Validation of an NSP-based (negative selection pattern) gene family identification strategy.
BACKGROUND
Gene family identification from ESTs can be a valuable resource for analysis of genome evolution but presents unique challenges in organisms for which the entire genome is not yet sequenced. We have developed a novel gene family identification method based on negative selection patterns (NSP) between family members to screen EST-generated contigs. This strategy was tested on five known gene families in Arabidopsis to see if individual paralogs could be identified with accuracy from EST data alone when compared to the actual gene sequences in this fully sequenced genome.


RESULTS
The NSP method uniquely identified family members in all the gene families tested. Two members of the FtsH gene family, three members each of the PAL, RF1, and ribosomal L6 gene families, and four members of the CAD gene family were correctly identified. Additionally all ESTs from the representative contigs when checked against MapViewer data successfully identify the gene locus predicted.


CONCLUSIONS
We demonstrate the effectiveness of the NSP strategy in identifying specific gene family members in Arabidopsis using only EST data and we describe how this strategy can be used to identify many gene families in agronomically important crop species where they are as yet undiscovered.
Frank
Ronald L
RL
Biological Sciences Department, Missouri S&T, Rolla, MO 65409, USA. rfrank@mst.edu
Kandoth
Cyriac
C
Ercal
Fikret
F
D017360:Arabidopsis / Q000235:genetics; D029681:Arabidopsis Proteins / Q000235:genetics*; D002874:Chromosome Mapping / Q000379:methods*; D020224:Expressed Sequence Tags; D018745:Genome, Plant / Q000235:genetics*; D005810:Multigene Family / Q000235:genetics*; D020543:Proteome / Q000235:genetics*; D012641:Selection, Genetic
D029681:Arabidopsis Proteins; D020543:Proteome
FEMS Microbiol Lett. 1999 May 15;174(2):247-50
10339815
Genome Res. 1999 Apr;9(4):373-82
10207159
BMC Bioinformatics. 2005 Jul 15;6 Suppl 2:S7
16026604
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W609-12
16845082
BMC Bioinformatics. 2003 Sep 2;4:35
12952558
BMC Plant Biol. 2005 Mar 30;5:5
15799777
Mol Biol Evol. 1986 Sep;3(5):418-26
3444411
Genomics. 2002 Sep;80(3):295-302
12213199
Plant Physiol. 2005 Sep;139(1):18-26
16166257
Mol Biol Evol. 1994 Jul;11(4):613-9
8078400
Science. 1991 Jun 21;252(5013):1651-6
2047873
Immunogenetics. 2007 Mar;59(3):233-46
17216438
Trends Genet. 2003 Aug;19(8):417-22
12902158
J Plant Physiol. 2006 Mar;163(4):445-51
16455358
BMC Bioinformatics. 2006 Sep 06;7 Suppl 2:S19
17118140
Nucleic Acids Res. 2003 Jun 1;31(11):2963-74
12771222
Trends Genet. 2005 Jan;21(1):60-5
15680516
Brief Bioinform. 2007 Jan;8(1):6-21
16772268
Nature. 1992 Feb 13;355(6361):632-4
1538749
Plant Physiol. 2006 Feb;140(2):411-32
16407444
BMC Genomics. 2006 Aug 09;7:204
16899135
AAPS PharmSci. 2003;5(1):E1
12713273
BMC Genomics. 2007 Apr 04;8:93
17407609
Genetics. 1999 Apr;151(4):1531-45
10101175
Annu Rev Genet. 2004;38:615-43
15568988
Genome Res. 1999 Sep;9(9):868-77
10508846
Bioinformatics. 2006 May 15;22(10):1269-71
16543274
Plant Mol Biol. 2004 Mar;54(4):519-32
15316287
BMC Genomics. 2006 Mar 07;7:44
16522197