Highlights of DNA Barcoding in identification of salient microorganisms like fungi

Dulla, E.L.; Kathera, Chandrasekhar; Gurijala, H.K.; Mallakuntla, T.R.; Pandiarajan, S.; Prasad, Vikram; Mopati, R.D.; Jasti, Pramodakumari

doi:10.1016/j.mycmed.2016.05.006

Cited by 7 publications

(3 citation statements)

References 54 publications

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“…Other reasons for exclusion include low nucleotide variation and a complete lack of mitochondria in some fungal linages (Wickes and Wiederhold 2018 ). Instead, the ITS region and the D1/D2 region of the large subunit ( LSU ) rDNA, both belonging to the nuclear ribosomal RNA genes, are the most widely used in all fungi from diverse environments (Dulla et al 2016 ; Schoch et al 2012 ; Scorzetti et al 2002 ). These two loci can be easily amplified using relatively universal primers, and have the largest amount of reference sequence data for fungi (Blackwell 2011 ; Suhr and Hallen-Adams 2015 ).…”

Section: How To Get a Barcodementioning

confidence: 99%

Life barcoded by DNA barcodes

Guo

Yuan

Tao

et al. 2022

Conservation Genet Resour

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The modern concept of DNA-based barcoding for cataloguing biodiversity was proposed in 2003 by first adopting an approximately 600 bp fragment of the mitochondrial COI gene to compare via nucleotide alignments with known sequences from specimens previously identified by taxonomists. Other standardized regions meeting barcoding criteria then are also evolving as DNA barcodes for fast, reliable and inexpensive assessment of species composition across all forms of life, including animals, plants, fungi, bacteria and other microorganisms. Consequently, global DNA barcoding campaigns have resulted in the formation of many online workbenches and databases, such as BOLD system, as barcode references, and facilitated the development of mini-barcodes and metabarcoding strategies as important extensions of barcode techniques. Here we intend to give an overview of the characteristics and features of these barcode markers and major reference libraries existing for barcoding the planet’s life, as well as to address the limitations and opportunities of DNA barcodes to an increasingly broader community of science and society.

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Section: How To Get a Barcodementioning

confidence: 99%

Life barcoded by DNA barcodes

Guo

Yuan

Tao

et al. 2022

Conservation Genet Resour

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“…Koch and Botha (1998) [ 21 ] and Frisvad et al (2008) [ 22 ] tested fatty acids. Many serology-based detection methods use ELISA for the detection of antibodies produced against Mucorales infection [ 23 , 24 ]. To date, the most accurate and successful method has been DNA barcoding which was identified in the level of species in the most neglected taxa.…”

Section: Introductionmentioning

confidence: 99%

Mucormycosis: A comparative update between conventional and molecular diagnosis strategies

Mudgal

Rao

Pai

2022

CMM

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Mucormycosis is an opportunistic, aggressive, and angioinvasive fungal infection associated with a high mortality rate as it disseminates and infects the whole body if not treated early. Most conventional diagnostic methods require time and may also generate false-negative reports due to the several lacunae associated. On the other hand, molecular methods are rapid, reliable, and can be applied to different biological samples, such as fresh tissue, formalin-fixed paraffin-embedded blocks, serum, and urine. Mucorales are angio-invasive, and many studies have found the circulating fungal DNA (a non-invasive form of DNA) in the blood and urine of the patient. In addition, with the increase in the usage of steroid drugs in this COVID scenario, the rate of mucormycosis infection has taken a sudden rise. In light of this situation, there is an imperative need to diagnose these infections at the earliest. Studies on the diagnosis of mucormycosis were explored and retrieved from Pubmed and Google Scholar. Histopathology and culture reports of patients diagnosed with mucormycosis in 2019-2020 were searched and retrieved from the hospital database (ethically permitted) to find the rate of concordance between the techniques. In this review study, different tested molecular techniques are encapsulated, and various primers are documented that are used to identify and classify different Mucoromycota fungi. An attempt has been made to compare the feasibility, accuracy adaptability, and time frame used among molecular and conventional methods for the diagnosis of mucormycosis.

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“…The use of molecular techniques with morphological traits offers a better fungal identification (Bernreiter, 2017, Dayarathne et al, 2020. Moreover, molecular identification is a standardized method that is fast and accurate to specieslevel identification based on gene phylogenies (Das et al, 2015;Dulla et al, 2016). Subsequently, the ITS operon has been identified by many studies as a potential primary DNA barcode marker for most fungi due to its ease in amplification and availability of a large number of Genbank sequences (Schoch et al, 2012;Badotti et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

Molecular and morphological identification of fungi causing canker and dieback diseases on Vangueria infausta (Burch) subsp. rotundata (Robyns) and Berchemia discolor (Klotzsch) Hemsl in lower Eastern Kenya

Susan¹,

Njuguna²,

Steven³

et al. 2022

Afr. J. Biotechnol.

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Drought-tolerant multipurpose fruit trees Vangueria infausta (Burch) subsp. rotundata (Robyns) and Berchemia discolor (Klotzsch) Hemsl are native to Kenya. These fruit tree species are suitable for dryland agroforestry and support local communities with food, medicine, fodder and other necessities. Reports by the local communities indicate that the two species suffer from diebacks and cankers. The aim of this study was to identify the fungi associated with V. rotundata and B. discolor and determine the cause of diebacks and cankers symptoms observed. Samples were collected from two sites (Tiva and Ikanga) in Kitui County and one site (Mkange) in Makueni County. Fungal isolations were carried out by incubating the samples on malt extract agar media supplemented with Streptomycin Sulphate. Morphological identification grouped the fungal isolates into 7 clusters. Botryosphaeriaceae and Nectriaceae had the highest frequency of occurrence (32.7 and 30.5%) respectively. DNA was extracted from pure fungal cultures, amplified and sequenced. Phylogenetic analysis of DNA sequences clustered the fungal isolates into seven families; Botryosphaeriaceae, Sporocadaceae, Nectriaceae, Trichosphaeriaceae, Pleosporaceae, Diaporthaceae and Glomerellaceae. Using Koch's postulates, this study showed that isolates of Botryosphaeriaceae within the genera Lasiodiplodia, Alanphillipsia and Dothiorella are pathogenic to B. discolor and other indigenous agroforestry species due to their ability to cause similar symptoms to those observed in the field. This is the first study to investigate the fungal flora linked to V. rotundata and B. discolor dieback and canker diseases.

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Highlights of DNA Barcoding in identification of salient microorganisms like fungi

Cited by 7 publications

References 54 publications

Life barcoded by DNA barcodes

Life barcoded by DNA barcodes

Mucormycosis: A comparative update between conventional and molecular diagnosis strategies

Molecular and morphological identification of fungi causing canker and dieback diseases on Vangueria infausta (Burch) subsp. rotundata (Robyns) and Berchemia discolor (Klotzsch) Hemsl in lower Eastern Kenya

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