assembly error or additional rearrangement?

1. Rearrangement Rate following the Whole-Genome Duplication in Teleosts -- Sémon and Wolfe 24 (3): 860 -- Molecular Biology and Evolution: "Rearrangement Rate following the Whole-Genome Duplication in Teleosts"

check out to see whether there is higher RR in zebrafish, theoretically.

2. ScienceDirect - Genomics : Phylogenetic analysis of three complete gap junction gene families reveals lineage-specific duplications and highly supported gene classes: "Note that in one of the zebrafish clusters the orientation of the two genes is inverted (cx41.8, cx44.1), suggesting an additional chromosomal rearrangement on the zebrafish chromosome."



3. Ancient duplicated conserved noncoding elements in vertebrates: A genomic and functional analysis -- McEwen et al. 16 (4): 451 -- Genome Research: "In only two cases were all dCNE family members found to be located in the introns of paralogous genes (NBEA and LRBA) that were not the likely target genes. In these two specific cases the predicted target genes, MAB21L1 and MAB21L2, are also located in introns of NBEA and LRBA, respectively."

very interesting and important case! New paper in PLoS One, "Ancient Origin of the New Developmental Superfamily DANGER" also mentioned the Mab21L1/2. Check out!