IMA genome-F18 The re-identification of Penicillium genomes available in NCBI and draft genomes for Penicillium species from dry cured meat, Penicillium biforme, P. brevicompactum, P. solitum, and P. cvjetkovicii, Pewenomyces kutranfy, Pew. lalenivora, Pew. tapulicola, Pew. kalosus, Teratosphaeria carnegiei, and Trichoderma atroviride SC1
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IMA genome-F18 The re-identification of Penicillium genomes available in NCBI and draft genomes for Penicillium species from dry cured meat, Penicillium biforme, P. brevicompactum, P. solitum, and P. cvjetkovicii, Pewenomyces kutranfy, Pew. lalenivora, Pew. tapulicola, Pew. kalosus, Teratosphaeria carnegiei, and Trichoderma atroviride SC1
Visagie, Cobus M.; Magista, Donato; Ferrara, Massimo; Balocchi, Felipe; Duong, Tuan A.; Eichmeier, Ales; Gramaje, David; Aylward, Janneke; Baker, Scott E.; Barnes, Irene; Calhoun, Sara; De Angelis, Maria; Frisvad, Jens C.; Hayes, Richard D.; Houbraken, Jos; Grigoriev, Igor V.; LaButti, Kurt; Leal, Catarina; Lipzen, Anna; Ng, Vivian; Pangilinan, Jasmyn; Pecenka, Jakub; Perrone, Giancarlo; Piso, Anja; Savage, Emily; Spetik, Milan; Wingfield, Michael J.; Zhang, Yu; Wingfield, Brenda D.
Sequencing fungal genomes has now become very common and the list of genomes in this manuscript reflects this. Particularly relevant is that the first announcement is a re-identification of Penicillium genomes available on NCBI. The fact that more than 100 of these genomes have been deposited without the correct species names speak volumes to the fact that we must continue training fungal taxonomists and the importance of the International Mycological Association (after which this journal is named). When we started the genome series in 2013, one of the essential aspects was the need to have a phylogenetic tree as part of the manuscript. This came about as the result of a discussion with colleagues in NCBI who were trying to deal with the very many incorrectly identified bacterial genomes (at the time) which had been submitted to NCBI. We are now in the same position with fungal genomes. Sequencing a fungal genome is all too easy but providing a correct species name and ensuring that the fungus has in fact been correctly identified seems to be more difficult. We know that there are thousands of fungi which have not yet been described. The availability of sequence data has made identification of fungi easier but also serves to highlight the need to have a fungal taxonomist in the project to make sure that mistakes are not made.
Description:
SUPPLEMENTARY INFORMATION : Additional file 1. Table 1. Summary of genomes analysed during this
study that were correctly identified.
AVAILABILITY OF DATA AND MATERIAL : Genome data for the Penicillium genomes are publicly available in the NCBI
genome database (https:// www. ncbi. nlm. nih. gov/ datas ets/ genome). The
datasets generated from Trichoderma atroviride during the current study are
available in the NCBI repository, https:// www. ncbi. nlm. nih. gov/ biopr oject/
923860. For the Penicillium species from dry cured meat the genome assembly
and annotations are available from JGI Fungal genome portal MycoCosm
under JGI Projects: 1,289,827 (ITEM 15300), 1,289,819 (ITEM 18316), 1,289,903
(ITEM 18327), and have been deposited to GenBank under BioProjects:
PRJNA970850 (ITEM 15300), PRJNA971651 (ITEM 18316), PRJNA970851
(ITEM 18327). Genome assembly and annotations are available from JGI
Fungal genome portal MycoCosm under JGI Project Id 1,289,847 and has
been deposited to GenBank under BioProject n.PRJNA971650 (BioSample n.
SAMN35051277; Project Accession n. SRP442271). The genomic sequences of
T. carnegiei have been deposited at DDJ/EMBL/GenBank under the accession
JANYMD000000000. This paper describes the first version. The genomes of the
Pewenomyces species have been deposited in the NCBI genome database.