scholarly journals Online Databases for Taxonomy and Identification of Pathogenic Fungi and Proposal for a Cloud-Based Dynamic Data Network Platform

2017 ◽  
Vol 55 (4) ◽  
pp. 1011-1024 ◽  
Author(s):  
Peralam Yegneswaran Prakash ◽  
Laszlo Irinyi ◽  
Catriona Halliday ◽  
Sharon Chen ◽  
Vincent Robert ◽  
...  

ABSTRACT The increase in public online databases dedicated to fungal identification is noteworthy. This can be attributed to improved access to molecular approaches to characterize fungi, as well as to delineate species within specific fungal groups in the last 2 decades, leading to an ever-increasing complexity of taxonomic assortments and nomenclatural reassignments. Thus, well-curated fungal databases with substantial accurate sequence data play a pivotal role for further research and diagnostics in the field of mycology. This minireview aims to provide an overview of currently available online databases for the taxonomy and identification of human and animal-pathogenic fungi and calls for the establishment of a cloud-based dynamic data network platform.

2016 ◽  
Vol 67 (3) ◽  
pp. 380 ◽  
Author(s):  
Michael Shackleton ◽  
Gavin N. Rees

Identification of macroinvertebrates is a key component of monitoring programs that seek to understand the condition of aquatic environments. Classical identification approaches underpin such programs, but molecular approaches are gaining recognition as valuable ways to identify organisms for research and monitoring programs. We applied DNA barcoding data to specimens collected as part of monitoring programs in the Murray–Darling Basin, to investigate the possible informational benefits these data may provide. We also tested the performances of two online DNA databases in assigning taxon names to our sequence data. We found that relying on the online databases to determine species identifications was currently problematic for the Australian freshwater fauna because of a lack of available sequence data. However, we also found that collecting and applying barcode data to our monitoring programs gave considerable informational benefits by providing greater resolution of specimen identity, highlighting the presence of potential cryptic species, providing information on larval and adult associations, demonstrating instances where misidentification had occurred though classical approaches, and providing conformation of the performance of diagnostic characters currently used in keys to determine species identities.


2021 ◽  
Author(s):  
Pedro W Crous ◽  
Amy Y Rossman ◽  
Catherine Aime ◽  
Cavan Allen ◽  
Treena Burgess ◽  
...  

Names of phytopathogenic fungi and oomycetes are essential to communicate knowledge about species and their biology, control, and quarantine as well as for trade and research purposes. Many plant pathogenic fungi are pleomorphic, meaning that they produce different asexual (anamorph) and sexual (teleomorph) morphs in their lifecycles. Because of this, more than one name has been applied to different morphs of the same species, which has confused users of names. The onset of DNA technologies makes it possible to connect different morphs of the same species, resulting in a move to a more natural classification system for fungi, in which a single name for a genus as well as species can now be used. The move to a single nomenclature, as well as the advent of molecular phylogeny and the introduction of polythetic taxonomic approaches has been the main driving force for the re-classification of fungi, including pathogens. Nonetheless, finding the correct name for species remains challenging, but there is a series of steps or considerations that could greatly simplify this process, as outlined here. In addition to various online databases and resources, a list of accurate names is herewith provided of the accepted names of the most common genera and species of phytopathogenic fungi.


Plant Disease ◽  
2019 ◽  
Vol 103 (6) ◽  
pp. 1156-1165 ◽  
Author(s):  
M. A. Bautista-Cruz ◽  
G. Almaguer-Vargas ◽  
S. G. Leyva-Mir ◽  
M. T. Colinas-León ◽  
K. C. Correia ◽  
...  

Persian lime (Citrus latifolia Tan.) is an important and widely cultivated fruit crop in several regions of Mexico. In recent years, severe symptoms of gummosis, stem cankers, and dieback were detected in the Persian lime-producing region in the states of Veracruz and Puebla, Mexico. The aims of this study were to identify the species of Lasiodiplodia associated with these symptoms, determine the distribution of these species, and test their pathogenicity and virulence on Persian lime plants. In 2015, symptomatic samples were collected from 12 commercial Persian lime orchards, and 60 Lasiodiplodia isolates were obtained. Fungal identification of 32 representative isolates was performed using a phylogenetic analysis based on DNA sequence data of the internal transcribed spacer region and part of the translation elongation factor 1-α and β-tubulin genes. Sequence analyses were carried out using the Maximum Likelihood and Bayesian Inference methods. Six Lasiodiplodia species were identified as Lasiodiplodia pseudotheobromae, Lasiodiplodia theobromae, Lasiodiplodia brasiliense, Lasiodiplodia subglobosa, Lasiodiplodia citricola, and Lasiodiplodia iraniensis. All Lasiodiplodia species of this study are reported for the first time in association with Persian lime in Mexico and worldwide. L. pseudotheobromae (46.9% of isolates) was the most frequently isolated species followed by L. theobromae (28.1%) and L. brasiliense (12.5%). Pathogenicity on Persian lime young plants using a mycelial plug inoculation method showed that all identified Lasiodiplodia species were able to cause necrotic lesions and gummosis, but L. subglobosa, L. iraniensis, and L. pseudotheobromae were the most virulent.


2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Quinton Marco Dos Santos ◽  
Annemariè Avenant-Oldewage

Abstract The use of molecular tools in the study of parasite taxonomy and systematics have become a substantial and crucial component of parasitology. Having genetic characterisation at the disposal of researchers has produced mostly useful, and arguably more objective conclusions. However, there are several groups for which limited genetic information is available and, coupled with the lack of standardised protocols, renders molecular study of these groups challenging. The Diplozoidae are fascinating and unique monogeneans parasitizing mainly freshwater cyprinid fishes in Europe, Asia and Africa. This group was studied from a molecular aspect since the turn of the century and as such, limitations and variability concerning the use of these techniques have not been clearly defined. In this review, all literature and molecular information, primarily from online databases such as GenBank, were compiled and scrupulously analysed for the Diplozoidae. This was done to review the information, detect possible pitfalls, and provide a “checkpoint” for future molecular studies of the family. Hindrances detected are the availability of sequence data for only a limited number of species, frequently limited to a single sequence per species, and the heavy reliance on one non-coding ribosomal marker (ITS2 rDNA) which is difficult to align objectively and displays massive divergences between taxa. Challenging species identification and limited understanding of diplozoid species diversity and plasticity are also likely restricting factors, all of which hamper the accurate taxonomic and phylogenetic study of this group. Thus, a more integrated taxonomic approach through the inclusion of additional markers, application of more rigorous morphological assessment, more structured barcoding techniques, alongside thorough capturing of species descriptions including genetypes, genophore vouchers and reference collections in open sources are encouraged. The pitfalls highlighted are not singular to the Diplozoidae, and the study of other groups may benefit from the points raised here as well.


2003 ◽  
Vol 4 (1) ◽  
pp. 4-15 ◽  
Author(s):  
Peter F. Giles ◽  
Darren M. Soanes ◽  
Nicholas J. Talbot

Fungal phytopathogens continue to cause major economic impact, either directly, through crop losses, or due to the costs of fungicide application. Attempts to understand these organisms are hampered by a lack of fungal genome sequence data. A need exists, however, to develop specific bioinformatics tools to collate and analyse the sequence data that currently is available. A web-accessible gene discovery database (http://cogeme.ex.ac.uk/biosynthesis.html) was developed as a demonstration tool for the analysis of metabolic and signal transduction pathways in pathogenic fungi using incomplete gene inventories. Using Bayesian probability to analyse the currently available gene information from pathogenic fungi, we provide evidence that the obligate pathogenBlumeria graminispossesses all amino acid biosynthetic pathways found in free-living fungi, such asSaccharomyces cerevisiae. Phylogenetic analysis was also used to deduce a gene history of succinate-semialdehyde dehydrogenase, an enzyme in the glutamate and lysine biosynthesis pathways. The database provides a tool and methodology to researchers to direct experimentation towards predicting pathway conservation in pathogenic microorganisms.


2017 ◽  
Author(s):  
Harun Mustafa ◽  
André Kahles ◽  
Mikhail Karasikov ◽  
Gunnar Rätsch

AbstractMuch of the DNA and RNA sequencing data available is in the form of high-throughput sequencing (HTS) reads and is currently unindexed by established sequence search databases. Recent succinct data structures for indexing both reference sequences and HTS data, along with associated metadata, have been based on either hashing or graph models, but many of these structures are static in nature, and thus, not well-suited as backends for dynamic databases.We propose a parallel construction method for and novel application of the wavelet trie as a dynamic data structure for compressing and indexing graph metadata. By developing an algorithm for merging wavelet tries, we are able to construct large tries in parallel by merging smaller tries constructed concurrently from batches of data.When compared against general compression algorithms and those developed specifically for graph colors (VARI and Rainbowfish), our method achieves compression ratios superior to gzip and VARI, converging to compression ratios of 6.5% to 2% on data sets constructed from over 600 virus genomes.While marginally worse than compression by bzip2 or Rainbowfish, this structure allows for both fast extension and query. We also found that additionally encoding graph topology metadata improved compression ratios, particularly on data sets consisting of several mutually-exclusive reference genomes.It was also observed that the compression ratio of wavelet tries grew sublinearly with the density of the annotation matrices.This work is a significant step towards implementing a dynamic data structure for indexing large annotated sequence data sets that supports fast query and update operations. At the time of writing, no established standard tool has filled this niche.


2020 ◽  
Author(s):  
Thomas KF Wong ◽  
Subha Kalyaanamoorthy ◽  
Karen Meusemann ◽  
David K Yeates ◽  
Bernhard Misof ◽  
...  

ABSTRACTMultiple sequence alignments (MSAs) play a pivotal role in studies of molecular sequence data, but nobody has developed a minimum reporting standard (MRS) to quantify the completeness of MSAs in terms of completely-specified nucleotides or amino acids. We present an MRS that relies on four simple completeness metrics. The metrics are implemented in AliStat, a program developed to support the MRS. A survey of published MSAs illustrates the benefits and unprecedented transparency offered by the MRS.


Plant Disease ◽  
2014 ◽  
Vol 98 (7) ◽  
pp. 991-991 ◽  
Author(s):  
W. J. Ma ◽  
X. Yang ◽  
X. R. Wang ◽  
Y. S. Zeng ◽  
M. D. Liao ◽  
...  

Hylocereus undatus widely grows in southern China. Some varieties are planted for their fruits, known as dragon fruits or Pitaya, while some varieties for their flowers known as Bawanghua. Fresh or dried flowers of Bawanghua are used as routine Chinese medicinal food. Since 2008, a serious anthracnose disease has led to great losses on Bawanghua flower production farms in the Baiyun district of Guangzhou city in China. Anthracnose symptoms on young stems of Bawanghua are reddish-brown, sunken lesions with pink masses of spores in the center. The lesions expand rapidly in the field or in storage, and may coalesce in the warm and wet environment in spring and summer in Guangzhou. Fewer flowers develop on infected stems than on healthy ones. The fungus overwinters in infected debris in the soil. The disease caused a loss of up to 50% on Bawanghua. Putative pathogenic fungi with whitish-orange colonies were isolated from a small piece of tissue (3 × 3 mm) cut from a lesion margin and cultured on potato dextrose agar in a growth chamber at 25°C, 80% RH. Dark colonies with acervuli bearing pinkish conidial masses formed 14 days later. Single celled conidia were 11 to 18 × 4 to 6 μm. Based on these morphological characteristics, the fungi were identified as Colletotrichum gloeosporioides (Penz.) Penz. & Sacc (2). To confirm this, DNA was extracted from isolate BWH1 and multilocus analyses were completed with DNA sequence data generated from partial ITS region of nrDNA, actin (ACT) and glutamine synthetase (GS) nucleotide sequences by PCR, with C. gloeosporioides specific primers as ITS4 (5′-TCCTCCGCTTATTGATATGC-3′) / CgInt (5′-GGCCTCCCGCCTCCGGGCGG-3′), GS-F (5′-ATGGCCGAGTACATCTGG-3′) / GS-R (5′-GAACCGTCGAAGTTCCAC-3′) and actin-R (5′-ATGTGCAAGGCCGGTTTCGC-3′) / actin-F (5′-TACGAGTCCTTCTGGCCCAT-3′). The sequence alignment results indicated that the obtained partial ITS sequence of 468 bp (GenBank Accession No. KF051997), actin sequence of 282 bp (KF712382), and GS sequence of 1,021 bp (KF719176) are 99%, 96%, and 95% identical to JQ676185.1 for partial ITS, FJ907430 for ACT, and FJ972589 for GS of C. gloeosporioides previously deposited, respectively. For testing its pathogenicity, 20 μl of conidia suspension (1 × 106 conidia/ml) using sterile distilled water (SDW) was inoculated into artificial wounds on six healthy young stems of Bawanghua using sterile fine-syringe needle. Meanwhile, 20 μl of SDW was inoculated on six healthy stems as a control. The inoculated stems were kept at 25°C, about 90% relative humidity. Three independent experiments were carried out. Reddish-brown lesions formed after 10 days, on 100% stems (18 in total) inoculated by C. gloeosporioides, while no lesion formed on any control. The pathogen was successfully re-isolated from the inoculated stem lesions on Bawanghua. Thus, Koch's postulates were fulfilled. Colletotrichum anthracnose has been reported on Pitaya in Japan (3), Malaysia (1) and in Brazil (4). To our knowledge, this is the first report of anthracnose disease caused by C. gloeosporioides on young stems of Bawanghua (H. undatus) in China. References: (1) M. Masyahit et al. Am. J. Appl. Sci. 6:902, 2009. (2) B. C. Sutton. Page 402 in: Colletotrichum Biology, Pathology and Control. J. A. Bailey and M. J. Jeger, eds. CAB International, Wallingford, UK, 1992. (3) S. Taba et al. Jpn. J. Phytopathol. 72:25, 2006. (4) L. M. Takahashi et al. Australas. Plant Dis. Notes 3:96, 2008.


Forests ◽  
2019 ◽  
Vol 10 (6) ◽  
pp. 488 ◽  
Author(s):  
Claudia Pinna ◽  
Benedetto T. Linaldeddu ◽  
Vitale Deiana ◽  
Lucia Maddau ◽  
Lucio Montecchio ◽  
...  

The black-banded oak borer, Coraebus florentinus, is an emerging pest of oak trees in the western Mediterranean region. Larvae of the insect are xylophagous and progressively excavate an annular gallery that interrupts sap flow, resulting in the death of the attacked branches. Until now, limited information has been available regarding the ecological interactions between C. florentinus and the main plant pathogenic fungi involved in the etiology of oak decline. Knowledge of these interactions is important in understanding their impact in natural ecosystems and developing appropriate management strategies. Therefore, in this study, we characterized the fungal communities occurring in the exoskeleton of adults and larvae of C. florentinus and associated with the necrotic wood tissues surrounding the branch galleries of declining oak trees. A total of 29 fungal species were identified based on DNA sequence data and morphological features, of which 14 were from symptomatic woody tissues, six from insect exoskeleton, and nine from both insects and symptomatic wood tissues. The most frequent fungal species, Cryphonectria naterciae (15.9% of isolates), Dothiorella iberica (11.3%), and Diplodia corticola (9.9%), were isolated from both insect and gallery systems. All three species are well-known oak pathogens and are reported here, for the first time, to be associated with C. florentinus. At the same time, 89.6% of the fungal taxa were isolated from one or two sites, highlighting the site-dependence of fungal community assemblages.


2020 ◽  
Vol 2 (2) ◽  
Author(s):  
Thomas K F Wong ◽  
Subha Kalyaanamoorthy ◽  
Karen Meusemann ◽  
David K Yeates ◽  
Bernhard Misof ◽  
...  

Abstract Multiple sequence alignments (MSAs) play a pivotal role in studies of molecular sequence data, but nobody has developed a minimum reporting standard (MRS) to quantify the completeness of MSAs in terms of completely specified nucleotides or amino acids. We present an MRS that relies on four simple completeness metrics. The metrics are implemented in AliStat, a program developed to support the MRS. A survey of published MSAs illustrates the benefits and unprecedented transparency offered by the MRS.


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