The chemoreceptor repertoire of D. silvatica
The chemosensory repertoire of chelicerates, particularly of spiders, is characterized by a high diversity in terms of copy number and sequence divergence, likely resulted from a constant and prolonged gene birth and death process, only altered by episodic bursts of gene duplication yielding lineage-specific expansions (Vizueta et al., 2018). Here, our comprehensive analysis using the BITACORA pipeline allowed the identification in the genome of D. silvatica of 545 chemoreceptor genes, corresponding to 134 Gr and 411 Ir (plus one homolog to the insect Ir25a and 24 iGluR ) sequences (Figure 4; Tables 3, S4 and S5). Although these family sizes are in agreement with the variability observed across spider genomes, the 411Ir reported here represents the largest repertoire found for this family in chelicerates, only surpassed by the extraordinary chemoreceptor repertoire found in the German cockroach genome (Robertson, Baits, Walden, Wada-Katsumata, & Schal, 2018). On the other hand, the number of Grs in D. silvatica is relatively low compared to other spiders (i.e. S MIN of 634 Grs in Parasteatoda tepidariorum ), which could suggest a different contribution of the gustatory repertories to the evolutionary, and probably adaptive history of these different spider lineages.
Noticeably, most identified chemoreceptor genes are complete (459 complete genes under the criterion considered in this article; see methods), yielding a S MIN of 540 genes (Table 3). This large proportion of complete copies is highly unusual in reports on these chemoreceptor families across arthropod genomes (Vizueta et al., 2018), clearly demonstrating the benefits of having a chromosome-level assembly to annotate, characterize and study multigene families in animal genomes. The new high-quality assembly has uncovered, for example, that the two studied gene families are unevenly distributed across pseudochromosomes. The X chromosome, representing the 23.3% of the genome assembly, harbors only 3.0% and 3.2% of the Gr andIr identified copies, respectively (Table 3); the members of these families, nevertheless, are more uniformly distributed across the other major pseudochromosomes. Even so, the number of chemoreceptors located in the small scaffolds, which only represent 11.8% of the total assembly, represents 23.1% and 59.6% of the Gr and Irrepertories, respectively. This uneven distribution, however, is not observed when considering all genes identified in the genome (Table 3). While the first feature likely hides some (unknown) particularities of the sex chromosome, the high representation of gene family members across the minor scaffolds could be explained by the assembly difficulties of these repetitive regions. Further studies including gene families with different family sizes will get insights into this genomic feature.