The complete chloroplast genome of Pharus latifolius (pharoideae; poaceae) and implications on the early evolution of the grasses.

摘要

This paper has detailed several characters that unite Poaceae as a monophyletic clade, including the genesis of an rpoC2 insert and the subsequent degradation of repeat structures therein, the reduction of the ycf1 and ycf2 pseudogene regions and the general reduction in the size of intergenic regions within whole plastomes. Other characters also support the monophyly of the family, including the preservation of three large inversions and the probable whole genome duplication in the ancestor of the grasses. The case for the exclusion of Anomochlooideae from Poaceae based on morphological characters, the absence of the spikelet floral suite, the absence of the rpoC1 intron and the lack &psgr;rpl23 has been made by other investigators of the basal grade of the family, but I contend that the classical inclusion of the subfamily should be maintained. The polyphyly of the rpoC1 intron loss, reported in several distantly related taxa including other members of Poales, is a conspicuous character and one that may be structurally primed for loss within the order. The other character supporting the familial classification beginning with Pharoideae, the translocation of rpl23 to the LSC, has likewise been reported in several lineages and in the case of Trifolium subterraneum has occurred six times. The simple absence/presence nature of these two characters further discounts their phylogenetic utility, while the sequence-based characters from pseudogenes and indels are far more powerful tools in determining ancestry.;The floral suite of characters that is the grass spikelet is somewhat more ambiguous in its phylogenetic significance, and originates either before the divergence of Anomochlooideae or before the divergence of Pharoideae, supporting the spikelet clade. The inclusion of Anomochlooideae within Poaceae requires either the loss of these floral characters by A. marantoidea at some point following its divergence, or the loss of characters in the ancestor of Anomochlooideae and subsequent reversal to the pseudospikelet state seen in the genus Streptochaeta. The presence of the spikelet-like character set within Streptochaeta suggests the development of similar characters in the ancestor of Poaceae with subsequent modifications in the Anomochlooideae lineage and the lineage leading to the spikelet clade. The reversion to spikelet-like floral characters within Poales has been observed within the families Restionaceae and Cyperaceae, but the apparent infrequency of these events within the order somewhat discounts the possibility of recurrent reversals within Streptochaeta and the spikelet clade. These characters, together with the above molecular characters, support the monophyly of Poaceae in accordance with the traditional system of classification for the family.