Comparative genomics of Gossypium and Arabidopsis: Unraveling the consequences of both ancient and recent polyploidy

Abstract

Both ancient and recent polyploidy, together with post-polyploidization loss of many duplicated gene copies, complicates angiosperm comparative genomics. To explore an approach by which these challenges might be mitigated, genetic maps of extant diploid and tetraploid cottons (Gossypium spp.) were used to infer the approximate order of 3016 loci along the chromosomes of their hypothetical common ancestor. The inferred Gossypium gene order corresponded more closely than the original maps did to a similarly inferred ancestral gene order predating an independent paleopolyploidization (␣) in Arabidopsis. At least 59% of the cotton map and 53% of the Arabidopsis transcriptome showed correspondence in multilocus gene arrangements based on one or both of two software packages (CrimeStatII, FISH). Genomic regions in which chromosome structural rearrangement has been rapid (obscuring gene order correspondence) have also been subject to greater divergence of individual gene sequences. About 26%-44% of corresponding regions involved multiple Arabidopsis or cotton chromosomes, in some cases consistent with known, more ancient, duplications. The genomic distributions of multiple-locus probes provided early insight into the consequences for chromosome structure of an ancient large-scale duplication in cotton. Inferences that mitigate the consequences of ancient duplications improve leveraging of genomic information for model organisms in the study of more complex genomes.

Gene copy number evolution during tetraploid cotton radiation

“…Even 'diploid' cotton has experienced at least one genome duplication as its divergence from a common ancestor shared with Arabidopsis (Rong et al, 2005), a period during which Arabidopsis has experienced two genome duplications. DR genes have lower copy number than randomly selected genes in 'diploid' cotton, indicating that the ancestors of modern diploid cotton may have experienced gene loss similar to that being observed now in tetraploid cotton.…”

“…In this same time period, cotton has independently experienced a paleoduplication (Rong et al, 2005) and the well-known polyploid formation. Nonetheless, cotton and Arabidopsis are relatively closely related in the angiosperm phylogeny (Bowers et al, 2003;Rong et al, 2005).…”

“…In this same time period, cotton has independently experienced a paleoduplication (Rong et al, 2005) and the well-known polyploid formation. Nonetheless, cotton and Arabidopsis are relatively closely related in the angiosperm phylogeny (Bowers et al, 2003;Rong et al, 2005). Correlated patterns of retention/loss of duplicated genes in the Arabidopsis and cotton genomes would lend further support to the notion that an underlying set of principles of molecular evolution may contribute to the fates of gene and genome duplications .…”

Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres

“…The combination of BES/markers hybridized to fingerprint contigs 32 , 2,800 markers in a genetic map for the D genome in an A t D t plant 33 and 262 markers from the tetraploid genetic map 34 , along with Vitis vinifera and T. cacao synteny was used to identify breaks in the initial assembly. Markers were aligned to the assembly using BLAT 35 (parameters: -t 5 dna -q 5 dna 2minScore 5 200 -extendThroughN).…”

Toward Sequencing Cotton (Gossypium) Genomes: Figure 1.

“…Some of these maps collectively include approximately 5,000 DNA markers (approximately 3,300 restriction fragment length polymorphisms, approximately 700 amplified fragment length polymorphisms, approximately 1,000 simple sequence repeats, and approximately 100 single nucleotide polymorphisms). In addition, sequence-tagged site-based maps consisting of 2,584 loci at 1.72-cM (approximately 600 kb) intervals in tetraploids (AD genomes), 1,014 loci at 1.42-cM (approximately 600 kb) intervals in diploids (D genome; Rong et al, 2004Rong et al, , 2005, and an EST-simple sequence repeat-based genetic map of 1,710 loci at 1.92-cM intervals in tetraploids (AD genomes; Guo et al, 2007) are available. There is a high degree of colinearity among the respective genome types .…”