Great hammerhead and shortfin mako gene annotation files

These preliminary annotation gff files of great hammerhead and shortfin
mako chromosome-level genomes are presented here, in hopes of being an
asset to the shark genomics community. These annotations were not used for
analysis in our associated paper which focused on conservation genomic
analyses involving levels of heterozygosity and demographic history of
these two species. These annotations should be regarded as preliminary
because of the paucity of quality tissue samples that were available to
us, from these endangered species, to acquire multiple sets of
transcriptomic data. As a result, this hammerhead annotation identifies
genes using ab initio predictions from the Maker2 pipeline (employing
Augustus and EvidenceModeler) combined with a single tissue transcriptome
for training the Augustus gene model (see Stanhope et al. for further
details), and evidence-based predictions for mako, using Stringtie2,
employing the limited RNA-seq available. The majority of the genes
reported here could nonetheless prove beneficial for a variety of
comparative analyses, however, the genomes should not be considered
thoroughly annotated and the full gene structure should be validated prior
to use for targeted analyses. The entire mako annotation is presented
(27,804 protein coding genes). A subset of the hammerhead ab
initio gene prediction pipeline is presented, representing a
total of 26,110 protein coding genes, that were supported by blast
evidence in the hammerhead heart transcriptome sequences. Additionally,
the gff file contains repeats that were soft masked using RepeatMasker
prior to annotation per the methods in Stanhope et al.