The maze of Zea: I. Chloroplast SSRs and evolution

The evolution of Zea and, especially, the domestication of maize have undergone multifaceted assessment for many decades. New analyses have often demonstrated inconsistencies that prompted new thinking. Reexamination of chloroplast microsatellite data from a broad sampling of Zea reveals clear phenetic patterns, notably: 1) The various teosinte taxa are related to each other as expected; 2) Chloroplasts of the tested maize landraces form two very different groups; 3) Mexican annual teosintes are closely linked to only one maize group. These and other results are supported by a wide range of older studies. The latter two patterns deserve careful consideration because they contradict the model that a Mexican annual teosinte was domesticated, then evolved to all present maizes. They do not contradict the model that a small, domesticated maize was greatly changed by introgression, probably by a teosinte in section Luxuriantes of Zea. The introgression probably also led to great evolutionary acceleration, several important bottlenecks and the enormous diversity of modern maize. These chloroplast microsatellite relationships have various implications and deserve careful attention in designing future studies (see discussion)

Analysis and functional classification of transcripts from the nematode Meloidogyne incognita

BACKGROUND: Plant parasitic nematodes are major pathogens of most crops. Molecular characterization of these species as well as the development of new techniques for control can benefit from genomic approaches. As an entrée to characterizing plant parasitic nematode genomes, we analyzed 5,700 expressed sequence tags (ESTs) from second-stage larvae (L2) of the root-knot nematode Meloidogyne incognita. RESULTS: From these, 1,625 EST clusters were formed and classified by function using the Gene Ontology (GO) hierarchy and the Kyoto KEGG database. L2 larvae, which represent the infective stage of the life cycle before plant invasion, express a diverse array of ligand-binding proteins and abundant cytoskeletal proteins. L2 are structurally similar to Caenorhabditis elegans dauer larva and the presence of transcripts encoding glyoxylate pathway enzymes in the M. incognita clusters suggests that root-knot nematode larvae metabolize lipid stores while in search of a host. Homology to other species was observed in 79% of translated cluster sequences, with the C. elegans genome providing more information than any other source. In addition to identifying putative nematode-specific and Tylenchida-specific genes, sequencing revealed previously uncharacterized horizontal gene transfer candidates in Meloidogyne with high identity to rhizobacterial genes including homologs of nodL acetyltransferase and novel cellulases. CONCLUSIONS: With sequencing from plant parasitic nematodes accelerating, the approaches to transcript characterization described here can be applied to more extensive datasets and also provide a foundation for more complex genome analyses