Lsc

R^— R^— Rz— Rz— R-^— R^— R^— Fz— F^— F^— F^— Rz— F^—

F—^ F—^ F—^ F—^ F—^ F—^ F—^ R—^ R—^ R—^ R—^ F—^ R—^

_rp!2 ndhB_rps7_rrn16_rrn5 rp!32_chIL rrn5_rrn16_rps7 ndhB psbA chIB

LSC IR SSC IR LSC Figure 6.4 Primer locations for the current study of plastid genome organization in ferns: (a) Adiantum and (b) Angiopteris.

Figure 6.5 Current understanding of plastid genome inversions (see Figure 6.1) marked on a simplified phylogenetic framework.

gleichenioid clade and its sister. Inversion 2 occurred on the branch leading to the common ancestor of the heterosporous fern clade and its sister group. Note that either parsimonious acquisition of inversion 1 requires that the gleiche-nioid ferns are not sister to the filmy ferns, as is possible with the unresolved tree in Figure 6.2. That sister relationship was recovered in only some of the analyses by Pryer et al. (2004); see Chapter 15.

The gene order data gathered so far suggest that major rearrangement events do occur in intervals, rather than during temporal hot spots. This being the case, rearrangement events, when present, yield another potential phylogenetic marker to be considered. The one caveat we should add is that our inferences are based on the sampling of only one taxon per major lineage. Although this should be sufficient to infer the sequence of events involved in the major, already characterized, inversions, we could be missing other structural changes that are significant, and even phylogenetically informative within specific lineages.

6.5 Conclusions and prospects

Although our overall understanding of fern plastid genome structure and evolution is increasing, we still lack knowledge of the variation within many groups of ferns, where DNA sequence data from a sample of genes is the preferred approach for phylogenetic studies. In general, the plastid genome structure remains evolutionarily conservative (or perhaps there is convergence to a stable structure), yet in certain clades the structure can become destabilized. Thus, within some angiosperm families, the plastid genome structure provides a wealth of phylogenetic data (Cosner et al., 2004; Kim et al., 2005). In ferns, only a few groups have been examined extensively at the structural level, one excellent example being the tree ferns (Conant et al., 1994). With the shift to sequenced based approaches, it is likely that some potentially very useful data may be missed. In addition to the traditional studies of plastid genome structure and evolution, it is likely that future studies will examine other aspects of plastid "genomics," especially investigations into plastid proteins (Peltier et al., 2000; van Wijk, 2000; Leister, 2003) as well as regulation of plastid-encoded genes (Wu et al, 1993; Eberhard et al, 2002; Robbens et al, 2005). With the variety and combination of genomic tools currently available, it is likely that the next decade will open up exciting new avenues of investigation.

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