Author's response: Following the Occham's razor principle, the simplest and most probable hypothesis is that in prokaryotes, after a duplication, both copies of the gene are conserved, usually in tandem or, less frequently, in a distant region of the chromosome.
For the few gene families that have been studied in core dinoflagellates, a general pattern of highly duplicated but conserved genes in tandem arrays has been seen for actin, proliferating cell nuclear antigen, and the peridinin chlorophyll protein [ 9, 11, 12, 14, 15].
To further support that osa-miR159a.2 osa-miR159a.2nal importance for rice we searchas for osa-miR159a.2-osa-miR159a.1 tandem structures conserved in more distant Oryza species with difunctionalnome types [ 23].
Finally we also identified by BLASTN analysis a nearly identical tandem osa-miR1428 gene conserved in Oryza sativa ssp indica, another rice subspecies, showing that the osa-miR1428 tandemiRNANA gene is conserved and could have an important function in rice (not shown).
In terms of the aminoacidic structure of MUC2, the core domains are poorly conserved and rich in tandem repeats.
In comparison, we found only eight of these tandem duplications to be conserved in E. cymbalariae (Table S3A).
We also identified a nearly identical tandem osa-miR1428 gene in Oryza sativa sp indica showing that this tandem miRNA gene has been conserved in other rice subspecies (not shown).
miR-221 and miR-222 are two highly homologous miRNAs encoded in tandem from human chromosome Xp11.3 and are highly conserved in vertebrates.
This may be related to the locus being atypical in having two pspC paralogues in tandem (Iannelli et al. 2002), an arrangement conserved in all isolates in the collection.
It also contained a novel EELR domain conserved in many eukaryote organisms (Figure 7B and 7C), as well as 4 tandem SSF motifs at its C-terminus (Figure 8A).
EB-MMG has tandem SxLP motifs, with the N-terminal one being highly conserved in vertebrate species.
