Phylogenetic analysis using this data revealed grouping of genomes comparable with previous studies. In total, 61 SNPs were detected in cotton genomes which include 53 substitutions and 8 Indels in the total 1920 bp genome length. The resultant PCR products amplifying partial gene sequences were sequenced. arboreum showing homology with genes encoding for mitochondrial small heat shock protein (MT-sHSP), histone H2B1, S-adenosyl methionine synthetase, cytochrome p450, actin-depolymerizing factor 2, C-terminal domain of helicases and histone H2B3for designing primers. We explored the expressed sequence tags (ESTs) data set of G.
Here we present the frequency of SNPs in the transcribed regions of the multiple genes, and their utility in resolving phylogenies among 11 diploid species representing five of the eight diploid genomes of the genus Gossypium. To the extent of our knowledge, frequency of single nucleotide polymorphisms (SNPs) has not been calculated in genes of multiple genomes of the genus Gossypium. Genus cotton has total 50 species, diploid species fall into 8 genomic groups (A–G, and K). Inferences that mitigate the consequences of ancient duplications improve leveraging of genomic information for model organisms in the study of more complex genomes. The genomic distributions of multiple-locus probes provided early insight into the consequences for chromosome structure of an ancient large-scale duplication in cotton. About 26%-44% of corresponding regions involved multiple Arabidopsis or cotton chromosomes, in some cases consistent with known, more ancient, duplications. 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. 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). The inferred Gossypium gene order corresponded more closely than the original maps did to a similarly inferred ancestral gene order predating an independent paleopolyploidization (alpha) in Arabidopsis. 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. Both ancient and recent polyploidy, together with post-polyploidization loss of many duplicated gene copies, complicates angiosperm comparative genomics.
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