In contrast to animals, the entire multicellular diploid generation of plants (along with the cuticle and thick-walled, non-motile spores) probably evolved after the transition to land [1,2]. All land plants display alternating multicellular generations – the sexual, haploid gametophyte and the asexual, diploid sporophyte. In early land plant fossils the gametophytic and sporophytic generation share about equal morphological complexity, making it likely that the gametophyte was reduced and the sporophyte became the dominant generation in vascular plants [1-3] while in “bryophytes” (mosses, hornworts and liverworts) the sporophyte generation was reduced and the gametophyte became dominant. Thus, “bryophytes” in comparison with vascular plants enable inference of early states of land plant evolution. Based upon spores found in the fossil record, the first plants had occupied the land in the Middle Ordovician, approximately 460 million years ago (MYA) [1]. The first splits among the Embryophyta separated the Bryopsida (mosses), Antocerotophyta (hornworts) and Marchantiophyta (liverworts) from the remainder of the land plants, the vascular plants. The oldest liverwort fossils are from the Late Devonian, ~360 MYA, the oldest mosses to be found in the fossil record are from the Permian, ~270 MYA [4,5]. The first deposits containing remnants of modern mosses are from the Jurassic and Cretaceous; based on these fossils some extant species exhibited only limited morphological change in the past 80 MY [5,6]. Most of the mosses deposited in European Miocene (24 MYA) are morphologically identical to extant European genera and even species [5,7]. Mosses embedded in Caribbean amber (20–45 MYA) could also be traced to a large extent to extant genera and species [8]. In summary, some moss species might be 40–80 MY old, whereas some genera might even be 80–100 MY old [6], which is also seconded by recent phylogenetic analyses [9,10].
Gene and genome duplications are a driving force of eukaryotic evolution [11,12]. Angiosperms (flowering plants) are paleopolyploids, i.e. the genome of their common ancestor was subject to a large-scale or even genome-wide duplication event during the Late Jurassic or Early Cretaceous, 100–160 MYA [13,14]. This duplication event might have triggered the angiosperm radiation during the Late Cretaceous, which is apparent in the fossil record [15]. There is evidence for several more large-scale or genome-wide duplication events among the angiosperms. The core eudicots apparently duplicated their genome in the Late Cretaceous, while the common ancestor of the Brassicales did so again in the Cenozoic [13,16]. Also poplar, of which the genome sequence has been determined recently, has undergone an additional genome duplication event ~60 MYA, independent of the one in the Brassicales [17]. Recently, paleopolyploidy has been suggested for several basal angiosperm species as well as for some gymnosperms [18]. Interestingly, the retention of genes after such large-scale duplication events has been shown to be biased towards certain functional classes [16,19,20] and it has been argued that such biased retention of duplicated genes has been a driving force for morphological complexity, increase in biological diversity and eukaryote adaptive radiation [13,21].
The aims of the current study were: (i) to reveal molecular evidence for genome duplications in non-seed plants, in particular in the moss Physcomitrella patens, (ii) to date the duplication event(s), and (iii) to study the possible evolutionary consequences by analyzing the retention of different functional classes of genes.
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