ceae)], and with two genera (Brassica and Zea) serving as exemplars (Palmer and Herbon, 1988; Fauron et al., 1995). The completion of the Arabidopsis mt genome sequence in 1997 (Unseld et al., 1997; Marienfeld et al., 1999) gave a more fine-grained and comprehensive picture of the extent to which foreign DNA uptake and internal duplication have influenced the size, structure, and evolutionary potential of a particular mt genome, but without significantly changing prior notions of the structural dynamics of plant mt genomes.
A few years ago, we set up a large-scale Southern blot survey, of 281 diverse angiosperms, to better elucidate the evolution of two fundamental classes of mt features—their content of genes and of introns—that were poorly characterized relative to the traits whose evolution is described above. Our hope was that by surveying hundreds of diverse plants, we could discern the basic tempo and pattern of gene and intron loss and gain and, furthermore, identify especially attractive candidates for follow-up study to learn about the processes and mechanisms underlying these kinds of structural changes. An additional, utilitarian goal, whose achievements (see, e.g., Qiu et al., 1998) will not be described in this report, was to use these presence/absence characters to help unravel the phylogeny of angiosperms and other land plants. This paper will summarize our results, both recently published and unpublished, on gene content and intron content evolution in angiosperm evolution. We show that rates of gene loss, of accompanying gene transfer to the nucleus, and of intron acquisition by cross-species horizontal transfer can be remarkably high for particular classes of these genetic elements, and that these rates also vary substantially across lineages of flowering plants. As a completely unexpected bonus, these surveys have also led to the discovery of two exceptional groups of plants with vastly elevated rates of synonymous substitutions.
We went to some lengths to sample angiosperm diversity, extracting total DNAs from 281 species that represent 278 genera and 169 families of angiosperms (species listed at www.bio.indiana.edu/~palmerlab). Twelve sets of pseudoreplicate filter-blots were made, each set containing one digest (with either BamHI or HindIII) of each of the 281 DNAs. The digested DNAs were arranged according to the presumptive phylogenetic relationships of their cognate plants as understood about 5 years ago. To date, the sets of blots have been sequentially hybridized with nearly 100 different probes, mostly for segments of various mt genes and introns, but also for several chloroplast genes and introns.