Development of genomic resources for the phylogenetic analysis of the <Emphasis Type="Italic">Brachionus plicatilis</Emphasis> species complex (Rotifera: Monogononta)

There has been a substantial leap forward in the quantity and quality of genomic resources available for research on rotifers in recent years. We used available genomic and bioinformatics resources to identify variable regions of the genome to design PCR and sequencing primers for the Brachionus plicatilis complex. We then tested their suitability for the study of systematics of this group. Eight amplified successfully for members of the B. plicatilis complex. We sequenced the amplified products, constructed a concatenated alignment (5,511 bp) and carried out phylogenetic analyses. The resulting tree, based on mitochondrial and nuclear genes for 11 clones of six species, was well supported even at relatively deep nodes, contrasting with results of previous studies using only mitochondrial genes, which provide little phylogenetic information for the deepest nodes. The same procedure could be used to design primers for more conserved regions to be used in a wider range of rotifer groups.