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Götesson, Fredrik, 2012. RDNA Barcodesystem. First cycle, G2E. Uppsala: SLU, Dept. of Forest Mycology and Plant Pathology

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Abstract

Frequently found ITS sequences that don’t match any species in GeneBank were further classified with two different barcode regions. This study aims to answer for which phylogenetic placement the unknown species belongs to and if the species belong to a new order. The two barcode regions that were used were 18S small ribosomal subunit and the 28S large ribosomal subunit. The study will as well investigate which of the small and the large ribosomal subunit is appropriate extending ITS in a two-marker barcode system. Problem with the PCR amplifications made it hard to amplify many of the samples. The sequenced sample was able to copy the 28S large ribosomal subunit. The phylogenetic analysis with sequences from all classes showed that the sample belonged to the group of Pezizomycotina fungus. The parsimony phylogenetic tree showed that the sequence was lined
along species from the order of Arthoniales with a bootstrap value on 98. The branch of Arthoniales is
divided into subbranches with species from the order of Dothideomycetes with a low confident value. The H0 sample was collected from needle samplings. Arthoniales is an order of lichens species which is unlikely to be found from needle samples. Most likely the sample belongs to a Dothideomycetes species which is highly similar to Arthoniales species. The 18S small subunit has fewer hypervariable than 28S subunit and by that it is more suitable for higher taxonomic identification. 28S subunit combined with the ITS region is considered to be a good universal barcode.

Main title:RDNA Barcodesystem
Authors:Götesson, Fredrik
Supervisor:Lindahl, Björn and Ihrmark, Katarina
Examiner:Elfstrand, Malin
Series:UNSPECIFIED
Volume/Sequential designation:UNSPECIFIED
Year of Publication:2012
Level and depth descriptor:First cycle, G2E
Student's programme affiliation:NK002 Biotechnology - Bachelor's Programme 180 HEC
Department:(NL, NJ) > Dept. of Forest Mycology and Plant Pathology
(S) > Dept. of Forest Mycology and Plant Pathology
Keywords:RDNA Barcodesystem, ITS sequences, Fungal species
URN:NBN:urn:nbn:se:slu:epsilon-s-1546
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-s-1546
Subjects:Plant genetics and breeding
Language:English
Deposited On:21 Aug 2012 14:34
Metadata Last Modified:21 Aug 2012 14:34

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