In planta gene expression analysis of Xanthomonas oryzae pathovar oryzae, African strain MAI1

BMC Microbiology

Table 3 Homologues of genes in strain MAI1 found near IS elements in the BAI3 genome

			Relative distance (kb) between differentially expressed genes and IS elements in genome:
Flanking sequence of IS element	Genes in vicinity	Putative function	BAI3	MAFF311018
FI978233			10001..10132	920135..920004
ISXo8 transposase (IS5 family)	FI978262	ISXo8 transposase (IS5 family)	- 2.0	- 3723
	FI978083	Putative transposase	+ 8.2	+ 621
	M1P4B2	No protein match	+ 1.2	- 3796
	FI978246	Transposase	+ 6.3	- 1089
	FI978279	ribonucleoside-diphosphate reductase, beta subunit	- 0.9	+ 153
	FI978268	No protein match	+ 7.8	+ 761
	FI978290	dTDP-glucose 4,6-dehydratase	- 10.1	+ 144
	FI978285	hypothetical protein XOO1934	- 1.2	+ 150
	FI978270	Putative transposase	- 3.8	+ 757
FI978246			10001..10299	2009657..2009789
transposase	FI978181	Cellulase	- 5.5	+ 1728
FI978274			13384..14161	14199973..1420912
ISXoo15 transposase (IS30 family)	FI978084	Putative transposase	+ 7.8	+13.8

Homologues of IS elements, found as differentially expressed in the African strain MAI1 of Xanthomonas oryzae pv. oryzae (Xoo) were identified in the Xoo BAI3 draft genome. Extractions (10 kb) were made from up- and downstream flanking regions of IS elements. BLAST searches were performed locally, using the MAI1 differentially expressed genes. For the sequences located within the 20-kb sequence flanking the IS elements, the relative distance of each sequence to the IS element in BAI3 was compared with the relative distance of their respective homologues in the Xoo MAFF311018 genome. The designation + indicates upstream location of the sequence relative to the IS element, and the designation - indicates downstream location. For IS elements, gene locations within the 20-kb sequence flanking the IS element in BAI3 and within the genome of Xoo MAFF311018 are presented.

ISSN: 1471-2180