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Manzoor, Shahid, 2010. Bioinformatics assembly and analysis and annotation of the Bacillus amyloliquefaciens strain 5036 genome. Second cycle, A2E. Uppsala: SLU, Dept. of Animal Breeding and Genetics

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Abstract

Plants are essential for both human and animal life, several agricultural practices have been adopted or are being developed in order to improve crop production by preventing or mitigating effects of biotic and abiotic stresses faced by plants. Biocontrol is a promising technique being cost effective, environment friendly and able to target pathogens difficult to control through traditional means. Bacteria that are associated with plant roots and exert beneficial effects on plant development are known as plant growth-promoting rhizobacteria (PGPR). Compared to plant growth-promoting Pseudomonas rhizobacteria, Bacillus species are advantageous due to their ability to form spores, which enable survival at high temperature, extreme pH, drought or mechanical and chemical stress and thus ideal for use as commercial biocontrol products. A PGPR may serve both as a biofertilizer and as a biological antagonist to pathogens. PGPR can be used for seed treatment supporting colonization in the rhizosphere on emerging roots. The mechanisms of protection may vary among different bacteria and include alteration of plant cell walls, production of biofilm on plant roots that prevent infection, competition for nutrients and space for growth and production of antibiotics and other damaging compounds to the pathogens. The Bacillus amyloliquefaciens strain UCMB-5036 has potential to serve as a biocontrol agent. This genome was assembled from short paired-end reads of 75bp size generated by Illumina multiplexed technology using a mapping assembly technique against the already published complete genome of B. amyloliquefaciens FZB42. The total size of draft genome is 3918701 bp, containing 4209 genes and 29 identified ribosomal RNA genes. After annotating the draft genome, it was observed that most of the genes responsible for colonization and plant growth-promotion in FZB42 also are present in UCMB-5036. De novo assembly for unmapped reads indicate the presence of some novel genes i.e. genes which are present in UCMB-5036 but not in reference genome of FZB42.

Main title:Bioinformatics assembly and analysis and annotation of the Bacillus amyloliquefaciens strain 5036 genome
Authors:Manzoor, Shahid
Supervisor:Bongcam-Rudloff, Erik and Maijer, Johan
Examiner:Andersson, Göran
Series:Examensarbete / SLU, Institutionen för husdjursgenetik
Volume/Sequential designation:323
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:Bacillus amyloliquefaciens UCMB-5036, Rhizosphere, Colonization, PGPR, Next generation sequencing, Paired-end Reads, Mapping assembly, De novo assembly
URN:NBN:urn:nbn:se:slu:epsilon-s-1734
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-s-1734
Subjects:Plant genetics and breeding
Plant diseases
Animal genetics and breeding
Language:English
Deposited On:05 Oct 2012 13:46
Metadata Last Modified:16 Jul 2013 23:15

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