Comparative sequence analysis of Solanum and Arabidopsis in a hot spot for pathogen resistance on potato chromosome V reveals a patchwork of conserved and rapidly evolving genome segments

被引:35
作者
Ballvora, Agim
Joecker, Anika
Viehoever, Prisca
Ishihara, Hirofumi
Paal, Juergen
Meksem, Khalid
Bruggmann, Remy
Schoof, Heiko
Weisshaar, Bernd
Gebhardt, Christiane
机构
[1] Max Planck Inst Zuchtungsforsch, D-50829 Cologne, Germany
[2] Univ Bielefeld, Inst Genomforsch, D-33615 Bielefeld, Germany
[3] So Illinois Univ, Dept Plant Soil & Gen Agr, Carbondale, IL 62901 USA
[4] GSF Forschungszentrum Umwelt & Gesundheit, Inst Bioinformat, D-85764 Neuherberg, Germany
关键词
D O I
10.1186/1471-2164-8-112
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
Background: Quantitative phenotypic variation of agronomic characters in crop plants is controlled by environmental and genetic factors (quantitative trait loci = QTL). To understand the molecular basis of such QTL, the identification of the underlying genes is of primary interest and DNA sequence analysis of the genomic regions harboring QTL is a prerequisite for that. QTL mapping in potato (Solanum tuberosum) has identified a region on chromosome V tagged by DNA markers GP21 and GP179, which contains a number of important QTL, among others QTL for resistance to late blight caused by the oomycete Phytophthora infestans and to root cyst nematodes. Results: To obtain genomic sequence for the targeted region on chromosome V, two local BAC (bacterial artificial chromosome) contigs were constructed and sequenced, which corresponded to parts of the homologous chromosomes of the diploid, heterozygous genotype P6/210. Two contiguous sequences of 417,445 and 202,781 base pairs were assembled and annotated. Gene- by- gene co- linearity was disrupted by non- allelic insertions of retrotransposon elements, stretches of diverged intergenic sequences, differences in gene content and gene order. The latter was caused by inversion of a 70 kbp genomic fragment. These features were also found in comparison to orthologous sequence contigs from three homeologous chromosomes of Solanum demissum, a wild tuber bearing species. Functional annotation of the sequence identified 48 putative open reading frames (ORF) in one contig and 22 in the other, with an average of one ORF every 9 kbp. Ten ORFs were classified as resistance- gene- like, 11 as F- box- containing genes, 13 as transposable elements and three as transcription factors. Comparing potato to Arabidopsis thaliana annotated proteins revealed five micro- syntenic blocks of three to seven ORFs with A. thaliana chromosomes 1, 3 and 5. Conclusion: Comparative sequence analysis revealed highly conserved collinear regions that flank regions showing high variability and tandem duplicated genes. Sequence annotation revealed that the majority of the ORFs were members of multiple gene families. Comparing potato to Arabidopsis thaliana annotated proteins suggested fragmented structural conservation between these distantly related plant species.
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共 62 条
[1]   Gapped BLAST and PSI-BLAST: a new generation of protein database search programs [J].
Altschul, SF ;
Madden, TL ;
Schaffer, AA ;
Zhang, JH ;
Zhang, Z ;
Miller, W ;
Lipman, DJ .
NUCLEIC ACIDS RESEARCH, 1997, 25 (17) :3389-3402
[2]  
[Anonymous], 2002, GENOME BIOL
[3]   InterPro - an integrated documentation resource for protein families, domains and functional sites [J].
Apweiler, R ;
Attwood, TK ;
Bairoch, A ;
Bateman, A ;
Birney, E ;
Biswas, M ;
Bucher, P ;
Cerutti, L ;
Corpet, F ;
Croning, MDR ;
Durbin, R ;
Falquet, L ;
Fleischmann, W ;
Gouzy, J ;
Hermjakob, H ;
Hulo, N ;
Jonassen, I ;
Kahn, D ;
Kanapin, A ;
Karavidopoulou, Y ;
Lopez, R ;
Marx, B ;
Mulder, NJ ;
Oinn, TM ;
Pagni, M ;
Servant, F ;
Sigrist, CJA ;
Zdobnov, EM .
BIOINFORMATICS, 2000, 16 (12) :1145-1150
[4]   The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000 [J].
Bairoch, A ;
Apweiler, R .
NUCLEIC ACIDS RESEARCH, 2000, 28 (01) :45-48
[5]   The R1 gene for potato resistance to late blight (Phytophthora infestans) belongs to the leucine zipper/NBS/LRR class of plant resistance genes [J].
Ballvora, A ;
Ercolano, MR ;
Weiss, J ;
Meksem, K ;
Bormann, CA ;
Oberhagemann, P ;
Salamini, F ;
Gebhardt, C .
PLANT JOURNAL, 2002, 30 (03) :361-371
[6]   LOCALIZATION BY RESTRICTION-FRAGMENT-LENGTH-POLYMORPHISM MAPPING IN POTATO OF A MAJOR DOMINANT GENE CONFERRING RESISTANCE TO THE POTATO CYST NEMATODE GLOBODERA-ROSTOCHIENSIS [J].
BARONE, A ;
RITTER, E ;
SCHACHTSCHABEL, U ;
DEBENER, T ;
SALAMINI, F ;
GEBHARDT, C .
MOLECULAR & GENERAL GENETICS, 1990, 224 (02) :177-182
[7]   Agrobacterium transient expression system as a tool for the isolation of disease resistance genes:: application to the Rx2 locus in potato [J].
Bendahmane, A ;
Querci, M ;
Kanyuka, K ;
Baulcombe, DC .
PLANT JOURNAL, 2000, 21 (01) :73-81
[8]   The genetic colinearity of rice and other cereals on the basis of genomic sequence analysis [J].
Bennetzen, JL ;
Ma, JX .
CURRENT OPINION IN PLANT BIOLOGY, 2003, 6 (02) :128-133
[9]  
BONIERBALE MW, 1988, GENETICS, V120, P1095
[10]   Evolution of DNA sequence nonhomologies among maize inbreds [J].
Brunner, S ;
Fengler, K ;
Morgante, M ;
Tingey, S ;
Rafalski, A .
PLANT CELL, 2005, 17 (02) :343-360