Displaying publications 1 - 20 of 842 in total

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  1. A more elaborative way to check codon quality: an open source program
    Shardiwal RK, Sohrab SS
    Int J Bioinform Res Appl, 2010;6(3):223-9.
    PMID: 20615831
    Relative Synonymous Codon Usage (RSCU) and Relative Adaptiveness of a Codon (RAC) table bias importance in gene expression are well documented in the literature. However, to improve the gene expression we need to figure out which codons are optimal for the expression in order to synthesise an appropriate DNA sequence. An alternative to the manual approach, which is obviously a tedious task, is to set up software on your computer to perform this. Though such kinds of programs are available on the internet, none of them are open-source libraries. Here, one can use our Perl program to do his or her task more easily and efficiently. It is free for everyone.
    Matched MeSH terms: Sequence Analysis, DNA/methods
  2. Revision of Chimarrogale (Lipotyphla: Soricidae) from Vietnam with comments on taxonomy and biogeography of Asiatic water shrews
    Abramov AV, Bannikova AA, Lebedev VS, Rozhnov VV
    Zootaxa, 2017 Feb 15;4232(2):zootaxa.4232.2.5.
    PMID: 28264392 DOI: 10.11646/zootaxa.4232.2.5
    We analyzed the complete mitochondrial cytochrome b (cytb) gene and fragments of four nuclear loci: ApoB, RAG2, IRBP1 and BRCA1. These data allowed us to provide new insights into the diversity of the Asiatic water shrews of Indochina. A new, highly divergent genetic lineage of Chimarrogale was found in southern Vietnam, and this lineage included specimens from the provinces of Kon Tum, Dak Lak, and Lam Dong. Such finding represents the newest and southernmost records of Chimarrogale in Indochina. Morphological analysis classified the specimens from southern Vietnam as C. varennei proper, which is restricted to that region, whereas the polymorphic C. himalayica, which contained at least four cytochrome b haplogroups, occurred in central and northern Vietnam and southern China. This distinct C. varennei lineage closely related to the C. platycephalus + C. leander clade suggests the existence of an unknown glacial refuge in Tay Nguyen Plateau, southern Vietnam. Because the Bornean C. phaeura (i) was sister-group of the rest of Chimarrogale sensu lato and (ii) had a high genetic divergence (~15% for cytochrome b) and geographical isolation, we suggest that C. phaeura be placed into a separate genus, Crossogale Thomas, 1921. This genus should also include C. sumatrana (Sumatra) and C. hantu (Peninsular Malaysia). On those grounds, we propose a new classification system for Asiatic water shrews.
    Matched MeSH terms: Sequence Analysis, DNA*
  3. Fulltext The next generation sequencing technologies
    MOHAMAD, O., HO, W. S.
    Buletin Persatuan Genetik Malaysia, 2011;18(1):33-35.
    MyJurnal
    Sanger sequencing has been the major method in directly sequencing DNA, and has dominated the DNA sequencing market for nearly past 30 years (Varshney et al., 2009). Along with PCR, we cannot underestimate how important this technology has been to research in various elds of molecular biology. It has revolutionized genetics by allowing us to gain unprecedented insights into the
    workings of different organisms.
    Matched MeSH terms: Sequence Analysis, DNA
  4. Fulltext Pattern Matching for DNA Sequencing Data Using Multiple Bloom Filters
    Najam M, Rasool RU, Ahmad HF, Ashraf U, Malik AW
    Biomed Res Int, 2019;2019:7074387.
    PMID: 31111064 DOI: 10.1155/2019/7074387
    Storing and processing of large DNA sequences has always been a major problem due to increasing volume of DNA sequence data. However, a number of solutions have been proposed but they require significant computation and memory. Therefore, an efficient storage and pattern matching solution is required for DNA sequencing data. Bloom filters (BFs) represent an efficient data structure, which is mostly used in the domain of bioinformatics for classification of DNA sequences. In this paper, we explore more dimensions where BFs can be used other than classification. A proposed solution is based on Multiple Bloom Filters (MBFs) that finds all the locations and number of repetitions of the specified pattern inside a DNA sequence. Both of these factors are extremely important in determining the type and intensity of any disease. This paper serves as a first effort towards optimizing the search for location and frequency of substrings in DNA sequences using MBFs. We expect that further optimizations in the proposed solution can bring remarkable results as this paper presents a proof of concept implementation for a given set of data using proposed MBFs technique. Performance evaluation shows improved accuracy and time efficiency of the proposed approach.
    Matched MeSH terms: Sequence Analysis, DNA
  5. Fulltext Design pattern mining using distributed learning automata and DNA sequence alignment
    Esmaeilpour M, Naderifar V, Shukur Z
    PLoS One, 2014;9(9):e106313.
    PMID: 25243670 DOI: 10.1371/journal.pone.0106313
    Over the last decade, design patterns have been used extensively to generate reusable solutions to frequently encountered problems in software engineering and object oriented programming. A design pattern is a repeatable software design solution that provides a template for solving various instances of a general problem.
    Matched MeSH terms: Sequence Analysis, DNA/methods*
  6. The complete mitogenome of the Morton Bay bug Thenus orientalis (Lund, 1793) (Crustacea: Decapoda: Scyllaridae) from a cooked sample and a new mitogenome order for the Decapoda
    Tan MH, Gan HM, Lee YP, Austin CM
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016;27(2):1277-8.
    PMID: 25103440 DOI: 10.3109/19401736.2014.945554
    The mitochondrial genome sequence of the Morton Bay bug, Thenus orientalis, is documented, which makes it the second mitogenome for species of the family Scyllaridae and the ninth for members of the superfamily Palinuroidae. Thenus orientalis has a mitogenome of 16,826 base pairs consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 23 transfer RNAs, and a non-coding AT-rich region. The base composition of the T. orientalis mitogenome is 31.31% for T, 23.77% for C, 31.05% for A, and 13.87% for G, with an AT bias of 62.36%. In addition to a duplicated trnS1 and several other tRNA gene rearrangements, the mitogenome gene order has novel protein coding gene order with the nad6 and cob genes translocated as a block to a location downstream of the nad3 gene.
    Matched MeSH terms: Sequence Analysis, DNA/methods*
  7. The complete mitogenome of the swimming crab Thalamita crenata (Rüppell, 1830) (Crustacea; Decapoda; Portunidae)
    Tan MH, Gan HM, Lee YP, Austin CM
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016;27(2):1275-6.
    PMID: 25090400 DOI: 10.3109/19401736.2014.945553
    The complete mitochondrial genome of the swimming crab Thalamita crenata was obtained from a partial genome scan using the MiSeq sequencing system. The Thalamita crenata mitogenome has 15,787 base pairs (70% A+T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a putative 897 bp non-coding AT-rich region. This Thalamita mitogenome sequence is the first for the genus and the eighth for the family Portunidae.
    Matched MeSH terms: Sequence Analysis, DNA/methods*
  8. The mitogenome of Pangasius sutchi (Teleostei, Siluriformes: Pangasiidae)
    Zhao H, Kong X, Zhou C
    Mitochondrial DNA, 2014 Oct;25(5):342-4.
    PMID: 23795847 DOI: 10.3109/19401736.2013.800492
    The Pangasius sutchi is an important ornamental and economic fish in Southeast Asia e.g. Thailand, Malaysia and China. The complete mitochondrial genome sequence of P. sutchi has been sequenced, which contains 22 tRNA genes, 13 protein-coding genes, 2 rRNA genes and a non-coding control region with the total length of 16,522 bp. The gene order and composition are similar to most of other vertebrates. Just like most other vertebrates, the bias of G and C was found in different region/genes statistics results. Most of the genes are encoded on heavy strand, except for eight tRNA and ND6 genes. The mitogenome sequence of P. sutchi would contribute to better understand population genetics, evolution of this lineage.
    Matched MeSH terms: Sequence Analysis, DNA/methods*
  9. Polymorphic microsatellite loci from an indigenous Asian fungus-growing termite, Macrotermes gilvus (Blattodea: Termitidae) and cross amplification in related taxa
    Singham GV, Vargo EL, Booth W, Othman AS, Lee CY
    Environ Entomol, 2012 Apr;41(2):426-31.
    PMID: 22507019 DOI: 10.1603/EN11228
    The fungus-growing termite, Macrotermes gilvus (Hagen), an indigenous species from Southeast Asia distributed from Myanmar to Indonesia and the Philippines, offers great potential as an ecological model system to elucidate the effects of geography on gene flow within this region. We used next generation sequencing (Roche 454 pyrosequencing) to identify microsatellite markers from the genomic DNA of M. gilvus. A modest sequencing volume generated 34,122 reads, with 1,212 (3.6%) reads contains microsatellites with di-, tri-, tetra-, penta-, and hexa-nucleotide repeat motifs. Thirty-seven loci were selected for primer development and tested for polymorphism across 22 colonies of M. gilvus. Eleven loci were found to be polymorphic with 2-4 alleles per locus. Observed and expected heterozygosities ranged between 0.091-0.727 and 0.090-0.540, respectively. Cross taxa amplification was successful across a panel of four related termite species and four multiplex groups were designed for future population genetic studies. These markers will open new avenues for the study of phylogeography and population genetics of this fungus-growing termite. This study also has effectively demonstrated the use of 454 pyrosequencing for the rapid development of informative microsatellite markers from a termite genome.
    Matched MeSH terms: Sequence Analysis, DNA/methods
  10. Construction of cDNA library and preliminary analysis of expressed sequence tags from green microalga Ankistrodesmus convolutus Corda
    Thanh T, Chi VT, Abdullah MP, Omar H, Noroozi M, Ky H, et al.
    Mol Biol Rep, 2011 Jan;38(1):177-82.
    PMID: 20354903 DOI: 10.1007/s11033-010-0092-4
    Green microalga Ankistrodesmus convolutus Corda is a fast growing alga which produces appreciable amount of carotenoids and polyunsaturated fatty acids. To our knowledge, this is the first report on the construction of cDNA library and preliminary analysis of ESTs for this species. The titers of the primary and amplified cDNA libraries were 1.1×10(6) and 6.0×10(9) pfu/ml respectively. The percentage of recombinants was 97% in the primary library and a total of 337 out of 415 original cDNA clones selected randomly contained inserts ranging from 600 to 1,500 bps. A total of 201 individual ESTs with sizes ranging from 390 to 1,038 bps were then analyzed and the BLASTX score revealed that 35.8% of the sequences were classified as strong match, 38.3% as nominal and 25.9% as weak match. Among the ESTs with known putative function, 21.4% of them were found to be related to gene expression, 14.4% ESTs to photosynthesis, 10.9% ESTs to metabolism, 5.5% ESTs to miscellaneous, 2.0% to stress response, and the remaining 45.8% were classified as novel genes. Analysis of ESTs described in this paper can be an effective approach to isolate and characterize new genes from A. convolutus and thus the sequences obtained represented a significant contribution to the extensive database of sequences from green microalgae.
    Matched MeSH terms: Sequence Analysis, DNA/methods*
  11. Fulltext Finding Nemo: hybrid assembly with Oxford Nanopore and Illumina reads greatly improves the clownfish (Amphiprion ocellaris) genome assembly
    Tan MH, Austin CM, Hammer MP, Lee YP, Croft LJ, Gan HM
    Gigascience, 2018 03 01;7(3):1-6.
    PMID: 29342277 DOI: 10.1093/gigascience/gix137
    Background: Some of the most widely recognized coral reef fishes are clownfish or anemonefish, members of the family Pomacentridae (subfamily: Amphiprioninae). They are popular aquarium species due to their bright colours, adaptability to captivity, and fascinating behavior. Their breeding biology (sequential hermaphrodites) and symbiotic mutualism with sea anemones have attracted much scientific interest. Moreover, there are some curious geographic-based phenotypes that warrant investigation. Leveraging on the advancement in Nanopore long read technology, we report the first hybrid assembly of the clown anemonefish (Amphiprion ocellaris) genome utilizing Illumina and Nanopore reads, further demonstrating the substantial impact of modest long read sequencing data sets on improving genome assembly statistics.

    Results: We generated 43 Gb of short Illumina reads and 9 Gb of long Nanopore reads, representing approximate genome coverage of 54× and 11×, respectively, based on the range of estimated k-mer-predicted genome sizes of between 791 and 967 Mbp. The final assembled genome is contained in 6404 scaffolds with an accumulated length of 880 Mb (96.3% BUSCO-calculated genome completeness). Compared with the Illumina-only assembly, the hybrid approach generated 94% fewer scaffolds with an 18-fold increase in N50 length (401 kb) and increased the genome completeness by an additional 16%. A total of 27 240 high-quality protein-coding genes were predicted from the clown anemonefish, 26 211 (96%) of which were annotated functionally with information from either sequence homology or protein signature searches.

    Conclusions: We present the first genome of any anemonefish and demonstrate the value of low coverage (∼11×) long Nanopore read sequencing in improving both genome assembly contiguity and completeness. The near-complete assembly of the A. ocellaris genome will be an invaluable molecular resource for supporting a range of genetic, genomic, and phylogenetic studies specifically for clownfish and more generally for other related fish species of the family Pomacentridae.

    Matched MeSH terms: Sequence Analysis, DNA/methods*
  12. Fulltext Museomics for reconstructing historical floristic exchanges: Divergence of stone oaks across Wallacea
    Strijk JS, Binh HT, Ngoc NV, Pereira JT, Slik JWF, Sukri RS, et al.
    PLoS One, 2020;15(5):e0232936.
    PMID: 32442164 DOI: 10.1371/journal.pone.0232936
    Natural history collections and tropical tree diversity are both treasure troves of biological and evolutionary information, but their accessibility for scientific study is impeded by a number of properties. DNA in historical specimens is generally highly fragmented, complicating the recovery of high-grade genetic material. Furthermore, our understanding of hyperdiverse, wide-spread tree assemblages is obstructed by extensive species ranges, fragmented knowledge of tropical tree diversity and phenology, and a widespread lack of species-level diagnostic characters, prohibiting the collecting of readily identifiable specimens which can be used to build, revise or strengthen taxonomic frameworks. This, in turn, delays the application of downstream conservation action. A sizable component of botanical collections are sterile-thus eluding identification and are slowing down progress in systematic treatments of tropical biodiversity. With rapid advances in genomics and bioinformatic approaches to biodiversity research, museomics is emerging as a new field breathing life into natural collections that have been built up over centuries. Using MIGseq (multiplexed ISSR genotyping by sequencing), we generated 10,000s of short loci, for both freshly collected materials and museum specimens (aged >100 years) of Lithocarpus-a widespread tropical tree genus endemic to the Asian tropics. Loci recovery from historical and recently collected samples was not affected by sample age and preservation history of the study material, underscoring the reliability and flexibility of the MIGseq approach. Phylogenomic inference and biogeographic reconstruction across insular Asia, highlights repeated migration and diversification patterns between continental regions and islands. Results indicate that co-occurring insular species at the extremity of the distribution range are not monophyletic, raising the possibility of multiple independent dispersals along the outer edge of Wallacea. This suggests that dispersal of large seeded tree genera throughout Malesia and across Wallacea may have been less affected by large geographic distances and the presence of marine barriers than generally assumed. We demonstrate the utility of MIGseq in museomic studies using non-model taxa, presenting the first range-wide genomic assessment of Lithocarpus and tropical Fagaceae as a proof-of-concept. Our study shows the potential for developing innovative genomic approaches to improve the capture of novel evolutionary signals using valuable natural history collections of hyperdiverse taxa.
    Matched MeSH terms: Sequence Analysis, DNA/methods*
  13. Fulltext Sex Chromosome Turnover in Bent-Toed Geckos (Cyrtodactylus)
    Keating SE, Blumer M, Grismer LL, Lin A, Nielsen SV, Thura MK, et al.
    Genes (Basel), 2021 01 19;12(1).
    PMID: 33477871 DOI: 10.3390/genes12010116
    Lizards and snakes (squamates) are known for their varied sex determining systems, and gecko lizards are especially diverse, having evolved sex chromosomes independently multiple times. While sex chromosomes frequently turnover among gecko genera, intrageneric turnovers are known only from Gekko and Hemidactylus. Here, we used RADseq to identify sex-specific markers in two species of Burmese bent-toed geckos. We uncovered XX/XY sex chromosomes in Cyrtodactylus chaunghanakwaensis and ZZ/ZW sex chromosomes in Cyrtodactylus pharbaungensis. This is the third instance of intrageneric turnover of sex chromosomes in geckos. Additionally, Cyrtodactylus are closely related to another genus with intrageneric turnover, Hemidactylus. Together, these data suggest that sex chromosome turnover may be common in this clade, setting them apart as exceptionally diverse in a group already known for diverse sex determination systems.
    Matched MeSH terms: Sequence Analysis, DNA/methods
  14. Fulltext Complete Genome Sequence and Methylome Analysis of Aeromonas hydrophila Strain YL17, Isolated from a Compost Pile
    Lim YL, Roberts RJ, Ee R, Yin WF, Chan KG
    Genome Announc, 2016 Mar 03;4(2).
    PMID: 26941143 DOI: 10.1128/genomeA.00060-16
    In this report, we announce the complete genome sequence of Aeromonas hydrophila strain YL17. Single-molecule real-time (SMRT) DNA sequencing was used to generate the complete genome sequence and the genome-wide DNA methylation profile of this environmental isolate. A total of five unique DNA methyltransferase recognition motifs were reported here.
    Matched MeSH terms: Sequence Analysis, DNA
  15. Suppression Subtractive Hybridization Versus Next-Generation Sequencing in Plant Genetic Engineering: Challenges and Perspectives
    Sahebi M, Hanafi MM, Azizi P, Hakim A, Ashkani S, Abiri R
    Mol Biotechnol, 2015 Oct;57(10):880-903.
    PMID: 26271955 DOI: 10.1007/s12033-015-9884-z
    Suppression subtractive hybridization (SSH) is an effective method to identify different genes with different expression levels involved in a variety of biological processes. This method has often been used to study molecular mechanisms of plants in complex relationships with different pathogens and a variety of biotic stresses. Compared to other techniques used in gene expression profiling, SSH needs relatively smaller amounts of the initial materials, with lower costs, and fewer false positives present within the results. Extraction of total RNA from plant species rich in phenolic compounds, carbohydrates, and polysaccharides that easily bind to nucleic acids through cellular mechanisms is difficult and needs to be considered. Remarkable advancement has been achieved in the next-generation sequencing (NGS) field. As a result of progress within fields related to molecular chemistry and biology as well as specialized engineering, parallelization in the sequencing reaction has exceptionally enhanced the overall read number of generated sequences per run. Currently available sequencing platforms support an earlier unparalleled view directly into complex mixes associated with RNA in addition to DNA samples. NGS technology has demonstrated the ability to sequence DNA with remarkable swiftness, therefore allowing previously unthinkable scientific accomplishments along with novel biological purposes. However, the massive amounts of data generated by NGS impose a substantial challenge with regard to data safe-keeping and analysis. This review examines some simple but vital points involved in preparing the initial material for SSH and introduces this method as well as its associated applications to detect different novel genes from different plant species. This review evaluates general concepts, basic applications, plus the probable results of NGS technology in genomics, with unique mention of feasible potential tools as well as bioinformatics.
    Matched MeSH terms: Sequence Analysis, DNA/economics; Sequence Analysis, DNA/methods
  16. Fulltext InCoB celebrates its tenth anniversary as first joint conference with ISCB-Asia
    Schönbach C, Tan TW, Kelso J, Rost B, Nathan S, Ranganathan S
    BMC Genomics, 2011 Nov 30;12 Suppl 3:S1.
    PMID: 22369160 DOI: 10.1186/1471-2164-12-S3-S1
    In 2009 the International Society for Computational Biology (ISCB) started to roll out regional bioinformatics conferences in Africa, Latin America and Asia. The open and competitive bid for the first meeting in Asia (ISCB-Asia) was awarded to Asia-Pacific Bioinformatics Network (APBioNet) which has been running the International Conference on Bioinformatics (InCoB) in the Asia-Pacific region since 2002. InCoB/ISCB-Asia 2011 is held from November 30 to December 2, 2011 in Kuala Lumpur, Malaysia. Of 104 manuscripts submitted to BMC Genomics and BMC Bioinformatics conference supplements, 49 (47.1%) were accepted. The strong showing of Asia among submissions (82.7%) and acceptances (81.6%) signals the success of this tenth InCoB anniversary meeting, and bodes well for the future of ISCB-Asia.
    Matched MeSH terms: Sequence Analysis, DNA
  17. Genetic analysis of saffold virus-Penang in relation to other newly discovered saffold viruses
    Voon K, Ng QM, Yu M, Wang LF, Chua KB
    Southeast Asian J. Trop. Med. Public Health, 2012 Jul;43(4):917-26.
    PMID: 23077814
    Viruses in the family Picornaviridae are classified into nine genera. Within the family Picornaviridae, two species: Encephalomyocarditis virus and Theilovirus, are listed under the genus Cardiovirus. A novel Theilovirus, Saffold virus (SAFV), was first reported in 2007. Since then, numerous SAFV isolates have been detected around the world and genetic recombinations have been reported among them. In 2009, SAFV-Penang was isolated from a febrile child with influenza-like illness in Malaysia. SAFV-Penang is a genotype 3 SAFV. In this study we investigated the genome features of SAFV-Penang to exclude the possibility it is a recombinant variant. SAFV-Penang was found not to be a recombinant variant but to have three unique non-synonymous substitutions, alanine [A689], lysine [K708] and isoleucine [I724] in the VP1 protein.
    Matched MeSH terms: Sequence Analysis, DNA
  18. Characterisation of 12 microsatellite loci in the Vietnamese commercial clam Lutraria rhynchaena Jonas 1844 (Heterodonta: Bivalvia: Mactridae) through next-generation sequencing
    Thai BT, Tan MH, Lee YP, Gan HM, Tran TT, Austin CM
    Mol Biol Rep, 2016 May;43(5):391-6.
    PMID: 26922181 DOI: 10.1007/s11033-016-3966-2
    The marine clam Lutraria rhynchaena is gaining popularity as an aquaculture species in Asia. Lutraria populations are present in the wild throughout Vietnam and several stocks have been established and translocated for breeding and aquaculture grow-out purposes. In this study, we demonstrate the feasibility of utilising Illumina next-generation sequencing technology to streamline the identification and genotyping of microsatellite loci from this clam species. Based on an initial partial genome scan, 48 microsatellite markers with similar melting temperatures were identified and characterised. The 12 most suitable polymorphic loci were then genotyped using 51 individuals from a population in Quang Ninh Province, North Vietnam. Genetic variation was low (mean number of alleles per locus = 2.6; mean expected heterozygosity = 0.41). Two loci showed significant deviation from Hardy-Weinberg equilibrium (HWE) and the presence of null alleles, but there was no evidence of linkage disequilibrium among loci. Three additional populations were screened (n = 7-36) to test the geographic utility of the 12 loci, which revealed 100 % successful genotyping in two populations from central Vietnam (Nha Trang). However, a second population from north Vietnam (Co To) could not be successfully genotyped and morphological evidence and mitochondrial variation suggests that this population represents a cryptic species of Lutraria. Comparisons of the Qang Ninh and Nha Trang populations, excluding the 2 loci out of HWE, revealed statistically significant allelic variation at 4 loci. We reported the first microsatellite loci set for the marine clam Lutraria rhynchaena and demonstrated its potential in differentiating clam populations. Additionally, a cryptic species population of Lutraria rhynchaena was identified during initial loci development, underscoring the overlooked diversity of marine clam species in Vietnam and the need to genetically characterise population representatives prior to microsatellite development. The rapid identification and validation of microsatellite loci using next-generation sequencing technology warrant its integration into future microsatellite loci development for key aquaculture species in Vietnam and more generally, aquaculture countries in the South East Asia region.
    Matched MeSH terms: Sequence Analysis, DNA
  19. Complete mitochondrial genomes of the tooth of a poached Bornean banteng (Bos javanicus lowi; Cetartiodactyla, Bovidae)
    Ishige T, Gakuhari T, Hanzawa K, Kono T, Sunjoto I, Sukor JR, et al.
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016 Jul;27(4):2453-4.
    PMID: 26075477 DOI: 10.3109/19401736.2015.1033694
    Here we report the complete mitochondrial genome of the Bornean banteng Bos javanicus lowi (Cetartiodactyla, Bovidae), which was determined using next-generation sequencing. The mitochondrial genome is 16,344 bp in length containing 13 protein-coding genes, 21 tRNAs and 2 rRNAs. It shows the typical pattern of bovine mitochondrial arrangement. Phylogenetic tree analysis of complete mtDNA sequences showed that Bornean banteng is more closely related to gaur than to other banteng subspecies. Divergence dating indicated that Bornean banteng and gaur diverged from their common ancestor approximately 5.03 million years ago. These results suggest that Bornean banteng might be a distinct species in need of conservation.
    Matched MeSH terms: Sequence Analysis, DNA
  20. Fulltext Mitogenomic phylogeny of the common long-tailed macaque (Macaca fascicularis fascicularis)
    Liedigk R, Kolleck J, Böker KO, Meijaard E, Md-Zain BM, Abdul-Latiff MA, et al.
    BMC Genomics, 2015 Mar 21;16:222.
    PMID: 25887664 DOI: 10.1186/s12864-015-1437-0
    BACKGROUND: Long-tailed macaques (Macaca fascicularis) are an important model species in biomedical research and reliable knowledge about their evolutionary history is essential for biomedical inferences. Ten subspecies have been recognized, of which most are restricted to small islands of Southeast Asia. In contrast, the common long-tailed macaque (M. f. fascicularis) is distributed over large parts of the Southeast Asian mainland and the Sundaland region. To shed more light on the phylogeny of M. f. fascicularis, we sequenced complete mitochondrial (mtDNA) genomes of 40 individuals from all over the taxon's range, either by classical PCR-amplification and Sanger sequencing or by DNA-capture and high-throughput sequencing.

    RESULTS: Both laboratory approaches yielded complete mtDNA genomes from M. f. fascicularis with high accuracy and/or coverage. According to our phylogenetic reconstructions, M. f. fascicularis initially diverged into two clades 1.70 million years ago (Ma), with one including haplotypes from mainland Southeast Asia, the Malay Peninsula and North Sumatra (Clade A) and the other, haplotypes from the islands of Bangka, Java, Borneo, Timor, and the Philippines (Clade B). The three geographical populations of Clade A appear as paraphyletic groups, while local populations of Clade B form monophyletic clades with the exception of a Philippine individual which is nested within the Borneo clade. Further, in Clade B the branching pattern among main clades/lineages remains largely unresolved, most likely due to their relatively rapid diversification 0.93-0.84 Ma.

    CONCLUSIONS: Both laboratory methods have proven to be powerful to generate complete mtDNA genome data with similarly high accuracy, with the DNA-capture and high-throughput sequencing approach as the most promising and only practical option to obtain such data from highly degraded DNA, in time and with relatively low costs. The application of complete mtDNA genomes yields new insights into the evolutionary history of M. f. fascicularis by providing a more robust phylogeny and more reliable divergence age estimations than earlier studies.

    Matched MeSH terms: Sequence Analysis, DNA
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