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Fulltext Mitochondrial Genome Supports Sibling Species of Angiostrongylus costaricensis (Nematoda: Angiostrongylidae)

Yong HS, Song SL, Eamsobhana P, Goh SY, Lim PE, Chow WL, et al.

PLoS One, 2015;10(7):e0134581.
PMID: 26230642 DOI: 10.1371/journal.pone.0134581

Angiostrongylus costaricensis is a zoonotic parasitic nematode that causes abdominal or intestinal angiostrongyliasis in humans. It is endemic to the Americas. Although the mitochondrial genome of the Brazil taxon has been published, there is no available mitochondrial genome data on the Costa Rica taxon. We report here the complete mitochondrial genome of the Costa Rica taxon and its genetic differentiation from the Brazil taxon. The whole mitochondrial genome was obtained from next-generation sequencing of genomic DNA. It had a total length of 13,652 bp, comprising 36 genes (12 protein-coding genes-PCGs, 2 rRNA and 22 tRNA genes) and a control region (A + T rich non-coding region). It is longer than that of the Brazil taxon (13,585 bp). The larger mitogenome size of the Costa Rica taxon is due to the size of the control region as the Brazil taxon has a shorter length (265 bp) than the Costa Rica taxon (318 bp). The size of 6 PCGs and the start codon for ATP6, CYTB and NAD5 genes are different between the Costa Rica and Brazil taxa. Additionally, the two taxa differ in the stop codon of 6 PCGs. Molecular phylogeny based on 12 PCGs was concordant with two rRNA, 22 tRNA and 36 mitochondrial genes. The two taxa have a genetic distance of p = 16.2% based on 12 PCGs, p = 15.3% based on 36 mitochondrial genes, p = 13.1% based on 2 rRNA genes and p = 10.7% based on 22 tRNA genes, indicating status of sibling species. The Costa Rica and Brazil taxa of A. costaricensis are proposed to be accorded specific status as members of a species complex.

Matched MeSH terms: Phylogeny
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: Phylogeny
Molecular identification and phylogeny of Armillaria isolates from South America and Indo-Malaysia

Coetzee MP, Wingfield BD, Bloomer P, Ridley GS, Wingfield MJ

Mycologia, 2003 Mar-Apr;95(2):285-93.
PMID: 21156614

Armillaria root rot is a serious disease, chiefly of woody plants, caused by many species of Armillaria that occur in temperate, tropical and subtropical regions of the world. Very little is known about Armillaria in South America and Southeast Asia, although Armillaria root rot is well known in these areas. In this study, we consider previously unidentified isolates collected from trees with symptoms of Armillaria root rot in Chile, Indonesia and Malaysia. In addition, isolates from basidiocarps resembling A. novae-zelandiae and A. limonea, originating from Chile and Argentina, respectively, were included in this study because their true identity has been uncertain. All isolates in this study were compared, based on their similarity in ITS sequences with previously sequenced Armillaria species, and their phylogenetic relationship with species from the Southern Hemisphere was considered. ITS sequence data for Armillaria also were compared with those available at GenBank. Parsimony and distance analyses were conducted to determine the phylogenetic relationships between the unknown isolates and the species that showed high ITS sequence similarity. In addition, IGS-1 sequence data were obtained for some of the species to validate the trees obtained from the ITS data set. Results of this study showed that the ITS sequences of the isolates obtained from basidiocarps resembling A. novae-zelandiae are most similar to those for this species. ITS sequences for isolates from Indonesia and Malaysia had the highest similarity to A. novae-zelandiae but were phylogenetically separated from this species. Isolates from Chile, for which basidiocarps were not found, were similar in their ITS and IGS-1 sequences to the isolate from Argentina that resembled A. limonea. These isolates, however, had the highest ITS and IGS-1 sequence similarity to authentic isolates of A. luteobubalina and were phylogenetically more closely related to this species than to A. limonea.

Matched MeSH terms: Phylogeny
Fulltext Biotic and abiotic variables influencing plant litter breakdown in streams: a global study

Boyero L, Pearson RG, Hui C, Gessner MO, Pérez J, Alexandrou MA, et al.

Proc Biol Sci, 2016 Apr 27;283(1829).
PMID: 27122551 DOI: 10.1098/rspb.2015.2664

Plant litter breakdown is a key ecological process in terrestrial and freshwater ecosystems. Streams and rivers, in particular, contribute substantially to global carbon fluxes. However, there is little information available on the relative roles of different drivers of plant litter breakdown in fresh waters, particularly at large scales. We present a global-scale study of litter breakdown in streams to compare the roles of biotic, climatic and other environmental factors on breakdown rates. We conducted an experiment in 24 streams encompassing latitudes from 47.8° N to 42.8° S, using litter mixtures of local species differing in quality and phylogenetic diversity (PD), and alder (Alnus glutinosa) to control for variation in litter traits. Our models revealed that breakdown of alder was driven by climate, with some influence of pH, whereas variation in breakdown of litter mixtures was explained mainly by litter quality and PD. Effects of litter quality and PD and stream pH were more positive at higher temperatures, indicating that different mechanisms may operate at different latitudes. These results reflect global variability caused by multiple factors, but unexplained variance points to the need for expanded global-scale comparisons.

Matched MeSH terms: Phylogeny
Fulltext Comprehensive genome analysis of a pangolin-associated Paraburkholderia fungorum provides new insights into its secretion systems and virulence

Tan KY, Dutta A, Tan TK, Hari R, Othman RY, Choo SW

PeerJ, 2020;8:e9733.
PMID: 32953261 DOI: 10.7717/peerj.9733

Background: Paraburkholderia fungorum (P. fungorum) is a Gram-negative environmental species that has been commonly used as a beneficial microorganism in agriculture as an agent for biocontrol and bioremediation. Its use in agriculture is controversial as many people believe that it could harm human health; however, there is no clear evidence to support.
Methodology: The pangolin P. fungorum (pangolin Pf) genome has a genomic size of approximately 7.7 Mbps with N50 of 69,666 bps. Our study showed that pangolin Pf is a Paraburkholderia fungorum supported by evidence from the core genome SNP-based phylogenetic analysis and the ANI analysis. Functional analysis has shown that the presence of a considerably large number of genes related to stress response, virulence, disease, and defence. Interestingly, we identified different types of secretion systems in the genome of pangolin Pf, which are highly specialized and responsible for a bacterium's response to its environment and in physiological processes such as survival, adhesion, and adaptation. The pangolin Pf also shared some common virulence genes with the known pathogenic member of the Burkholderiales. These genes play important roles in adhesion, motility, and invasion.
Conclusion: This study may provide better insights into the functions, secretion systems and virulence of this pangolin-associated bacterial strain. The addition of this genome sequence is also important for future comparative analysis and functional work of P. fungorum.

Matched MeSH terms: Phylogeny
Fulltext Taxonomy and phylogeny of the genus Gastrocentrum Gorham (Coleoptera, Cleridae, Tillinae), with the description of five new species

Yang G, Yang X, Shi H

Zookeys, 2020;979:99-132.
PMID: 33192133 DOI: 10.3897/zookeys.979.53765

The genus Gastrocentrum Gorham, 1876 is revised to include nine species. Five new species are described in this genus: G. magnumsp. nov. (NE India), G. regularesp. nov. (Cameron Highlands, Malaysia), G. xiaodongisp. nov. (Gyirong, Xizang, China), G. zayuensesp. nov. (Zayü, Xizang, China), and G. gaoligongensesp. nov. (Fugong, Yunnan, China). Gastrocentrum nitidum Schenkling, 1916 is transferred to the genus Tillus as a new combination. All the species in this genus are described (except G. brevicolle), and a key is provided for their identification. Illustrations of male genitalia, female reproductive organs, and other important structures are provided. An interspecific phylogeny-estimate of Gastrocentrum is presented based on morphological data, with two main clades recognized: a clade containing G. unicolor and G. laterimaculatum, and a clade containing the remaining six species (the latter a polytomy consisting of G. magnumsp. nov., G. dux, and G. regularesp. nov., and a well-supported sub-clade representing the remaining species). Additionally, the taxonomic and phylogenetic importance of female reproductive organs is discussed.

Matched MeSH terms: Phylogeny
Fulltext Geographical structure, narrow species ranges, and Cenozoic diversification in a pantropical clade of epiphyllous leafy liverworts

Bechteler J, Schäfer-Verwimp A, Lee GE, Feldberg K, Pérez-Escobar OA, Pócs T, et al.

Ecol Evol, 2017 01;7(2):638-653.
PMID: 28116059 DOI: 10.1002/ece3.2656

The evolutionary history and classification of epiphyllous cryptogams are still poorly known. Leptolejeunea is a largely epiphyllous pantropical liverwort genus with about 25 species characterized by deeply bilobed underleaves, elliptic to narrowly obovate leaf lobes, the presence of ocelli, and vegetative reproduction by cladia. Sequences of three chloroplast regions (rbcL, trnL-F, psbA) and the nuclear ribosomal ITS region were obtained for 66 accessions of Leptolejeunea and six outgroup species to explore the phylogeny, divergence times, and ancestral areas of this genus. The phylogeny was estimated using maximum-likelihood and Bayesian inference approaches, and divergence times were estimated with a Bayesian relaxed clock method. Leptolejeunea likely originated in Asia or the Neotropics within a time interval from the Early Eocene to the Late Cretaceous (67.9 Ma, 95% highest posterior density [HPD]: 47.9-93.7). Diversification of the crown group initiated in the Eocene or early Oligocene (38.4 Ma, 95% HPD: 27.2-52.6). Most species clades were established in the Miocene. Leptolejeunea epiphylla and L. schiffneri originated in Asia and colonized African islands during the Plio-Pleistocene. Accessions of supposedly pantropical species are placed in different main clades. Several monophyletic morphospecies exhibit considerable sequence variation related to a geographical pattern. The clear geographic structure of the Leptolejeunea crown group points to evolutionary processes including rare long-distance dispersal and subsequent speciation. Leptolejeunea may have benefitted from the large-scale distribution of humid tropical angiosperm forests in the Eocene.

Matched MeSH terms: Phylogeny
Fulltext Morphological and molecular datasets for Kaempferia species

Labrooy C, Abdullah TL, Stanslas J

Data Brief, 2018 Dec;21:1678-1685.
PMID: 30505900 DOI: 10.1016/j.dib.2018.10.097

This study compared morphological and molecular data for identification of Kaempferia species. Each species was deposited in Institute of Bioscience (IBS), Universiti Putra Malaysia (UPM) as voucher specimens and ITS sequences of each species deposited in NCBI (https://www.ncbi.nlm.nih.gov/) as GenBank accessions. DNA was extracted using a modified CTAB method and PCR amplification was completed using Internal Transcribed Spacer (ITS4 and ITS5) markers. PCR amplification of products were viewed under gel electrophoresis. Sequencing was performed and sequence characteristics of ITS rDNA in Kaempferia is shown. Qualitative and qualitative scoring of morphological characters and measuring techniques for Kaempferia species are included. In addition, a brief review of molecular markers used in phylogenetic studies of Zingiberaceae is included in this dataset.

Matched MeSH terms: Phylogeny
Fulltext Rapid birth-death evolution and positive selection in detoxification-type glutathione S-transferases in mammals

Tan HM, Low WY

PLoS One, 2018;13(12):e0209336.
PMID: 30586459 DOI: 10.1371/journal.pone.0209336

Glutathione S-Transferases (GSTs) are phase II detoxification enzymes that may have evolved in response to changes of environmental substrates. GST genes formed a multigene family and in mammals, there are six classes known as Alpha, Mu, Omega, Pi, Theta, and Zeta. Recent studies in phase I detoxification system specifically the cytochrome P450s provided a general explanation on why genes from a common origin such as those in a multigene family have both phylogenetically stable and unstable genes. Genes that participate in core functions of organisms such as development and physiology are stable whereas genes that play a role in detoxification are unstable and evolve in a process known as birth-death evolution, which is characterised by frequent gene gains and losses. The generality of the birth-death model at explaining the evolution of detoxification enzymes beyond the phase I enzyme has not been comprehensively explored. This work utilized 383 Gst genes and 300 pseudogenes across 22 mammalian species to study gene gains and losses. GSTs vary greatly in their phylogenetic stability despite their overall sequence similarity. Stable Gst genes from Omega and Zeta classes do not show fluctuation in gene numbers from human to opossum. These genes play a role in biosynthesis related functions. Unstable genes that include Alpha, Mu, Pi and Theta undergo frequent gene gain and loss in a process known as birth-death evolution. Gene members of these four classes are well known for their roles in detoxification. Our positive selection screen identified five positively selected sites in mouse GSTA3. Previous studies showed two of these sites (108H and 208E) were biochemically tested as important residues that conferred catalytic activity against the toxic aflatoxin B1-8,9-epoxide. The functional significance against aflatoxin of the remaining three positively selected sites warrant further investigation.

Matched MeSH terms: Phylogeny
Population genetic analysis of oceanic paddle crab (varuna litterata) in Thailand

Uthamas Suppapan, Jamjun Pechsiri, Sompong O-thong, Arunrat Vanichanon, Pradit Sangthong, Verakiat Supmee

Sains Malaysiana, 2017;46:2251-2261.

Population genetic structure of Varuna litterata living along the coast of Thailand were examined in this study. The samples were collected from 3 coastal regions: The Andaman sea (Satun, Trang, Phang Nga), the lower Gulf of Thailand (Pattani, Songkhla, Nakhon Si Thammarat) and the upper Gulf of Thailand (Petchburi, Samut Songkram, Rayong, Trat). Intraspecific variation was determined based on partial sequences of the cytochrome oxidase subunits I gene. A total of 182 samples were collected but only 32 haplotypes were obtained from these samples. An excess of rare haplotypes indicated that the female effective population size of V. litterata living along the coast of Thailand is large. Estimated values of haplotype diversity and nucleotide diversity were 0.790 and 0.003, respectively. The AMOVA (analysis of molecular variance) and phylogenetic analysis results showed that based on genetic variation, the population of this organism was found to have 2 genetically different populations: The Andaman sea population and the Gulf of Thailand population. Genetic exchange of V. litterata among populations inhabiting along the coast of Thailand could be described by the stepping stone model. The results of neutrality tests, both Tajima's D and Fu's Fs statistics, yielded negative values (-1.992 and -26.877, respectively) and statistically significant deviation from the neutrality, indicating that the V. litterata living along the Thailand coast had experienced population expansion. Mismatch distribution analysis indicated that a possible expansion occurred 211,428 years ago during the Pleistocene glaciations period.

Matched MeSH terms: Phylogeny
Fulltext Optimisation of biomass, exopolysaccharide and intracellular polysaccharide production from the mycelium of an identified Ganoderma lucidum strain QRS 5120 using response surface methodology

Supramani S, Ahmad R, Ilham Z, Annuar MSM, Klaus A, Wan-Mohtar WAAQI

AIMS Microbiol, 2019;5(1):19-38.
PMID: 31384700 DOI: 10.3934/microbiol.2019.1.19

Wild-cultivated medicinal mushroom Ganoderma lucidum was morphologically identified and sequenced using phylogenetic software. In submerged-liquid fermentation (SLF), biomass, exopolysaccharide (EPS) and intracellular polysaccharide (IPS) production of the identified G.lucidum was optimised based on initial pH, starting glucose concentration and agitation rate parameters using response surface methodology (RSM). Molecularly, the G. lucidum strain QRS 5120 generated 637 base pairs, which was commensurate with related Ganoderma species. In RSM, by applying central composite design (CCD), a polynomial model was fitted to the experimental data and was found to be significant in all parameters investigated. The strongest effect (p < 0.0001) was observed for initial pH for biomass, EPS and IPS production, while agitation showed a significant value (p < 0.005) for biomass. By applying the optimized conditions, the model was validated and generated 5.12 g/L of biomass (initial pH 4.01, 32.09 g/L of glucose and 102 rpm), 2.49 g/L EPS (initial pH 4, 24.25 g/L of glucose and 110 rpm) and 1.52 g/L of IPS (and initial pH 4, 40.43 g/L of glucose, 103 rpm) in 500 mL shake flask fermentation. The optimized parameters can be upscaled for efficient biomass, EPS and IPS production using G. lucidum.

Matched MeSH terms: Phylogeny
Comment on Seri Masran and Ab Majid 2017

Tseng SP, Yang CS

J Med Entomol, 2017 09 01;54(5):1107-1108.
PMID: 28874021 DOI: 10.1093/jme/tjx136
Matched MeSH terms: Phylogeny
Presbytis neglectus or P. femoralis, Colobine Molecular Phylogenies, and GenBank Submission of Newly Generated DNA Sequences

Nijman V

Folia Primatol., 2020;91(3):228-239.
PMID: 31578029 DOI: 10.1159/000502093

Great progress has been made in unravelling the evolutionary history of Asian colobines, largely through the use of dated molecular phylogenies based on multiple markers. The Presbytis langurs are a case in point, with more allopatric species being identified, recognition of Presbytis thomasi from Sumatra rather than P. potenziani from the Mentawai Islands as being the most basal species of the group, and the discovery that P. rubicunda from Borneo is nested among the Sumatran species and only made it to Borneo in the last 1.3 million years. Based on variation in mitochondrial d-loop, it has recently been argued that Malaysia's P. femoralis femoralis is actually P. neglectus neglectus. Unfortunately, despite being available, sequences from the type locality, Singapore, were excluded from the analysis, and none of the newly generated sequences was deposited in GenBank. I manually reconstructed these sequences, which allowed me to present a molecular phylogeny that includes 8 additional sequences from West Malaysia and Singapore. P. neglectus from Malaysia and P. femoralis from Singapore form one monophyletic clade, with minimal divergence. I conclude that recognition of P. neglectus is erroneous and the name is a junior synonym of P. femoralis. Colobine taxonomy and systematics have advanced, and continue to advance, mostly by considering evidence from a wide range of individuals, species and data sets (molecular, behavioural and morphological) rather than focusing on single molecular markers from 1 or 2 species from one small geographic area. For an orderly taxonomic debate where evidence can be evaluated and reinterpreted it is essential that newly generated sequences are deposited in public repositories.

Matched MeSH terms: Phylogeny
Fulltext Characterization of the mitogenomes of long-tailed giant rat, Leopoldamys sabanus and a comparative analysis with other Leopoldamys species

Jahari PNS, Mohd Azman S, Munian K, Ahmad Ruzman NH, Shamsir MS, Richter SR, et al.

Mitochondrial DNA B Resour, 2021 Feb 11;6(2):502-504.
PMID: 33628904 DOI: 10.1080/23802359.2021.1872433

Two mitogenomes of long-tailed giant rat, Leopoldamys sabanus (Thomas, 1887), which belongs to the family Muridae were sequenced and assembled in this study. Both mitogenomes have a length of 15,973 bp and encode 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes and one control region. The circular molecule of L. sabanus has a typical vertebrate gene arrangement. Phylogenetic and BLASTn analysis using 10 Leopoldamys species mitogenomes revealed sequence variation occurred within species from different time zones. Along with the taxonomic issues, this suggests a landscape change might influence genetic connectivity.

Matched MeSH terms: Phylogeny
Fulltext The complete chloroplast genome and phylogenetic analysis of Nephelium lappaceum (rambutan)

Liu J, Zheng C, Liu ZY, Niu YF

Mitochondrial DNA B Resour, 2021 Feb 09;6(2):485-487.
PMID: 33628898 DOI: 10.1080/23802359.2021.1872449

Nephelium lappaceum is a popular tropical fruit belonging to the Sapindaceae family. The plant originated in Malaysia and Indonesia and is commonly called rambutan. Because of its refreshing flavor and exotic appearance, rambutan is widely accepted in the World. Due to its significant medicinal properties, the fruit has also been employed in traditional medicine for centuries. The chloroplast genome of rambutan was sequenced, assembled, and annotated in the present study. The chloroplast genome length was 161,356 bp and contained 132 genes, including 87 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. It possessed the typical quadripartite circle structure with a large single-copy region (86,009 bp), a small single-copy region (18,153 bp), and two inverted repeat regions (28,597 bp). A total of 35 SSR markers were found in the chloroplast genome of Nephelium lappaceum, of which 33 were monomer, 1 was dimer and 1 was tetramer. Phylogenetic analysis based on the complete chloroplast genome sequences of 21 plant species showed that rambutan was closely related to Pometia tomentosa. These results provide a foundation for further phylogenetic and evolutionary studies of the Sapindaceae family.

Matched MeSH terms: Phylogeny
Taxonomy and toxicity of a bloom-forming Ostreopsis species (Dinophyceae, Gonyaulacales) in Tahiti island (South Pacific Ocean): one step further towards resolving the identity of O. siamensis

Chomérat N, Bilien G, Viallon J, Hervé F, Réveillon D, Henry K, et al.

Harmful Algae, 2020 09;98:101888.
PMID: 33129466 DOI: 10.1016/j.hal.2020.101888

Among dinoflagellates responsible for benthic harmful algal blooms, the genus Ostreopsis primarily described from tropical areas has been increasingly reported from subtropical and temperate areas worldwide. Several species of this toxigenic genus produce analogs of palytoxin, thus representing a major threat to human and environmental health. The taxonomy of several species needs to be clarified as it was based mostly on morphological descriptions leading in some cases to ambiguous interpretations and misidentifications. The present study aims at reporting a benthic bloom that occurred in April 2019 in Tahiti island, French Polynesia. A complete taxonomic investigation of the blooming Ostreopsis species was realized using light, epifluorescence and field emission electron microscopy and phylogenetic analyses inferred from LSU rDNA and ITS-5.8S rDNA regions. Toxicity of a natural sample and strains isolated from the bloom was assessed using both neuroblastoma cell-based assay and LC-MS/MS analyses. Morphological observations showed that cells were round to oval, large, 58.0-82.5 µm deep (dorso-ventral length) and 45.7-61.2 µm wide. The cingulum was conspicuously undulated, forming a 'V' in ventral view. Thecal plates possessed large pores in depressions, with a collar rim. Detailed observation also revealed the presence of small thecal pores invisible in LM. Phylogenetic analyses were congruent and all sequences clustered within the genotype Ostreopsis sp. 6, in a subclade closely related to sequences from the Gulf of Thailand and Malaysia. No toxicity was found on the field sample but all the strains isolated from the bloom were found to be cytotoxic and produced ostreocin D, a lower amount of ostreocins A and B and putatively other compounds. Phylogenetic data demonstrate the presence of this species in the Gulf of Thailand, at the type locality of O. siamensis, and morphological data are congruent with the original description and support this identification.

Matched MeSH terms: Phylogeny
Fulltext Genetic diversity of Sabah rice cultivars using random amplified polymorphic dna (rapd) markers

Alvina Simon, Vijay Kumar Subbiah, Chee, Fong Tyng, Noor Hydayaty Md Yusuf

Borneo International Journal of Biotechnology, 2020;1(1):35-43.
MyJurnal

Rice is the most important staple crop in Malaysia and is cultivated all over the country, including the state of Sabah. The uniqueness of rice cultivation in Sabah lies in the type of rice itself, deriving mainly from local or non-commercial cultivars but with distinctive characteristics including long grains, aromatic properties, and drought tolerance. However, despite having these important agricultural traits, information on the genetic diversity of Sabah rice remains limited. Hence, the purpose of this study was to determine the genetic polymorphisms of Sabah rice using random amplification of polymorphic DNA (RAPD) markers. A total of 101 alleles were profiled, from which 94% were identified as polymorphic. Phylogenetic analysis grouped the rice samples into three clusters, with two clusters classifying the ability of rice to grow under different planting conditions, suitable for growth irrigate and upland condition. The first cluster was dominated by cultivars that could survive in wet (irrigated) areas, while the other featured those that were found in dry (upland) areas. Furthermore, two alleles, OPA-05-B2 and OPA-01-B11, were found to be unique to cultivars within the upland cluster and were thus proposed to be involved in dry environmental adaptation. The results of the present study provide an insight into the genetic relationships and diversity of Sabah rice.

Matched MeSH terms: Phylogeny
Fulltext Fusarium Species in Mangrove Soil in Northern Peninsular Malaysia and the Soil Physico-Chemical Properties

Mohamed Zubi WS, Mohd MH, Mohamed Nor NMI, Zakaria L

Microorganisms, 2021 Feb 26;9(3).
PMID: 33652900 DOI: 10.3390/microorganisms9030497

Fusarium genus comprises important saprophytic and phytopathogenic fungi and is widespread in nature. The present study reports the occurrence of Fusarium spp. in soils from two mangrove forests in northern Peninsular Malaysia and analyzed physico-chemical properties of the mangrove soil. Based on TEF-1α sequences, nine Fusarium species were identified: Fusarium solani species complex (FSSC) (n = 77), Fusarium verticillioides (n = 20), Fusarium incarnatum (n = 10), Fusarium proliferatum (n = 7), Fusarium lateritium (n = 4), Fusarium oxysporum (n = 3), Fusarium rigidiuscula (n = 2), Fusarium chlamydosporum (n = 1), and Fusarium camptoceras (n = 1); FSSC isolates were the most prevalent. Phylogenetic analysis of the combined TEF-1α and ITS sequences revealed diverse phylogenetic affinities among the FSSC isolates and potentially new phylogenetic clades of FSSC. Soil analysis showed varied carbon content, pH, soil moisture, and salinity, but not nitrogen content, between sampling locations. Regardless of the physico-chemical properties, various Fusarium species were recovered from the mangrove soils. These were likely saprophytes; however, some were well-known plant pathogens and opportunistic human pathogens. Thus, mangrove soils might serve as inoculum sources for plant and human pathogenic Fusarium species. The present study demonstrates the occurrence of various Fusarium species in the extreme environment of mangrove soil, thereby contributing to the knowledge on species diversity in Fusarium.

Matched MeSH terms: Phylogeny
Fulltext The complete mitochondrial genome of Malayan Gaur (Bos gaurus hubbacki) from Peninsular Malaysia

Rosli N, Sitam FT, Rovie-Ryan JJ, Gan HM, Lee YP, Hartini Ithnin, et al.

Mitochondrial DNA B Resour, 2019 Jul 13;4(2):2535-2536.
PMID: 33365614 DOI: 10.1080/23802359.2019.1640085

Here, we present the first complete mitochondrial genome of Malayan Gaur (Bos gaurus hubbacki) inferred using next-generation sequencing. The mitogenome is 16,367 bp in length with the structural organization of a typical bovine mitochondrial arrangement comprising 13 protein-coding genes, 21 tRNAs, and 2 rRNAs. No internal stop codon was found in the protein-coding genes. Phylogenetic tree analysis revealed that Malayan gaur is more closely related to Burmese banteng instead of gaur.

Matched MeSH terms: Phylogeny
Fulltext Complete mitochondrial genome of the black-winged fly, Felderimyia fuscipennis (Diptera: Tephritidae) and its phylogenetic relationship within family Tephritidae

Yang MJ, Liu JH, Wan XS, Zhang QL, Fu DY, Wang XB, et al.

Mitochondrial DNA B Resour, 2020 Oct 27;5(3):3638-3639.
PMID: 33367040 DOI: 10.1080/23802359.2020.1831984

The black-winged fly, Felderimyia fuscipennis (Diptera: Tephritidae), is an insect pest of bamboo shoot, mainly distributed in Thailand, Malaysia and Yunnan Province and Guangxi Autonomous Region, China. The complete sequence of the mitogenome of F. fuscipennis has been determined in this study. The whole mitogenome sequence is 16,536 bp in length, which totally contains 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and a non-coding region (putative control region, CR). The phylogeny indicates that F. fuscipennis of subfamily Trypetinae was monophyletic and clearly separated from both Dacinae and Tephritinae with high bootstrap value supported.

Matched MeSH terms: Phylogeny

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