From Chlamydomonas to rice: the evolution of green P450s A link to my talk given in Los Angeles August 21, 2002
Note the japonica rice strain has been revised 9/19/2007. See the two links below for an Excel spreadsheet of all japonica P450s Including name, possible function, references and accession numbers. The second file contains the sequences.
- Rice P450 Blast Server now with indica, japonica and combined setsRice and Arabidopsis P450 list New Jan. 21, 2003side by side list of all rice and Arab. P450sRice Cytochrome P450s chr. 1 New Dec. 29, 2003A comparison of IRGSP annotation with my annotationRice Cytochrome P450 annotation status New Dec. 29, 2003list of partial and complete P450sRice Cytochrome P450 FASTA file New Dec. 30, 2003FASTA format of rice sequences452 named Rice Cytochrome P450 genes New Dec. 29, 2003Revised sequences458 named Rice Cytochrome P450 genes New Sept 25, 2002
Includes ortholog pairs and 953 sequences from japonica and indica
- 514 Rice Cytochrome P450 Contigs REVISED August 12, 2002
- 534 Rice indica Cytochrome P450 sequences REVISED August 12, 2002
- 341 Rice japonica Cytochrome P450 sequences REVISED August 9, 2002
- Rice Cytochrome P450 sequences FASTA format
- japonica Rice accession numbers
- Rice Cytochrome P450 accession numbers sorted by CYP names finished 9/25/02
- Rice Cytochrome P450 Report Nov. 14, 2001
- Rice CYP72As (9 gene cluster)
- Rice P450 tree of 90 new unnamed sequences
- Rice P450 tree of new sequences + named plant group A sequences
- Rice P450 tree of the 86 clan sequences
- Rice P450 tree of some 76 family sequences
- Rice P450 tree of the 71 family sequences
Sept. 25, 2002, There are 458 different P450 gene sequences in rice. Some of these are short pseudogene fragments of only one exon or part of one exon. I count 309 full length, probably functional, P450 genes and another 14 that are now incomplete but may become completed as the genome is finished. That would give 323 full length P450s and 135 pseudogenes.
This compares to 249 full length P450s in Arabidopsis and 23 pseudogenes.
Several sequences may join together to form complete sequences. (98A17 and 98A18), (714D1 and 714D2), (various CYP730 fragments) this may reduce the gene count by three or four.
August 9, 2002, 875 total rice contigs, 341 are japonica, 534 are indica 250 japonica sequences are full length. 293 rice sequences are full length (from both subspecies)
<p”>I will be trying to name all the rice genes before August 20. All gene pieces have been sorted into family bins and many have been named but some like the 94 family still need to be sorted into subfamilies. (8/19/02)
As of March 1, 2002 I have updated the rice P450 page. There are now 202 full length P450s, 61 pseudogene fragments and 61 incomplete sequences. A blast server for the rice P450 sequences is available. The 324 sequence contigs are non-redundant, meaning I have blasted them against each other and combined overlapping fragments into contigs. I have done systematic searches of the Genbank Database for rice P450 ESTs, GSSs, sequences in nr and HTGS hits. These are compiled into the set of sequences on the blast server. The public data has now been completely searched. I will now be looking at the private 5X coverage of rice, but the results from this cannot be presented until they are approved according to legal agreements, so I will not be able to add them daily. </p.
Note from Oct. 16, 2001
Since 1993, there are 197241 rice entries in Genbank.
The majority are recent additions.
Several sequences may join together to form complete sequences.(98A17 and 98A18), (714D1 and 714D2), (various CYP730 fragments)this may reduce the gene count by three or four.
August 9, 2002, 875 total rice contigs, 341 are japonica, 534 are indica250 japonica sequences are full length. 293 rice sequences are full length (from both subspecies)I will be trying to name all the rice genes before August 20. All gene pieces have been sorted into family bins and many have been named but some like the 94 family still need to be sorted into subfamilies.
(8/19/02)
As of March 1, 2002 I have updated the rice P450 page. There are now 202 full length P450s, 61 pseudogene fragments and 61 incomplete sequences.
A blast server for the rice P450 sequences is available. The 324 sequence contigs are non-redundant, meaning I have blasted them against each other and combined overlapping fragments into contigs. I have done systematic searches of the Genbank Database for rice P450 ESTs, GSSs, sequences in nr and HTGS hits. These are compiled into the set of sequences on the blast server. The public data has now been completely searched. I will now be looking at the private 5X coverage of rice, but the results from this cannot be presented until they are approved according to legal agreements, so I will not be able to add them daily.Note from Oct. 16, 2001 Since 1993, there are 197241 rice entries in Genbank.
The majority are recent additions.
2001 32693 up to Oct. 16, 2001
2000 43284
1999 67898
1998 34465
1997 8170
1996 1529
1995 3733
1994 3468
1993 4866
no entries before 1993
Of the total number of entries 197241,
93164 are GSS sequences = Genome Survey Sequence (from BAC ends)
92634 are ESTs
553 are STS (Sequence Tagged Sites for mapping)
277 are patents
1145 are HTGS high throughput genomic
6667 are microsatellite repeats from the Monsanto data
(in NR section with accession numbers starting with AY)
2801 are other NR section sequences, mRNAs, genes and finished BACs
in 1999 the activity was
01/ 6291
02/ 4294
03/ 688
04/ 4191
05/ 4860 1709 GSSs + 3094 ESTs
06/ 10776 6162 GSSs + 4527 ESTs
07/ 6370 5050 GSSs + 1284 ESTs
08/ 3785 3239 GSSS + 444 ESTs
09/ 1577 1188 GSSs + 360 ESTs
10/ 1089 839 GSSs + 216 ESTs
11/ 18077 17800 GSSs + 261 ESTs
12/ 11507 11412 GSSs + 72 ESTs
in 2000 the activity was
43284 20085 GSSs + 22558 ESTs for the whole year
in 2001 the activity was
32639 62 GSSs + 23831 ESTs (up to 10/16/01)
01/ 916 0 GSSs + 793 ESTs
02/ 7063 0 GSSs + 1276 ESTs 5637 = microsatellite sequences
03/ 1833 51 GSSs + 1614 ESTs
04/ 1311 0 GSSs + 1212 ESTs
05/ 2766 0 GSSs + 2632 ESTs
06/ 702 0 GSSs + 595 ESTs
07/ 3647 2 GSSs + 3355 ESTs
08/ 576 0 GSSs + 85 ESTs
09/ 420 9 GSSs + 420 ESTs
10/ 13405 0 GSSs + 12269 ESTs 12269 ESTs deposited Oct. 5