Evolutionary hierarchies of conserved blocks in 5'-noncoding sequences of dicot rbcS genes

摘要: Evolutionary processes in gene regulatory regions are major determinants of organismal evolution, but exceptionally challenging to study. We explored the possibilities evolutionary analysis phylogenetic footprints 5'-noncoding sequences (NCS) from 27 ribulose-1,5-bisphosphate carboxylase small subunit (rbcS) genes, three dicot families (Brassicaceae, Fabaceae and Solanaceae). Sequences up 400 bp encompassing proximal promoter 5'-untranslated were analyzed. conducted footprinting by several alternative methods: generalized Lempel-Ziv complexity (C LZ ), multiple alignments with DIALIGN ALIGN-M, MOTIF SAMPLER Gibbs sampling algorithm. These tools collectively defined 36 conserved blocks mean length 12.8 bp. On average, 12.5 found each 5'-NCS. The occurred arrays whose relative order was absolutely conserved, confirming existence 'conserved modular arrays' promoters. Identities half confirmed past rbcS research, including versions I-box, G-box, GT-1 sites such as Box II. Over 90% overlapped DNase-protected tomato Regions characterized low C sliding-window analyses also frequently associated DNase-protection. Blocks could be assigned hierarchies based on taxonomic distribution estimated age. Lineage divergence dates implied that 13 all plant Cretaceous antiquity, while other family-specific much younger. dated formation multigene families, using genome coding sequence information. Dendrograms relations 5'-NCS produced methods, including: cluster pairwise values; trees alignments; cladistic blocks. Dicot contain recurrent blocks, which coincident functional elements. amenable interpretation ancient, taxonomically widespread can distinguished more recent, taxon-specific ones.