Comparative studies of amniotes have been hindered by a dearth of reptilian molecular sequences. With the genomic assembly of the green anole, Anolis carolinensis available, non-avian reptilian genes can now be compared to mammalian, avian, and amphibian homologs. Furthermore, with more than 350 extant species in the genus Anolis, anoles are an unparalleled example of tetrapod genetic diversity and divergence. As an important ecological, genetic and now genomic reference, it is imperative to develop a standardized Anolis gene nomenclature alongside associated vocabularies and other useful metrics.
Here we report the formation of the Anolis Gene Nomenclature Committee (AGNC) and propose a standardized evolutionary characterization code that will help researchers to define gene orthology and paralogy with tetrapod homologs, provide a system for naming novel genes in Anolis and other reptiles, furnish abbreviations to facilitate comparative studies among the Anolis species and related iguanid squamates, and classify the geographical origins of Anolis subpopulations.
This report has been generated in close consultation with members of the Anolis and genomic research communities, and using public database resources including NCBI and Ensembl. Updates will continue to be regularly posted to new research community websites such as lizardbase. We anticipate that this standardized gene nomenclature will facilitate the accessibility of reptilian sequences for comparative studies among tetrapods and will further serve as a template for other communities in their sequencing and annotation initiatives.
As the rate of generating new sequence assemblies continues to accelerate, the final bottleneck that remains is annotation. While automated pipelines have been developed, it is still up to community initiatives to pool, evaluate, integrate, and disseminate the necessary resources required for functional and comparative annotations that support research needs. The presence of multiple tools and resources, and changing assemblies and annotations, presents “moving-target” challenges for those attempting to assign function, orthology, nomenclature and other common vocabulary to genetic loci. One challenge is that many assemblies are, or will be, periodically updated due to resequencing efforts that aim to fill in ever-present gaps, initiatives to provide a consensus reference sequence that takes into account the polymorphism present in a species, or a re-deployment of different assembly algorithms. The second challenge is that the generation of confidently assigned gene models on a fixed assembly generally correlates with the amount of effort that a community puts into annotating their genome of interest. A third challenge relates to the principle that orthologous (and by association, functional) assignments are interdependent on the quality and quantity of annotations from closely related genomes.