Next-generation insect digitization: combining phenomics and genomics by subsequent synchrotron X-ray imaging and DNA sequencing

Recent technological advances allow for the large-scale acquisition of genetic and morphological data: high-throughput sequencing has transformed the field of genomics while synchrotron X-ray microtomography enables rapid, noninvasive 3D imaging. However, integrating these approaches for the same specimens is challenging because X-rays can fragment DNA, and DNA extraction damages internal morphology, particularly relevant for small bodied organisms, such as insects. We systematically tested multiple extraction protocols and irradiation conditions across three model insect species. We irradiated more than 1,000 specimens under varying conditions and tested DNA quality through DNA barcoding and UCE sequencing. Our results demonstrate that high-quality DNA and high-resolution tomograms can be obtained from the same individuals, provided that the parameters are carefully optimized and rapid SR-CT scanning precedes DNA extraction. In this respect, our findings establish practical guidelines for combining genomics and phenomics, paving the way for comprehensive integrative digitization of biodiversity.