Plant genome evolution: Lessons from comparative genomics at the DNA level

Plant Molecular Biology

Volumn 48, Issue 1-2, 2002, Pages 21-37

  Schmidt, Renate ^a,b  

^a Max Delbruck Laboratorium der Max Planck Gesellschaft   (Germany)

^b MAX PLANCK INSTITUTE OF MOLECULAR PLANT PHYSIOLOGY   (Germany)

Author keywords

Collinearity; Comparative mapping; Comparative sequence analysis; Genome; Retroelement; Sequence conservation

Indexed keywords

DNA; GENES; GENETIC ENGINEERING;

GENE ARRANGEMENTS;

PLANTS (BOTANY);

EMBRYOPHYTA; MAGNOLIOPHYTA;

PLANT DNA;

COMPARATIVE STUDY; DNA BASE COMPOSITION; GENE; GENETICS; GENOME; GENOMICS; MOLECULAR EVOLUTION; PLANT; REVIEW;

BASE COMPOSITION; DNA, PLANT; EVOLUTION, MOLECULAR; GENES, PLANT; GENOME, PLANT; GENOMICS; PLANTS;

EID: 0036007664     PISSN: 01674412     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1013788306201     Document Type: Review

References (100)

1. Comparative genome analysis reveals extensive conservation of genome organisation for Arabidopsis thaliana and Capsella rubella
2. Comparative linkage maps of the rice and maize genomes
3. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
4. Nuclear DNA content of some important plant species
5. Gene identification in a complex chromosomal continuum by local genomic cross-referencing
6. Amphidiploid Brassica juncea contains conserved progenitor genomes
7. Insights into the structural and functional evolution of plant genomes afforded by the nucleotide sequences of chromosomes 2 and 4 of Arabidopsis thaliana
8. Duplicate and diverge: The evolution of plant genome microstructure
9. The use of the Monsanto draft rice genome sequence in research
10. Plant genome values: How much do we know?
11. Nuclear DNA amounts in angiosperms
12. Nuclear DNA amounts in angiosperms
13. Nuclear DNA amounts in angiosperms
14. Comparative sequence analysis of plant nuclear genomes: Microcolinearity and its many exceptions
15. Grass genomes
16. Extensive duplication and reshuffling in the Arabidopsis genome
17. Alignment of the conserved C genomes of Brassica oleracea and Brassica napus
18. The association of flowering time quantitative trait loci with duplicated regions and candidate loci in Brassica oleracea
19. RFLP maps based on a common set of clones reveal modes of chromosomal evolution in potato and tomato
20. Collinearity between a 30-centimorgan segment of Arabidopsis thaliana chromosome 4 and duplicated regions within the Brassica napus genome
21. RFLP-based genetic maps of wheat homoeologous group 7 chromosomes
22. Microcolinearity in sh2-homologous regions of the maize, rice, and sorghum genomes
23. Sequence organization and conservation in sh2/a1-homologous regions of sorghum and rice
24. Comparative mapping of the Brassica S locus region and its homeolog in Arabidopsis: Implications for the evolution of mating systems in the Brassicaceae
25. The genetic maps of wheat and their potential in plant breeding
26. Genome relationships: The grass model in current research
27. Arabidopsis-rice: Will colinearity allow gene prediction across the eudicot-monocot divide?
28. Comparative mapping reveals a complex relationship between the pearl millet genome and those of foxtail millet and rice
29. Toward integration of comparative genetic, physical, diversity, and cytomolecular maps for grasses and grains, using the sorghum genome as a foundation
30. Physical mapping of the barley stem rust resistance gene rpg4
31. m of Triticum monococcum and its recognition by the wheat Ph1 locus
32. Comparative sequence analysis of collinear barley and rice bacterial artificial chromosomes
33. High gene density is conserved at syntenic loci of small and large grass genomes
34. The molecular characterization and organization of plant chromosomal DNA sequences
35. Detailed comparative mapping of cereal chromosome regions corresponding to the Ph1 locus in wheat
36. The two genes homologous to Arabidopsis FAEI co-segregate with the two loci governing erucic acid content in Brassica napus
37. The genetics of stamenoid petal production in oilseed rape (Brassica napus) and equivalent variation in Arabidopsis thaliana
38. Comparative genetics in the grasses
39. Independent deletions of a pathogen-resistance gene in Brassica and Arabidopsis
40. Genome organization in dicots: Genome duplication in Arabidopsis and synteny between soybean and Arabidopsis
41. Sequence analysis of a rice BAC covering the syntenous barley Rpg1 region
42. Identification of the genomic locations of duplicate nucleotide sequences in maize by analysis of restriction fragment length polymorphisms
43. Genetic mapping and characterization of sorghum and related crops by means of maize DNA probes
44. Comparative fluorescence in situ hybridization mapping of a 431-kb Arabidopsis thaliana bacterial artificial chromosome contig reveals the role of chromosomal duplications in the expansion of the Brassica rapa genome
45. Rice-barley synteny and its application to saturation mapping of the barley Rpg1 region
46. Towards map-based cloning of the barley stem rust resistance genes Rpg1 and rpg4 using rice as an intergenomic cloning vehicle
47. Evidence for homology of flowering-time genes VFR2 from Brassica rapa and FLC from Arabidopsis thaliana
48. Comparative mapping of Arabidopsis thaliana and Brassica oleracea chromosomes reveals islands of conserved organization
49. Comparing sequenced segments of the tomato and Arabidopsis genomes: Large-scale duplication followed by selective gene loss creates a network of synteny
50. Comparative mapping between Arabidopsis thaliana and Brassica nigra indicates that Brassica genomes have evolved through extensive genome replication accompanied by chromosome fusions and frequent rearrangements
51. Comparative genome mapping in Brassica
52. Comparative mapping in Arabidopsis and Brassica, fine scale genome collinearity and congruence of genes controlling flowering time
53. Comparative mapping of quantitative trait loci sculpting the curd of Brassica oleracea
54. An EST-enriched comparative map of Brassica oleracea and Arabidopsis thaliana
55. Rapid reorganization of resistance gene homologues in cereal genomes
56. Phylogenetic analysis of DNA C-values provides evidence for a small ancestral genome size in flowering plants
57. Comparative analysis of QTLs affecting plant height and maturity across the Poaceae, in reference to an interspecific sorghum population
58. Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana
59. Genome mapping in Capsicum and the evolution of genome structure in the Solanaceae
60. The evolutionary fate and consequences of duplicate genes
61. Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana
62. Importance of anchor genomes for any plant genome project
63. Was there a single ancestral cereal chromosome?
64. Centromeric sites and cereal chromosome evolution
65. Pronounced intraspecific haplotype divergence at the RPP5 complex disease resistance locus of Arabidopsis
66. Comparative physical mapping of segments of the genome of Brassica oleracea var. alboglabra that are homoeologous to sequenced regions of chromosomes 4 and 5 of Arabidopsis thaliana
67. Comparison of flowering time genes in Brassica rapa, B. napus and Arabidopsis thaliana
68. Identification of the A and C genomes of amphidiploid Brassica napus (oilseed rape)
69. Convergent domestication of cereal crops by independent mutations at corresponding genetic loci
70. Toward a unified genetic map of higher plants, transcending the monocot-dicot divergence
71. Comparative genomics of plant chromosomes
72. Evaluation of gene prediction software using a genomic data set: Application to Arabidopsis thaliana sequences
73. 'Green revolution' genes encode mutant gibberellin response modulators
74. Arabidopsis and Brassica comparative genomics: Sequence, structure and gene content in the ABII-Rps2-Ck1 chromosomal segment and related regions
75. Differential methylation of genes and retrotransposons facilitates shotgun sequencing of the maize genome
76. Comparative sequence analysis reveals extensive microcolinearity in the Lateral suppressor regions of the tomato, Arabidopsis and Capsella genomes
77. Organization of an Arabidopsis thaliana gene cluster on chromosome 4 including the RPS2 gene in the Brassica nigra genome
78. Genetic and physical mapping in Brassica diploid species of a gene cluster defined in Arabidopsis thaliana
79. Nested retrotransposons in the intergenic regions of the maize genome
80. Desaturase multigene families of Brassica napus arose through genome duplication
81. Synteny: Recent advances and future prospects
82. Comparative structural genomics in the Brassicaceae family
83. Arabidopsis thaliana: A source of candidate disease-resistance genes for Brassica napus
84. Linkage arrangement of restriction fragment length polymorphism loci in Brassica oleracea
85. Angiosperm phylogeny inferred from multiple genes as a tool for comparative biology
86. A linkage map of Brassica rapa (syn. campestris) based on restriction fragment length polymorphism loci
87. Rapid genome change in synthetic polyploids of Brassica and its implications for polyploid evolution
88. Subgenome chromosome walking in wheat: A 450-kb physical contig in Triticum monococcum L. spans the Lr10 resistance locus in hexaploid wheat (Triticum aestivum L.)
89. Conservation of gene repertoire but not gene order in pepper and tomato
90. High density molecular linkage maps of the tomato and potato genomes
91. The complete sequence of 340 kb of DNA around the rice Adh1-Adh2 region reveals interrupted colinearity with maize chromosome 4
92. Evidence for an ancient chromosomal duplication in Arabidopsis thaliana by sequencing and analyzing a 400-kb contig at the Apetala2 locus on chromosome 4
93. Colinearity and its exceptions in orthologous adh regions of maize and sorghum
94. Structure and organization of the B genome based on a linkage map in Brassica nigra
95. Identification and analysis of homoeologous segments of the genomes of rice and Arabidopsis thaliana
96. The origins of genomic duplications in Arabidopsis
97. Genome evolution in polyploids
98. Yesterday's polyploids and the mystery of diploidization
99. Physical mapping of duplicated genomic regions of two chromosome ends in rice
100. Rice bioinformatics. Analysis of rice sequence data and leveraging the data to other plant species