Molecular identification of poisonous mushrooms using nuclear ITS region and peptide toxins: a retrospective study on fatal cases in Thailand

Most species in the genus Amanita are ectomycorrhizal fungi comprising both edible and poisonous mushrooms. Some species produce potent cyclic peptide toxins, such as α-amanitin, which places them among the deadliest organisms known to mankind. These toxins and related cyclic peptides are encoded by genes of the “MSDIN” family (named after the first five amino acid residues of the precursor peptides), and it is largely unknown to what extent these genes are expressed in the basidiocarps. In the present study, Amanita rimosa and Amanita exitialis were sequenced through the PacBio and Illumina techniques. Together with our two previously sequenced genomes, Amanita subjunquillea and Amanita pallidorosea, in total, 46 previously unknown MSDIN genes were discovered. The expression of over 80% of the MSDIN genes was demonstrated in A. subjunquillea. Through a combination of genomics and mass spectrometry, 12 MSDIN genes were shown to produce novel cyclic peptides. To further confirm the results, three of the cyclic peptides were chemically synthesized. The tandem mass spectrometry (MS/MS) spectra of the natural and the synthetic peptides shared a majority of the fragment ions, demonstrating an identical structure between each peptide pair. Collectively, the results suggested that the genome-guided approach is reliable for identifying novel cyclic peptides in Amanita species and that there is a large peptide reservoir in these mushrooms.

Download Full-text

WildTermitomycesSpecies Collected from Ondo and Ekiti States Are More Related to African Species as Revealed by ITS Region of rDNA

The Scientific World JOURNAL ◽

10.1100/2012/689296 ◽

2012 ◽

Vol 2012 ◽

pp. 1-5 ◽

Cited By ~ 2

Author(s):

Victor Olusegun Oyetayo

Keyword(s):

Sequence Analysis ◽

Phylogenetic Tree ◽

Molecular Identification ◽

Internal Transcribed Spacer ◽

Its Region ◽

Its Sequence ◽

African Countries ◽

African Species ◽

Its Sequence Analysis ◽

Degree Of Similarity

Molecular identification of eighteenTermitomycesspecies collected from two states, Ondo and Ekiti in Nigeria was carried out using the internal transcribed spacer (ITS) region. The amplicons obtained from rDNA ofTermitomycesspecies were compared with existing sequences in the NCBI GenBank. The results of the ITS sequence analysis discriminated between all theTermitomycesspecies (obtained from Ondo and Ekiti States) andTermitomycessp. sequences obtained from NCBI GenBank. The degree of similarity of T1 to T18 to gene ofTermitomycessp. obtained from NCBI ranges between 82 and 99 percent.Termitomycesspecies from Garbon with ascension number AF321374 was the closest relative of T1 to T18 except T12 that has T. eurhizus and T. striatus as the closet relative. Phylogenetic tree generated with ITS sequences obtained from NCBI GenBank data revealed that T1 to T18 are more related toTermitomycesspecies indigenous to African countries such as Senegal, Congo, and Gabon.

Download Full-text

Morphological and molecular identification of phytophthora species from maple trees in Serbia

Genetika ◽

10.2298/gensr1402353m ◽

2014 ◽

Vol 46 (2) ◽

pp. 353-368 ◽

Cited By ~ 1

Author(s):

Ivan Milenkovic ◽

Justyna Nowakowska ◽

Tomasz Oszako ◽

Katarina Mladenovic ◽

Aleksandar Lucic ◽

...

Keyword(s):

Molecular Identification ◽

Genomic Dna ◽

Its Region ◽

Phytophthora Species ◽

Morphological Identification ◽

First Report ◽

Phytophthora Spp ◽

Isolated Species

The paper presents the results of the study performed with aims to determine the presence and diversity of Phytophthora species on maple trees in Serbia. Due to high aggressiveness and their multicyclic nature, presence of these pathogens is posing significant threat to forestry and biodiversity. In total, 29 samples of water, soil and tissues were taken from 10 different localities, and six different maple hosts were tested. After the isolation tests, 17 samples from five different maple hosts were positive for the presence of Phytophthora spp., and 31 isolates were obtained. After the detailed morphological and physiological classification, four distinct groups of isolates were separated. DNA was extracted from selected representative isolates and molecular identification with sequencing of ITS region was performed. Used ITS4 and ITS6 primers successfully amplified the genomic DNA of chosen isolates and morphological identification of obtained isolates was confirmed after the sequencing. Four different Phytophthora species were detected, including P. cactorum, P. gonapodyides, P. plurivora and P. lacustris. The most common isolated species was homothallic, and with very variable and semipapillate sporangia, P. plurivora with 22 obtained isolates. This is the first report of P. plurivora and P. gonapodyides on A. campestre, P. plurivora and P. lacustris on Acer heldreichii and first report of P. lacustris on A. pseudoplatanus and A. tataricum in Serbia.

Download Full-text

Biatora Britannica sp. Nov. and the Occurrence of Biatora Efflorescens in the British Isles

The Lichenologist ◽

10.1006/lich.2000.0319 ◽

2001 ◽

Vol 33 (3) ◽

pp. 181-187 ◽

Cited By ~ 6

Author(s):

Christian Printzen ◽

H. Thorsten Lumbsch ◽

Alan Orange

Keyword(s):

Its Region ◽

Molecular Data ◽

Sister Taxon ◽

British Isles ◽

Close Relationship ◽

Nuclear Its ◽

Relationship Of

AbstractBiatora Britannica sp. nov is described from Wales. The species is the sorediate sister taxon of the Madeiran Biatora hertelii. The close relationship is supported by the presence of the hymenial pigment Hertelii-green, which is hitherto known only from these two species. Molecular data from the nuclear ITS-region of 14 Bratora¯ species renders further support for the close relationship of both species. Sterile, sorediate material from the British Isles earlier referred to B. efflorescens may in fact belong to B. britannica.

Download Full-text

Molecular systematics of Australian Podolepis (Asteraceae: Gnaphalieae): evidence from DNA sequences of the nuclear ITS region and the chloroplast matK gene

Australian Systematic Botany ◽

10.1071/sb99030 ◽

2000 ◽

Vol 13 (5) ◽

pp. 709 ◽

Cited By ~ 7

Author(s):

N. Konishi ◽

K. Watanabe ◽

K. Kosuge

Keyword(s):

Dna Sequences ◽

Its Region ◽

Chromosomal Evolution ◽

Internal Transcribed Spacers ◽

Nuclear Ribosomal Dna ◽

Base Number ◽

Monophyletic Clade ◽

Matk Gene ◽

Nuclear Its ◽

Generic Relationships

The generic circumscription and intra-generic relationships of the genus Podolepis Labill., with various chromosome numbers from n = 12 to n = 3, were examined by sequences of the internal transcribed spacers (ITS) of nuclear ribosomal DNA and the matK gene of chloroplast DNA. The topology of the ITS tree for 17 species and the matK tree for 18 species of the genus Podolepis sensu Davis (1957) and Anderberg (1991) and 15 taxa from eight related genera (Anderberg 1989, 1991, 1994) are basically concordant. Except for P. georgei Diels andP. kendallii F.Muell., parsimony analyses support the monophyly of the genus Podolepis sensu Davis (1957) and Anderberg (1991). The genera of Asteridea Lindl. and Pterochaeta Steetz are sisters toPodolepis in the combined tree based on the ITS and matK sequences. Within the monophyletic clade of the genus Podolepis, three lineages are identified. The chromosome base number of x = 12 may be ancestral in the genus Podolepis. The dysploidal reduction in chromosome number from n = 12 to n = 10 and 9, from n = 12 to n = 8 and 7, and from n = 12 to n = 11 and 3 in three lineages, respectively, is the primary mode of chromosomal evolution in this genus. Total karyotypic length (= genome size) is much greater in perennials than in annuals within the genus Podolepis. The number of pappus bristles on outer female florets tends to decrease and they are absent in some annuals of this genus, while myxogenic cells on the pericarp become prominent.

Download Full-text

Molecular identification of tick-borne pathogens in asymptomatic individuals with human immunodeficiency virus type 1 (HIV-1) infection: a retrospective study

BMC Infectious Diseases ◽

10.1186/s12879-018-3140-7 ◽

2018 ◽

Vol 18 (1) ◽

Cited By ~ 3

Author(s):

Renata Welc-Falęciak ◽

Justyna D. Kowalska ◽

Małgorzata Bednarska ◽

Magdalena Szatan ◽

Agnieszka Pawełczyk

Keyword(s):

Human Immunodeficiency Virus ◽

Retrospective Study ◽

Human Immunodeficiency Virus Type ◽

Virus Type ◽

Molecular Identification ◽

Immunodeficiency Virus ◽

Asymptomatic Individuals ◽

Hiv 1

Download Full-text

Two new Oxalis (Oxalidaceae) species, including 5 varieties, from the Richtersveld of South Africa

Phytotaxa ◽

10.11646/phytotaxa.314.2.4 ◽

2017 ◽

Vol 314 (2) ◽

pp. 231

Author(s):

LÉANNE L. DREYER ◽

FRANCOIS ROETS ◽

KENNETH C. OBERLANDER

Keyword(s):

New Species ◽

Its Region ◽

Morphological Characters ◽

Phylogenetic Position ◽

African Species ◽

Widespread Species ◽

Taxonomic Descriptions ◽

Granite Outcrops ◽

Nuclear Its ◽

Typical Variety

Two new species of Oxalis (Oxalidaceae) from the Richtersveld are described, namely Oxalis canaliculata and O. magnifolia. These widespread species are morphologically distinct and easily identified, but both contain populations in which individuals consistently differ morphologically from typical varieties. The typical variety of Oxalis canaliculata is widespread throughout the Richtersveld, while O. canaliculata var. trifoliolata is known from a single population and O. canaliculata var. graniticola is known only from granite outcrops. Oxalis magnifolia includes the typical variety that is widespread and Oxalis magnifolia var. reduplicata, which is only known from two populations in close proximity to one another. Morphological characters, preliminary phylogenetic position based on data from the nuclear ITS region, habitat description and formal taxonomic descriptions are provided for all taxa. The diagnostic characters of the new species are compared to all phenotypically similar southern African species.

Download Full-text

Ectomycorrhizae of Tomentella badia: description and molecular identification

Acta Mycologica ◽

10.5586/am.2013.018 ◽

2013 ◽

Vol 48 (2) ◽

pp. 155-171 ◽

Cited By ~ 3

Author(s):

Andrea Binder ◽

Derek Peršoh ◽

Nourou S. Yorou ◽

Rita Verma ◽

Claus Bässler ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Picea Abies ◽

Molecular Identification ◽

Its Region ◽

Molecular Phylogenetic Analysis ◽

Functional Characteristics ◽

Molecular Phylogenetic ◽

Dark Blue

Species within the genera Tomentella are among the most important ECM in forests. However, our knowledge about their functional characteristics is still rather limited. The ectomycorrhizae of Tomentella badia on Picea abies are described here in detail and compared to the non-identified ECM Piceirhiza obscura. A pseudoparenchymatous mantle formed by epidermoid cells is covered by heaps of epidermoid cells. This mantle type is regarded as a new one and designated as mantle type R. Many cells filled with dark blue contents and/or blue granules, together with clampless hyphae, are distinct characters of these ectomycorrhizae. Molecular-phylogenetic analysis of the ITS region was used for identification.

Download Full-text

Molecular identification and technological properties of yeasts isolated from spontaneously fermented cassava waste pulp

Nova Biotechnologica et Chimica ◽

10.36547/nbc.898 ◽

2021 ◽

Vol 20 (2) ◽

pp. e898

Author(s):

Adelodun L. Kolapo ◽

Raoofat O. Salami ◽

Gbemisola O. Onipede

Keyword(s):

Bile Salt ◽

Molecular Identification ◽

Starter Culture ◽

Its Region ◽

Viable Count ◽

Haemolytic Activity ◽

Good Growth ◽

Technological Properties ◽

Specific Tolerance ◽

Cassava Waste

The aim of this work was to report on molecular identification and technological properties of the yeast flora isolated from spontaneously fermented cassava waste pulp. This was done with a view of obtaining yeast strains that could be used as a starter culture for the fermentation of cassava waste pulp. Molecular identification was based on the nucleotide sequence of the ITS region of the genomic DNA of the yeast isolates while the technological properties evaluated include linamarase (U/mL), gelatinase, and haemolytic activity; growth at pH 2.5 and tolerance to 2 % bile salt. All the representative five isolated yeasts were identified as Geotrichum silvicola KLP04 – KLP08. The isolates exhibited linamarase activity ranging between 3.3 and 4.2 with strain KLP04 having the highest value and strain KLP05 the least. None of the isolates demonstrated gelatinase and haemolytic activity except strain KLP08 which was partially haemolytic. All the examined yeasts exhibited good growth at pH 2.5, with strain KLP08 having the highest viable counts of 4.1 log10cfu/ml and strain KLP04 the least value of 3.5 log10cfu/ml after 72 h of growth. All the identified yeasts showed strain-specific tolerance to 2% bile salt with strain KLP04 having the highest viable count of 4.3 log10cfu/ml and strain KLP08 the least value of 2.2 log10cfu/ml at the end of 72 h of incubation. Based on all the examined technological properties, Candida silvicola KLP04 strain had the highest potential to be considered for starter culture for the fermentation of cassava waste pulp.

Download Full-text

Eutrema racemosum (Eutremeae, Brassicaceae), a new tetraploid species from southwest China

Phytotaxa ◽

10.11646/phytotaxa.224.2.5 ◽

2015 ◽

Vol 224 (2) ◽

pp. 185 ◽

Cited By ~ 4

Author(s):

Guoqian Hao ◽

Ihsan Al-Shehbaz ◽

Qian Wang ◽

Qianlong Liang ◽

Jianquan Liu

Keyword(s):

Southwest China ◽

Phylogenetic Analyses ◽

Its Region ◽

Distinct Species ◽

Molecular Data ◽

Small Genome ◽

Sequence Variations ◽

Nuclear Its ◽

Well Differentiated ◽

Germination Experiments

The new species Eutrema racemosum is described, and its relationship to the closely related E. heterophyllum and E. edwardsii are discussed based on morphological, cytological, and molecular data. The novelty differs from E. heterophyllum by having elongated racemes and from E. edwardsii by somewhat reflexed fruiting pedicels. Four chloroplast DNA fragments and nuclear ITS region were sequenced for multiple individuals of each species. Three species show distinct and stable sequence variations. Eutrema racemosum and E. heterophyllum form a clade sister to that of E. edwardsii in phylogenetic analyses of sequence variations. Our cytological studies revealed that E. heterophyllum is a diploid with the small genome size, while E. racemosum is a tetraploid with duplicate genomes. These available data support the recognition of E. racemosum as a distinct species well differentiated morphologically and genetically, as well as well-isolated reproductively from its sister species E. heterophyllum. We further found some interspecific triploid hybrids between tetraploid E. racemosum and diploid E. heterophyllum, which seem to be sterile according to our germination experiments.

Download Full-text