TY - JOUR
T1 - FUSARIUM-ID v.3.0
T2 - An Updated, Downloadable Resource for Fusarium Species Identification
AU - Torres-Cruz, Terry J.
AU - Whitaker, Briana K.
AU - Proctor, Robert H.
AU - Broders, Kirk
AU - Laraba, Imane
AU - Kim, Hye Seon
AU - Brown, Daren W.
AU - O’Donnell, Kerry
AU - Estrada-Rodríguez, Tania L.
AU - Lee, Yong Hwan
AU - Cheong, Kyeongchae
AU - Wallace, Emma C.
AU - McGee, Chyanna T.
AU - Kang, Seogchan
AU - Geiser, David M.
N1 - Publisher Copyright:
© 2022 The American Phytopathological Society
PY - 2022/6
Y1 - 2022/6
N2 - Species within Fusarium are of global agricultural, medical, and food/ feed safety concern and have been extensively characterized. However, accurate identification of species is challenging and usually requires DNA sequence data. FUSARIUM-ID (http://isolate.fusariumdb.org/blast. php) is a publicly available database designed to support the identification of Fusarium species using sequences of multiple phylogenetically informative loci, especially the highly informative ∼680-bp 59 portion of the translation elongation factor 1-alpha (TEF1) gene that has been adopted as the primary barcoding locus in the genus. However, FUSARIUM-ID v. 1.0 and 2.0 had several limitations, including inconsistent metadata annotation for the archived sequences and poor representation of some species complexes and marker loci. Here, we present FUSARIUM-ID v.3.0, which provides the following improvements: (i) additional and updated annotation of metadata for isolates associated with each sequence, (ii) expanded taxon representation in the TEF1 sequence database, (iii) availability of the sequence database as a downloadable file to enable local BLAST queries, and (iv) a tutorial file for users to perform local BLAST searches using either freely available software, such as SequenceServer, BLAST+ executable in the command line, and Galaxy, or the proprietary Geneious software. FUSARIUM-ID will be updated on a regular basis by archiving sequences of TEF1 and other loci from newly identified species and greater in-depth sampling of currently recognized species.
AB - Species within Fusarium are of global agricultural, medical, and food/ feed safety concern and have been extensively characterized. However, accurate identification of species is challenging and usually requires DNA sequence data. FUSARIUM-ID (http://isolate.fusariumdb.org/blast. php) is a publicly available database designed to support the identification of Fusarium species using sequences of multiple phylogenetically informative loci, especially the highly informative ∼680-bp 59 portion of the translation elongation factor 1-alpha (TEF1) gene that has been adopted as the primary barcoding locus in the genus. However, FUSARIUM-ID v. 1.0 and 2.0 had several limitations, including inconsistent metadata annotation for the archived sequences and poor representation of some species complexes and marker loci. Here, we present FUSARIUM-ID v.3.0, which provides the following improvements: (i) additional and updated annotation of metadata for isolates associated with each sequence, (ii) expanded taxon representation in the TEF1 sequence database, (iii) availability of the sequence database as a downloadable file to enable local BLAST queries, and (iv) a tutorial file for users to perform local BLAST searches using either freely available software, such as SequenceServer, BLAST+ executable in the command line, and Galaxy, or the proprietary Geneious software. FUSARIUM-ID will be updated on a regular basis by archiving sequences of TEF1 and other loci from newly identified species and greater in-depth sampling of currently recognized species.
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U2 - 10.1094/PDIS-09-21-2105-SR
DO - 10.1094/PDIS-09-21-2105-SR
M3 - Article
C2 - 34879732
AN - SCOPUS:85131271003
SN - 0191-2917
VL - 106
SP - 1610
EP - 1616
JO - Plant disease
JF - Plant disease
IS - 6
ER -