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DNA barcoding survey of Trichoderma diversity in soil and litter of the Colombian lowland Amazonian rainforest reveals Trichoderma strigosellum sp. nov. and other species.

López-Quintero CA, Atanasova L, Franco-Molano AE, Gams W, Komon-Zelazowska M, Theelen B, Müller WH, Boekhout T, Druzhinina I - Antonie Van Leeuwenhoek (2013)

Bottom Line: DNA barcoding of 107 strains based on the internal transcribed spacers 1 and 2 (ITS1 and 2) of the ribosomal RNA gene cluster and the partial sequence of the translation elongation factor 1 alpha (tef1) gene revealed that the diversity of Trichoderma was dominated (71 %) by three common cosmopolitan species, namely Trichoderma harzianum sensu lato (41 %), Trichoderma spirale (17 %) and Trichoderma koningiopsis (13 %).Multigene phylogenetic analysis and phenotype profiling of four strains with an ITS1 and 2 phylotype similar to Trichoderma strigosum revealed a new sister species of the latter that is described here as Trichoderma strigosellum sp. nov.Sequence similarity searches revealed that this species also occurs in soils of Malaysia and Cameroon, suggesting a pantropical distribution.

View Article: PubMed Central - PubMed

Affiliation: CBS Fungal Biodiversity Centre (CBS-KNAW), Utrecht, The Netherlands.

ABSTRACT
The diversity of Trichoderma (Hypocreales, Ascomycota) colonizing leaf litter as well as the rhizosphere of Garcinia macrophylla (Clusiaceae) was investigated in primary and secondary rain forests in Colombian Amazonia. DNA barcoding of 107 strains based on the internal transcribed spacers 1 and 2 (ITS1 and 2) of the ribosomal RNA gene cluster and the partial sequence of the translation elongation factor 1 alpha (tef1) gene revealed that the diversity of Trichoderma was dominated (71 %) by three common cosmopolitan species, namely Trichoderma harzianum sensu lato (41 %), Trichoderma spirale (17 %) and Trichoderma koningiopsis (13 %). Four ITS 1 and 2 phylotypes (13 strains) could not be identified with certainty. Multigene phylogenetic analysis and phenotype profiling of four strains with an ITS1 and 2 phylotype similar to Trichoderma strigosum revealed a new sister species of the latter that is described here as Trichoderma strigosellum sp. nov. Sequence similarity searches revealed that this species also occurs in soils of Malaysia and Cameroon, suggesting a pantropical distribution.

Show MeSH
ITS2 based oligonucleotide barcodes for T. strigosum and T. strigosellum sp. nov. GSH4 corresponds to the genus-specific hallmark as indicated in Druzhinina et al. 2005
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Fig5: ITS2 based oligonucleotide barcodes for T. strigosum and T. strigosellum sp. nov. GSH4 corresponds to the genus-specific hallmark as indicated in Druzhinina et al. 2005

Mentions: We compared ITS1 and 2 phylotypes of T. strigosellum sp. nov. and T. strigosum and found that five out of eight available sequences for T. strigosellum sp. nov. had a ‘species-specific’ oligonucleotide barcode in the 5′ area of the ITS2 locus that immediately follows the genus-specific hallmark four (Druzhinina et al. 2005). Compared to T. strigosum this hallmark contained one indel (an extra C), one T → C transition and one G → T transversion (Fig. 5). However, three strains of T. strigosellum sp. nov. displayed a phylotype identical to that of T. strigosum (Fig. 5). Thus the ITS barcode alone cannot reliably identify both species, but may attribute them to the T. strigosum clade. The two species are reliably differentiated in phylogenetic analyses of the tef1 large intron.Fig. 5


DNA barcoding survey of Trichoderma diversity in soil and litter of the Colombian lowland Amazonian rainforest reveals Trichoderma strigosellum sp. nov. and other species.

López-Quintero CA, Atanasova L, Franco-Molano AE, Gams W, Komon-Zelazowska M, Theelen B, Müller WH, Boekhout T, Druzhinina I - Antonie Van Leeuwenhoek (2013)

ITS2 based oligonucleotide barcodes for T. strigosum and T. strigosellum sp. nov. GSH4 corresponds to the genus-specific hallmark as indicated in Druzhinina et al. 2005
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3824238&req=5

Fig5: ITS2 based oligonucleotide barcodes for T. strigosum and T. strigosellum sp. nov. GSH4 corresponds to the genus-specific hallmark as indicated in Druzhinina et al. 2005
Mentions: We compared ITS1 and 2 phylotypes of T. strigosellum sp. nov. and T. strigosum and found that five out of eight available sequences for T. strigosellum sp. nov. had a ‘species-specific’ oligonucleotide barcode in the 5′ area of the ITS2 locus that immediately follows the genus-specific hallmark four (Druzhinina et al. 2005). Compared to T. strigosum this hallmark contained one indel (an extra C), one T → C transition and one G → T transversion (Fig. 5). However, three strains of T. strigosellum sp. nov. displayed a phylotype identical to that of T. strigosum (Fig. 5). Thus the ITS barcode alone cannot reliably identify both species, but may attribute them to the T. strigosum clade. The two species are reliably differentiated in phylogenetic analyses of the tef1 large intron.Fig. 5

Bottom Line: DNA barcoding of 107 strains based on the internal transcribed spacers 1 and 2 (ITS1 and 2) of the ribosomal RNA gene cluster and the partial sequence of the translation elongation factor 1 alpha (tef1) gene revealed that the diversity of Trichoderma was dominated (71 %) by three common cosmopolitan species, namely Trichoderma harzianum sensu lato (41 %), Trichoderma spirale (17 %) and Trichoderma koningiopsis (13 %).Multigene phylogenetic analysis and phenotype profiling of four strains with an ITS1 and 2 phylotype similar to Trichoderma strigosum revealed a new sister species of the latter that is described here as Trichoderma strigosellum sp. nov.Sequence similarity searches revealed that this species also occurs in soils of Malaysia and Cameroon, suggesting a pantropical distribution.

View Article: PubMed Central - PubMed

Affiliation: CBS Fungal Biodiversity Centre (CBS-KNAW), Utrecht, The Netherlands.

ABSTRACT
The diversity of Trichoderma (Hypocreales, Ascomycota) colonizing leaf litter as well as the rhizosphere of Garcinia macrophylla (Clusiaceae) was investigated in primary and secondary rain forests in Colombian Amazonia. DNA barcoding of 107 strains based on the internal transcribed spacers 1 and 2 (ITS1 and 2) of the ribosomal RNA gene cluster and the partial sequence of the translation elongation factor 1 alpha (tef1) gene revealed that the diversity of Trichoderma was dominated (71 %) by three common cosmopolitan species, namely Trichoderma harzianum sensu lato (41 %), Trichoderma spirale (17 %) and Trichoderma koningiopsis (13 %). Four ITS 1 and 2 phylotypes (13 strains) could not be identified with certainty. Multigene phylogenetic analysis and phenotype profiling of four strains with an ITS1 and 2 phylotype similar to Trichoderma strigosum revealed a new sister species of the latter that is described here as Trichoderma strigosellum sp. nov. Sequence similarity searches revealed that this species also occurs in soils of Malaysia and Cameroon, suggesting a pantropical distribution.

Show MeSH