Gemeinholzer, B. | bioRxiv Science

bioRxiv2021

Metabarcoding malaise trap plant components enables monitoring the diversity of plant-insect interactions

The declines observed in insect abundance and diversity in the past decades has also been observed in plants, and these events are most certainly correlated. Rapid largescale biomonitoring of both plants and insects can help monitor these changes and inform decisions for land management and species protection. Malaise traps have been used for nearly 80 years for passive insect sampling of primarily flying insects, and when they enter these traps, they carry the fragments of the plants they have visited, either as plant fragments and pollen on the body surface, or as digested food material in gut contents. DNA metabarcoding is a potential method to identify these plant traces in the ethanol of the malaise bottles, which is not possible with traditional microscopy. Metabarcoding could offer more insight into what plants insects are directly interacting with at a given time, and allow for the detection of rare plants, and neophyte species visited by insects. This study, to our knowledge, is the first examination of DNA metabarcoding plant traces from Malaise trap samples, we examine 105 samples from 21 sites throughout Germany collected in a 2-week period in May of 2020. Here we report on the feasibility of sequencing these sample types, analysis of the resulting taxa, the usage of cultivated plants by insects near nature conservancy areas, and the detection of rare and neophyte species.

molecular biology↗

bioRxiv2021

GBS and a newly developed mRNA-GBS approach to link population genetic and transcriptome analyses reveal pattern differences between sites and treatments in red clover (Trifolium pratense L.)

The important worldwide forage crop red clover (Trifolium pratense L.) is widely cultivated as cattle feed and for soil improvement. Wild populations and landraces have great natural diversity that could be used to improve cultivated red clover. However, to date, there is still insufficient knowledge about the natural genetic and phenotypic diversity of the species. Here, we developed a low-cost transcriptome analysis (mRNA-GBS) with reduced complexity and compared the results with population genetic (GBS) and previously published mRNA-Seq data, to assess whether analysis of intraspecific variation within and between populations and transcriptome responses is possible simultaneously. The mRNA-GBS approach was successful. SNP analyses from the mRNA-GBS approach revealed comparable patterns to the GBS results, but it was not possible to link transcriptome analyses with reduced complexity and sequencing depth to previously published greenhouse and field expression studies. The use of short sequences upstream of the poly(A) tail of mRNA to reduce complexity are promising approaches that combine population genetics and expression profiling to analyze many individuals with trait differences simultaneously and cost-effectively, even in non-model species. Our mRNA-GBS approach revealed too many additional short mRNA sequences, hampering sequence alignment depth and SNP recovery. Optimizations are being discussed. Nevertheless, our study design across different regions in Germany was also challenging as the use of differential expression analyses with reduced complexity, in which mRNA is fragmented at specific sites rather than randomly, is most likely counteracted under natural conditions by highly complex plant reactions at low sequencing depth.

plant biology↗