Only a Single Taxonomically Restricted Gene Family in the Drosophila melanogaster Subgroup Can Be Identified with High Confidence.

Taxonomically restricted genes (TRGs) are genes that are present only in one clade. Protein-coding TRGs may evolve de novo from previously noncoding sequences: functional ncRNA, introns, or alternative reading frames of older protein-coding genes, or intergenic sequences. A major challenge in studying de novo genes is the need to avoid both false-positives (nonfunctional open reading frames and/or functional genes that did not arise de novo) and false-negatives. Here, we search conservatively for high-confidence TRGs as the most promising candidates for experimental studies, ensuring functionality through conservation across at least two species, and ensuring de novo status through examination of homologous noncoding sequences. Our pipeline also avoids ascertainment biases associated with preconceptions of how de novo genes are born. We identify one TRG family that evolved de novo in the Drosophila melanogaster subgroup. This TRG family contains single-copy genes in Drosophila simulans and Drosophila sechellia. It originated in an intron of a well-established gene, sharing that intron with another well-established gene upstream. These TRGs contain an intron that predates their open reading frame. These genes have not been previously reported as de novo originated, and to our knowledge, they are the best Drosophila candidates identified so far for experimental studies aimed at elucidating the properties of de novo genes.

The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces.

The Orthologous Matrix (OMA) is a leading resource to relate genes across many species from all of life. In this update paper, we review the recent algorithmic improvements in the OMA pipeline, describe increases in species coverage (particularly in plants and early-branching eukaryotes) and introduce several new features in the OMA web browser. Notable improvements include: (i) a scalable, interactive viewer for hierarchical orthologous groups; (ii) protein domain annotations and domain-based links between orthologous groups; (iii) functionality to retrieve phylogenetic marker genes for a subset of species of interest; (iv) a new synteny dot plot viewer; and (v) an overhaul of the programmatic access (REST API and semantic web), which will facilitate incorporation of OMA analyses in computational pipelines and integration with other bioinformatic resources. OMA can be freely accessed at https://omabrowser.org.

Faecal egg counts and immune markers in a line of Scottish Cashmere goats selected for resistance to gastrointestinal nematode parasite infection.

This study aimed to investigate the effect of selection for low faecal egg count (FEC) in Scottish Cashmere goats in comparison to a control line of unselected goats grazing the same pasture. Goats from generations F2 through to F9 were monitored for FEC, bodyweight, peripheral eosinophilia and IgG, IgA and IgE response against Teladorsagia circumcincta from the end of their first grazing season, through winter housing (during which a single artificial challenge dose of 10,000 drug susceptible T. circumcincta was given) and the following full grazing season. The study demonstrated that selected line animals excreted a significantly lower number of parasite eggs (P<0.01) in the majority of generations examined. Liveweight productivity was unaffected by selection. Although selected line animals had greater numbers of circulating eosinophils in many of the generations (four generations of males and six generations of females, P<0.05), there was no direct link between eosinophilia and reduced FEC. Immunoglobulin levels showed no consistent difference between selected and control lines. IgG, IgA and IgE levels were not different between lines over the whole dataset (P>0.05), although the selected line had significantly elevated or reduced levels (P<0.05) for all three within individual generations. There were significant associations between increased IgG and reduced FEC under artificial infection conditions (P=0.02). Increased IgA was also significantly associated with elevated FEC during the second grazing season (P<0.001). The study demonstrates that selection produced a line of goats with consistently reduced FEC compared with control animals, but did not identify a clear relationship between any of the immune markers measured and faecal egg output.