Scolanthus callimorphus Ultra Conserved Noncoding Elements
Excerpt from Zimmerman et. al., 2021
Genomic Distribution of Ultraconserved Non-coding Elements
Longer stretches of unusually highly conserved non-coding genomic regions have been studied thoroughly in vertebrates with varying methodologies. These ultraconserved non-coding elements (UCNEs) are generally posited to be cis-regulatory regions, but the precise mechanistic requirement for such high conservation is not fully understood. While some previous studies have argued that the degree of conservation observed in UCNEs is specific to vertebrates, a more recent study has asserted that UCNEs are present in smaller numbers within Drosophila. We were therefore interested to find out how many, and to what extent, UCNEs are present in Edwardsiidae. We adopted criteria previously used to detect UCNEs between chicken and humans and found 145 regions in the Nematostella genome that were highly conserved with Scolanthus. 116 of these regions fell into 37 syntenic clusters of at most 500 kb intervening gaps, and the remaining 29 were singletons. Several such clusters were close to NK paralogs, such as one containing 12 UCNEs and spanning 70 kb surrounding the NK3-4 cluster on chromosome 5 and three UCNEs upstream of the NK2.2 cluster on chromosome 2, a pattern previously reported in vertebrates. Additionally, we detected a single UCNE neighboring the PaxC gene. While Pax-associated UCNEs have been previously reported in vertebrates, this neural developmental gene appears to have arisen from a cnidarian-specific duplication, implying that the accompanying UCNE also arose independently. On the other hand, no UCNEs are found near the edwardsiid Irx gene, despite their ubiquity among Bilateria. Likewise, our stringent criteria did not detect the previously reported UCNE at the 3’end of the SoxB2 gene, as previously reported, suggesting that more relaxed parameters might reveal additional conserved elements shared between more distantly related species.