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Niazi, Adnan, 2010. Whole genome assembly, annotation and bioinformatics analysis of Bacillus amyloliquefaciens strain UCMB5113". Second cycle, A2E. Uppsala: SLU, Dept. of Animal Breeding and Genetics

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Abstract

Bacillus amyloliquefaciens strain UCMB5113 is a Gram negative rhizo-bacterium, that produces antimicrobial compounds and induce plant basal defense with unknown genetic mechanism that suppress soil-borne plants and pathogens. Paired-end reads of length 75 bp with insert size of ~230 bp were sequenced from the genome of UCMB5113 by Illumina multiplex technology. Reference-guided assembly of the paired-end reads was performed using Bacillus amyloliquefaciens FZB42 as reference sequence which was found to be closely related to UCMB5113 strain. A draft of UCMB5113 genome obtained after mapping the reads with reference sequence containing 4,169 genes excluding 90 tRNA and 29 rRNA genes. The draft genome of UCMB5113 harbors cluster of genes, which were found in B. amyloliquefaciens FZB42 and involved in synthesis of secondary metabolites like surfactin, fengycin, bacillomycinD, bacillibactin, and bacilysin, by pathways not involving ribosomes. Initial analysis reveals that UCMB5113 genome lacks an operon NRS involved in synthesis of putative secondary metabolite. The determination of draft genome sequence of UCMB5113 provided very basic analysis of set of genes involved in plant bacterium interaction and plant growth and protection. Further analysis is required to understand the genetic mechanism of interaction and protection mediated by CMB5113.

Main title:Whole genome assembly, annotation and bioinformatics analysis of Bacillus amyloliquefaciens strain UCMB5113"
Authors:Niazi, Adnan
Supervisor:Bongcam-Rudloff, Erik and Fuxelius, Hans Henrik and Meijer, Johan
Examiner:Andersson, Göran
Series:Examensarbete / SLU, Institutionen för husdjursgenetik
Volume/Sequential designation:335
Year of Publication:2010
Level and depth descriptor:Second cycle, A2E
Student's programme affiliation:Other
Department:(VH) > Dept. of Animal Breeding and Genetics
Keywords:genome assembly, Bacillus amyloliquefaciens UCMB5113, plant growth and protection, bacterial biocontrol, antimicrobial genes
URN:NBN:urn:nbn:se:slu:epsilon-s-1694
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-s-1694
Subjects:Plant genetics and breeding
Language:English
Deposited On:02 Oct 2012 08:04
Metadata Last Modified:16 Jul 2013 23:15

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