COMPARISON OF THE GENOMES OF FOUR Xanthomonas PATHOGEN STRAINS

Verawaty, Marieska (2006) COMPARISON OF THE GENOMES OF FOUR Xanthomonas PATHOGEN STRAINS. INTERNATIONAL CONFERENCE ON MATHEMATICS AND NATURAL SCIENCES.

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Abstract

Genome comparison of Xanthomonas oryzae pv oryzicola (Xoc) with Xanthomonas campestris pv campestris (Xcc), Xanthomonas axonopodis pv citri (Xac) and Xanthomonas oryzae pv oryzae (Xoo) had been analyzed in Bioinformatics and Plant Pathology Department, Iowa State University, USA. Xac and Xoc both are non vascular host type infection; Xac infected dicots host but Xoc infected monocots host. On the other hand Xcc and Xoo both are vascular host type infection; Xcc infected dycot host but Xoo infected monocot host. The aim of this research was to find the unique genes both in vascular and non vascular host type infection and the unique genes both in dicots and monocots host type classification. On this research Open Reading Frames (ORFs) were identified using dnatopro. Sequence similarity searches were done with stand alone Basic Local Alignment Search Tool (BLAST) and NET-BLAST. Multi-query Sequence Box (MuSeqBox) was using to parse BLAST output and store attributes of BLAST hits in tabular form. It was found that there were 3,085 qualifying ORFs in the Xoc genome sequence with minimal ORF length set to 300 amino acids. From this research we found that there are 318 candidate non-vascular specific proteins. There are 361 candidates of vascular specific proteins. There are 572 candidates of dicots specific proteins. There are 1097 candidate monocots specific proteins. And also we found that there are 58 proteins potentially really unique in the Non-Vascular species and 134 proteins potentially really unique in the vascular species.

Item Type:	Article
Subjects:	#3 Repository of Lecturer Academic Credit Systems (TPAK) > Corresponding Author
Divisions:	08-Faculty of Mathematics and Natural Science > 46101-Biology (S2)
Depositing User:	Dr. Marieska Verawaty
Date Deposited:	11 Apr 2023 10:35
Last Modified:	11 Apr 2023 10:35
URI:	http://repository.unsri.ac.id/id/eprint/94944

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