Displaying publications 1 - 20 of 73 in total

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  1. Fulltext Two sympatric types of Plasmodium ovale and discrimination by molecular methods
    Zaw MT, Lin Z
    J Microbiol Immunol Infect, 2017 Oct;50(5):559-564.
    PMID: 28065415 DOI: 10.1016/j.jmii.2016.08.004
    Plasmodium ovale is widely distributed in tropical countries, whereas it has not been reported in the Americas. It is not a problem globally because it is rarely detected by microscopy owing to low parasite density, which is a feature of clinical ovale malaria. P.o. curtisi and P.o. wallikeri are widespread in both Africa and Asia, and were known to be sympatric in many African countries and in southeast Asian countries. Small subunit ribosomal RNA (SSUrRNA) gene, cytochrome b (cytb) gene, and merozoite surface protein-1 (msp-1) gene were initially studied for molecular discrimination of P.o. curtisi and P.o. wallikeri using polymerase chain reaction (PCR) and DNA sequencing. DNA sequences of other genes from P. ovale in Southeast Asia and the southwestern Pacific regions were also targeted to differentiate the two sympatric types. In terms of clinical manifestations, P.o. wallikeri tended to produce higher parasitemia levels and more severe symptoms. To date, there have been a few studies that used the quantitative PCR method for discrimination of the two distinct P. ovale types. Conventional PCR with consequent DNA sequencing is the common method used to differentiate these two types. It is necessary to identify these two types because relapse periodicity, drug susceptibility, and mosquito species preference need to be studied to reduce ovale malaria. In this article, an easier method of molecular-level discrimination of P.o. curtisi and P.o. wallikeri is proposed.
    Matched MeSH terms: Genes, rRNA/genetics
  2. Tropical soil bacterial communities in Malaysia: pH dominates in the equatorial tropics too
    Tripathi BM, Kim M, Singh D, Lee-Cruz L, Lai-Hoe A, Ainuddin AN, et al.
    Microb Ecol, 2012 Aug;64(2):474-84.
    PMID: 22395784 DOI: 10.1007/s00248-012-0028-8
    The dominant factors controlling soil bacterial community variation within the tropics are poorly known. We sampled soils across a range of land use types--primary (unlogged) and logged forests and crop and pasture lands in Malaysia. PCR-amplified soil DNA for the bacterial 16S rRNA gene targeting the V1-V3 region was pyrosequenced using the 454 Roche machine. We found that land use in itself has a weak but significant effect on the bacterial community composition. However, bacterial community composition and diversity was strongly correlated with soil properties, especially soil pH, total carbon, and C/N ratio. Soil pH was the best predictor of bacterial community composition and diversity across the various land use types, with the highest diversity close to neutral pH values. In addition, variation in phylogenetic structure of dominant lineages (Alphaproteobacteria, Beta/Gammaproteobacteria, Acidobacteria, and Actinobacteria) is also significantly correlated with soil pH. Together, these results confirm the importance of soil pH in structuring soil bacterial communities in Southeast Asia. Our results also suggest that unlike the general diversity pattern found for larger organisms, primary tropical forest is no richer in operational taxonomic units of soil bacteria than logged forest, and agricultural land (crop and pasture) is actually richer than primary forest, partly due to selection of more fertile soils that have higher pH for agriculture and the effects of soil liming raising pH.
    Matched MeSH terms: Genes, rRNA
  3. Fulltext The whole mitochondrial genome of the mangrove crab, Metopograpsus frontalis (Miers, 1880) (Decapoda, Grapsidae) and its phylogenetic relationship
    Guan M, Liu X, Lin F, Xie Z, Fazhan H, Ikhwanuddin M, et al.
    Mitochondrial DNA B Resour, 2018 Mar 14;3(1):368-369.
    PMID: 33490509 DOI: 10.1080/23802359.2018.1450685
    In this study, we sequenced and analyzed the whole mitochondrial genome of Metopograpsus frontalis Miers, 1880 (Decapoda, Grapsidae). The circular genome is 15,587 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, as well as a control region. Both atp8/atp6 and nad4L/nad4 share 7 nucleotides in their adjacent overlapping region, which is identical to those observed in other Grapsidae crabs. The genome composition and gene order follow a classic crab-type arrangement regulation. The phylogenetic analysis suggested that Grapsidae crabs formed a solid monophyletic group. The newly described mitochondrial genome may provide genetic marker for studies on phylogeny of the grapsid crabs.
    Matched MeSH terms: Genes, rRNA
  4. Fulltext The whole mitochondrial genome and phylogenetic analysis of Lupocycloporus gracilimanus (Stimpson, 1858) (Decapoda, portunidae)
    Guan M, Tan H, Fazhan H, Xie Z, Shi X, Zhang Y, et al.
    Mitochondrial DNA B Resour, 2018 Oct 26;3(2):1244-1245.
    PMID: 33474478 DOI: 10.1080/23802359.2018.1532345
    The mitochondrial genome plays an important role in studies on phylogeography and population genetic diversity. Here we report the complete mitochondrial genome of Lupocycloporus gracilimanus (Stimpson, 1858) which is the first mitochondrial genome reported in genus Lupocycloporus by now. The mitogenome is 15,990 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and a putative control region. The phylogenetic analysis showed that L. gracilimanus was closest to genus Scylla. The present research should provide valuable information for phylogenetic analysis and classification of Portunidae.
    Matched MeSH terms: Genes, rRNA
  5. Fulltext The first mitochondrial genome data of an old world fruit bat, Cynopterus sphinx from Malaysia
    Jahari PNS, Mohd Azman S, Munian K, Zakaria NA, Omar MSS, Richter SR, et al.
    Mitochondrial DNA B Resour, 2021 Jan 12;6(1):53-55.
    PMID: 33521264 DOI: 10.1080/23802359.2020.1846472
    We assembled the complete mitogenome of Cynopterus sphinx (Vahl, 1797) of the family Pteropodidae originating from Malaysia. The total mitogenome size was 16,710bp which consists of 37 genes (13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and one control region). A phylogenetic and BLASTn result showed the mitogenome sequence in this study varies by nearly 7% (93.48% similarity) from the same species in Cambodia. The next closest match of BLASTn was at 92% similarity to the C. brachyotis. This suggests the species-complex in Cynopterus sp. has given rise to the genetic variability.
    Matched MeSH terms: Genes, rRNA
  6. Fulltext The first complete mitochondrial genome data of Geoffroy's rousette, Rousettus amplexicaudatus originating from Malaysia
    Jahari PNS, Mohd Azman S, Munian K, M Fauzi NF, Shamsir MS, Richter SR, et al.
    Mitochondrial DNA B Resour, 2020 Sep 01;5(3):3262-3264.
    PMID: 33458132 DOI: 10.1080/23802359.2020.1812449
    The increasing interest in understanding the evolutionary relationship between members of the Pteropodidae family has been greatly aided by genomic data from the Old World fruit bats. Here we present the complete mitogenome of Geoffroy's rousette, Rousettus amplexicaudatus found in Peninsular Malaysia . The mitogenome constructed is 16,511bp in length containing 37 genes; 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a D-loop region. The overall base composition is estimated to be 32.28% for A, 25.64% for T, 14.09% for G and 27.98% for C, indicating a slightly AT rich feature (57.93%). A phylogenetic and BLASTn analysis against other available mitogenomes showed Malaysian R. amplexicaudatus matched 98% similarity to the same species in Cambodia and Vietnam. However, it differed considerably (92.53% similarity) with the same species in the Philippines. This suggests flexibility in Rousettus sp. with regards to adapting to mesic and dry habitats, ability for long-distance dispersal and remarkably precise lingual echolocation thus supporting its wide-range distribution and colonization. Further taxonomical and mitogenomic comparatives are required in resolving the evolutionary relationship between Rousettus spp.
    Matched MeSH terms: Genes, rRNA
  7. Fulltext The complete mitochondrial genome of the cavity-nesting honeybee, Apis koschevnikovi (Insecta: Hymenoptera: Apidae)
    Wakamiya T, Tingek S, Okuyama H, Kiyoshi T, Takahashi JI
    Mitochondrial DNA B Resour, 2017 Jan 17;2(1):24-25.
    PMID: 33490434 DOI: 10.1080/23802359.2016.1275847
    In this study, we analyzed the complete mitochondrial genome of the cavity-nesting honeybee, A. koschevnikovi. The mitochondrial genome of A. koschevnikovi was observed to be a circular molecule of 15,278 bp and was similar to that of the other cavity-nesting honeybee species. The average AT content in the A. koschevnikovi mitochondrial genome was 84%. It was predicted to contain 13 protein-coding, 24 tRNA and two rRNA genes, along with one A + T-rich control region, besides three tRNA-Met repeats.
    Matched MeSH terms: Genes, rRNA
  8. Fulltext The complete mitochondrial genome of the cavity-nesting honeybee, Apis cerana (Insecta: Hymenoptera: Apidae) from Borneo
    Okuyama H, Tingek S, Takahashi JI
    Mitochondrial DNA B Resour, 2017 Jul 31;2(2):475-476.
    PMID: 33473869 DOI: 10.1080/23802359.2017.1361344
    The complete mitochondrial genome of the cavity-nesting honeybee Apis cerana from Sabah on Borneo Island was analyzed using next-generation sequencing. The mitochondrial genome of A. cerana was a circular molecule of 15,884 bp and was similar to that of the other cavity-nesting honeybee species. The average AT content in the A. cerana mitochondrial genome was 84.4%. It was predicted to contain 13 protein-coding, 22 tRNA, and two rRNA genes, along with one A + T-rich control region.
    Matched MeSH terms: Genes, rRNA
  9. The complete mitochondrial genome of the Blue-face angelfish, Pomacanthus xanthometapon (Perciformes: Pomacanthidae)
    Shen KN, Loh KH, Chen CH, Hsiao CD
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016 11;27(6):4122-4123.
    PMID: 25585497
    In this study, the complete mitogenome sequence of the Blue-face angelfish, Pomacanthus xanthometapon (Perciformes: Pomacanthidae) has been sequenced by the next-generation sequencing method. The assembled mitogenome consisting of 16,533 bp includes 13 protein coding genes, 22 transfer RNAs, and two ribosomal RNAs genes. The overall base composition of Blue-face angelfish is 28.7% for A, 28.9% for C, 15.9% for G, 26.6% for T and show 84% identities to flame angelfish Centropyge loriculus. The complete mitogenome of the Blue-face angelfish provides essential and important DNA molecular data for further phylogeography and evolutionary analysis for marine angelfish phylogeny.
    Matched MeSH terms: Genes, rRNA/genetics
  10. Fulltext The complete mitochondrial genome of Varuna yui (Decapoda: Brachyura: Varunidae) and its phylogeny
    Lin F, Xie Z, Fazhan H, Baylon JC, Yang X, Tan H, et al.
    Mitochondrial DNA B Resour, 2018 Feb 23;3(1):263-264.
    PMID: 33474136 DOI: 10.1080/23802359.2018.1443043
    The complete mitochondrial genome plays an important role in the research on phylogenetic relationship. Here, we reported the first complete mitochondrial genome sequence of Varuna yui Hwang & Takeda, 1986 (Varunidae). The complete mtDNA (15,915 bp in length) consisted of 13 protein-coding genes, 22 tRNAs, two rRNA genes, and a control region. The gene arrangement was identical to those observed in the Varunidae species. The phylogenetic analysis suggested that V. yui had close relationship with other Varunidae species (Helicetient sinensis, Eriocher sinesis, etc.). The newly described genome may facilitate further comparative mitogenomic analysis within Varunidae species.
    Matched MeSH terms: Genes, rRNA
  11. Fulltext The complete mitochondrial genome of Amyda cartilaginea (Testudines: Trionychidae)
    Cui L, Rao D, Zhang M
    Mitochondrial DNA B Resour, 2020 Nov 03;5(3):3670-3672.
    PMID: 33367054 DOI: 10.1080/23802359.2020.1832595
    The Asiatic softshell turtle, also known as the black-rayed softshell turtle (Amyda cartilaginea; Accession no: MT039230), is found in northeastern India (Mizoram), Brunei Darussalam, Indonesia, Malaysia, Singapore, Myanmar, Laos, Vietnam, Cambodia, and Thailand. This turtle is thought to have been introduced into the Sunda Islands, Sulawesi, and Yunnan, China, through the Malay Peninsula to Sumatra, Java, and Borneo. Herein, we determined the complete mitochondrial genome of A. cartilaginea for the first time using next-generation sequencing (NGS). The assembled mitogenome was 16,763 bp in length and encoded 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA genes (12S rRNA and 16S rRNA), and one control region (CR). The PCGs based maximum-likelihood phylogeny discriminated A. cartilaginea from other Testudines and clusters within family Trionychidae with the sister taxa of Nilssonia nigricans.
    Matched MeSH terms: Genes, rRNA
  12. Fulltext The complete mitochondrial DNA sequence of endemic honeybee Apis nuluensis (Insecta: Hymenoptera: Apidae) inhabiting Mount Kinabalu in Sabah Province, Borneo Island
    Takahashi JI, Tingek S, Okuyama H
    Mitochondrial DNA B Resour, 2017 Sep 05;2(2):585-586.
    PMID: 33473910 DOI: 10.1080/23802359.2017.1372714
    The cavity-nesting honeybee Apis nuluensis inhabits only the highlands of Mount Kinabalu of Sabah, Borneo Island. The mitochondrial genome is a circular molecule of approximately 1.6 kb that includes 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one AT-rich control region. The average AT content was 84.5%. The start codons ATC, ATG, and ATT were found in one, three, and nine genes, respectively, whereas the stop codon TAA was observed in all genes. The phylogenetic relationship, inferred using 13 PCGs, was consistent with that reported in previous studies that predicted a sister taxon relationship between A. nuluensis and A. cerana.
    Matched MeSH terms: Genes, rRNA
  13. Fulltext The Whole Genome Sequence and mRNA Transcriptome of the Tropical Cyclopoid Copepod Apocyclops royi
    Jørgensen TS, Nielsen BLH, Petersen B, Browne PD, Hansen BW, Hansen LH
    G3 (Bethesda), 2019 05 07;9(5):1295-1302.
    PMID: 30923136 DOI: 10.1534/g3.119.400085
    Copepoda is one of the most ecologically important animal groups on Earth, yet very few genetic resources are available for this Subclass. Here, we present the first whole genome sequence (WGS, acc. UYDY01) and the first mRNA transcriptome assembly (TSA, Acc. GHAJ01) for the tropical cyclopoid copepod species Apocyclops royi Until now, only the 18S small subunit of ribosomal RNA gene and the COI gene has been available from A. royi, and WGS resources was only available from one other cyclopoid copepod species. Overall, the provided resources are the 8th copepod species to have WGS resources available and the 19th copepod species with TSA information available. We analyze the length and GC content of the provided WGS scaffolds as well as the coverage and gene content of both the WGS and the TSA assembly. Finally, we place the resources within the copepod order Cyclopoida as a member of the Apocyclops genus. We estimate the total genome size of A. royi to 450 Mb, with 181 Mb assembled nonrepetitive sequence, 76 Mb assembled repeats and 193 Mb unassembled sequence. The TSA assembly consists of 29,737 genes and an additional 45,756 isoforms. In the WGS and TSA assemblies, >80% and >95% of core genes can be found, though many in fragmented versions. The provided resources will allow researchers to conduct physiological experiments on A. royi, and also increase the possibilities for copepod gene set analysis, as it adds substantially to the copepod datasets available.
    Matched MeSH terms: Genes, rRNA
  14. Fulltext Short technical communication yeast identification from domestic ragi for food fermentation by PCR method
    Siti Hajar, M.D., Noorhisham, T.K., Nurina, A.
    International Food Research Journal, 2012;19(2):775-777.
    MyJurnal
    In this study polymerase chain reaction (PCR) was used to identify yeast in domestic ragi obtained
    from two local markets in Sarawak and Pahang. These ragi are normally used as a dry starter in food fermentation (tapai) for Pahang (ST2) and Sarawak (ST3) and tuak (ST1) which is an alcoholic drink in Sarawak. Universal primer, NL1 and NL4 were used as a primer in this study to amplify D1/D2 fragment. Based on the result from the sequencing and after the BLAST search of the nucleotide sequences, the strain was confirmed as Candida glabrata (FN424108.) partial 26S rRNA gene, strain IMUFRJ 51955 for ST1, Saccharomyces cerevisiae(EU285514.1) isolate 35 26S ribosomal RNA gene, partial sequence for ST2 sample and Candida glabrata (FN393990.1) partial 26S rRNA gene, strain MUCL 51244 for ST3. All these strains were found in domestic ragi used for food fermentation.
    Matched MeSH terms: Genes, rRNA
  15. Phylogeny of sea cucumber (Echinodermata: Holothuroidea) as inferred from 16S mitochondrial rRNa gene sequences
    Kamarul Rahim Kamarudin, Ridzwan Hashim, Usup G
    Sains Malaysiana, 2010;39:209-218.
    This study aimed to determine phylogenetic relationship between and among selected species of sea cucumbers (Echinodermata: Holothuroidea) using 16S mitochondrial ribosomal RNA (rRNA) gene. Phylogenetic analyses of 37 partial sequences of 16S mitochondrial rRNA gene using three main methods namely neighbour joining (NJ), maximum parsimony (MP) and maximum likelihood (ML) showed the presence of five main genera of sea cucumbers: Molpadia from order Molpadiida and four genera of order Aspidochirotida namely Holothuria, Stichopus, Bohadschia and Actinopyga. All of the 17 species obtained from Malaysia distributed among the main genera except within Actinopyga. Interestingly, Holothuria excellens was out of Holothuria group causing Holothuria to be paraphyletic. High bootstrap value and consistent clustering made Molpadia, Stichopus, Bohadschia and Actinopyga monophyletic. The relationship of Actinopyga with the other genera was unclarified and Stichopus was sister to Molpadia. The latter finding caused the resolution at order level unclear. The pairwise genetic distance calculated using Kimura 2-parameter model further supported and verified findings from the phylogenetic trees. Further studies with more samples and different mitochondrial DNA genes need to be done to get a better view and verification on the molecular phylogeny of sea cucumbers.
    Matched MeSH terms: Genes, rRNA
  16. Phylogeny and species delineation in the marine diatom Pseudo-nitzschia (Bacillariophyta) using cox1, LSU, and ITS2 rRNA genes: A perspective in character evolution
    Lim HC, Tan SN, Teng ST, Lundholm N, Orive E, David H, et al.
    J Phycol, 2018 04;54(2):234-248.
    PMID: 29377161 DOI: 10.1111/jpy.12620
    Analyses of the mitochondrial cox1, the nuclear-encoded large subunit (LSU), and the internal transcribed spacer 2 (ITS2) RNA coding region of Pseudo-nitzschia revealed that the P. pseudodelicatissima complex can be phylogenetically grouped into three distinct clades (Groups I-III), while the P. delicatissima complex forms another distinct clade (Group IV) in both the LSU and ITS2 phylogenetic trees. It was elucidated that comprehensive taxon sampling (sampling of sequences), selection of appropriate target genes and outgroup, and alignment strategies influenced the phylogenetic accuracy. Based on the genetic divergence, ITS2 resulted in the most resolved trees, followed by cox1 and LSU. The morphological characters available for Pseudo-nitzschia, although limited in number, were overall in agreement with the phylogenies when mapped onto the ITS2 tree. Information on the presence/absence of a central nodule, number of rows of poroids in each stria, and of sectors dividing the poroids mapped onto the ITS2 tree revealed the evolution of the recently diverged species. The morphologically based species complexes showed evolutionary relevance in agreement with molecular phylogeny inferred from ITS2 sequence-structure data. The data set of the hypervariable region of ITS2 improved the phylogenetic inference compared to the cox1 and LSU data sets. The taxonomic status of P. cuspidata and P. pseudodelicatissima requires further elucidation.
    Matched MeSH terms: Genes, rRNA
  17. Phylogenetic relationships within the genus holothuria inferred from 16S mitochondiral rRNA gene sequences
    Kamarul Rahim Kamarudin, ‘Aisyah Mohamed Rehan, Ridzwan Hashim, Usup G, Maryam Mohamed Rehan
    Sains Malaysiana, 2016;45:1079-1087.
    This study aimed to resolve the taxonomic status of a morphologically undetermined sea cucumber species of order Apodida
    from Malaysia (GenBank accession no.: FJ223867) using partial 16S mitochondrial rRNA gene sequences and subsequently
    to determine the validity of morphological taxonomy of Holothuria species into its current subgenera. The undetermined
    species clustered with all taxa of Holothuria in previous study. Phylogenetic analyses using maximum parsimony and
    Bayesian methods suggest that the undetermined species was genetically closer to Holothuria (Lessonothuria) pardalis and
    Holothuria (Acanthotrapeza) coluber; and its position in both phylogenetic trees further suggests its status as a Holothuria
    taxon. Subgenera of Holothuria, Merthensiothuria and Metriatyla are monophyletic with strong bootstrap supports and
    posterior probabilities of clades, thus strengthening their morphological taxonomies. Nonetheless, the non-monophyly of
    subgenera of Halodeima, Microthele and Platyperona suggests a requirement for their taxonomic revisions using integrative
    taxonomy. The status of Holothuria (Halodeima) edulis subgroups in the maximum parsimony and Bayesian trees is
    indistinct and further taxonomic revisions are necessary. In terms of sister relationship, both phylogenetic trees suggest
    that subgenus Holothuria is a sister taxon of subgenus Roweothuria while the other sister relationships were unclear due
    to the undetermined species, paraphyly and polyphyly of a number of subgenera. Further studies with more specimens of
    genus Holothuria from broader geographical locations and various mtDNA genes along with morphological approaches
    may facilitate to provide better insights into the molecular phylogeny of subgenera of Holothuria.
    Matched MeSH terms: Genes, rRNA
  18. Fulltext Phylogenetic analysis of simian Plasmodium spp. infecting Anopheles balabacensis Baisas in Sabah, Malaysia
    Chua TH, Manin BO, Daim S, Vythilingam I, Drakeley C
    PLoS Negl Trop Dis, 2017 Oct;11(10):e0005991.
    PMID: 28968395 DOI: 10.1371/journal.pntd.0005991
    BACKGROUND: Anopheles balabacensis of the Leucospyrus group has been confirmed as the primary knowlesi malaria vector in Sabah, Malaysian Borneo for some time now. Presently, knowlesi malaria is the only zoonotic simian malaria in Malaysia with a high prevalence recorded in the states of Sabah and Sarawak.

    METHODOLOGY/PRINCIPAL FINDINGS: Anopheles spp. were sampled using human landing catch (HLC) method at Paradason village in Kudat district of Sabah. The collected Anopheles were identified morphologically and then subjected to total DNA extraction and polymerase chain reaction (PCR) to detect Plasmodium parasites in the mosquitoes. Identification of Plasmodium spp. was confirmed by sequencing the SSU rRNA gene with species specific primers. MEGA4 software was then used to analyse the SSU rRNA sequences and bulid the phylogenetic tree for inferring the relationship between simian malaria parasites in Sabah. PCR results showed that only 1.61% (23/1,425) of the screened An. balabacensis were infected with one or two of the five simian Plasmodium spp. found in Sabah, viz. Plasmodium coatneyi, P. inui, P. fieldi, P. cynomolgi and P. knowlesi. Sequence analysis of SSU rRNA of Plasmodium isolates showed high percentage of identity within the same Plasmodium sp. group. The phylogenetic tree based on the consensus sequences of P. knowlesi showed 99.7%-100.0% nucleotide identity among the isolates from An. balabacensis, human patients and a long-tailed macaque from the same locality.

    CONCLUSIONS/SIGNIFICANCE: This is the first study showing high molecular identity between the P. knowlesi isolates from An. balabacensis, human patients and a long-tailed macaque in Sabah. The other common simian Plasmodium spp. found in long-tailed macaques and also detected in An. balabacensis were P. coatneyi, P. inui, P. fieldi and P. cynomolgi. The high percentage identity of nucleotide sequences between the P. knowlesi isolates from the long-tailed macaque, An. balabacensis and human patients suggests a close genetic relationship between the parasites from these hosts.

    Matched MeSH terms: Genes, rRNA
  19. Peltaster gemmifer: A new species in the sooty blotch and flyspeck species complex from the United States
    Rosli H, Batzer JC, Harrington TC, Gleason ML
    Mycologia, 2018 09 21;110(5):822-834.
    PMID: 30240341 DOI: 10.1080/00275514.2018.1486679
    Sooty blotch and flyspeck (SBFS) fungi infect the cuticle of fruit, including apple fruit, and produce pigmented colonies. A new member of this fungal complex in the genus Peltaster is described on the basis of molecular and morphological evidence. The SBFS complex is a diverse group of ectophytic fungi that reside primarily within the order Capnodiales. Sooty blotch and flyspeck isolates from apple orchards in the central United States were subjected to parsimony and Bayesian analyses based on the internal transcribed spacer regions of nuc rDNA, the partial translation elongation factor 1-α gene, and the partial mitochondrial small subunit rRNA gene. Phylogenetic analysis delineated a new species, Peltaster gemmifer, from P. cerophilus and P. fructicola. Peltaster gemmifer conidiophores bear primary conidia that produce secondary conidia either through budding or through microcyclic conidiation; these were not seen in cultures of P. cerophilus and P. fructicola. On cellulose membrane that was placed on water agar amended with apple juice, P. gemmifer produced brown to black pycnothyria in a superficial brownish mycelial mat, similar to the colonies produced on apple fruit. Findings from the present study add to the >80 named and putative SBFS species so far described worldwide.
    Matched MeSH terms: Genes, rRNA
  20. Fulltext PHYLOGENETIC ANALYSIS OF Komagataeibacter sp.: A CELLULOSE-PRODUCER BACTERIA BASED ON 16S rRNA GENE SEQUENCES+-
    Nur Aisyah Atikah Alizan, Sarah S. Zakaria
    Journal of Academia Universiti Teknologi MARA Negeri Sembilan, 2021;9(1):97-105.
    MyJurnal
    Bacteria of the genus Komagataeibacter are described to be the most noteworthy for having several of its species being efficient and strong cellulose producers. The 16S ribosomal RNA (rRNA) gene analysis is often used for the identification and taxonomic classification of these bacteria species. In order to observe the phylogenetic relationship among Komagataeibacter sp., twelve sequences of the 16S rRNA gene with three sequences each for species namely Komagataeibacter europaeus, Komagataeibacter hansenii, Komagataeibacter intermedius and Komagataeibacter xylinus were retrieved from NCBI GenBank database. The sequences were aligned and analysed using PAUP, OrthoANI and BLAST, followed by the phylogenetic tree construction using a Maximum Likelihood method. The parsimony character diagnostic analysis showed very few numbers of parsimony- informative characters present in the aligned sequences which is only 1.5% of the total characters. The inferred phylogenetic relationships demonstrated the unexpected positioning of K. xylinus (GQ240638: Gluconacetobacter xylinus strain) and K. xylinus (KC11853: G. xylinus strain) into the clades of K. europaeus and K. hansenii respectively. The also very low bootstrap values of the branch points linking the K. europaeus species indicated low support for the produced topologies. The findings of this study indicate that more phylogenies information can be attained by increasing the taxon sampling. In addition, more robust molecular data are needed to infer the phylogenetic relationships between the Komagataeibacter species more accurately.
    Matched MeSH terms: Genes, rRNA
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