Primitive Duplicate Hox Clusters in the European Eel's Genome

Abstract

The enigmatic life cycle and elongated body of the European eel (Anguilla anguilla L., 1758) have long motivated scientific enquiry. Recently, eel research has gained in urgency, as the population has dwindled to the point of critical endangerment. We have assembled a draft genome in order to facilitate advances in all provinces of eel biology. Here, we use the genome to investigate the eel's complement of the Hox developmental transcription factors. We show that unlike any other teleost fish, the eel retains fully populated, duplicate Hox clusters, which originated at the teleost-specific genome duplication. Using mRNA-sequencing and in situ hybridizations, we demonstrate that all copies are expressed in early embryos. Theories of vertebrate evolution predict that the retention of functional, duplicate Hox genes can give rise to additional developmental complexity, which is not immediately apparent in the adult. However, the key morphological innovation elsewhere in the eel's life history coincides with the evolutionary origin of its Hox repertoire.

Whole-genome duplication in teleost fishes and its evolutionary consequences

“…Notably, the eels (European and Japanese eel) are currently the only fishes in which the complete set of the original eight Hox clusters has been observed (Guo et al, 2009;Henkel et al, 2012). Since Elopomorpha is the most basal teleost group (Arratia, 1997;Near et al, 2012) this strongly suggests that the ancestor of all living teleosts also possessed eight Hox clusters, consistent with a WGD at the base of teleost evolution (Figure 1).…”

“…Although duplicated Hox genes have also been identified in other teleosts, it was initially not clear whether the increase in the number of Hox clusters is universal for teleosts (Prohaska and Stadler, 2004). Recently, duplicated Hox gene clusters were found in the two most basal extant groups of teleost fishes, the Elopomorpha (including eels and tarpons) (Guo et al, 2009;Henkel et al, 2012). and Osteoglossomorpha (including bony tongues and elephantfish) (Chambers et al, 2009).…”

Assessing patterns of hybridization between North Atlantic eels using diagnostic single-nucleotide polymorphisms

“…Sequence reads were aligned to the European eel genome draft (www.eelgenome.com) (Henkel et al, 2012) using the ungapped aligner Bowtie version 0.12.8 (Langmead et al, 2009). A maximum of two mismatches between the individual reads and the genome were allowed and alignments were suppressed for a particular read when more than one reportable alignment existed, thereby decreasing the risk of paralogous sequences in the data.…”

Population Genomics of Marine Fishes: Next-Generation Prospects and Challenges

“…Since there is little published information available to assess whether this prediction holds true, we used data from two published studies to estimate levels of linkage disequilibrium in European eel (SNP data from a single geographical sample from Pujolar et al, 2014a) and Atlantic cod (SNP data from a single population sample from Hemmer- Hansen et al, 2013) as a function of distance between genetic markers. In European eel, we used the published genome sequence (Henkel et al, 2012a) to infer genomic location and found that linkage disequilibrium decayed to background levels, estimated as levels of linkage disequilibrium between non-syntenic markers, within a few kilobases (10 -20 kb or less; Fig. 4a, b).…”