Comparative assessment of rcd1 specific wwe domain in making evolutionary patterns against conserved genomic regions

Conserved genomic sequences are of evolutionary importance, as they give information regarding speciation and divergence of taxa. Some sequences that have been used in the determination of plant taxonomic relationships through DNA are rbcL, MatK, atpB-rbcL intergenic spacer with varying success. With the increase in genomic data, the sro family of genes have been found conserved within the kingdom plantae. Among a subset of sro members, the wwe is a domain encoding short stretch of nucleotides that is easily amplified and exists in low copy number per genome. The nucleotides of this domain vary between different species of a plant family while it clusters plants belonging to a same family into statistically supported clades during phylogenetic analyses. This fact raised a need to identify the relationships it forms phylogenetically. To achieve this end, the plants belonging to diverse genera were analysed using wwe, rbcL and rcd1 sequences after amplification from genome and sequence retrieval from online databases. It was found that the plants were clustered by the wwe sequences into their taxonomic families with high bootstrap support. The trees were constructed by using Physcomitrella patens as outgroup as it belongs to order Funariales which is quite divergent to the angiosperms that harbour monocots and dicots. The results demonstrate a potential for using the wwe domain specific to sro family as a molecular marker either alone or in combination with other markers in DNA barcoding and phylogenetics studies, as it has shown to resolve all analysed plants at sub-familial level with high bootstrap support.