Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps

Abstract

Large-scale (segmental or whole) genome duplication has been recurring in angiosperm evolution. Subsequent gene loss and rearrangements further affect gene copy numbers and fractionate ancestral gene linkages across multiple chromosomes. The fragmented "multiple-to-multiple" correspondences resulting from this distinguishing feature of angiosperm evolution complicates comparative genomic studies. Using a robust computational framework that combines information from multiple orthologous and duplicated regions to construct local syntenic networks, we show that a shared ancient hexaploidy event (or perhaps two roughly concurrent genome fusions) can be inferred based on the sequences from several divergent plant genomes. This "paleo-hexaploidy" clearly preceded the rosid-asterid split, but it remains equivocal whether it also affected monocots. The model resulting from our multi-alignments lays the foundation for approximating the number and arrangement of genes in the last universal common ancestor of angiosperms. Comparative analysis of inferred homologous genes derived from this model shows patterns of preferential gene retention or loss after polyploidy and reveals large variability of nucleotide substitution rates among plant nuclear genomes.

Polyploid Evolution of the Brassicaceae during the Cenozoic Era

“…The three well-known ancient a, b, and g paleopolyploidization events that have marked the evolutionary history of the Brassicaceae were initially thought to have occurred around 14.5 to 86, 170 to 235, and 300 Mya, respectively (Bowers et al, 2003). Several subsequent attempts at determining the precise age of these ancient polyploidy events and their relative position in the context of Brassicaceae phylogeny have provided ambiguous estimates (Lynch and Conery, 2000;Blanc et al, 2003;Ermolaeva et al, 2003;De Bodt et al, 2005;Schranz and Mitchell-Olds, 2006;Ming et al, 2008;Tang et al, 2008;Barker et al, 2009). A limitation of many of these previous analyses has been the lack of extensive taxonomic breadth, as many of these studies focused only on A. thaliana.…”

“…The g WGD is probably shared by all core eudicots (Bowers et al, 2003;Jaillon et al, 2007;Lyons et al, 2008;Tang et al, 2008;Barker et al, 2009). Considering significant variation in molecular evolutionary rate and lack of precise estimate of nucleotide substitution rate among eudicots, the precise age of the g WGD could not be established.…”

Phylogenomic Synteny Network Analysis of MADS-Box Transcription Factor Genes Reveals Lineage-Specific Transpositions, Ancient Tandem Duplications, and Deep Positional Conservation

“…We analyzed all protein models from these genomes for all possible intra-and interspecies wholegenome comparisons ( Figure 2A). We then built a database that contains all the links between syntenic gene pairs present in syntenic genomic blocks identified by the tool MCScanX (Tang et al, 2008b;Wang et al, 2012). This database contains in total 921,074 nodes (i.e., genes that were connected by synteny with another gene) and 8,045,487 edges (i.e., pairwise syntenic connections); the data can be downloaded from GitHub (https:// github.com/zhaotao1987/SynNet-Pipeline).…”

“…The construction of synteny networks uses three main steps: (1) pairwise whole-genome comparisons, (2) detection of syntenic blocks and data fusion, and (3) network clustering. The first two steps provide a database of syntenic relationships between homologous genes for the genomes analyzed using standard programs, such as BLAST (Altschul et al, 1990) for genome comparisons and MCScan (Tang et al, 2008b) for synteny detection. The final step, the network clustering, can make use of a wide range of clustering algorithms and methods (reviewed in Lancichinetti and Fortunato, 2009;Fortunato, 2010) and are at the heart of our synteny network analysis.…”

Gene copy number evolution during tetraploid cotton radiation

“…Genes in some specific functional categories duplicate and reduplicate. Genes duplicated by gene duplication survive much longer than those duplicated individually (Lynch and Conery, 2000), and some gene functional groups are preferentially preserved in duplicate (Blanc and Wolfe, 2004;Seoighe and Gehring, 2004;Maere et al, 2005;Chapman et al, 2006;Paterson et al, 2006;Tang et al, 2008b). Coding regions of genes preserved in duplicate tend to be functionally complex , under purifying selection (Brunet et al, 2006;Chapman et al, 2006), and may evolve in concert (Gao and Innan, 2004;Wang et al, 2007).…”