Types, levels and patterns of low-copy DNA sequence divergence, and phylogenetic implications, for Gossypium genome types

Abstract

To explore types, levels and patterns of genetic divergence among diploid Gossypium (cotton) genomes, 780 cDNA, genomic DNA and simple sequence repeat (SSR) loci were re-sequenced in Gossypium herbaceum (A1 genome), G. arboreum (A2), G. raimondii (D5), G. trilobum (D8), G. sturtianum (C1) and an outgroup, Gossypioides kirkii. Divergence among these genomes ranged from 7.32 polymorphic base pairs per 100 between G. kirkii and G. herbaceum (A1) to only 1.44 between G. herbaceum (A1) and G. arboreum (A2). SSR loci are least conserved with 12.71 polymorphic base pairs and 3.77 polymorphic sites per 100 base pairs, whereas expressed sequence tags are most conserved with 3.96 polymorphic base pairs and 2.06 sites. SSR loci also exhibit the highest percentage of 'extended polymorphisms' (spanning multiple consecutive nucleotides). The A genome lineage was particularly rapidly evolving, with the D genome also showing accelerated evolution relative to the C genome. Unexpected asymmetry in mutation rates was found, with much more transition than transversion mutation in the D genome after its divergence from a common ancestor shared with the A genome. This large quantity of orthologous DNA sequence strongly supports a phylogeny in which A-C divergence is more recent than A-D divergence, a subject that is of much importance in view of A-D polyploid formation being key to the evolution of the most productive and finest-quality cottons. Loci that are monomorphic within A or D genome types, but polymorphic between genome types, may be of practical importance for identifying locus-specific DNA markers in tetraploid cottons including leading cultivars.

Converting restriction fragment length polymorphism to single‐strand conformation polymorphism markers and its application in the fine mapping of a trichome gene in cotton

“…) and new marker development (Rong et al. ). However, due to the drawbacks of RFLP marker as mentioned above, cotton genetic maps that were constructed more recently invariably used SSR markers (Han et al.…”

Extensive and Biased Intergenomic Nonreciprocal DNA Exchanges Shaped a Nascent Polyploid Genome, Gossypium (Cotton)

“…The D-genome has higher GC content than the Agenome in the heterochromatin where A t -to-D t conversion is enriched, and the A-genome has higher GC content than the D-genome in the euchromatin where D t -to-A t conversion is enriched (Figure 2). The high correlation of tetraploid cotton gene conversion with the GC ratio between the two progenitor genomes (R 2 = 0.506) (Figure 3A), may explain the 30% more A-to-G and T-to-C mutations in the D-genome than the A-genome since their divergence (Rong et al 2012).To investigate genomic features related to HeGCEs, we compared regions with highly (HC)-or little (LC)-biased conversion. Across the genome, the log-ratio of A t -to-D t vs. Figure 4A).…”