Biology subjects

Breeschoten, T.

Publications and source records attributed to Breeschoten, T..

3 recordsLinked to original sources

bioRxiv2021

Genome and transcriptome analysis of the beet armyworm Spodoptera exigua reveals targets for pest control

BackgroundThe genus Spodoptera (Lepidoptera: Noctuidae) includes some of the most infamous insect pests of cultivated plants including Spodoptera frugiperda, Spodoptera litura and Spodoptera exigua. To effectively develop targeted pest control strategies for diverse Spodoptera species, genomic resources are highly desired. To this aim, we provide the genome assembly and developmental transcriptome comprising all major life stages of S. exigua, the beet armyworm. Spodoptera exigua is a polyphagous herbivore that can feed from > 130 host plants including several economically important crops. ResultsThe 419 Mb beet armyworm genome was sequenced from a female S. exigua pupa. Using a hybrid genome sequencing approach (Nanopore long read data and Illumina short read), a high-quality genome assembly was achieved (N50=1.1 Mb). An official gene set (OGS, 18,477 transcripts) was generated by automatic annotation and by using transcriptomic RNA-seq data sets of 18 S. exigua samples as supporting evidence. In-depth analyses of developmental stage-specific expression in combination with gene tree analyses of identified homologous genes across Lepidoptera genomes revealed potential Spodoptera-specific genes of interest such as mg7 and REPAT46 upregulated during 1st and 3rd instar larval stages for targeted pest-outbreak management. ConclusionsThe beet armyworm genome sequence and developmental transcriptome covering all major developmental stages provides critical insights into the biology of this devastating polyphagous insect pest species with a worldwide distribution. In addition, comparative genomic analyses across Lepidoptera significantly advance our knowledge to further control other invasive Spodoptera species and reveals potential lineage-specific target genes for pest control strategies.

genomics↗

bioRxiv2018

Snail shell colour evolution in urban heat islands detected via citizen science

The extreme environmental conditions that prevail in cities are known to cause selection pressures leading to adaptive changes in wild, city-dwelling, organisms (\"urban evolution\"). The urban heat island, elevated temperatures in the city centre due to a combination of generation, reflection, and trapping of heat, is one of the best recognised and most widespread urban environmental factors. Here, we used a citizen-science approach to study the effects of urban heat on genetically-determined shell colour in the land snail Cepaea nemoralis in the Netherlands. We used smartphone applications to obtain colour data on almost 8,000 snails throughout the country. Our analysis shows that snails in urban centres are more likely to be yellow than pink, an effect predicted on the basis of thermal selection. Urban yellow snails are also more likely to carry dark bands at the underside of the shell; these bands might affect thermoregulation in yet underexplored ways.

evolutionary biology↗

bioRxiv2018

The contribution of mitochondrial metagenomics to largescale data mining and phylogenetic analysis of Coleoptera

A phylogenetic tree at the species level is still far off for highly diverse insect orders, including the Coleoptera, but the taxonomic breadth of public sequence databases is growing. In addition, new types of data may contribute to increasing taxon coverage, such as metagenomic shotgun sequencing for assembly of mitogenomes from bulk specimen samples. The current study explores the application of these techniques for large-scale efforts to build the tree of Coleoptera. We used shotgun data from 17 different ecological and taxonomic datasets (5 unpublished) to assemble a total of 1942 mitogenome contigs of >3000 bp. These sequences were combined into a single dataset together with all mitochondrial data available at GenBank, in addition to nuclear markers widely used in molecular phylogenetics. The resulting matrix of nearly 16000 species with two or more loci produced trees (RAxML) showing overall congruence with the Linnaean taxonomy at hierarchical levels from suborders to genera. We tested the role of full-length mitogenomes in stabilizing the tree from GenBank data, as mitogenomes might link terminals with non-overlapping gene representation. However, the mitogenome data were only partly useful in this respect, presumably because of the purely automated approach to assembly and gene delimitation, but improvements in future may be possible by using multiple assemblers and manual curation. In conclusion, the combination of data mining and metagenomic sequencing of bulk samples provided the largest phylogenetic tree of Coleoptera to date, which represents a summary of existing phylogenetic knowledge and a defensible tree of great utility, in particular for studies at the intra-familial level, despite some shortcomings for resolving basal nodes.

evolutionary biology↗