ABSTRACT
Understanding the organization of eukaryotic centromeres has both fundamental and applied importance because of their roles in chromosome segregation, karyotypic stability, and artificial chromosome-based cloning and expression vectors. Using clone-by-clone sequencing methodology, we obtained the complete genomic sequence of the centromeric region of rice (Oryza sativa) chromosome 8. Analysis of 1.97 Mb of contiguous nucleotide sequence revealed three large clusters of CentO satellite repeats (68.5 kb of 155-bp repeats) and >220 transposable element (TE)-related sequences; together, these account for approximately 60% of this centromeric region. The 155-bp repeats were tandemly arrayed head to tail within the clusters, which had different orientations and were interrupted by TE-related sequences. The individual 155-bp CentO satellite repeats showed frequent transitions and transversions at eight nucleotide positions. The 40 TE elements with highly conserved sequences were mostly gypsy-type retrotransposons. Furthermore, 48 genes, showing high BLAST homology to known proteins or to rice full-length cDNAs, were predicted within the region; some were close to the CentO clusters. We then performed a genome-wide survey of the sequences and organization of CentO and RIRE7 families. Our study provides the complete sequence of a centromeric region from either plants or animals and likely will provide insight into the evolutionary and functional analysis of plant centromeres.
Subject(s)
Chromosomes, Plant/genetics , Oryza/genetics , Base Composition , Base Sequence , Centromere/genetics , Chromosomes, Artificial, Bacterial/genetics , Chromosomes, Artificial, P1 Bacteriophage/genetics , Conserved Sequence , DNA Transposable Elements/genetics , DNA, Plant/chemistry , DNA, Plant/genetics , DNA, Satellite/genetics , Genome, Plant , Molecular Sequence Data , Physical Chromosome Mapping , Repetitive Sequences, Nucleic AcidABSTRACT
We developed seven Q-chromosome-specific DNA markers in Nicotiana tabacum by random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) analysis using two hybrid lines, and we were able to identify tobacco monosomic plants among F1 progeny derived from the cross N. tabacum Haplo-QxN. tabacum cv. Samsun NN using Q-chromosome-specific DNA markers. Based on the results, we discuss the roles of the Q chromosome in embryo sac development and embryogenesis. Here, we propose a new method for identifying DNA markers for a particular chromosome in the genus Nicotiana.
Subject(s)
Chromosomes, Plant/genetics , Genes, Plant/genetics , Monosomy/genetics , Nicotiana/growth & development , Nicotiana/genetics , Chimera/genetics , Gene Expression Regulation, Plant/genetics , Genetic Markers/genetics , Seeds/cytology , Seeds/genetics , Seeds/growth & developmentABSTRACT
The rice species Oryza sativa is considered to be a model plant because of its small genome size, extensive genetic map, relative ease of transformation and synteny with other cereal crops. Here we report the essentially complete sequence of chromosome 1, the longest chromosome in the rice genome. We summarize characteristics of the chromosome structure and the biological insight gained from the sequence. The analysis of 43.3 megabases (Mb) of non-overlapping sequence reveals 6,756 protein coding genes, of which 3,161 show homology to proteins of Arabidopsis thaliana, another model plant. About 30% (2,073) of the genes have been functionally categorized. Rice chromosome 1 is (G + C)-rich, especially in its coding regions, and is characterized by several gene families that are dispersed or arranged in tandem repeats. Comparison with a draft sequence indicates the importance of a high-quality finished sequence.
