Table 1 Selected ‘hidden genome’ elements and their corresponding studies that are referenced by this Review, by species

From: Discovering the hidden function in fungal genomes

Hidden genome element

Species

Referenced studies

Microproteins/sORFs

A. fumigatus, A. nidulans, A. niger, A. oryzae, Ag. bisporus, C. albicans, C. dubliniensis, Cr. gattii, Cr. neoformans, D. hansenii, E. cuniculi, E. intestinalis, Er. cymbalariae, Er. gossypii,, G. zeae, K. africana, Kl. lactis, L. thermotolerans, M. grisea, My. thermophila, N. glabrata, Na. castellii, Na. dairenensis, P. pastoris, P. stipitis, S. cerevisiae, Sc. pombe, T. delbrueckii, Te. phaffii, Th. terrestris, Y. lipolytica, Z. rouxii

16,17,18,19,20,21

Alternatively spliced proteinsd

A. fumigatus, A. nidulans, C. albicans, C. parapsilosis, Cr. neoformans, H. capsulatum, Li. corymbifera, M. oryzae, N. glabrata, Ne. crassa, S. cerevisiae, Sch. commune, Sh. bambusicola

29,31,32,33,34,35,38,39,40,42,43,44,45,46,47

Long non-coding RNAs

A. flavus, A. sydowii, C. albicans, C. auris, C. parapsilosis, C. tropicalis, Co. militaris, Cr. neoformans, F. graminearum, Me. robertsii, N. glabrata, Ne. crassa, No. ceranae, S. cerevisiae, Sc. pombe, P. pastoris, U. maydis

58,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81

Micro/Micro-like RNAs, small non-coding RNAs

A. fumigatus, B. bassiana, Bo. cinerea, C. albicans, Cr. neoformans, F. graminearum, F. oxysporum, F. verticillioides, Me. anisopliae, Mu. circinelloides, Ne. crassa, Ne. tetrasperma, Neo. fischeri, Pe. marneffei, Pu. graminis, Py. tritici-repentis, Scl. sclerotiorum, So. macrospora, Sp. reilianum, Tr. reesei, Tri. rubrum, U. maydis, V. dahliae, Va. mali

58,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97a

Circular RNAs

As. apis, Ga. lucidum, No. ceranae, M. oryzae, S. cerevisiae, Sc. pombe, Tri. rubrum

98,99,100,101,102,103

Transposable elements

A. fumigatus, Am. brunnescens, Am. inopinata, Am. muscaria, Am. polypyramis, Am. thiersii, Bo. cinerea, C. albicans, Cr. deneoformans, Cr. neoformans, F. graminearum, F. oxysporum, La. bicolor, M. oryzae, Mi. osmundae, N. glabrata, Ne. crassa, Ph. carnosa, Ph. chrysosporium, Pl. ostreatus, Ps. antarctica, Ps. hubeiensis, Pu. graminis, Pu. striiformis, S. cerevisiae, Sc. pombe, Se. lacrymans, Vo. volvacea, Zy. tritici

127,128,129b,130,131,132,133,134,135,136

Starshipse

A. felis, A. flavus, A. fumigatus, A. niger, A. oryzae, A. sojae, Al. alternata, Al. gaisen, Al. solani, Al. tenuissima, Ar. ostoyae, Bot. dothidea, Bi. sorokiniana, Cl. psammophila, F. culmorum, F. fujikuroi, F. oxysporum, Fo. nubica, Fo. pedrosoi, Le. lupina, Mo. importuna, Ma. phaseolina, O. oligospora, Pa. lecythidis, Pa. variotii, Par. nodorum, Pe. fuscoglaucum, Pe. roqueforti, Po. anserina, Po. comata, Po. pauciseta, Py. tritici-repentis, Tr. asperellum, Ta. marneffei

128,137–143,144c

  1. Abbreviatious used for genera: A., Aspergillus; Ag., Agaricus; Al., Alternaria; Am., Amanita; Ar., Armillaria; As., Ascosphaera; B., Beauveria; Bi., Bipolaris; Bo., Botrytis; Bot., Botryosphaeria; C., Candida; Cl., Cladophialophora; Co., Cordyceps; Cr., Cryptococcus; D., Debaryomyces; E., Encephalitozoon; Er., Eremothecium; F., Fusarium; Fo., Fonsecaea; H., Histoplasma; G., Gibberella; Ga., Ganoderma; K., Kazachstania; Kl., Kluyveromyces; L., Lachancea; La., Laccaria; Le., Letharia; Li., Lichtheimia; M., Magnaporthe; Ma., Macrophomina; Me., Metarhizium; Mi., Mixia; Mo., Morchella; Mu., Mucor; My., Myceliophthora; N., Nakaseomyces; Na., Naumovozyma; Ne., Neurospora; Neo., Neosartorya; No., Nosema; O., Orbilia; P., Pichia; Pa., Paecilomyces; Par., Parastagonospora; Pe., Penicillium; Ph., Phanerochaete; Pl., Pleurotus; Po., Podospora; Ps., Pseudozyma; Pu., Puccinia; Py., Pyrenophora; S., Saccharomyces; Sc., Schizosaccharomyces; Sch., Schizophyllum; Scl., Sclerotinia; Se., Serpula; Sh., Shiraia; So., Sordaria; Sp., Sporisorium; T., Torulaspora; Ta., Talaromyces; Te., Tetrapisispora; Th., Thielavia; Tr., Trichoderma; Tri., Trichophyton; U., Ustilago; V., Verticillium; Va., Valsa; Vo., Volvariella; Y., Yarrowia; Z., Zygosaccharomyces; Zy., Zymoseptoria.
  2. aThe comprehensive set of species in ref. 97 is not listed due to the contentious presence of bona fide miRNA/milRNA/sRNAs (or lack thereof) in some species.
  3. bNot all species could be listed here as ref. 129 included 625 publicly available genomic assemblies, including 27 Aspergillus isolates, 30 Candida isolates, 19 Cryptococcus isolates, 26 Fusarium isolates, 15 Penicillium isolates, 25 Saccharomyces isolates, 20 Trichophyton isolates, and more.
  4. cComputational annotations of Starships from ref. 144 have been left out due to space constraints, encompassing 2899 genomes from 1649 fungal species.
  5. dAlternative splicing has already been described in a number of fungal taxa that would exceed the space available in this table (see refs. 28,30,41). This list only includes those species with well characterized instances of alternatively spliced proteins that are specifically discussed in this Review.
  6. eThe existence of bona fide Starships in some listed species remains putative. This list of species that contain characterized Starships is not necessarily comprehensive, even amongst the literature cited in this Review.
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