Chemoreceptor genes are unevenly distributed across the genome of
D. silvatica
Despite that not all chemoreceptor genes could be mapped on the
scaffolds corresponding to the main cytological described chromosomes,
the new high-quality assembly allowed us to study the genomic
organization and evolution of a great number of paralogous copies of
each family. According to our criterion (see methods), we identified 83
genomic clusters, 17 and 66 of them including Gr and Irgenes, respectively (Figures 5A, 5C, S2A and S2C). These clusters, which
harbor up to 10 copies of the same family, were found in all major
scaffolds of D. silvatica.
To gain insights into the evolutionary meaning of such gene clustering
structure we investigated the relationship between pairwise evolutionary
divergences, measured as dij (the number of amino
acid substitutions per site between two sequences), and physical
distances (in kb). We found that C ST values are
high in all pseudochromosomes, ranging from 0.418 to 0.982 and from
0.428 to 0.894 for the Gr and Ir gene families, respectively,
considering all identified sequences (Table 3); these values are similar
when using only the complete data set (Table S4). These highC ST values translate into statistically lower
evolutionary distances among family copies included in clusters than
those dispersed along the genome, both at the chromosome (Mann–Whitney
U-test, p -values < 0.05 for nearly all
pseudochromosomes) but also at the whole genome levels (p -values
< 0.001 in all cases) (Tables 3 and S4; Figures 5 and S2).
This result, jointly with the large number of genomic clusters found
across the D. silvatica genome, point to the recent origin of
many of the chemoreceptors in this species, and to the unequal
crossing-over as a major mechanism accounting for this origin. After
gene duplication, the paralogs that are retained long enough (i.e.,
those that are not lost by genetic drift or purifying selection),
continuously diverged at the sequence, and likely at the functional
level (at least in terms of ligand specificity or signaling
characteristics). We expect, therefore, that over time, evolutionary
distances of these retained copies increase with physical distance, just
as we have found (Figures 5B, 5D, S2B and S2D). This genomic
architecture could have relevant functional and evolutionary
implications. For instance, the presence of distantly related family
members within the same genomic cluster, could be the hallmark of the
interaction between functional and gene regulation constraints
preventing cluster breaking. A more comprehensive analysis of these
specific cases deserves to be further evaluated.