We analyzed the complete mitochondrial DNA (mtDNA) sequences of three humans (African, European, and Japanese), three African apes (common and pygmy chimpanzees, and gorilla), and one orangutan in an attempt to estimate most accurately the substitution rates and divergence times of hominoid mtDNAs. Nonsynonymous substitutions and substitutions in RNA genes have accumulated with an approximately clock-like regularity. From these substitutions and under the assumption that the orangutan and African apes diverged 13 million years ago, we obtained a divergence time for humans and chimpanzees of 4.9 million years. This divergence time permitted calibration of the synonymous substitution rate (3.89 x 10(-8)/site per year). To obtain the substitution rate in the displacement (D)-loop region, we compared the three human mtDNAs and measured the relative abundance of substitutions in the D-loop region and at synonymous sites. The estimated substitution rate in the D-loop region was 7.00 x 10(-8)/site per year. Using both synonymous and D-loop substitutions, we inferred the age of the last common ancestor of the human mtDNAs as 143,000 +/- 18,000 years. The shallow ancestry of human mtDNAs, together with the observation that the African sequence is the most diverged among humans, strongly supports the recent African origin of modern humans, Homo sapiens sapiens.

Mutagenized Arabidopsis seedlings (ecotype Columbia) were screened for the ability to grow photoautotrophically on solid medium containing 200 mM NaCl. A novel mutant line, designated pst1 (for photoautotrophic salt tolerance1), was obtained. There were no significant differences between pst1 and wild-type plants with regard to their ability to induce proline as an osmoregulatory solute. In addition, the content of monovalent cations in pst1 plants grown with or without salt stress was equal to that in the wild type. We observed that light, even at moderate intensities, increased the effects of salt stress on wild-type plants. The pst1 seedlings were nearly 10 times more tolerant to methyl viologen than were wild-type seedlings. We also found that the activities of the active oxygen scavengers superoxide dismutase and ascorbate peroxidase were enhanced significantly in pst1 plants. The pst1 plants also were tolerant to other stresses, such as high light intensity and toxic monovalent cations. The recessive nature of the pst1 mutation indicates that the potential for salt-stress tolerance is blocked in wild-type Arabidopsis.

DNA methylation is a type of epigenetic marking that strongly influences chromatin structure and gene expression in plants and mammals. Over the past decade, DNA methylation has been intensively investigated in order to elucidate its control mechanisms. These studies have shown that small RNAs are involved in the induction of DNA methylation, that there is a relationship between DNA methylation and histone methylation, and that the base excision repair pathway has an important role in DNA demethylation. Some aspects of DNA methylation have also been shown to be shared with mammals, suggesting that the regulatory pathways are, in part at least, evolutionarily conserved. Considerable progress has been made in elucidating the mechanisms that control DNA methylation; however, many aspects of the mechanisms that read the information encoded by DNA methylation and mediate this into downstream regulation remain uncertain, although some candidate proteins have been identified. DNA methylation has a vital role in the inactivation of transposons, suggesting that DNA methylation is a key factor in the evolution and adaptation of plants.

Summary: While characterized mutable alleles caused by DNA transposons have been abundant in maize since the discovery of Dissociation conferring variegation by Barbara McClintock, only a few mutable alleles have been described in rice even though the rice genome contains various transposons. Here, we show that a spontaneous mutable virescent allele, pyl‐v, is caused by the disruption of the nuclear‐coded essential chloroplast protease gene, OsClpP5, due to insertion of a 607‐bp non‐autonomous DNA transposon, non‐autonomous DNA‐based active rice transposon one (nDart1), belonging to the hAT superfamily. The transposition of nDart1 can be induced by crossing with a line containing an autonomous element, aDart, and stabilized by segregating out of aDart. We also identified a novel mutable dwarf allele thl‐m caused by an insertion of nDart1. The japonica cultivar Nipponbare carries no aDart, although it contains epigenetically silenced Dart element(s), which can be activated by 5‐azacytidine. Nipponbare bears four subgroups of about 3.6‐kb Dart‐like sequences, three of which contain potential transposase genes, and around 3.6‐kb elements without an apparent transposase gene, as well as three subgroups of about 0.6‐kb nDart1‐related elements that are all internal deletions of the Dart‐like sequences. Both nDart1 and 3.6‐kb Dart‐like elements were also present in indica varieties 93‐11 and Kasalath. nDart1 appears to be the most active mutagen among nDart1‐related elements contributing to generating natural variations. A candidate for an autonomous element, aDart, and a possible application of nDart1 for transposon tagging are discussed.