Biology subjects

Chua, P. Y. S.

Publications and source records attributed to Chua, P. Y. S..

4 recordsLinked to original sources

bioRxiv2022

Assessing flower-visiting arthropod diversity in apple orchards through environmental DNA flower metabarcoding and visual census

Arthropods are essential to maintaining healthy and productive agricultural systems. Apples are cultivated worldwide and rely on pollination. Honey bees are used for pollination but wild bees and other arthropods also contribute to pollination. Flower visitors can also be natural enemies or herbivores. In some cases, such as Syrphids, a group can have more than one role, adults being pollinators and the larvae being natural enemies of pests. In the present study, we assessed the biodiversity of arthropod flower visitors in four Danish apple orchards and compared the use of molecular and non-molecular techniques to study arthropod communities in agricultural ecosystems. Arthropod DNA collected from apple flowers was analysed by metabarcoding and pollinators were recorded through visual assessment in the orchards. These techniques resulted in two complementary lists of arthropods detected. Non-bee arthropods constituted a big part of the community of apple flower visitors by both methods. Metabarcoding detected 14 taxa and had 72% species resolution while visual census identified 7 different taxa with 14% species resolution. This study showed the importance of using different sampling methodologies to obtain a more accurate picture of fauna present. It also revealed the high presence of non-bee arthropods visiting flowers in apple orchards. The outcome of our study provides information regarding the effects of management practices on arthropod biodiversity, which can contribute to informing on suitable management practices to increase crop yield and maintain healthy agricultural systems.

ecology↗

bioRxiv2021

A two-step metagenomics approach for prey identification from the blood meals of common vampire bats (Desmodus rotundus)

The feeding behaviour of the sanguivorous common vampire bat (Desmodus rotundus) facilitates the transmission of pathogens that can impact both human and animal health. To formulate effective strategies in controlling the spread of diseases, there is a need to obtain information on which animals they feed on. One DNA-based approach, shotgun sequencing, can be used to obtain such information. Even though it is costly, shotgun sequencing can be used to simultaneously retrieve prey and vampire bat mitochondrial DNA for population studies within one round of sequencing. However, due to the challenges of analysing shotgun sequenced metagenomic data such as false negatives/positives and typically low proportion of reads mapped to diet items, shotgun sequencing has not been used for the identification of prey from common vampire bat blood meals. To overcome these challenges and generate longer mitochondrial contigs which could be useful for prey population studies, we shotgun sequenced common vampire bat blood meal samples (n=8) and utilised a two-step metagenomic approach based on combining existing bioinformatic workflows (alignment and de novo mtDNA assembly) to identify prey. Further, we validated our results to detections made through metabarcoding. We accurately identified the common vampire bats prey in seven out of eight samples without any false positives. We also generated prey mitochondrial contig lengths between 138bp to 3231bp (mean=985bp, SD=981bp). As we develop more computationally efficient bioinformatics pipelines and reduce sequencing costs, we can expect an uptake in metagenomics dietary studies in the near future.

molecular biology↗

bioRxiv2021

Towards the extended barcode concept: Generating DNA reference data through genome skimming of danish plants

BackgroundRecently, there has been a push towards the extended barcode concept of utilising chloroplast genomes (cpGenome) and nuclear ribosomal DNA (nrDNA) sequences for molecular identification of plants instead of the standard barcode regions. These extended barcodes has a wide range of applications, including biodiversity monitoring and assessment, primer design, and evolutionary studies. However, these extended barcodes are not well represented in global reference databases. To fill this gap, we generated cpGenomes and nrDNA reference data from genome skims of 184 plant species collected in Denmark. We further explored the application of our generated reference data for molecular identifications of plants in an environmental DNA metagenomics study. ResultsWe assembled partial cpGenomes for 82.1% of sequenced species and full or partial nrDNA sequences for 83.7% of species. We added all assemblies to GenBank, of which chloroplast reference data from 101 species and nuclear reference data from 6 species were not previously represented. On average, we recovered 45 genes per species. The rate of recovery of standard barcodes was higher for nuclear barcodes (>89%) than chloroplast barcodes (< 60%). Extracted DNA yield did not affect assembly outcome, whereas high GC content did so negatively. For the in silico simulation of metagenomic reads, taxonomic assignments using the reference data generated had better species resolution (94.9%) as compared to GenBank (18.1%) without any identification errors. ConclusionsGenome skimming generates reference data of both standard barcodes and other loci, contributing to the global DNA reference database for plants.

genomics↗

bioRxiv2021

Molecular dietary analyses of western capercaillies (Tetrao urogallus) reveal a diverse diet

Conservation strategies centred around species habitat protection rely on species dietary information. One species at the focal point of conservation efforts is the herbivorous grouse, the western capercaillie (Tetrao urogallus). Traditional microhistological analysis of crop contents or faeces and/or direct observations are time-consuming and at low taxonomic resolution. Thus, limited knowledge on diet is hampering conservation efforts. Here we use non-invasive environmental DNA (eDNA) metabarcoding on DNA extracted from faeces to present the first large-scale molecular dietary analysis of capercaillies. Faecal samples were collected from seven populations located in Norway (Finnmark, Troms, Trondelag, Innlandet) and France (Vosges, Jura, Pyrenees) (n=172). We detected 122 plant taxa belonging to 46 plant families of which 37.7% of the detected taxa could be identified at species level. The average dietary richness of each sample was 7 {+/-} 5 SD taxa. The most frequently occurring plant groups with the highest relative read abundance (RRA) were trees and dwarf shrubs, in particular, Pinus and Vaccinium myrtillus, respectively. There was a difference in dietary composition (RRA) between samples collected from the different locations (adonis F5,86= 11.01, p <0.05) and seasons (adonis F2,03= 0.64, p <0.05). Dietary composition also differed between sexes at each location (adonis F1,47 = 2.77, p <0.05), although not significant for all data combined. In total, 35 taxa (36.84% of taxa recorded) were new capercaillie food items compared to existing knowledge. The non-invasive molecular dietary analysis applied in this study provides new ecological understanding of capercaillies diet which can have real conservation implications. The broad variety of diet items indicates that vegetation does not limit food intake. This plasticity in diet suggests that other factors including disturbed mating grounds and not diet could be the main threat to their survival.

ecology↗