Dataset Information

?-tubulin paralogue tubC is frequently misidentified as the benA gene in Aspergillus section Nigri taxonomy: primer specificity testing and taxonomic consequences.

ABSTRACT: ?-tubulin (benA, tub-2) and calmodulin (caM) are crucial genes in the taxonomy of Aspergillus section Nigri. Widely used ?-tubulin primers are not specific for the benA gene for some taxa and preferentially amplify the tubC paralogue. Sequences of the tubC paralogue are widely combined with benA sequences in recent taxonomical works as well as other works, resulting in incongruent trees. In this study we newly provide benA sequences for several ex-type strains, which were characterised using the tubC gene only. We designed a highly specific forward primer to benA designated Ben2f for use in Aspergillus section Nigri, and tested specificity of numerous primer combinations to ?-tubulin paralogs. The primer pairs with the highest specificity to the benA gene and functional across species in section Nigri includes Ben2f/Bt2b, Ben2f/T22 and T10/T22. We also provide tools based on codon usage bias analysis that reliably distinguish both paralogues. Exon/intron arrangement is the next distinctive characteristic, although this tool is not valid outside section Nigri. The species identity of taxa from the A. aculeatus clade used in previous molecular studies was revised using combined molecular data (ITS, benA, caM). These data together with two different PCR-fingerprinting methods indicated that A. japonicus should be treated as a synonym of A. violaceofuscus. Similarly, A. fijiensis is reduced to synonymy with A. brunneoviolaceus.

SUBMITTER: Hubka V

PROVIDER: S-EPMC3589786 | biostudies-literature | 2012 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

β-tubulin paralogue tubC is frequently misidentified as the benA gene in Aspergillus section Nigri taxonomy: primer specificity testing and taxonomic consequences.

Hubka V V Kolarik M M

Persoonia 20121009

β-tubulin (benA, tub-2) and calmodulin (caM) are crucial genes in the taxonomy of Aspergillus section Nigri. Widely used β-tubulin primers are not specific for the benA gene for some taxa and preferentially amplify the tubC paralogue. Sequences of the tubC paralogue are widely combined with benA sequences in recent taxonomical works as well as other works, resulting in incongruent trees. In this study we newly provide benA sequences for several ex-type strains, which were characterised using the ...[more]

PMID: 23606761

Similar Datasets

Project description:Four new species, Aspergillus eucalypticola, A. neoniger, A. fijiensis and A. indologenus are described and illustrated. Aspergillus eucalypticola was isolated from Eucalyptus leaf from Australia, and is related to A. tubingensis and A. costaricaensis, but could clearly be distinguished from them based on either ?-tubulin or calmodulin sequence data. Aspergillus eucalypticola produced pyranonigrin A, funalenone, aurasperone B and other naphtho-?-pyrones. Aspergillus neoniger is also a biseriate species isolated from desert sand in Namibia, and mangrove water in Venezuela, which produces aurasperone B and pyranonigrin A. Aspergillus fijiensis is a uniseriate species related to A. aculeatinus, and was isolated from soil in Fiji, and from Lactuca sativa in Indonesia. This species is able to grow at 37 °C, and produces asperparalines and okaramins. Aspergillus indologenus was isolated from soil, India. This species also belongs to the uniseriate group of black aspergilli, and was found to be related to, but clearly distinguishable from A. uvarum based on ?-tubulin, calmodulin and ITS sequence data. Aspergillus indologenus produced the insecticidal compounds okaramins A, B, H, and two types of indol-alkaloids which have not been structure elucidated. Two other species, A. violaceofuscus and A. acidus, are revalidated based on molecular and extrolite data. Aspergillus violaceofuscus was found to be related to A. japonicus, and produced some of the same interesting indol-alkaloids as A. indologenus, and also produced several families of partially characterised extrolites that were also found in A. heteromorphus. Aspergillus acidus (previously known as A. foetidus var. pallidus and A. foetidus var. acidus) is also a valid species, while A. foetidus is a synonym of A. niger based on molecular and physiological data. Two other species described previously, A. coreanus and A. lacticoffeatus, were found to be colour mutants of A. acidus and A. niger, respectively. Methods which could be used to distinguish the two closely related and economically important species A. niger and A. awamori are also detailed. Although these species differ in their occurrence and several physiological means (elastase activities, abilities to utilise 2-deoxy-D-glucose as sole carbon source), our data indicate that only molecular approaches including sequence analysis of calmodulin or ?-tubulin genes, AFLP analysis, UP-PCR analysis or mtDNA RFLP analysis can be used reliably to distinguish these sibling species. Aspergillus section Nigri now includes 26 taxa.

Project description:Species of Penicillium section Citrina have a worldwide distribution and occur commonly in soils. The section is here delimited using a combination of phenotypic characters and sequences of the nuclear ribosomal RNA gene operon, including the internal transcribed spacer regions ITS1 and ITS2, the 5.8S nrDNA (ITS) and partial RPB2 sequences. Species assigned to section Citrina share the production of symmetrically biverticillate conidiophores, flask shaped phialides (7.0-9.0 μm long) and relatively small conidia (2.0-3.0 μm diam). Some species can produce greyish-brown coloured cleistothecia containing flanged ascospores. In the present study, more than 250 isolates presumably belonging to section Citrina were examined using a combined analysis of phenotypic and physiological characters, extrolite profiles and ITS, β-tubulin and/or calmodulin sequences. Section Citrina includes 39 species, and 17 of those are described here as new. The most important phenotypic characters for distinguishing species are growth rates and colony reverse colours on the agar media CYA, MEA and YES; shape, size and ornamentation of conidia and the production of sclerotia or cleistothecia. Temperature-growth profiles were made for all examined species and are a valuable character characters for species identification. Species centered around P. citrinum generally have a higher maximum growth temperature (33-36 °C) than species related to P. westlingii (27-33 °C). Extrolite patterns and partial calmodulin and β-tubulin sequences can be used for sequence based identification and resolved all species. In contrast, ITS sequences were less variable and only 55 % of the species could be unambiguously identified with this locus.Taxonomic noveltiesPenicillium argentinense Houbraken, Frisvad & Samson, P. atrofulvum Houbraken, Frisvad & Samson, P. aurantiacobrunneum Houbraken, Frisvad & Samson, P. cairnsense Houbraken, Frisvad & Samson, P. christenseniae Houbraken, Frisvad & Samson, P. copticola Houbraken, Frisvad & Samson, P. cosmopolitanum Houbraken, Frisvad & Samson, P. neomiczynskii Cole, Houbraken, Frisvad & Samson, P. nothofagi Houbraken, Frisvad & Samson, P. pancosmium Houbraken, Frisvad & Samson, P. pasqualense Houbraken, Frisvad & Samson, P. quebecense Seifert, Houbraken, Frisvad & Samson, P. raphiae Houbraken, Frisvad & Samson, P. terrigenum Seifert, Houbraken, Frisvad & Samson, P. ubiquetum Houbraken, Frisvad & Samson, P. vancouverense Houbraken, Frisvad & Samson, P. wellingtonense Cole, Houbraken, Frisvad & Samson.

Dataset Information

?-tubulin paralogue tubC is frequently misidentified as the benA gene in Aspergillus section Nigri taxonomy: primer specificity testing and taxonomic consequences.

Publications

β-tubulin paralogue tubC is frequently misidentified as the benA gene in Aspergillus section Nigri taxonomy: primer specificity testing and taxonomic consequences.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets