INAUGURAL ARTICLES: Rapid recent growth and divergence of rice nuclear genomes

By Jonathan Ma. 2004

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Archaeogenetic study of prehistoric rice remains from Thailand and India: evidence of early japonica in South and Southeast Asia (2016, background): “Backcrossing to the indicamother population is implied by the many studies that have identified a deep whole genome and chloroplast divergence between indica and japonica (Ma and Bennetzen 2004; Tang et al. 2004; Vitte et al. 2004).”
Consilience of genetics and archaeobotany in the entangled history of rice (2010, background): “Whole genome comparisons of representative accessions for the nuclear genome suggest a similarly deep divergence on the orders of 100,000 s of years (Vitte et al. 2004; Ma and Bennetzen 2004), whilst various genes or gene systems also point to differences such as pSINEs (Ohtsubo et al.”
Genome sequencing and analysis of the model grass Brachypodium distachyon (2010, background): “Scaffolds not included in the final assembly were: unanchored rDNA (51); mitochondrial (2); chloroplastic (14); and small unanchored repetitive scaffolds as defined by 95% of the 24mers occurring greater than four times in the large scaffolds (43) or were less than 1kb in sequence length (2).”
Genetic Structure and Diversity in Oryza sativa L. (2005, background): “Deviation of allelic diversity and heterozygosity from mutation-drift equilib- and Morishima 2002; Ma and Bennetzen 2004; Yamanaka et al. 2004).”