Abstract
As a model plant to study perennial trees in the Salicaceae family, the poplar (Populus trichocarpa) genome was sequenced, revealing recurrent paleo-polyploidizations during its evolution. A comparative and hierarchical alignment of its genome to a well-selected reference genome would help us better understand poplar’s genome structure and gene family evolution. Here, by adopting the relatively simpler grape (Vitis vinifera) genome as reference, and by inferring both intra- and inter-genomic gene collinearity, we produced a united alignment of these two genomes and hierarchically distinguished the layers of paralogous and orthologous genes, as related to recursive polyploidizations and speciation. We uncovered homologous blocks in the grape and poplar genomes and also between them. Moreover, we characterized the genes missing and found that poplar had two considerably similar subgenomes (≤0.05 difference in gene deletion) produced by the Salicaceae-common tetraploidization, suggesting its autotetraploid nature. Taken together, this work provides a timely and valuable dataset of orthologous and paralogous genes for further study of the genome structure and functional evolution of poplar and other Salicaceae plants.
Highlights
Poplar (Populus trichocarpa), a Salicaceae plant, is important for providing raw fuel material for the manufacturing industry and it plays an important ecological role in protecting the natural environment (Wang, 2007)
The poplar genome was affected by an extra tetraploidization, or whole-genome duplication, which was inferred to have occurred c. 60 million of years ago, and which is shared by other Salicaceae plants (Tuskan et al, 2006; Dai et al, 2014)
3030 genes were found in 126 blocks that contained more than 10 colinear genes, while in poplar, there were 14 590 colinear genes found in 202 blocks
Summary
Poplar (Populus trichocarpa), a Salicaceae plant, is important for providing raw fuel material for the manufacturing industry and it plays an important ecological role in protecting the natural environment (Wang, 2007). Polyploidy is an important genetic phenomenon of land plants, and it possibly contributed to their evolutionary origins and diversifications (Paterson et al, 2004; Soltis et al, 2008; Jiao et al, 2011). It is considered one of the main factors in the formation of the angiosperms, a large flowering plant group wherein recurring polyploidizations and extensive genome rearrangements rewire the combination of genes (Tang et al, 2008a). Recursive polyploidizations have produced thousands of duplicated genes, providing enormous opportunities for genetic innovation (Taylor and Raes, 2004)
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