Rice pseudomolecule-anchored cross-species DNA sequence alignments indicate regional genomic variation in expressed sequence conservation.
BACKGROUND
Various methods have been developed to explore inter-genomic relationships among plant species. Here, we present a sequence similarity analysis based upon comparison of transcript-assembly and methylation-filtered databases from five plant species and physically anchored rice coding sequences.


RESULTS
A comparison of the frequency of sequence alignments, determined by MegaBLAST, between rice coding sequences in TIGR pseudomolecules and annotations vs 4.0 and comprehensive transcript-assembly and methylation-filtered databases from Lolium perenne (ryegrass), Zea mays (maize), Hordeum vulgare (barley), Glycine max (soybean) and Arabidopsis thaliana (thale cress) was undertaken. Each rice pseudomolecule was divided into 10 segments, each containing 10% of the functionally annotated, expressed genes. This indicated a correlation between relative segment position in the rice genome and numbers of alignments with all the queried monocot and dicot plant databases. Colour-coded moving windows of 100 functionally annotated, expressed genes along each pseudomolecule were used to generate 'heat-maps'. These revealed consistent intra- and inter-pseudomolecule variation in the relative concentrations of significant alignments with the tested plant databases. Analysis of the annotations and derived putative expression patterns of rice genes from 'hot-spots' and 'cold-spots' within the heat maps indicated possible functional differences. A similar comparison relating to ancestral duplications of the rice genome indicated that duplications were often associated with 'hot-spots'.


CONCLUSIONS
Physical positions of expressed genes in the rice genome are correlated with the degree of conservation of similar sequences in the transcriptomes of other plant species. This relative conservation is associated with the distribution of different sized gene families and segmentally duplicated loci and may have functional and evolutionary implications.
Armstead
Ian
I
Institute of Grassland and Environmental Research, Plas Gogerddan, Aberystwyth, Ceredigion, SY23 3EB, UK. ian.armstead@bbsrc.ac.uk
Huang
Lin
L
King
Julie
J
Ougham
Helen
H
Thomas
Howard
H
King
Ian
I
D017360:Arabidopsis / Q000235:genetics / Q000254:growth & development; D017124:Conserved Sequence; D019175:DNA Methylation; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D049810:Genetic Speciation; D014644:Genetic Variation; D018745:Genome, Plant; D001467:Hordeum / Q000235:genetics / Q000254:growth & development; D008129:Lolium / Q000235:genetics / Q000254:growth & development; D012275:Oryza / Q000235:genetics* / Q000254:growth & development; D010802:Phylogeny; D011544:Pseudogenes; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods; D012689:Sequence Homology, Nucleic Acid; D012984:Software; D013025:Glycine max / Q000235:genetics / Q000254:growth & development; D003313:Zea mays / Q000235:genetics / Q000254:growth & development
Nat Genet. 1999 Nov;23(3):305-8
10545948
Curr Opin Plant Biol. 2006 Dec;9(6):631-8
17005440
New Phytol. 2005 Mar;165(3):937-46
15720704
Biochem Soc Trans. 2004 Aug;32(Pt 4):571-4
15270678
Genome Res. 2005 Dec;15(12):1643-50
16339361
Genome Res. 2005 Apr;15(4):487-95
15805490
Plant J. 2006 Jul;47(1):63-74
16824180
Genome Res. 2003 Aug;13(8):1818-27
12902377
Plant Cell. 2004 Jul;16(7):1679-91
15208398
Plant Physiol. 2004 Sep;136(1):2621-32
15375207
PLoS Biol. 2005 Jan;3(1):e13
15660154
Curr Opin Plant Biol. 2005 Apr;8(2):122-8
15752990
Nature. 2003 Jan 2;421(6918):63-6
12511954
Plant Cell. 2005 Jun;17(6):1641-57
15863518
Nat Rev Genet. 2006 Mar;7(3):174-84
16485017
BMC Genomics. 2006 Oct 26;7:275
17067373
Genetics. 1998 Dec;150(4):1595-603
9832535
Genetics. 2006 Sep;174(1):179-90
16751662
BMC Evol Biol. 2004 Jul 06;4:22
15238160
Plant Mol Biol. 2005 Sep;59(1):7-26
16217598
Plant Cell. 2004 Aug;16(8):2089-103
15269332
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D771-6
16381977
Genetics. 1999 Apr;151(4):1531-45
10101175
Curr Opin Plant Biol. 2004 Aug;7(4):391-9
15231261
Trends Genet. 2005 Nov;21(11):602-7
16140417
Trends Genet. 2006 Nov;22(11):597-602
16979781
BMC Biol. 2005 Sep 27;3:20
16188032
BMC Genomics. 2006 Oct 24;7:272
17062153
Curr Opin Plant Biol. 2006 Apr;9(2):149-56
16459129
Genetics. 2005 Oct;171(2):765-81
16020789
Proc Natl Acad Sci U S A. 2005 Sep 13;102(37):13206-11
16141333
Proc Natl Acad Sci U S A. 2006 Feb 21;103(8):2730-5
16467140
Curr Opin Plant Biol. 2005 Apr;8(2):155-62
15752995
J Comput Biol. 2000 Feb-Apr;7(1-2):203-14
10890397
Genetics. 2002 May;161(1):315-24
12019245
Mol Biol Evol. 2006 Sep;23(9):1808-16
16809621
Nucleic Acids Res. 2007 Jan;35(Database issue):D846-51
17088284
Proc Natl Acad Sci U S A. 2004 Jun 29;101(26):9903-8
15161969
Plant Physiol. 2005 Aug;138(4):1898-902
16172096
Evolution. 2005 Jun;59(6):1245-58
16050101
Plant Physiol. 2006 Apr;140(4):1169-82
16607030
Plant Cell. 2005 Jan;17(1):4-11
15632052
Am J Bot. 2004 Oct;91(10):1656-65
21652315
Trends Genet. 2003 Mar;19(3):141-7
12615008
Curr Opin Plant Biol. 2006 Aug;9(4):383-90
16713729
Theor Appl Genet. 2006 Jul;113(2):186-95
16791686