Plant Tannins and Essential Oils Have an Additive Deterrent Effect on Diet Choice by Kangaroos

Tannins and essential oils are well recognised as antiherbivore compounds. We investigated the relative effectiveness of the polyphenol, tannin, and the essential oils, 1,8-cineole and pine oil, as feeding deterrents against western grey kangaroos. Both groups of secondary metabolites are naturally abundant in many Australian plants. These three metabolite groups were incorporated separately or together into standard pellets for presentation to kangaroos, and their behaviour (sequence of food choice and feeding time) and amounts consumed were observed. The control (with no secondary metabolites) was much preferred. There was a sharp reduction in the ingestion of pellets containing tannins, 1,8-cineole or pine oil. Combinations of the metabolites resulted in almost no consumption. In association with tannin, pellets containing either 1,8-cineole or pine oil were as effective deterrents as both combined. There was a strong correlation between time spent feeding on the different diets and the amount of food consumed, although the rate of intake was markedly slower when secondary metabolites were present. Behavioural observations showed that the amount of food ingested is initially guided by the presence/absence of essential oils, apparently detected by smell, and later by the presence/absence of tannins, by taste. Both groups of secondary metabolites work in concert by stimulating different senses that minimise herbivory by marsupials, such as the western grey kangaroo, and help to explain their abundance in the Australian flora.

Effective machine-learning assembly for next-generation amplicon sequencing with very low coverage

Background In short-read DNA sequencing experiments, the read coverage is a key parameter to successfully assemble the reads and reconstruct the sequence of the input DNA. When coverage is very low, the original sequence reconstruction from the reads can be difficult because of the occurrence of uncovered gaps. Reference guided assembly can then improve these assemblies. However, when the available reference is phylogenetically distant from the sequencing reads, the mapping rate of the reads can be extremely low. Some recent improvements in read mapping approaches aim at modifying the reference according to the reads dynamically. Such approaches can significantly improve the alignment rate of the reads onto distant references but the processing of insertions and deletions remains challenging. Results Here, we introduce a new algorithm to update the reference sequence according to previously aligned reads. Substitutions, insertions and deletions are performed in the reference sequence dynamically. We evaluate this approach to assemble a western-grey kangaroo mitochondrial amplicon. Our results show that more reads can be aligned and that this method produces assemblies of length comparable to the truth while limiting error rate when classic approaches fail to recover the correct length. Finally, we discuss how the core algorithm of this method could be improved and combined with other approaches to analyse larger genomic sequences. Conclusions We introduced an algorithm to perform dynamic alignment of reads on a distant reference. We showed that such approach can improve the reconstruction of an amplicon compared to classically used bioinformatic pipelines. Although not portable to genomic scale in the current form, we suggested several improvements to be investigated to make this method more flexible and allow dynamic alignment to be used for large genome assemblies.

Estimating kangaroo age from lens weight

In a recent publication, Mayberry et al. (2017) presented a method for estimating western grey kangaroo age from the weights of dried eye lenses. The drying conditions are inadequate and may lead to erroneous age estimates. It is suggested that well documented methods in general use be used for future studies.

Effective Machine-Learning Assembly For Next-Generation Sequencing With Very Low Coverage

ABSTRACTIn short-read DNA sequencing experiments, the read coverage is a key parameter to successfully assemble the reads and reconstruct the sequence of the input DNA. When coverage is very low, the original sequence reconstruction from the reads can be difficult because of the occurrence of uncovered gaps. Reference guided assembly can then improve these assemblies. However, when the available reference is phylogenetically distant from the sequencing reads, the mapping rate of the reads can be extremely low. Some recent improvements in read mapping approaches aim at modifying the reference according to the reads dynamically. Such approaches can significantly improve the alignment rate of the reads onto distant references but the processing of insertions and deletions remains challenging. Here, we introduce a dynamic programming algorithm to update the reference sequence according to previously aligned reads. Substitutions, insertions and deletions are performed in the reference sequence dynamically. We evaluate this approach to assemble a western-grey kangaroo mitochondrial amplicon. Our results show that more reads can be aligned and that this method produces assemblies of length comparable to the truth while limiting error rate when classic approaches fail to recover the correct length. Our method allows us to assemble the first full mitochondrial genome for the western-grey kangaroo. Finally, we discuss how the core algorithm of this method could be improved and combined with other approaches to analyse larger genomic sequences.