Multiple hybridization events and repeated evolution of homoeologue expression bias in parthenogenetic, polyploid New Zealand stick insects.

During hybrid speciation, homoeologues combine in a single genome. Homoeologue expression bias (HEB) occurs when one homoeologue has higher gene expression than another. HEB has been well characterized in plants but rarely investigated in animals, especially invertebrates. Consequently, we have little idea as to the role that HEB plays in allopolyploid invertebrate genomes. If HEB is constrained by features of the parental genomes, then we predict repeated evolution of similar HEB patterns among hybrid genomes formed from the same parental lineages. To address this, we reconstructed the history of hybridization between the New Zealand stick insect genera Acanthoxyla and Clitarchus using a high-quality genome assembly from Clitarchus hookeri to call variants and phase alleles. These analyses revealed the formation of three independent diploid and triploid hybrid lineages between these genera. RNA sequencing revealed a similar magnitude and direction of HEB among these hybrid lineages, and we observed that many enriched functions and pathways were also shared among lineages, consistent with repeated evolution due to parental genome constraints. In most hybrid lineages, a slight majority of the genes involved in mitochondrial function showed HEB towards the maternal homoeologues, consistent with only weak effects of mitonuclear incompatibility. We also observed a proteasome functional enrichment in most lineages and hypothesize this may result from the need to maintain proteostasis in hybrid genomes. Reference bias was a pervasive problem, and we caution against relying on HEB estimates from a single parental reference genome.

Prevalence of gastrointestinal helminths and parasites in smallholder pigs reared in the central Free State Province.

Pigs are kept by farmers as a source of livelihood and food. Unfortunately, helminthiasis and other internal parasites are major setbacks to profitable pig production in Africa. There is a lack of information on the prevalence and intensity of gastrointestinal helminths and parasites plaguing resource-poor pig farmers in the Free State. Knowledge of these endemic parasites can be used as baseline data to help design future intervention plans. The aim of this study was to identify and quantify the types of gastrointestinal helminths and parasites prevalent in smallholder pigs reared in the central Free State Province. Faecal samples were randomly collected from 77 pigs and parasitologically analysed. Quantification was done using the McMaster counting technique. Farming system, age, gender and health status were the risk factors considered. The study was conducted between January and March 2016. Overall, results showed that 61 samples (79.2%) tested positive for one or more gastrointestinal parasites, which were observed as single or mixed infections. Amongst the positive samples, 44.5% were infected with Ascaris suum, 50.6% with Trichuris suis, 26.0% and 72.7% were infected with Oesophagostomum dentatum and coccidia, respectively. There were significant differences (p < 0.05) between the rate of infection in the intensive and semi-intensive systems and between the dewormed and non-dewormed pigs. Piglets and female pigs recorded a higher prevalence in their categories. Pigs excreted mostly low (eggs per gram [EPG] ≤ 100) to moderate (EPG > 100 < 500) levels of helminth eggs. It is concluded that different species of gastrointestinal parasites are present in most pigs reared by smallholder farmers in this study area.

Placental Hypomethylation Is More Pronounced in Genomic Loci Devoid of Retroelements.

The human placenta is hypomethylated compared to somatic tissues. However, the degree and specificity of placental hypomethylation across the genome is unclear. We assessed genome-wide methylation of the human placenta and compared it to that of the neutrophil, a representative homogeneous somatic cell. We observed global hypomethylation in placenta (relative reduction of 22%) compared to neutrophils. Placental hypomethylation was pronounced in intergenic regions and gene bodies, while the unmethylated state of the promoter remained conserved in both tissues. For every class of repeat elements, the placenta showed lower methylation but the degree of hypomethylation differed substantially between these classes. However, some retroelements, especially the evolutionarily younger Alu elements, retained high levels of placental methylation. Surprisingly, nonretrotransposon-containing sequences showed a greater degree of placental hypomethylation than retrotransposons in every genomic element (intergenic, introns, and exons) except promoters. The differentially methylated fragments (DMFs) in placenta and neutrophils were enriched in gene-poor and CpG-poor regions. The placentally hypomethylated DMFs were enriched in genomic regions that are usually inactive, whereas hypermethylated DMFs were enriched in active regions. Hypomethylation of the human placenta is not specific to retroelements, indicating that the evolutionary advantages of placental hypomethylation go beyond those provided by expression of retrotransposons and retrogenes.

Retrotransposon hypomethylation in melanoma and expression of a placenta-specific gene.

In the human placenta, DNA hypomethylation permits the expression of retrotransposon-derived genes that are normally silenced by methylation in somatic tissues. We previously identified hypomethylation of a retrotransposon-derived transcript of the voltage-gated potassium channel gene KCNH5 that is expressed only in human placenta. However, an RNA sequence from this placental-specific transcript has been reported in melanoma. This study examined the promoter methylation and expression of the retrotransposon-derived KCNH5 transcript in 25 melanoma cell lines to determine whether the acquisition of 'placental' epigenetic marks is a feature of melanoma. Methylation and gene expression analysis revealed hypomethylation of this retrotransposon in melanoma cell lines, particularly in those samples that express the placental KCNH5 transcript. Therefore we propose that hypomethylation of the placental-specific KCNH5 promoter is frequently associated with KCNH5 expression in melanoma cells. Our findings show that melanoma can develop hypomethylation of a retrotransposon-derived gene; a characteristic notably shared with the normal placenta.

Waste-handling practices at red meat abattoirs in South Africa.

Abattoir waste disposal must be carefully managed because the wastes can be a source of food-borne diseases (Nemerow & Dasgupta Industrial and Hazardous Waste Treatment, p. 284, Van Nostrand Reinhold, New York, 1991; Bradshaw et al. The Treatment and Handling of Wastes, p. 183, The Royal Society, Chapman & Hall, London, 1992). Disposal of food that has been condemned because it is known to be diseased is of particular concern, and this paper looks at current disposal methods for such waste in the light of new scientific developments and waste-management strategies. Questionnaires were presented to management and workers at low- and high-throughput red meat abattoirs in the Free State Province, South Africa to determine current waste-handling procedures for condemned products. The waste-handling practices, almost without exception, did not fully comply with the requirements of the South African Red Meat Regulations of 2004, framed under the Meat Safety Act (Act 40 of 2000). The survey highlighted the need to improve current waste-handling strategies to prevent condemned products from re-entering the food chain and contributing to environmental pollution.