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.

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.

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.