Computational finishing of large sequence contigs reveals interspersed nested repeats and gene islands in the rf1-associated region of maize.
The architecture of grass genomes varies on multiple levels. Large long terminal repeat retrotransposon clusters occupy significant portions of the intergenic regions, and islands of protein-encoding genes are interspersed among the repeat clusters. Hence, advanced assembly techniques are required to obtain completely finished genomes as well as to investigate gene and transposable element distributions. To characterize the organization and distribution of repeat clusters and gene islands across large grass genomes, we present 961- and 594-kb contiguous sequence contigs associated with the rf1 (for restorer of fertility1) locus in the near-centromeric region of maize (Zea mays) chromosome 3. We present two methods for computational finishing of highly repetitive bacterial artificial chromosome clones that have proved successful to close all sequence gaps caused by transposable element insertions. Sixteen repeat clusters were observed, ranging in length from 23 to 155 kb. These repeat clusters are almost exclusively long terminal repeat retrotransposons, of which the paleontology of insertion varies throughout the cluster. Gene islands contain from one to four predicted genes, resulting in a gene density of one gene per 16 kb in gene islands and one gene per 111 kb over the entire sequenced region. The two sequence contigs, when compared with the rice (Oryza sativa) and sorghum (Sorghum bicolor) genomes, retain gene colinearity of 50% and 71%, respectively, and 70% and 100%, respectively, for high-confidence gene models. Collinear genes on single gene islands show that while most expansion of the maize genome has occurred in the repeat clusters, gene islands are not immune and have experienced growth in both intragene and intergene locations.
Kronmiller
Brent A
BA
Bioinformatics and Computational Biology, Iowa State University, Ames, Iowa 50011-1020, USA.
Wise
Roger P
RP
D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics; D032461:Chromosomes, Plant / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D020451:Contig Mapping / Q000379:methods*; D004251:DNA Transposable Elements / Q000235:genetics; D017343:Genes, Plant; D020071:Interspersed Repetitive Sequences / Q000235:genetics*; D008969:Molecular Sequence Data; D005810:Multigene Family / Q000235:genetics*; D012275:Oryza / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D045868:Sorghum / Q000235:genetics; D020079:Terminal Repeat Sequences / Q000235:genetics; D003313:Zea mays / Q000235:genetics*
D004251:DNA Transposable Elements
Genome Res. 2000 Nov;10(11):1772-87
11076862
Genome Res. 2006 Oct;16(10):1262-9
16963705
Genome Res. 2000 Apr;10(4):516-22
10779491
Science. 2003 Dec 19;302(5653):2115-7
14684820
Proc Natl Acad Sci U S A. 2005 Aug 23;102(34):12282-7
16103354
Proc Natl Acad Sci U S A. 2000 Feb 1;97(3):1160-5
10655501
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D16-20
16381837
Trends Ecol Evol. 2000 Mar;15(3):95-99
10675923
Nucleic Acids Res. 2003 Jul 1;31(13):3597-600
12824374
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W273-9
15215394
Nature. 2000 Dec 14;408(6814):796-815
11130711
J Mol Evol. 1980 Dec;16(2):111-20
7463489
Plant J. 2003 Apr;34(2):249-55
12694599
Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12404-10
15240870
Genome Res. 2000 Sep;10(9):1304-6
10984448
Nat Genet. 1999 Nov;23(3):305-8
10545948
Genetics. 1996 Jul;143(3):1383-94
8807309
Genome Res. 2001 Oct;11(10):1660-76
11591643
Anal Biochem. 1983 Jul 1;132(1):6-13
6312838
Comput Appl Biosci. 1989 Apr;5(2):101-6
2720459
Genome Biol. 2002;3(12):RESEARCH0079
12537568
Ann Bot. 2005 Jan;95(1):127-32
15596462
Nature. 2009 Jan 29;457(7229):551-6
19189423
Genetics. 1961 Oct;46:1245-52
13888759
Bioinformatics. 2000 Nov;16(11):1046-7
11159318
Plant Physiol. 2002 Dec;130(4):1594-7
12481042
J Hered. 1999 May-Jun;90(3):380-5
10355122
Nat Genet. 1998 Sep;20(1):43-5
9731528
Genome Res. 2003 Jan;13(1):97-102
12529311
Genome Res. 1998 Mar;8(3):195-202
9521923
Plant Cell. 2005 Feb;17(2):343-60
15659640
Plant Physiol. 2002 Jan;128(1):9-12
11788746
Plant Physiol. 2005 Dec;139(4):1612-24
16339807
PLoS Comput Biol. 2005 Jul;1(2):166-75
16110336
Genome Biol. 2002;3(12):RESEARCH0084
12537573
Science. 2003 Dec 19;302(5653):2118-20
14684821
Genome Res. 1998 Mar;8(3):186-94
9521922
Genome Res. 2003 Jan;13(1):73-80
12529308
Plant Physiol. 2005 May;138(1):116-26
15888684
Genome Res. 2001 Nov;11(11):1817-25
11691845
Nucleic Acids Res. 1998 Feb 15;26(4):1107-15
9461475
Genome Res. 2006 Oct;16(10):1241-51
16902087
Curr Opin Plant Biol. 2006 Apr;9(2):149-56
16459129
Nature. 2001 Feb 15;409(6822):860-921
11237011
Genome Res. 1999 Sep;9(9):868-77
10508846
Genome Res. 2000 Jul;10(7):982-90
10899147
Genome Res. 2003 Apr;13(4):721-31
12654723
Plant Physiol. 2001 Dec;127(4):1572-8
11743101
Genome Res. 2002 Oct;12(10):1599-610
12368253
Genome Res. 1998 Mar;8(3):175-85
9521921
Science. 1996 Nov 1;274(5288):765-8
8864112
PLoS Genet. 2007 Jul;3(7):e123
17658954
Genome Res. 2006 Oct;16(10):1252-61
16954538
Comput Appl Biosci. 1997 Oct;13(5):523-35
9367125
Plant Physiol. 2008 Jan;146(1):45-59
18032588
Genome Res. 1997 Nov;7(11):1072-84
9371743
Nature. 2005 Aug 11;436(7052):793-800
16100779
Nature. 2002 Dec 5;420(6915):520-62
12466850