ena-STUDY-CENTRE FOR GEOGENETICS-19-07-2021-14:34:46:397-312
Uncovering the genomic and metagenomic research potential in old ethanol-preserved snakes
Natural history museum collections worldwide represent a tremendous resource of information on past and present biodiversity. Fish, reptiles, amphibians and many invertebrate collections have often been preserved in ethanol for decades or centuries and our knowledge on the genomic and metagenomic research potential of such material is limited. Here, we use ancient DNA protocols, combined with shot-gun sequencing to test the molecular preservation in liver, skin and bone tissue from five old (1842 to 1964) museum specimens of the Common garter snake (Thamnophis sirtalis). When mapping reads to a T. sirtalis reference genome, we find that the DNA molecules are highly damaged with short average sequence lengths (38-64 bp)and high C-T deamination, ranging from 9% to 21% at the first position. Despite this, the samples display a relatively high endogenous DNA contents, ranging from 26% to 56%, revealing that genome-scale analyses are indeed possible from all specimensand tissues included here. Of the three tested types of tissue, bone show highest DNA quality. At least one of the snakes had been exposed to formalin but with the protocolsapplied here, this has not hampered neither the concentration nor the quality of the obtained DNA. Lastly, we demonstrate that these specimens display a diverse and tissue-specific microbial genetic profile, thus offering authentic metagenomic data despite being submerged in ethanol for many years. Our results emphasize thathistorical museum collections continue to offer an invaluable source of information, also in the era of genomics.
Natural history museum collections worldwide represent a tremendous resource of information on past and present biodiversity. Fish, reptiles, amphibians and many invertebrate collections have often been preserved in ethanol for decades or centuries and our knowledge on the genomic and metagenomic research potential of such material is limited. Here, we use ancient DNA protocols, combined with shot-gun sequencing to test the molecular preservation in liver, skin and bone tissue from five old (1842 to 1964) museum specimens of the Common garter snake (Thamnophis sirtalis). When mapping reads to a T. sirtalis reference genome, we find that the DNA molecules are highly damaged with short average sequence lengths (38-64 bp)and high C-T deamination, ranging from 9% to 21% at the first position. Despite this, the samples display a relatively high endogenous DNA contents, ranging from 26% to 56%, revealing that genome-scale analyses are indeed possible from all specimensand tissues included here. Of the three tested types of tissue, bone show highest DNA quality. At least one of the snakes had been exposed to formalin but with the protocolsapplied here, this has not hampered neither the concentration nor the quality of the obtained DNA. Lastly, we demonstrate that these specimens display a diverse and tissue-specific microbial genetic profile, thus offering authentic metagenomic data despite being submerged in ethanol for many years. Our results emphasize thathistorical museum collections continue to offer an invaluable source of information, also in the era of genomics.