Integration of hybridization-based markers (overgos) into physical maps for comparative and evolutionary explorations in the genus Oryza and in Sorghum

BACKGROUND: With the completion of the genome sequence for rice (Oryza sativa L.), the focus of rice genomics research has shifted to the comparison of the rice genome with genomes of other species for gene cloning, breeding, and evolutionary studies. The genus Oryza includes 23 species that shared a common ancestor 8–10 million years ago making this an ideal model for investigations into the processes underlying domestication, as many of the Oryza species are still undergoing domestication. This study integrates high-throughput, hybridization-based markers with BAC end sequence and fingerprint data to construct physical maps of rice chromosome 1 orthologues in two wild Oryza species. Similar studies were undertaken in Sorghum bicolor, a species which diverged from cultivated rice 40–50 million years ago. RESULTS: Overgo markers, in conjunction with fingerprint and BAC end sequence data, were used to build sequence-ready BAC contigs for two wild Oryza species. The markers drove contig merges to construct physical maps syntenic to rice chromosome 1 in the wild species and provided evidence for at least one rearrangement on chromosome 1 of the O. sativa versus Oryza officinalis comparative map. When rice overgos were aligned to available S. bicolor sequence, 29% of the overgos aligned with three or fewer mismatches; of these, 41% gave positive hybridization signals. Overgo hybridization patterns supported colinearity of loci in regions of sorghum chromosome 3 and rice chromosome 1 and suggested that a possible genomic inversion occurred in this syntenic region in one of the two genomes after the divergence of S. bicolor and O. sativa. CONCLUSION: The results of this study emphasize the importance of identifying conserved sequences in the reference sequence when designing overgo probes in order for those probes to hybridize successfully in distantly related species. As interspecific markers, overgos can be used successfully to construct physical maps in species which diverged less than 8 million years ago, and can be used in a more limited fashion to examine colinearity among species which diverged as much as 40 million years ago. Additionally, overgos are able to provide evidence of genomic rearrangements in comparative physical mapping studies

Deciphering the genome structure and paleohistory of _Theobroma cacao_

We sequenced and assembled the genome of _Theobroma cacao_, an economically important tropical fruit tree crop that is the source of chocolate. The assembly corresponds to 76% of the estimated genome size and contains almost all previously described genes, with 82% of them anchored on the 10 _T. cacao_ chromosomes. Analysis of this sequence information highlighted specific expansion of some gene families during evolution, for example flavonoid-related genes. It also provides a major source of candidate genes for _T. cacao_ disease resistance and quality improvement. Based on the inferred paleohistory of the T. cacao genome, we propose an evolutionary scenario whereby the ten _T. cacao_ chromosomes were shaped from an ancestor through eleven chromosome fusions. The _T. cacao_ genome can be considered as a simple living relic of higher plant evolution

The oryza map alignment project (OMAP): a new resource for comparative genome studies within oryza

Rice (Oryza sativa L.) is the most important human food crop in the world. The agronomic importance of rice, its shared evolutionary history with major cereal crops, and small genome size have led to the generation of a high-quality finished genome sequence by the International Rice Genome Sequencing Project (2005). The highly accurate and public IRGSP sequence now serves as a unifying research platform for a complete functional characterization of the rice genome. Such an analysis will investigate the rice transcriptome, proteome, and metabolome, with the goal of understanding the biological function of all 35,000 to 40,000 rice genes and applying that information to improve rice production and quality. This comprehensive analysis will utilize a variety of techniques and resources from expression and genome tiling arrays to collections of tagged mutant populations developed in elite cultivars grown around the world. Comparative genomics between the cereal genomes and within the genus Oryza will also play a critical role in our understanding of the rice genome (Ahn et al. 1993; Ahn and Tanksley 1993; Bennetzen and Ma 2003; Han and Xue 2003; Huang and Kochert 1994; Jena et al. 1994; Ma and Bennetzen 2004). By comparing genome organization, genes, and intergenic regions between cereal species, one can identify regions of the genome that are highly conserved or rapidly evolving. Such regions are expected to yield key insights into genome evolution, speciation, and domestication. The study of conserved noncoding sequences (CNSs) between cereal genomes will also increase our ability to understand and isolate regulatory elements required for precise developmental and temporal gene expression (Kaplinsky et al. 2002). The genus Oryza is composed of two cultivated (O. sativa and O. glaberrima) and 21 wild species (Khush 1997; Vaughan et al. 2003). Based on recent phylogenetic data, Ge et al. (1999) proposed that Porteresia coarctata should be included in the genus as the 24th Oryza species. Cultivated rice is classified as an AA genome diploid and has 6 wild AA genome relatives. The remaining 15 wild species are classified into 9 other genome types that include both diploid and tetraploid species. Figure 15.1 shows a proposed phylogenetic tree of the genus Oryza as described by Ge et al. (1999) based on the analysis of two nuclear genes and one chloroplast gene. The wild rice species offer a largely untapped resource of agriculturally important genes that have the potential to solve many of the problems in rice production that we face today, such as yield, drought, and salt tolerance as well as disease and insect resistance. To better understand the wild species of rice and take advantage of the IRGSP genome sequence, we have embarked on an ambitious comparative genomics program entitled the Oryza Map Alignment Project (OMAP). The long-term objective of OMAP is to create a genome-level closed experimental system for the genus Oryza that can be used as a research platform to study evolution, development, genome organization, polyploidy, domestication, gene regulatory networks, and crop improvement. The specific objectives of OMAP are to (1) construct deep-coverage large-insert bacterial artificial chromosome (BAC) libraries from 11 wild and 1 cultivated African Oryza species (O. glaberrima); (2) fingerprint and end-sequence clones from all 12 BAC libraries; (3) construct physical maps for all 12 Oryza species and align them to the IRGSP genome sequence; and (4) perform a detailed reconstruction of rice chromosomes 1, 3, and 10 across all 12 Oryza species (Wing et al. 2005). This chapter presents our current progress for OMAP and some early glimpses into the results we are finding

The genome of Theobroma cacao.

We sequenced and assembled the draft genome of Theobroma cacao, an economically important tropical-fruit tree crop that is the source of chocolate. This assembly corresponds to 76% of the estimated genome size and contains almost all previously described genes, with 82% of these genes anchored on the 10 T. cacao chromosomes. Analysis of this sequence information highlighted specific expansion of some gene families during evolution, for example, flavonoid-related genes. It also provides a major source of candidate genes for T. cacao improvement. Based on the inferred paleohistory of the T. cacao genome, we propose an evolutionary scenario whereby the ten T. cacao chromosomes were shaped from an ancestor through eleven chromosome fusions