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Hybridization brings together chromosome sets from two or more distinct progenitor species. Genome duplication associated with hybridization, or allopolyploidy, allows these chromosome sets to persist as distinct subgenomes during subsequent meioses. Here, we present a general method for identifying the subgenomes of a polyploid based on shared ancestry as revealed by the genomic distribution of repetitive elements that were active in the progenitors. This subgenome-enriched transposable element signal is intrinsic to the polyploid, allowing broader applicability than other approaches that depend on the availability of sequenced diploid relatives. We develop the statistical basis of the method, demonstrate its applicability in the well-studied cases of tobacco, cotton, and Brassica napus , and apply it to several cases: allotetraploid cyprinids, allohexaploid false flax, and allooctoploid strawberry. These analyses provide insight into the origins of these polyploids, revise the subgenome identities of strawberry, and provide perspective on subgenome dominance in higher polyploids. Assigning assembled chromosomes to subgenome in allopolypoid genome analysis is challenging. Here, the authors report a statistical formwork for identifying evolutionarily coherent subgneomes relying on transposable elements to group chromosomes into sets with shared ancestry and apply it in cyprinids, false flax and strawberry.

To explore the origins and consequences of tetraploidy in the African clawed frog, we sequenced the Xenopus laevis genome and compared it to the related diploid X. tropicalis genome. We characterize the allotetraploid origin of X. laevis by partitioning its genome into two homoeologous subgenomes, marked by distinct families of ‘fossil’ transposable elements. On the basis of the activity of these elements and the age of hundreds of unitary pseudogenes, we estimate that the two diploid progenitor species diverged around 34 million years ago (Ma) and combined to form an allotetraploid around 17–18 Ma. More than 56% of all genes were retained in two homoeologous copies. Protein function, gene expression, and the amount of conserved flanking sequence all correlate with retention rates. The subgenomes have evolved asymmetrically, with one chromosome set more often preserving the ancestral state and the other experiencing more gene loss, deletion, rearrangement, and reduced gene expression. The two homoeologous subgenomes in the allotetraploid frog Xenopus laevis evolved asymmetrically; one often retained the ancestral state, whereas the other experienced gene loss, deletion, rearrangement and reduced gene expression. Genomic evolution in Xenopus laevis Xenopus laevis , also known as the African clawed frog or platanna, is an important model organism that is used in the study of vertebrate cell and developmental biology. It is a palaeotetraploid—the product of genome duplications that occurred many millions of years ago. This makes X. laevis ideal for the study of polyploidy, but has greatly complicated genome sequencing. Here an international research collaboration reports the X. laevis genome sequence and compares it to that of the related X. tropicalis . Their analyses confirm that X. laevis is an allotetraploid and distinguishes two subgenomes that evolved asymmetrically—one often retained the ancestral state and the other was subject to gene loss, deletion, rearrangement and reduced expression. The two diploid progenitor species diverged about 34 million years ago, combining to form an allotetraploid about 18 million years ago.

Miscanthus is a perennial wild grass that is of global importance for paper production, roofing, horticultural plantings, and an emerging highly productive temperate biomass crop. We report a chromosome-scale assembly of the paleotetraploid M. sinensis genome, providing a resource for Miscanthus that links its chromosomes to the related diploid Sorghum and complex polyploid sugarcanes. The asymmetric distribution of transposons across the two homoeologous subgenomes proves Miscanthus paleo-allotetraploidy and identifies several balanced reciprocal homoeologous exchanges. Analysis of M. sinensis and M. sacchariflorus populations demonstrates extensive interspecific admixture and hybridization, and documents the origin of the highly productive triploid bioenergy crop M. × giganteus . Transcriptional profiling of leaves, stem, and rhizomes over growing seasons provides insight into rhizome development and nutrient recycling, processes critical for sustainable biomass accumulation in a perennial temperate grass. The Miscanthus genome expands the power of comparative genomics to understand traits of importance to Andropogoneae grasses. The perennial grass Miscanthus is a promising biomass crop. Here, via genomics and transcriptomics, the authors reveal its allotetraploid origin, characterize gene expression associated with rhizome development and nutrient recycling, and describe the hybrid origin of the triploid M. x giganteus .

Duplication has long been recognized as an evolutionary source of novelty. The relaxation of purifying selection following duplication allows for normally deleterious mutations to persist long enough to give rise to novel phenotypes. Whole-genome duplications (WGDs) are a specific type of duplication, in which a species suddenly finds itself with two copies of all of its genomic loci. While the fate of most of the duplicated loci is to be lost, those that persist are thought to underlie the innovations seen in groups with a history of polyploidy, such as flowering plants, yeast, Paramecium, and vertebrates. These ancient events give us an idea of how WGDs can drive the radiation of large and diverse phyla, but do not give us any information on the genomic response immediately following polyploidy. This thesis provides insights into the origins of polyploidy and its effects on genome dynamics. There are two models for the mechanism of polyploidy: autopolyploidy and allopolyploidy. Autopolyploids are formed by doubling the somatic chromosomes in the zygote or early embryo. Allopolyploids are formed by the hybridization of two related, but genetically distinct, species, followed by chromosome doubling. If there are no extant diploid relatives, it can be difficult to distinguish between these two models. One feature of allopolyploids is the lack of recombination between their homeologous chromosomes. The end result is that any markers that were unique to each species while apart, such as transposable element subfamilies, will be asymmetrically distributed on the progenitor chromosomes in an organism that recently underwent a WGD. Xenopus laevis is an important vertebrate model in developmental and cell biology that has experienced a recent WGD (~40 million years ago [MYA], based on cDNA alignments (Hellsten, 2007). Its diploid cousin Xenopus tropicalis has become a popular genetic model frog. Comparative analysis of these two frog genomes gives us an excellent opportunity to study genome dynamics following whole genome duplication. The discovery of asymmetrically distributed transposon subfamilies supports the model that cross-species hybridization through allotetraploidy is the mechanism underlying the polyploid Xenopus radiation. Thus, the sub-genome sequence divergence of 40 MYA dates the divergence of the progenitor species, not the hybridization event. The asymmetric distribution of these elements between homeologous sequences allows us to assign chromosomes to progenitor species, named “A” and “B”, making X. laevis a unique system to study sub-genome-specific evolution. The wealth of transcriptome and epigenetic data available for Xenopus allows me to assay how these genomic changes affect gene expression as well as gene retention. The combination of these resources with genomic data gives me the resolution needed to date the hybridization both by studying the decay of unitary pseudogenes and by comparative analysis of the transposable elements discussed above. The sub-genome from progenitor species “A” has more assembled length, longer chromosomes, a higher rate of gene retention, and higher average expression in the adult frog. The B sub-genome has higher synonymous and nonsynonymous mutation rates. The chromosomes orthologous to X. tropicalis 9 and 10 are fused in both sub-genomes of X. laevis, forming homeologous chromosomes 15 and 18, and deviate from the A/B trends discussed above. The regions of these X. laevis chromosomes orthologous to X. tropicalis chromosome 10 have a lower density of diagnostic repeats, no sub-genome bias in gene retention, and have a higher silent substitution rate. This divergence from the rest of the genome is not shared by the regions orthologous to X. tropicalis 9. I hypothesize that the short length of X. tropicalis 10 plays a role in these deviations due to a higher rate of gene conversion on shorter chromosomes.

Long-term climate change and periodic environmental extremes threaten food and fuel security 1 and global crop productivity 2 – 4 . Although molecular and adaptive breeding strategies can buffer the effects of climatic stress and improve crop resilience 5 , these approaches require sufficient knowledge of the genes that underlie productivity and adaptation 6 —knowledge that has been limited to a small number of well-studied model systems. Here we present the assembly and annotation of the large and complex genome of the polyploid bioenergy crop switchgrass ( Panicum virgatum ). Analysis of biomass and survival among 732 resequenced genotypes, which were grown across 10 common gardens that span 1,800 km of latitude, jointly revealed extensive genomic evidence of climate adaptation. Climate–gene–biomass associations were abundant but varied considerably among deeply diverged gene pools. Furthermore, we found that gene flow accelerated climate adaptation during the postglacial colonization of northern habitats through introgression of alleles from a pre-adapted northern gene pool. The polyploid nature of switchgrass also enhanced adaptive potential through the fractionation of gene function, as there was an increased level of heritable genetic diversity on the nondominant subgenome. In addition to investigating patterns of climate adaptation, the genome resources and gene–trait associations developed here provide breeders with the necessary tools to increase switchgrass yield for the sustainable production of bioenergy. The genome of the biofuel crop switchgrass ( Panicum virgatum ) reveals climate–gene–biomass associations that underlie adaptation in nature and will facilitate improvements of the yield of this crop for bioenergy production.