PMID: 21182768;PMCID: PMC3046485;Abstract:
Background: Allotetraploids carry pairs of diverged homoeologs for most genes. With the genome doubled in size, the number of putative interactions is enormous. This poses challenges on how to coordinate the two disparate genomes, and creates opportunities by enhancing the phenotypic variation. New combinations of alleles co-adapt and respond to new environmental pressures. Three stages of the allopolyploidization process - parental species divergence, hybridization, and genome duplication - have been well analyzed. The last stage of evolutionary adjustments remains mysterious.Results: Homoeolog-specific retention and use were analyzed in Arabidopsis suecica (As), a species derived from A. thaliana (At) and A. arenosa (Aa) in a single event 12,000 to 300,000 years ago. We used 405,466 diagnostic features on tiling microarrays to recognize At and Aa contributions to the As genome and transcriptome: 324 genes lacked Aa contributions and 614 genes lacked At contributions within As. In leaf tissues, 3,458 genes preferentially expressed At homoeologs while 4,150 favored Aa homoeologs. These patterns were validated with resequencing. Genes with preferential use of Aa homoeologs were enriched for expression functions, consistent with the dominance of Aa transcription. Heterologous networks - mixed from At and Aa transcripts - were underrepresented.Conclusions: Thousands of deleted and silenced homoeologs in the genome of As were identified. Since heterologous networks may be compromised by interspecies incompatibilities, these networks evolve co-biases, expressing either only Aa or only At homoeologs. This progressive change towards predominantly pure parental networks might contribute to phenotypic variability and plasticity, and enable the species to exploit a larger range of environments. © 2010 Chang et al.; licensee BioMed Central Ltd.
Amorpheae (Fabaceae: Papilionoideae) was first considered a natural group by Rupert Barneby in his illustrated monograph Daleae Imagines. Amorpheae currently comprise eight genera, ca. 250 spp., and extensive floral diversity, including loss of corolla and addition of a stemonozone. The Amorpheae and many of Barneby's subtribal groups are supported as monophyletic by previous phylogenetic analysis of nuclear ribosomal and chloroplast sequence data. However, some relationships remain unclear. A nuclear marker derived from a genomic study in Medicago, CNGC4, was sequenced in selected Amorpheae. This is one of the first applications of this marker for phylogenetic study. The new data confirm some relationships inferred using trnK and ITS, but also provide evidence for new arrangements. Combined data were used to explore several aspects of Barneby's taxonomic framework. The phylogeny, in concert with data on floral morphology, implies that simplification of the complex papilionoid flower has occurred several times in the history of the Amorpheae. © 2005, by The New York Botanical Garden Press.