Annotation of the chemoreceptor genes
We performed a comprehensive curation of all members of the major
chemoreceptor gene families encoded in the genome of D.
silvatica , namely the Gustatory-receptor (Gr ) and Ionotropic
(glutamate) receptor (Ir/iGluR ) families (Vizueta, Escuer,
Frıas-Lopez, et al., 2020; Vizueta et al., 2018). For this task, we used
the pipeline BITACORA (Vizueta, Escuer, Sánchez-Gracia, & Rozas, 2020;
Vizueta, Sánchez-Gracia, & Rozas, 2020), along with the homologous
sequence data set and hidden Markov model (HMM) profiles used in Vizueta
et al. (2018) and using the annotated gene models and genome sequence as
input. The resulting identified proteins were validated, and
re-annotated when necessary, in the Apollo genome browser (Lee et al.,
2013). We classified a gene as “complete” if the length of the encoded
protein contains, at least, 80% of the protein domain length
characteristic of the family (235 and 180 amino acids, for the GR and
IR/iGluR proteins, respectively). The remaining incomplete gene models
that could not be recovered using Apollo were classified as “partial”
fragments. For each chemoreceptor family, we computed the minimum number
of chemoreceptor sequences that could be unequivocally attributed to
different genes (S MIN) as in Vizueta et al.
(2018).