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although hybridization occurs frequently in many grasses, including many agriculturally important crops [ 30 ], it is less common that the products of interspecific hybridization can lead to speciation [ 31 ], with increased interspecific hybridization (i.e., the introgression) recently recognized as being an important and important biological process in plant evolution [ 32, 33 ].

we document 122 gene losses, 25 translocations and six inversions in the plastome of e. arvense. the plastome is highly rearranged with respect to those of other land plants. in addition, the plastome of e. arvense is very at-rich, suggesting that one of its plastome inversions is due to the recently evolved at-richness of this lineage. we also document increased sequence divergence at boundaries of inverted repeats, suggesting that this feature was selected for early in land plant evolution. we have examined nucleotide composition, codon usage and gene content across these early lineages, finding a number of patterns of genomic variation. we found that genomic rearrangements occurred early in land plant history and were not isolated events but rather commonly shared features of the plastome of early land plants. furthermore, these features seem to have evolved rapidly within lineages and have been maintained through millions of years of independent evolution. we hope that data generated here will be useful for understanding early land plant evolution and the evolution of the plastome.

all land plants (embryophytes) are seedless, with the plastid being the organelle of photosynthesis. it is also the site of dna replication, and the site of gene expression and protein translation. the plastid genome is small, ranging from 140 to 250 kilobases, and is often organized into a single large circular chromosome. the plastid genome of the moss physcomitrella patens has been sequenced [ 13 ], and this was the first complete plastome sequence available to the scientific community. the analysis of the physcomitrella plastome is a landmark in plant genomics and as a result we have been able to identify a number of features that have been overlooked or poorly understood in previous studies. in contrast to the highly conserved organization of the plastome, which has been reflected in the evolution of functionally important genes, structural variation, and alterations in base composition, the plastome is unusual in that it is highly differentiated between individuals and taxa. the plastome of physcomitrella is unusual in having high levels of heterogeneity in gene content and gene order. moreover, there is evidence of a number of different genome rearrangements between the plastomes of p. patens and marchantia polymorpha [ 14 ].




It has been known since the 1980s that the basal angiosperms, or monocots, and, less obviously, basal eudicots, have much smaller and highly conserved genomes than are found in the more derived seed plants [ 12 ], i.e., angiosperms. Our knowledge of this dramatic reduction in size follows from attempts to estimate the sizes of angiosperm plastomes based on gene content and linear DNA length. The small-plastome/large-nuclear genome conundrum, as it is known, can be resolved if the number and sizes of plastome introns in basal eudicots are determined. Consequently, the partial plastomes of two congeneric species of Acacia (Fabaceae) were sequenced in order to determine the number and length of introns. These data provide a minimum size of the plastid genome and some evidence for the importance of gene and intron length in the evolution of higher plants [ 13, 14 ]. Perhaps early hybrid populations contained less adaptive genetic material from the parental species, resulting in the hybrid swarm having greater potential for adaptive introgression [ 18 ]. Alternatively, highly divergent morphologies may be a result of multiple, successive invasions by allopolyploid hybrids, which have been observed elsewhere [ 42 ]. Evolutionary relationships among harrisoni and S. xanthioides are poorly known, but the greatest functional variation lies within species, not between them. As with Cynanchum and other former hybrids, the time for zelicaon-like ancestry to predominate may be short and contingent upon a series of rare but highly reproductive hybrid swarms. 5ec8ef588b


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