Molecular diversity of phospholipase D in angiosperms

BMC Genomics

Table 2 Summary on PLD genes in rice. All PLD genes that could be found in public sequence databases and in the Monsanto database of the rice genome draft are listed. Sequences of PLD genes found in the Monsanto database but not yet sequenced by the IRGSP (i.e. OsPLDβ2, OsPLDv2, and OsPLDλ) have been deposited into GenBank. All sequences are derived from the Nipponbare cultivar, unless otherwise stated.

proposed gene name	original gene name	chromosome^a	number of coding exons^b	GenBank/EMBL/ DDBJ accession numbers^c	Monsanto contigs^c	number of ESTs	Reference
OsPLDα1	PLD1	1	3	AB001920^d, AP003215 (5' end), AP003282 (3' end), D73411^d (cDNA)	-	18	[20, 21]
OsPLDα2		5	3?^e	AC087553	OSM15574 (5' end), OSM15576, OSM15582	2	-
OsPLDβ1		10	10	AC078894	OSM15748+ OSM15750	3	-
OsPLDβ2		?	10	AF411221	OSM12022	0	-
OsPLDδ		?	?	nbxb0077G10 (GSS sequence), BE040461 (EST), AU058024 (EST)^f	-	2?	-
OsPLDη1	PLD2	6	3⁸	AB001919^d, AP003629,	OSM12111	2	[21]
OsPLDη2	RPLD3	6	3	AF271356^h, AP003629	OSM12115	0	McGee et al., unpubl.
OsPLDη3	RPLD4	6	3	AF271357^h, AP003629	OSM12115	0	McGee et al., unpubl.
OsPLDθ		8	3	AP004659	OSM12593	0	-
OsPLDκ		2	6	AP004078	OSM128517 +OSM128518 + OSM128519	0	-
OsPLDλ		?	3	AF411223	OSM15282	3	-
OsPLDμ		3	4	AC099323	-	0	-
OsPLDv1	RPLD5	3	10ⁱ	AF271358^h, AC096856	OSM1620	1	McGee et al., unpubl.
OsPLDv2		7	10?^j	AF414565 +AF414566, AP003756(3' end)	OSM11825+ OSM11834	2	-
OsPLDp1		5	20	AC 104272	OSM151594	1	-
OsPLDp2		1	20	AP003934	OSM15141+ OSM15138	4	-

^aChromosome locations are not known for genes originally found only in the Monsanto rice genome database. ^bThe exon numbers with the question mark (?) should be considered preliminary, since the corresponding gene sequences are available incomplete only. ^cIn the case of several genes sequences had to be assembled from two or three contigs (contig numbers linked with "+"), the sequences are therefore incomplete and contain gaps (see Additional files). ^dSequence derived from the Koshihikari cultivar. ^eA portion from within the 1^st supposed intron has not yet been sequenced. ^fThe three sequences may potentially represent two distinct PLDδ isoforms, since the last one does not overlap with the former two. ^gErroneously reported to have two coding exons [2]. ^hSequence derived from the Indica variety, cultivar IR54. ⁱProposed annotation corrected: the 3^rd exon shortened by 12 nucleotides at the 3' end according to EST AA751500. ^jAvailable sequence incomplete, the very beginning of the 1^st exon truncated, the 3' end of the 4^th exon, a supposed intron and the 5' end of the 5^th exon lacking.

ISSN: 1471-2164