipated, novel addition to the current melange of commercial sequencers. Driven by the nanopore sequencing mechanism that requires minimal sample manipulation, the device is capable of generating long sequence reads in sizes (up to or exceeding 50 kb) that surpass those of all other platforms. One notable advantage of this feature is that long-range haplotypes can be more accurately resolved; such advantage is particularly pertinent to the genotyping of complex loci such as genes encoding the human leukocyte antigens, which are pivotal determinants of drug hypersensitivity. With this timely, albeit brief, review, we set out to examine the applications on which MinION has been tested thus far, the bioinformatics workflow tailored to the unique characteristics of its extended sequence reads, the device's potential utility in the detection of genetic markers for drug hypersensitivity, and how it may eventually evolve to become fit for diagnostic purposes in the clinical setting.

Matched MeSH terms: Haplotypes
Fulltext A preliminary study of genetic differentiation of two important cultured oyster species, Crassostrea iredalei and C. belcheri in Malaysia based on cytochrome oxidase I (COI) gene

Suzana M., Siti Azizah M. N., Devakie, M. N.

Buletin Persatuan Genetik Malaysia, 2009;14(1):14-17.
MyJurnal

This paper reports on a preliminary genetic investigation of two commercially cultured oyster species, white and black scar oysters, Crassostrea belcheri and C. iredalei, respectively. A total
of 68 individuals from three different areas in Malaysia namely a C. belcheri sample from Semporna (Sabah) and two populations of C. iredalei from Trai (Sabah) and Setiu (Terengganu) were
collected and analysed based on sequence analysis of cytochrome oxidase subunit I (COI). Alignment of COI gene was done using Alignment Explorer/CLUSTAL in Mega4.1. Genetic distances
within and between populations were calculated using Kimura 2-parameter. Phylogenetic dendograms were generated by Neighbour-Joining (NJ) and Maximum Parsimony (MP) methods.
The ingroup taxa were divided into two main clusters separating C. iredalei and C. belcheri with 99% bootstrap value. The two C. iredalei populations were homogeneous suggesting high
connectivity in the South China Sea for this species. The common central haplotype in the minimum spanning networks programme is believed to be the ancestral variant for the two species. The
findings from this study provides important baseline data for the aquaculture, management and monitoring of cultured populations of the oyster species.

Matched MeSH terms: Haplotypes
Fulltext Diversity and natural selection on the thrombospondin-related adhesive protein (TRAP) gene of Plasmodium knowlesi in Malaysia

Ahmed MA, Lau YL, Quan FS

Malar J, 2018 Jul 27;17(1):274.
PMID: 30053885 DOI: 10.1186/s12936-018-2423-1

BACKGROUND: Plasmodium knowlesi a parasite of the macaques is currently the most common cause of human malaria in Malaysia. The thrombospondin-related adhesive protein (TRAP) gene is pre-erythrocytic stage antigen. It is a well-characterized vaccine candidate in Plasmodium vivax and Plasmodium falciparum, however, no study has been done in the orthologous gene of P. knowlesi. This study investigates nucleotide diversity, haplotypes, natural selection and population differentiation of full-length pktrap genes in clinical samples from Malaysia.
METHODS: Forty full-length pktrap sequences from clinical isolates of Malaysia along with the reference H-strain were downloaded from published databases. Genetic diversity, polymorphism, haplotype and natural selection were determined using DnaSP 5.10 software. McDonald-Kreitman test was conducted using P. vivax and Plasmodium coatneyi as ortholog sequence in DnaSP 5.10 software. Population genetic differentiation index (FST) of parasite populations was determined using Arlequin v3.5. Phylogenetic relationships between trap ortholog genes were determined using MEGA 5.0 software.
RESULTS: Comparison of 40 full-length pktrap sequences along with the H-strain identified 74 SNPs (53 non-synonymous and 21 synonymous substitutions) resulting in 29 haplotypes. Analysis of the full-length gene showed that the nucleotide diversity was lower compared to its nearest ortholog pvtrap. Domain-wise analysis indicated that the proline/asparagine rich region had higher nucleotide diversity compared to the von Willebrand factor domain and the thrombospondin-type-1 domain. McDonald-Kreitman test identified that the ratio of the number of nonsynonymous to synonymous polymorphic sites within P. knowlesi was significantly higher than that of the number of nonsynonymous to synonymous fixed sites between P. knowlesi and P. vivax. The von Willebrand factor domain also indicated balancing selection using MK test, however, it did not give significant results when tested with P. coatneyi as an outgroup. Phylogenetic analysis of full-length genes identified three distinct sub-clusters of P. knowlesi, one originating from Peninsular Malaysia and two originating from Malaysian Borneo. High population differentiation values was observed within samples from Peninsular Malaysia and Malaysian Borneo.
CONCLUSIONS: This study is the first to report on the genetic diversity and natural selection of full-length pktrap. Low level of genetic diversity was found across the full-length gene of pktrap. Balancing selection of the von Willebrand factor domain indicated that TRAP could be a target in inducing immune response against P. knowlesi infections. However, higher number of samples would be necessary to further confirm the findings.

Matched MeSH terms: Haplotypes
Haplotype analysis of leptin gene polymorphisms in obesity among Malays in Terengganu, Malaysia population

Wan Rohani WT, Aryati A, Amiratul Athirah S

Med J Malaysia, 2018 10;73(5):281-285.
PMID: 30350805 MyJurnal

INTRODUCTION: The prevalence of overweight and obesity has developed the critical global threat which leads to metabolic risks and mortality. A Leptin hormone that regulates the food intake as well as food expenditure is encoded by Leptin gene. The gene has shown a pivotal role in obesity pathogenesis. This study was sought to determine the SNPs and haplotype association of the Leptin gene that were assigned as G2548A, H1328080, and A19G with obesity among Malays in Terengganu, Malaysia.
METHODOLOGY: This study comprised of 249 participants (148 overweight/ obese as a case group and 101 lean participants as controls). The PCR-RFLP technique was performed to distinguish the genotype distribution of Leptin gene polymorphisms. The allele and genotype frequencies were assessed for single and haplotype analyses.
RESULT: Single association analysis of G2548A (P=0.74), A19G (P=0.38), and H1328080 (P=0.56) polymorphisms yielded no statistically significant association. However, haplotype association analysis showed a suggestive indication of AAG haplotype (G2548A, H1328080, and A19G sequence) with susceptibility effect towards obesity predisposition [P=0.002, OR=8.897 (1.59-9.78)].
CONCLUSION: This data on single and haplotype might disclose the preliminary exposure and pave the way for the obesity development with an evidence of revealed susceptibility to obesity.

Matched MeSH terms: Haplotypes
Chrysomya bezziana: a case report in a dog from Southern China and review of the Chinese literature

Fang F, Chang Q, Sheng Z, Zhang Y, Yin Z, Guillot J

Parasitol Res, 2019 Dec;118(12):3237-3240.
PMID: 31655903 DOI: 10.1007/s00436-019-06464-x

Chrysomya bezziana is an obligate, myiasis-causing fly in humans and warm-blooded animals throughout the tropical and subtropical Old World. We report a case of cutaneous myiasis due to C. bezziana in a dog from Guangxi province in China. A total of 35 maggots were removed from the lesions. Direct sequencing of the mitochondrial cytochrome b gene showed that the specimen belonged to haplotype CB_bezz02, which was previously reported in Malaysia and the Gulf region. This paper also reviews reported cases of screwworm myiasis from humans and animals in China. Geographical records indicate that the distribution of C. bezziana is expanding, suggesting that an integrated pest management control should be taken into consideration in China.

Matched MeSH terms: Haplotypes
Fulltext Population structure and genetic diversity of Aedes aegypti and Aedes albopictus in Penang as revealed by mitochondrial DNA cytochrome oxidase I

Md Naim D, Kamal NZM, Mahboob S

Saudi J Biol Sci, 2020 Mar;27(3):953-967.
PMID: 32127775 DOI: 10.1016/j.sjbs.2020.01.021

The population genetics study is crucial as it helps in understanding the epidemiological aspects of dengue and help improving a vector control measures. This research aims to investigate the population genetics structure of two common species of Aedes mosquitoes in Penang; Aedes aegypti and Aedes albopictus using Cytochrome Oxidase I (COI) mitochondrial DNA (mtDNA) marker. Molecular investigations were derived from 440 bp and 418 bp mtDNA COI on 125 and 334 larvae of Aedes aegypti and Aedes albopictus respectively, from 32 locations in Penang. All samples were employed in the BLASTn for species identification. The haplotype diversity, nucleotide diversity, neutrality test and mismatch distribution analysis were conducted in DnaSP version 5.10.1. AMOVA analysis was conducted in ARLEQUIN version 3.5 and the phylogenetic reconstructions based on maximum likelihood (ML) and neighbor-joining (NJ) methods were implemented in MEGA X. The relationships among haplotypes were further tested by creating a minimum spanning tree using Network version 4.6.1. All samples were genetically identified and clustered into six distinct species. Among the species, Ae. albopictus was the most abundant (67.2%), followed by Ae. aegypti (25.2%) and the rest were counted for Culex sp. and Toxorhynchites sp. Both Ae. aegypti and Ae. albopictus show low nucleotide diversity (π) and high haplotype diversity (h), while the neutrality test shows a negative value in most of the population for both species. There are a total of 39 and 64 haplotypes recorded for Ae. aegypti and Ae. albopictus respectively. AMOVA analysis revealed that most of the variation occurred within population for both species. Mismatch distribution analysis showed bimodal characteristic of population differentiation for Ae. aegypti but Ae. albopictus showed unimodal characteristics of population differentiation. Genetic distance based on Tamura-Nei parameter showed low genetic divergent within population and high genetic divergent among population for both species. The maximum likelihood tree showed no obvious pattern of population genetic structure for both Ae. aegypti and Ae. albopictus from Penang and a moderate to high bootstrap values has supported this conclusion. The minimum spanning network for Ae. aegypti and Ae. albopictus showed five and three dominant haplotypes respectively, which indicates a mixture of haplotypes from the regions analysed. This study revealed that there is no population genetic structure exhibited by both Ae. aegypti and Ae. albopictus in Penang. Mutation has occurred rapidly in both species and this will be challenging in controlling the populations. However, further analysis needed to confirm this statement.

Matched MeSH terms: Haplotypes
Rediscovery of nycticebus coucang insularis robinson, 1917 (primates: lorisidae) at tioman island and its mitochondrial genetic assessment

Jeffrine J. Rovie-Ryan, Millawati Gani, Norsyamimi Rosli, Han Ming Gan, Gilmoore G. Bolongon, Tan Cheng Cheng, et al.

Sains Malaysiana, 2018;47:2533-2542.

Slow lorises (Nycticebus) consist of eight species native to Southeast Asia while three species are recognised in
Malaysia - N. coucang, N. menagensis and N. kayan. This study reports on the rediscovery of the subspecies N. coucang
insularis Robinson, 1917 in Tioman Island and the genetic assessment of its mitochondrial DNA variation. Morphological
measurements conform the specimen as the putative N. coucang but with distinct colour and markings. Two mitochondrial
DNA segments (cytochrome b and control region) were produced from the subspecies representing their first registered
sequences in GenBank. Genetically, the subspecies showed 99% of nucleotide similarity to N. coucang species type for
both the DNA segments and constitute its own unique haplotype. Phylogenetic trees constructed using three methods
(neighbour joining, maximum likelihood and Bayesian inference) showed two major groups within Nycticebus; the
basal group was formed by N. pygmaeus while the second group consisted of the remaining Nycticebus species. The
phylogenetic position of the subspecies, however, remains unresolved due to the observed mixing between N. coucang and
N. bengalensis. Several reasons could lead to this condition including the lack of well documented voucher specimens and
the short DNA fragments used. In addition, the possibility of hybridisation event between N. coucang and N. bengalensis
could not be excluded as a possible explanation since both species occur sympatrically at the Isthmus of Kra region
until the Thailand-Malaysia border. The rediscovery of this subspecies displays the unique faunal diversity that justifies
the importance of Tioman Island as a protected area.

Matched MeSH terms: Haplotypes
Fulltext Maternal ancestry analyses of red tilapia strains based on D-loop sequences of seven tilapia populations

Jiang B, Fu J, Dong Z, Fang M, Zhu W, Wang L

PeerJ, 2019;7:e7007.
PMID: 31179190 DOI: 10.7717/peerj.7007

Background: Many tilapia species or varieties have been widely introduced and have become an economically important food fish in China. Information on the genetic backgrounds of these populations is deficient and requires more research, especially for red tilapia strains.
Methods: In the present study, displacement loop (D-loop) sequences were used to evaluate the genetic relationship and diversity of seven tilapia populations that are widely cultured in China; this was done specifically to speculate on the maternal ancestry of red tilapia strains. Three red tilapia varieties of Oreochromis ssp., Taiwan (TW), Israel (IL), and Malaysia (MY) strains and other populations, including O. aureus (AR), O. niloticus (NL), O. mossambicus (MS), and the GIFT strain of O. niloticus, were collected and analyzed in this study.
Results: A total of 146 polymorphic sites and 32 haplotypes of D-loop sequences were detected among 332 fish and four major haplotypes were shared among the populations. The TW and NL populations had a greater number of haplotypes (20 and 8, respectively). The haplotype diversity (Hd) and nucleotide diversity (π) of each population ranged from 0.234 to 0.826, and 0 to 0.060, respectively. The significant positive Tajima's D value of neutral test were detected in the NL, IL, and MY populations (P 0.05). The nearest K2P genetic distance (D = 0.014) was detected between the MS and TW populations, whereas, the farthest (D = 0.101) was found between the GIFT and AR populations. The results from the molecular variance analysis (AMOVA) showed that there was an extremely significant genetic variation observed among the populations (P

Matched MeSH terms: Haplotypes
Global genetic diversity of Spirometra tapeworms

Hong X, Liu SN, Xu FF, Han LL, Jiang P, Wang ZQ, et al.

Trop Biomed, 2020 Mar 01;37(1):237-250.
PMID: 33612735

Spirometra larvae are etiological agents of human sparganosis. However, the systematics of spirometrid cestodes has long been controversial. In order to determine the current knowledge on the evolution and genetic structure of Spirometra, an exhaustive population diversity analysis of spirometrid cestodes using the mitochondrial gene: cytochrome c oxidase subunit 1 (cox1) was performed. All publicly available cox1 sequences available in the GenBank and 127 new sequencing genes from China were used as the dataset. The haplotype identify, network, genetic differentiation and phylogenetic analysis were conducted successively. A total of 488 sequences from 20 host species, representing four spirometrid tapeworms (S. decipiens, S. ranarum, S. erinaceieuropaei and Sparganum proliferum) and several unclassified American and African isolates from 113 geographical locations in 17 countries, identified 45 haplotypes. The genetic analysis revealed that there are four clades of spirometrid cestodes: Clade 1 (Brazil + USA) and Clade 2 (Argentina + Venezuela) included isolates from America, Clade 3 contained African isolates and one Korean sample, and the remainders from Asia and Australia belonged to Clade 4; unclassified Spirometra from America and Africa should be considered the separate species within the genus; and the taxonomy of two Korea isolates (S. erinaceieuropaei KJ599680 and S. decipiens KJ599679) was still ambiguous and needs to be further identified. In addition, the demographical analyses supported population expansion for the total spirometrid population. In summary, four lineages were found in the spirometrid tapeworm, and further investigation with deeper sampling is needed to elucidate the population structure.

Matched MeSH terms: Haplotypes
Genetic diversity of the full length apical membrane antigen-1 of Plasmodium knowlesi clinical isolates from Peninsular Malaysia

Ng YL, Fong MY, Lau YL

Trop Biomed, 2021 Jun 01;38(2):159-164.
PMID: 34172705 DOI: 10.47665/tb.38.2.052

The Plasmodium knowlesi apical membrane antigen-1 (PkAMA-1) plays an important role in the invasion of the parasite into its host erythrocyte, and it has been regarded as a potential vaccine candidate against human knowlesi malaria. This study investigates genetic diversity and natural selection of the full length PkAMA-1 of P. knowlesi clinical isolates from Peninsular Malaysia. Blood samples were collected from P. knowlesi malaria patients from Peninsular Malaysia. The PkAMA-1 gene was amplified from DNA samples using PCR, cloned into a plasmid vector and sequenced. Results showed that nucleotide diversity of the full length PkAMA-1 from Peninsular Malaysia isolates (π: 0.006) was almost similar to that of Sarawak (π: 0.005) and Sabah (π: 0.004) isolates reported in other studies. Deeper analysis revealed Domain I (π: 0.007) in the PkAMA-1 had the highest diversity as compared to Domain II (π: 0.004) and Domain III (π: 0.003). Z-test indicated negative (purifying) selection of the gene. Combined alignment analysis at the amino acid level for the Peninsular Malaysia and Sarawak PkAMA-1 sequences revealed 34 polymorphic sites. Thirty-one of these sites were dimorphic, and 3 were trimorphic. The amino acid sequences could be categorised into 31 haplotypes. In the haplotype network, PkAMA-1 from Peninsular Malaysia and Sarawak were separated into two groups.

Matched MeSH terms: Haplotypes
DNA barcoding and phylogenetic analysis of Malaysian groupers (Subfamily: Epinephelinae) using mitochondrial Cytochrome c oxidase I (COI) gene

Aziz NMA, Esa Y, Arshad A

J Environ Biol, 2016 07;37(4 Spec No):725-33.
PMID: 28779732

The present study was carried out to examine the species identification and phylogenetic relationships of groupers in Malaysia using mitochondrial Cytochrome c Oxidase I (COI) gene, commonly known as barcoding gene. A total of 63 individuals comprising 10 species from three genera were collected from the coastal areas of Johor, Kelantan, Pahang, Perak, Selangor and Terengganu. All the individuals were morphologically identified and molecular works involved polymerase chain reaction (PCR) and sequencing of COI barcoding fragment (655 base pairs). Results from the BLAST search showed that 55 sequences could be assigned to 10 grouper species with high percentage identity index (≥95% to 100%), while eight grouper individuals showed discrepancies in their taxonomic identification based on the morphology and the COI barcoding results. The histogram of distances showed that there was a clear-cut barcode gap present in the sequences indicating a clear separation between intraspecific and interspecific distances. The pairwise genetic distances showed lowest pairwise distance between P. leopardus and P. maculatus (4.4%), while the highest pairwise distance was between E. bleekeri and P. maculatus (23.5%), supporting their morphological and habitat similarities and differences. Phylogenetic analysis (Neighbor-Joining) showed the presence of two major clades (1) genus Epinephelus vs (2) genus Plectropomus and Cephalopholis). In conclusion, the present study has managed to show the accuracy of DNA barcoding method for species identification, and utilization of COI gene for phylogenetic study among groupers. ?

Matched MeSH terms: Haplotypes
Fulltext Association between alleles, haplotypes, and amino acid variations in HLA class II genes and type 1 diabetes in Kuwaiti children

Dashti M, Nizam R, Jacob S, Al-Kandari H, Al Ozairi E, Thanaraj TA, et al.

Front Immunol, 2023;14:1238269.
PMID: 37638053 DOI: 10.3389/fimmu.2023.1238269

Type 1 diabetes (T1D) is a complex autoimmune disorder that is highly prevalent globally. The interactions between genetic and environmental factors may trigger T1D in susceptible individuals. HLA genes play a significant role in T1D pathogenesis, and specific haplotypes are associated with an increased risk of developing the disease. Identifying risk haplotypes can greatly improve the genetic scoring for early diagnosis of T1D in difficult to rank subgroups. This study employed next-generation sequencing to evaluate the association between HLA class II alleles, haplotypes, and amino acids and T1D, by recruiting 95 children with T1D and 150 controls in the Kuwaiti population. Significant associations were identified for alleles at the HLA-DRB1, HLA-DQA1, and HLA-DQB1 loci, including DRB1*03:01:01, DQA1*05:01:01, and DQB1*02:01:01, which conferred high risk, and DRB1*11:04:01, DQA1*05:05:01, and DQB1*03:01:01, which were protective. The DRB1*03:01:01~DQA1*05:01:01~DQB1*02:01:01 haplotype was most strongly associated with the risk of developing T1D, while DRB1*11:04-DQA1*05:05-DQB1*03:01 was the only haplotype that rendered protection against T1D. We also identified 66 amino acid positions across the HLA-DRB1, HLA-DQA1, and HLA-DQB1 genes that were significantly associated with T1D, including novel associations. These results validate and extend our knowledge on the associations between HLA genes and T1D in Kuwaiti children. The identified risk alleles, haplotypes, and amino acid variations may influence disease development through effects on HLA structure and function and may allow early intervention via population-based screening efforts.

Matched MeSH terms: Haplotypes
Fulltext Complete mitochondrial genome of Zeugodacus tau (Insecta: Tephritidae) and differentiation of Z. tau species complex by mitochondrial cytochrome c oxidase subunit I gene

Yong HS, Song SL, Lim PE, Eamsobhana P

PLoS One, 2017;12(12):e0189325.
PMID: 29216281 DOI: 10.1371/journal.pone.0189325

The tephritid fruit fly Zeugodacus tau (Walker) is a polyphagous fruit pest of economic importance in Asia. Studies based on genetic markers indicate that it forms a species complex. We report here (1) the complete mitogenome of Z. tau from Malaysia and comparison with that of China as well as the mitogenome of other congeners, and (2) the relationship of Z. tau taxa from different geographical regions based on sequences of cytochrome c oxidase subunit I gene. The complete mitogenome of Z. tau had a total length of 15631 bp for the Malaysian specimen (ZT3) and 15835 bp for the China specimen (ZT1), with similar gene order comprising 37 genes (13 protein-coding genes-PCGs, 2 rRNA genes, and 22 tRNA genes) and a non-coding A + T-rich control region (D-loop). Based on 13 PCGs and 15 mt-genes, Z. tau NC_027290 (China) and Z. tau ZT1 (China) formed a sister group in the lineage containing also Z. tau ZT3 (Malaysia). Phylogenetic analysis based on partial sequences of cox1 gene indicates that the taxa from China, Japan, Laos, Malaysia, Bangladesh, India, Sri Lanka, and Z. tau sp. A from Thailand belong to Z. tau sensu stricto. A complete cox1 gene (or 13 PCGs or 15 mt-genes) instead of partial sequence is more appropriate for determining phylogenetic relationship.

Matched MeSH terms: Haplotypes

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