@article {67762, title = {Coding sequence-independent homology search identifies highly divergent homopteran putative effector gene family}, journal = {bioRxiv}, year = {2021}, month = {2021 Sep 25}, abstract = {

Many genomes contain rapidly evolving and highly divergent genes whose homology to genes of known function often cannot be determined from sequence similarity alone. However, coding sequence-independent features of genes, such as intron-exon boundaries, often evolve more slowly than coding sequences and can provide complementary evidence for homology. We found that a linear logistic regression classifier using only structural features of rapidly evolving\ bicycle\ aphid effector genes identified many putative\ bicycle\ homologs in aphids, phylloxerids, and scale insects, whereas sequence similarity search methods yielded few homologs in most aphids and no homologs in phylloxerids and scale insects. Subsequent examination of sequence features and intron locations supported homology assignments. Differential expression studies of newly-identified\ bicycle\ homologs, together with prior proteomic studies, support the hypothesis that BICYCLE proteins act as plant effector proteins in many aphid species and perhaps also in phylloxerids and scale insects.

}, doi = {https://doi.org/10.1101/2021.09.24.461719}, author = {Stern, David and Han, Claire} }