Genomic treasure troves: complete genome sequencing of herbarium and insect museum specimens

Pathogen prospecting of museums: Reconstructing malaria epidemiology

Malaria is a disease of global significance. Ongoing changes to the earth's climate, antimalarial resistance, insecticide resistance, and socioeconomic decline test the resilience of malaria prevention programs. Museum insect specimens present an untapped resource for studying vector-borne pathogens, spurring the question: Do historical mosquito collections contain Plasmodium DNA, and, if so, can museum specimens be used to reconstruct the historical epidemiology of malaria? In this Perspective, we explore molecular techniques practical to pathogen prospecting, which, more broadly, we define as the science of screening entomological museum specimens for human, animal, or plant pathogens. Historical DNA and pathogen prospecting provide a means of describing the coevolution of human, vector, and parasite, informing the development of insecticides, diagnostics, therapeutics, and vaccines.

Phylogenomics of the psychoactive mushroom genus Psilocybe and evolution of the psilocybin biosynthetic gene cluster

Psychoactive mushrooms in the genus Psilocybe have immense cultural value and have been used for centuries in Mesoamerica. Despite the recent surge of interest in these mushrooms due to the psychotherapeutic potential of their natural alkaloid psilocybin, their phylogeny and taxonomy remain substantially incomplete. Moreover, the recent elucidation of the psilocybin biosynthetic gene cluster is known for only five of ~165 species of Psilocybe, four of which belong to only one of two major clades. We set out to improve the phylogeny of Psilocybe using shotgun sequencing of fungarium specimens, from which we obtained 71 metagenomes including from 23 types, and conducting phylogenomic analysis of 2,983 single-copy gene families to generate a fully supported phylogeny. Molecular clock analysis suggests the stem lineage of Psilocybe arose ~67 mya and diversified ~56 mya. We also show that psilocybin biosynthesis first arose in Psilocybe, with 4 to 5 possible horizontal transfers to other mushrooms between 40 and 9 mya. Moreover, predicted orthologs of the psilocybin biosynthetic genes revealed two distinct gene orders within the biosynthetic gene cluster that corresponds to a deep split within the genus, possibly a signature of two independent acquisitions of the cluster within Psilocybe.

Retrieval of long DNA reads from herbarium specimens

High-throughput sequencing of herbarium specimens' DNA with short-read platforms has helped explore many biological questions. Here, for the first time, we investigate the potential of using herbarium specimens as a resource for long-read DNA sequencing technologies. We use target capture of 48 low-copy nuclear loci in 12 herbarium specimens of Silene as a basis for long-read sequencing using SMRT PacBio Sequel. The samples were collected between 1932 and 2019. A simple optimization of size selection protocol enabled the retrieval of both long DNA fragments (>1 kb) and long on-target reads for nine of them. The limited sampling size does not enable statistical evaluation of the influence of specimen age to the DNA fragmentation, but our results confirm that younger samples, that is, collected after 1990, are less fragmented and have better sequencing success than specimens collected before this date. Specimens collected between 1990 and 2019 yield between 167 and 3403 on-target reads > 1 kb. They enabled recovering between 34 loci and 48 (i.e. all loci recovered). Three samples from specimens collected before 1990 did not yield on-target reads > 1 kb. The four other samples collected before this date yielded up to 144 reads and recovered up to 25 loci. Young herbarium specimens seem promising for long-read sequencing. However, older ones have partly failed. Further exploration would be necessary to statistically test and understand the potential of older material in the quest for long reads. We would encourage greatly expanding the sampling size and comparing different taxonomic groups.

Genomes from historical Drosophila melanogaster specimens illuminate adaptive and demographic changes across more than 200 years of evolution

The ability to perform genomic sequencing on long-dead organisms is opening new frontiers in evolutionary research. These opportunities are especially notable in the case of museum collections, from which countless documented specimens may now be suitable for genomic analysis-if data of sufficient quality can be obtained. Here, we report 25 newly sequenced genomes from museum specimens of the model organism Drosophila melanogaster, including the oldest extant specimens of this species. By comparing historical samples ranging from the early 1800s to 1933 against modern-day genomes, we document evolution across thousands of generations, including time periods that encompass the species' initial occupation of northern Europe and an era of rapidly increasing human activity. We also find that the Lund, Sweden population underwent local genetic differentiation during the early 1800s to 1933 interval (potentially due to drift in a small population) but then became more similar to other European populations thereafter (potentially due to increased migration). Within each century-scale time period, our temporal sampling allows us to document compelling candidates for recent natural selection. In some cases, we gain insights regarding previously implicated selection candidates, such as ChKov1, for which our inferred timing of selection favors the hypothesis of antiviral resistance over insecticide resistance. Other candidates are novel, such as the circadian-related gene Ahcy, which yields a selection signal that rivals that of the DDT resistance gene Cyp6g1. These insights deepen our understanding of recent evolution in a model system, and highlight the potential of future museomic studies.

Chloroplast genome, nuclear ITS regions, mitogenome regions, and Skmer analysis resolved the genetic relationship among Cinnamomum species in Sri Lanka

Cinnamomum species have gained worldwide attention because of their economic benefits. Among them, C. verum (synonymous with C. zeylanicum Blume), commonly known as Ceylon Cinnamon or True Cinnamon is mainly produced in Sri Lanka. In addition, Sri Lanka is home to seven endemic wild cinnamon species, C. capparu-coronde, C. citriodorum, C. dubium, C. litseifolium, C. ovalifolium, C. rivulorum and C. sinharajaense. Proper identification and genetic characterization are fundamental for the conservation and commercialization of these species. While some species can be identified based on distinct morphological or chemical traits, others cannot be identified easily morphologically or chemically. The DNA barcoding using rbcL, matK, and trnH-psbA regions could not also resolve the identification of Cinnamomum species in Sri Lanka. Therefore, we generated Illumina Hiseq data of about 20x coverage for each identified species and a C. verum sample (India) and assembled the chloroplast genome, nuclear ITS regions, and several mitochondrial genes, and conducted Skmer analysis. Chloroplast genomes of all eight species were assembled using a seed-based method.According to the Bayesian phylogenomic tree constructed with the complete chloroplast genomes, the C. verum (Sri Lanka) is sister to previously sequenced C. verum (NC_035236.1, KY635878.1), C. dubium and C. rivulorum. The C. verum sample from India is sister to C. litseifolium and C. ovalifolium. According to the ITS regions studied, C. verum (Sri Lanka) is sister to C. verum (NC_035236.1), C. dubium and C. rivulorum. Cinnamomum verum (India) shares an identical ITS region with C. ovalifolium, C. litseifolium, C. citriodorum, and C. capparu-coronde. According to the Skmer analysis C. verum (Sri Lanka) is sister to C. dubium and C. rivulorum, whereas C. verum (India) is sister to C. ovalifolium, and C. litseifolium. The chloroplast gene ycf1 was identified as a chloroplast barcode for the identification of Cinnamomum species. We identified an 18 bp indel region in the ycf1 gene, that could differentiate C. verum (India) and C. verum (Sri Lanka) samples tested.

New insights into the plastome evolution of Lauraceae using herbariomics

BACKGROUND

The family Lauraceae possesses ca. 50 genera and 2,500-3,000 species that are distributed in the pantropics. Only half of the genera of the family were represented in previously published plastome phylogenies because of the difficulty of obtaining research materials. Plastomes of Hypodaphnideae and the Mezilaurus group, two lineages with unusual phylogenetic positions, have not been previously reported and thus limit our full understanding on the plastome evolution of the family. Herbariomics, promoted by next generation sequencing technology, can make full use of herbarium specimens, and provides opportunities to fill the sampling gap.

RESULTS

In this study, we sequenced five new plastomes (including four genera which are reported for the first time, viz. Chlorocardium, Hypodaphnis, Licaria and Sextonia) from herbarium specimens using genome skimming to conduct a comprehensive analysis of plastome evolution of Lauraceae as a means of sampling representatives of all major clades of the family. We identified and recognized six types of plastomes and revealed that at least two independent loss events at the IR-LSC boundary and an independent expansion of SSC occurred in the plastome evolution of the family. Hypodaphnis possesses the ancestral type of Lauraceae with trnI-CAU, rpl23 and rpl2 duplicated in the IR regions (Type-I). The Mezilaurus group shares the same plastome structure with the core Lauraceae group in the loss of trnI-CAU, rpl23 and rpl2 in the IRa region (Type-III). Two new types were identified in the Ocotea group: (1) the insertion of trnI-CAU between trnL-UAG and ccsA in the SSC region of Licaria capitata and Ocotea bracteosa (Type-IV), and (2) trnI-CAU and pseudogenizated rpl23 inserted in the same region of Nectandra angustifolia (Type-V). Our phylogeny suggests that Lauraceae are divided into nine major clades largely in accordance with the plastome types. The Hypodaphnideae are the earliest diverged lineage supported by both robust phylogeny and the ancestral plastome type. The monophyletic Mezilaurus group is sister to the core Lauraceae.

CONCLUSIONS

By using herbariomics, we built a more complete picture of plastome evolution and phylogeny of the family, thus providing a convincing case for further use of herbariomics in phylogenetic studies of the Lauraceae.

Horizon scan of DNA-based methods for quality control and monitoring of herbal preparations

Herbal medicines and preparations are widely used in healthcare systems globally, but concerns remain about their quality and safety. New herbal products are constantly being introduced to the market under varying regulatory frameworks, with no global consensus on their definition or characterization. These biologically active mixtures are sold through complex globalized value chains, which create concerns around contamination and profit-driven adulteration. Industry, academia, and regulatory bodies must collaborate to develop innovative strategies for the identification and authentication of botanicals and their preparations to ensure quality control. High-throughput sequencing (HTS) has significantly improved our understanding of the total species diversity within DNA mixtures. The standard concept of DNA barcoding has evolved over the last two decades to encompass genomic data more broadly. Recent research in DNA metabarcoding has focused on developing methods for quantifying herbal product ingredients, yielding meaningful results in a regulatory framework. Techniques, such as loop-mediated isothermal amplification (LAMP), DNA barcode-based Recombinase Polymerase Amplification (BAR-RPA), DNA barcoding coupled with High-Resolution Melting (Bar-HRM), and microfluidics-based methods, offer more affordable tests for the detection of target species. While target capture sequencing and genome skimming are considerably increasing the species identification resolution in challenging plant clades, ddPCR enables the quantification of DNA in samples and could be used to detect intended and unwanted ingredients in herbal medicines. Here, we explore the latest advances in emerging DNA-based technologies and the opportunities they provide as taxa detection tools for evaluating the safety and quality of dietary supplements and herbal medicines.

Predictors of sequence capture in a large-scale anchored phylogenomics project

Next-generation sequencing (NGS) technologies have revolutionized phylogenomics by decreasing the cost and time required to generate sequence data from multiple markers or whole genomes. Further, the fragmented DNA of biological specimens collected decades ago can be sequenced with NGS, reducing the need for collecting fresh specimens. Sequence capture, also known as anchored hybrid enrichment, is a method to produce reduced representation libraries for NGS sequencing. The technique uses single-stranded oligonucleotide probes that hybridize with pre-selected regions of the genome that are sequenced via NGS, culminating in a dataset of numerous orthologous loci from multiple taxa. Phylogenetic analyses using these sequences have the potential to resolve deep and shallow phylogenetic relationships. Identifying the factors that affect sequence capture success could save time, money, and valuable specimens that might be destructively sampled despite low likelihood of sequencing success. We investigated the impacts of specimen age, preservation method, and DNA concentration on sequence capture (number of captured sequences and sequence quality) while accounting for taxonomy and extracted tissue type in a large-scale butterfly phylogenomics project. This project used two probe sets to extract 391 loci or a subset of 13 loci from over 6,000 butterfly specimens. We found that sequence capture is a resilient method capable of amplifying loci in samples of varying age (0–111 years), preservation method (alcohol, papered, pinned), and DNA concentration (0.020 ng/μl - 316 ng/ul). Regression analyses demonstrate that sequence capture is positively correlated with DNA concentration. However, sequence capture and DNA concentration are negatively correlated with sample age and preservation method. Our findings suggest that sequence capture projects should prioritize the use of alcohol-preserved samples younger than 20 years old when available. In the absence of such specimens, dried samples of any age can yield sequence data, albeit with returns that diminish with increasing age.

Nine new species of Trigonopterus Fauvel (Coleoptera, Curculionidae) from Sundaland

The DNA of Trigonopterus specimens from the Sundaland region stored between ten and 32 years in museums could be used for next-generation sequencing. The availability of their cox1 sequence allowed the description of the following nine new species: Trigonopterusgrimmi sp. nov., T.johorensis sp. nov., T.lambirensis sp. nov., T.linauensis sp. nov., T.microreticulatus Riedel, Trnka & Wahab sp. nov., T.mulensis sp. nov., T.sarawakensis sp. nov., T.siamensis sp. nov., and T.singaporensis sp. nov. The alternative original spelling of the name T.tounensis Narakusumo & Riedel is chosen to prevail over T.tounaensis Narakusumo & Riedel. The new species represent the first country records of Trigonopterus for Brunei, Singapore, and Thailand. Thus, the genus´ known area of distribution in the Sundaland region is significantly extended. A key and a catalogue are provided to the Trigonopterus species from Borneo, W-Malaysia, Singapore, and Thailand.

Assessing the performance of historical skins and bones for museomics using wolf specimens as a case study

Advances in the field of museomics have promoted a high sampling demand for natural history collections (NHCs), eventually resulting in damage to invaluable resources to understand historical biodiversity. It is thus essential to achieve a consensus about which historical tissues present the best sources of DNA. In this study, we evaluated the performance of different historical tissues from Iberian wolf NHCs in genome-wide assessments. We targeted three tissues—bone (jaw and femur), maxilloturbinal bone, and skin—that have been favored by traditional taxidermy practices for mammalian carnivores. Specifically, we performed shotgun sequencing and target capture enrichment for 100,000 single nucleotide polymorphisms (SNPs) selected from the commercial Canine HD BeadChip across 103 specimens from 1912 to 2005. The performance of the different tissues was assessed using metrics based on endogenous DNA content, uniquely high-quality mapped reads after capture, and enrichment proportions. All samples succeeded as DNA sources, regardless of their collection year or sample type. Skin samples yielded significantly higher amounts of endogenous DNA compared to both bone types, which yielded equivalent amounts. There was no evidence for a direct effect of tissue type on capture efficiency; however, the number of genotyped SNPs was strictly associated with the starting amount of endogenous DNA. Evaluation of genotyping accuracy for distinct minimum read depths across tissue types showed a consistent overall low genotyping error rate (<7%), even at low (3x) coverage. We recommend the use of skins as reliable and minimally destructive sources of endogenous DNA for whole-genome and target enrichment approaches in mammalian carnivores. In addition, we provide a new 100,000 SNP capture array validated for historical DNA (hDNA) compatible to the Canine HD BeadChip for high-quality DNA. The increasing demand for NHCs as DNA sources should encourage the generation of genomic datasets comparable among studies.

Ancient DNA extraction methods for herbarium specimens: When is it worth the effort?

PREMISE

Herbaria harbor a tremendous number of plant specimens that are rarely used for molecular systematic studies, largely due to the difficulty in extracting sufficient amounts of high-quality DNA from the preserved plant material.

METHODS

We compared the standard Qiagen DNeasy Plant Mini Kit and a specific protocol for extracting ancient DNA (aDNA) (the N-phenacylthiazolium bromide and dithiothreitol [PTB-DTT] extraction method) from two different plant genera (Xanthium and Salix). The included herbarium materials covered about two centuries of plant collections. To analyze the success of DNA extraction using each method, a subset of samples was subjected to a standard library preparation as well as target-enrichment approaches.

RESULTS

The PTB-DTT method produced a higher DNA yield of better quality than the Qiagen kit; however, extracts from the Qiagen kit over a certain DNA yield and quality threshold produced comparable sequencing results. The sequencing resulted in high proportions of endogenous reads. We were able to successfully sequence 200-year-old samples.

DISCUSSION

This method comparison revealed that, for younger specimens, DNA extraction using a standard kit might be sufficient. For old and precious herbarium specimens, aDNA extraction methods are better suited to meet the requirements for next-generation sequencing.

Tracing the invasion of a leaf-mining moth in the Palearctic through DNA barcoding of historical herbaria

The lime leaf-miner, Phyllonorycter issikii is an invasive micromoth with an unusually higher number of haplotypes in the invaded area (Europe, Western Siberia) compared to its putative native region (East Asia). The origin of the genetic diversity in the neocolonized region remains unclear. We surveyed over 15 thousand herbarium specimens of lime trees (Tilia spp.) collected across the Palearctic over a period of 252 years (1764-2016) looking for preserved larvae within the archival leaf mines. We found 203 herbarium specimens with leaf mines of Ph. issikii collected in East Asia, one of them dating back to 1830, i.e. 133 years before the description of the species. In contrast, only 22 herbarium specimens collected in the West Palearctic in the last three decades (1987-2015) carried leaf mines. DNA barcoding of archival specimens revealed 32 haplotypes out of which 23 were novel (not known from modern populations) and found exclusively in East Asia. Six haplotypes are shared between both native and invaded areas and only two were responsible for the recent invasion of the Western Palearctic. The remarkable number of newly discovered haplotypes in archival populations supports East Asia as the native region and the source area of invasion.

EBP-Colombia and the bioeconomy: Genomics in the service of biodiversity conservation and sustainable development

The 2016 Peace Agreement has increased access to Colombia’s unique ecosystems, which remain understudied and increasingly under threat. The Colombian government has recently announced its National Bioeconomic Strategy (NBS), founded on the sustainable characterization, management, and conservation of the nation's biodiversity as a means to achieve sustainability and peace. Molecular tools will accelerate such endeavors, but capacity remains limited in Colombia. The Earth Biogenome Project's (EBP) objective is to characterize the genomes of all eukaryotic life on Earth through networks of partner institutions focused on sequencing either specific taxa or eukaryotic communities at regional or national scales. Colombia’s immense biodiversity and emerging network of stakeholders have inspired the creation of the national partnership “EBP-Colombia.” Here, we discuss how this Colombian-driven collaboration between government, academia, and the private sector is integrating research with sustainable, environmentally focused strategies to develop Colombia’s postconflict bioeconomy and conserve biological and cultural diversity. EBP-Colombia will accelerate the uptake of technology and promote partnership and exchange of knowledge among Colombian stakeholders and the EBP’s global network of experts; assist with conservation strategies to preserve Colombia’s vast biological wealth; and promote innovative approaches among public and private institutions in sectors such as agriculture, tourism, recycling, and medicine. EBP-Colombia can thus support Colombia’s NBS with the objective of sustainable and inclusive development to address the many social, environmental, and economic challenges, including conflict, inequality, poverty, and low agricultural productivity, and so, offer an alternative model for economic development that similarly placed countries can adopt.

Sixteenth-century tomatoes in Europe: who saw them, what they looked like, and where they came from

BACKGROUND

Soon after the Spanish conquest of the Americas, the first tomatoes were presented as curiosities to the European elite and drew the attention of sixteenth-century Italian naturalists. Despite of their scientific interest in this New World crop, most Renaissance botanists did not specify where these 'golden apples' or 'pomi d'oro' came from. The debate on the first European tomatoes and their origin is often hindered by erroneous dating, botanical misidentifications and inaccessible historical sources. The discovery of a tomato specimen in the sixteenth-century 'En Tibi herbarium' kept at Leiden, the Netherlands, triggered research on its geographical provenance and morphological comparison to other tomato specimens and illustrations from the same time period.

METHODS

Recent digitization efforts greatly facilitate research on historic botanical sources. Here we provide an overview of the ten remaining sixteenth-century tomato specimens, early descriptions and 13 illustrations. Several were never published before, revealing what these tomatoes looked like, who saw them, and where they came from. We compare our historical findings with recent molecular research on the chloroplast and nuclear DNA of the 'En Tibi' specimen.

RESULTS

Our survey shows that the earliest tomatoes in Europe came in a much wider variety of colors, shapes and sizes than previously thought, with both simple and fasciated flowers, round and segmented fruits. Pietro Andrea Matthioli gave the first description of a tomato in 1544, and the oldest specimens were collected by Ulisse Aldrovandi and Francesco Petrollini in c. 1551, possibly from plants grown in the Pisa botanical garden by their teacher Luca Ghini. The oldest tomato illustrations were made in Germany and Switzerland in the early 1550s, but the Flemish Rembert Dodoens published the first image in 1553. The names of early tomatoes in contemporary manuscripts suggest both a Mexican and a Peruvian origin. The 'En Tibi' specimen was collected by Petrollini around 1558 and thus is not the oldest extant tomato. Recent molecular research on the ancient nuclear and chloroplast DNA of the En Tibi specimen clearly shows that it was a fully domesticated tomato, and genetically close to three Mexican landraces and two Peruvian specimens that probably also had a Mesoamerican origin. Molecular research on the other sixteenth-century tomato specimens may reveal other patterns of genetic similarity, past selection processes, and geographic origin. Clues on the 'historic' taste and pest resistance of the sixteenth-century tomatoes will be difficult to predict from their degraded DNA, but should be rather sought in those landraces in Central and South America that are genetically close to them. The indigenous farmers growing these traditional varieties should be supported to conserve these heirloom varieties in-situ.

Phylogenomic analysis points to a South American origin of Manihot and illuminates the primary gene pool of cassava

The genus Manihot, with around 120 known species, is native to a wide range of habitats and regions in the tropical and subtropical Americas. Its high species richness and recent diversification only c. 6 million years ago have significantly complicated previous phylogenetic analyses. Several basic elements of Manihot evolutionary history therefore remain unresolved. Here, we conduct a comprehensive phylogenomic analysis of Manihot, focusing on exhaustive sampling of South American taxa. We find that two recently described species from northeast Brazil's Atlantic Forest were the earliest to diverge, strongly suggesting a South American common ancestor of Manihot. Ancestral state reconstruction indicates early Manihot diversification in dry forests, with numerous independent episodes of new habitat colonization, including into savannas and rainforests within South America. We identify the closest wild relatives to Manihot esculenta, including the crop cassava, and we quantify extensive wild introgression into the cassava gene pool from at least five wild species, including Manihot glaziovii, a species used widely in breeding programs. Finally, we show that this wild-to-crop introgression substantially shapes the mutation load in cassava. Our findings provide a detailed case study for neotropical evolutionary history in a diverse and widespread group, and a robust phylogenomic framework for future Manihot and cassava research.

A customised target capture sequencing tool for molecular identification of Aloe vera and relatives

Plant molecular identification studies have, until recently, been limited to the use of highly conserved markers from plastid and other organellar genomes, compromising resolution in highly diverse plant clades. Due to their higher evolutionary rates and reduced paralogy, low-copy nuclear genes overcome this limitation but are difficult to sequence with conventional methods and require high-quality input DNA. Aloe vera and its relatives in the Alooideae clade (Asphodelaceae, subfamily Asphodeloideae) are of economic interest for food and health products and have horticultural value. However, pressing conservation issues are increasing the need for a molecular identification tool to regulate the trade. With > 600 species and an origin of ± 15 million years ago, this predominantly African succulent plant clade is a diverse and taxonomically complex group for which low-copy nuclear genes would be desirable for accurate species discrimination. Unfortunately, with an average genome size of 16.76 pg, obtaining high coverage sequencing data for these genes would be prohibitively costly and computationally demanding. We used newly generated transcriptome data to design a customised RNA-bait panel targeting 189 low-copy nuclear genes in Alooideae. We demonstrate its efficacy in obtaining high-coverage sequence data for the target loci on Illumina sequencing platforms, including degraded DNA samples from museum specimens, with considerably improved phylogenetic resolution. This customised target capture sequencing protocol has the potential to confidently indicate phylogenetic relationships of Aloe vera and related species, as well as aid molecular identification applications.

Twenty-eight new species of Trigonopterus Fauvel (Coleoptera, Curculionidae) from Central Sulawesi

Here we present 28 new species of Trigonopterus from Central Sulawesi, mostly from Mt Dako and Mt Pompangeo: Trigonopterusacutussp. nov., T.ancorasp. nov., T.arcanussp. nov., T.coronasp. nov., T.dakoensissp. nov., T.daunsp. nov., T.ewoksp. nov., T.gundalasp. nov., T.hopplasp. nov., T.kakimerahsp. nov., T.katopasensissp. nov., T.matakensissp. nov., T.moduaisp. nov., T.monssp. nov., T.paramoduaisp. nov.T.pomberimbensissp. nov., T.pompangeensissp. nov., T.puspoisp. nov., T.rosichonisp. nov., T.rubidussp. nov., T.sarinoisp. nov., T.sutrisnoisp. nov., T.tanahsp. nov., T.tejokusumoisp. nov., T.toboliensissp. nov., T.tolitoliensissp. nov., T.tounaensissp. nov., T.unyilsp. nov. This fills important areas of distribution and brings the number of Trigonopterus species recorded from Sulawesi to 132.

Global high-throughput genotyping of organellar genomes reveals insights into the origin and spread of invasive starry stonewort (Nitellopsis obtusa)

Aquatic invasive species are damaging to native ecosystems. Preventing their spread and achieving comprehensive control measures requires an understanding of the genetic structure of an invasive population. Organellar genomes (plastid and mitochondrial) are useful for population level analyses of invasive plant distributions. In this study we generate complete organellar reference genomes using PacBio sequencing, then use these reference sequences for SNP calling of high-throughput, multiplexed, Illumina based organellar sequencing of fresh and historical samples from across the native and invasive range of Nitellopsis obtusa (Desv. in Loisel.) J.Groves, an invasive macroalgae. The data generated by the analytical pipeline we develop indicate introduction to North America from Western Europe. A single nucleotide transversion in the plastid genome separates a group of five samples from Michigan and Wisconsin that either resulted from introductions of two closely related genotypes or a mutation that has arisen in the invasive range. This transversion will serve as a useful tool to understand how Nitellopsis obtusa moves across the landscape. The methods and analyses described here are broadly applicable to invasive and native plant and algae species, and allow efficient genotyping of variable quality samples, including 100-year-old herbarium specimens, to determine population structure and geographic distributions.

Scenopinusjerei, a new species of window fly (Diptera, Scenopinidae) from Finland

A new species of window fly (Diptera: Scenopinidae), Scenopinusjereisp. nov., with characteristic bicoloured legs and completely black halteres, is described from Finland. To exclude potential previously named species, a survey of the relevant type specimens as well as original descriptions of the Palearctic and Nearctic Scenopinus species has been conducted, including old Scenopinusfenestralis (Linnaeus) synonyms. Scenopinusjereisp. nov. is likely to be an overlooked, boreal forest specialist living in the nests of cavity-nesting birds. An identification key to the European species is provided.

A Minimally Morphologically Destructive Approach for DNA Retrieval and Whole-Genome Shotgun Sequencing of Pinned Historic Dipteran Vector Species

Museum collections contain enormous quantities of insect specimens collected over the past century, covering a period of increased and varied insecticide usage. These historic collections are therefore incredibly valuable as genomic snapshots of organisms before, during, and after exposure to novel selective pressures. However, these samples come with their own challenges compared with present-day collections, as they are fragile and retrievable DNA is low yield and fragmented. In this article, we tested several DNA extraction procedures across pinned historic Diptera specimens from four disease vector genera: Anopheles, Aedes, Culex, and Glossina. We identify an approach that minimizes morphological damage while maximizing DNA retrieval for Illumina library preparation and sequencing that can accommodate the fragmented and low yield nature of historic DNA. We identify several key points in retrieving sufficient DNA while keeping morphological damage to a minimum: an initial rehydration step, a short incubation without agitation in a modified low salt Proteinase K buffer (referred to as "lysis buffer C" throughout), and critical point drying of samples post-extraction to prevent tissue collapse caused by air drying. The suggested method presented here provides a solid foundation for exploring the genomes and morphology of historic Diptera collections.

Unlocking inaccessible historical genomes preserved in formalin

Museum specimens represent an unparalleled record of historical genomic data. However, the widespread practice of formalin preservation has thus far impeded genomic analysis of a large proportion of specimens. Limited DNA sequencing from formalin-preserved specimens has yielded low genomic coverage with unpredictable success. We set out to refine sample processing methods and to identify specimen characteristics predictive of sequencing success. With a set of taxonomically diverse specimens collected between 1962 and 2006 and ranging in preservation quality, we compared the efficacy of several end-to-end whole genome sequencing workflows alongside a k-mer-based trimming-free read alignment approach to maximize mapping of endogenous sequence. We recovered complete mitochondrial genomes and up to 3× nuclear genome coverage from formalin-preserved tissues. Hot alkaline lysis coupled with phenol-chloroform extraction out-performed proteinase K digestion in recovering DNA, while library preparation method had little impact on sequencing success. The strongest predictor of DNA yield was overall specimen condition, which additively interacts with preservation conditions to accelerate DNA degradation. Here, we demonstrate a significant advance in capability beyond limited recovery of a small number of loci via PCR or target-capture sequencing. To facilitate strategic selection of suitable specimens for genomic sequencing, we present a decision-making framework that utilizes independent and nondestructive assessment criteria. Sequencing of formalin-preserved specimens will contribute to a greater understanding of temporal trends in genetic adaptation, including those associated with a changing climate. Our work enhances the value of museum collections worldwide by unlocking genomes of specimens that have been disregarded as a valid molecular resource.

Mining museums for historical DNA: advances and challenges in museomics

Historical DNA (hDNA), obtained from museum and herbarium specimens, has yielded spectacular new insights into the history of organisms. This includes documenting historical genetic erosion and extinction, discovering species new to science, resolving evolutionary relationships, investigating epigenetic effects, and determining origins of infectious diseases. However, the development of best-practices in isolating, processing, and analyzing hDNA remain under-explored, due to the substantial diversity of specimen preparation types, tissue sources, archival ages, and collecting histories. Thus, for hDNA to reach its full potential, and justify the destructive sampling of the rarest specimens, more experimental work using time-series collections, and the development of improved methods to correct for data asymmetries and biases due to DNA degradation are required.

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 shotgun 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 displayed relatively high endogenous DNA content, ranging from 26% to 56%, revealing that genome-scale analyses are indeed possible from all specimens and tissues included here. Of the three tested types of tissue, bone shows marginally but significantly higher DNA quality in these metrics. Though at least one of the snakes had been exposed to formalin, neither the concentration nor the quality of the obtained DNA was affected. 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 that historical museum collections continue to offer an invaluable source of information in the era of genomics.

Genomic library preparation and hybridization capture of formalin-fixed tissues and allozyme supernatant for population genomics and considerations for combining capture- and RADseq-based single nucleotide polymorphism data sets

Until recently many historical museum specimens were largely inaccessible to genomic inquiry, but high-throughput sequencing (HTS) approaches have allowed researchers to successfully sequence genomic DNA from dried and fluid-preserved museum specimens. In addition to preserved specimens, many museums contain large series of allozyme supernatant samples, but the amenability of these samples to HTS has not yet been assessed. Here, we compared the performance of a target-capture approach using alternative sources of genomic DNA from 10 specimens of spring salamanders (Plethodontidae: Gyrinophilus porphyriticus) collected between 1985 and 1990: allozyme supernatants, allozyme homogenate pellets and formalin-fixed tissues. We designed capture probes based on double-digest restriction-site associated sequencing (RADseq) derived loci from frozen blood samples available for seven of the specimens and assessed the success and consistency of capture and RADseq approaches. This study design enabled direct comparisons of data quality and potential biases among the different data sets for phylogenomic and population genomic analyses. We found that in phylogenetic analyses, all enrichment types for a given specimen clustered together. In principal component space all capture-based samples clustered together, but RADseq samples did not cluster with corresponding capture-based samples. Single nucleotide polymorphism calls were on average 18.3% different between enrichment types for a given individual, but these discrepancies were primarily due to differences in heterozygous/homozygous single nucleotide polymorphism calls. We demonstrate that both allozyme supernatant and formalin-fixed samples can be successfully used for population genomic analyses and we discuss ways to identify and reduce biases associated with combining capture and RADseq data.

Genome skims analysis of betel palms (Areca spp., Arecaceae) and development of a profiling method to assess their plastome diversity

The betel nut (Areca catechu L., Arecaceae) is a monoecious cultivated palm tree that is widespread in tropical regions. It is mainly cultivated for producing areca nuts, from which seeds are extracted and chewed by local populations principally in the Indo-Pacific region. Seeds contain alkaloids which are central nervous system stimulants and are highly addictive. Wild relatives of the betel nut are distributed in South Asia and Australasia, with ca. 40-50 Areca species currently recognized. The geographic origin(s) of the betel nut and its subsequent diffusion and diversification remains poorly documented. Here, a genome skimming approach was applied to screen nucleotidic variation in the most abundant genomic regions. Low coverage sequencing data allowed us to assemble full plastomes, mitochondrial regions (either full mitogenomes or the full set of mitochondrial genes) and the nuclear ribosomal DNA cluster for nine representatives of the Areca genus collected in the field and herbarium collections (including a 182-years old specimen collected during the Dumont d'Urville's expedition). These three genomic compartments provided similar phylogenetic signals, and revealed very low genomic diversity in our sample of cultivated betel nut. We finally developed a genotyping method targeting 34 plastid DNA microsatellites. This plastome profiling approach is useful for tracing the spread of matrilineages, and in combination with nuclear genomic data, can resolve the history of the betel nut. Our method also proves to be efficient for analyzing herbarium specimens, even those collected >100 years ago.

HyRAD-X Exome Capture Museomics Unravels Giant Ground Beetle Evolution

Advances in phylogenomics contribute toward resolving long-standing evolutionary questions. Notwithstanding, genetic diversity contained within more than a billion biological specimens deposited in natural history museums remains recalcitrant to analysis owing to challenges posed by its intrinsically degraded nature. Yet that tantalizing resource could be critical in overcoming taxon sampling constraints hindering our ability to address major evolutionary questions. We addressed this impediment by developing phyloHyRAD, a new bioinformatic pipeline enabling locus recovery at a broad evolutionary scale from HyRAD-X exome capture of museum specimens of low DNA integrity using a benchtop RAD-derived exome-complexity-reduction probe set developed from high DNA integrity specimens. Our new pipeline can also successfully align raw RNAseq transcriptomic and ultraconserved element reads with the RAD-derived probe catalog. Using this method, we generated a robust timetree for Carabinae beetles, the lack of which had precluded study of macroevolutionary trends pertaining to their biogeography and wing-morphology evolution. We successfully recovered up to 2,945 loci with a mean of 1,788 loci across the exome of specimens of varying age. Coverage was not significantly linked to specimen age, demonstrating the wide exploitability of museum specimens. We also recovered fragmentary mitogenomes compatible with Sanger-sequenced mtDNA. Our phylogenomic timetree revealed a Lower Cretaceous origin for crown group Carabinae, with the extinct Aplothorax Waterhouse, 1841 nested within the genus Calosoma Weber, 1801 demonstrating the junior synonymy of Aplothorax syn. nov., resulting in the new combination Calosoma  burchellii (Waterhouse, 1841) comb. nov. This study compellingly illustrates that HyRAD-X and phyloHyRAD efficiently provide genomic-level data sets informative at deep evolutionary scales.

Reversing extinction trends: new uses of (old) herbarium specimens to accelerate conservation action on threatened species

Although often not collected specifically for the purposes of conservation, herbarium specimens offer sufficient information to reconstruct parameters that are needed to designate a species as 'at-risk' of extinction. While such designations should prompt quick and efficient legal action towards species recovery, such action often lags far behind and is mired in bureaucratic procedure. The increase in online digitization of natural history collections has now led to a surge in the number new studies on the uses of machine learning. These repositories of species occurrences are now equipped with advances that allow for the identification of rare species. The increase in attention devoted to estimating the scope and severity of the threats that lead to the decline of such species will increase our ability to mitigate these threats and reverse the declines, overcoming a current barrier to the recovery of many threatened plant species. Thus far, collected specimens have been used to fill gaps in systematics, range extent, and past genetic diversity. We find that they also offer material with which it is possible to foster species recovery, ecosystem restoration, and de-extinction, and these elements should be used in conjunction with machine learning and citizen science initiatives to mobilize as large a force as possible to counter current extinction trends.

From e-voucher to genomic data: Preserving archive specimens as demonstrated with medically important mosquitoes (Diptera: Culicidae) and kissing bugs (Hemiptera: Reduviidae)

Scientific collections such as the U.S. National Museum (USNM) are critical to filling knowledge gaps in molecular systematics studies. The global taxonomic impediment has resulted in a reduction of expert taxonomists generating new collections of rare or understudied taxa and these large historic collections may be the only reliable source of material for some taxa. Integrated systematics studies using both morphological examinations and DNA sequencing are often required for resolving many taxonomic issues but as DNA methods often require partial or complete destruction of a sample, there are many factors to consider before implementing destructive sampling of specimens within scientific collections. We present a methodology for the use of archive specimens that includes two crucial phases: 1) thoroughly documenting specimens destined for destructive sampling—a process called electronic vouchering, and 2) the pipeline used for whole genome sequencing of archived specimens, from extraction of genomic DNA to assembly of putative genomes with basic annotation. The process is presented for eleven specimens from two different insect subfamilies of medical importance to humans: Anophelinae (Diptera: Culicidae)—mosquitoes and Triatominae (Hemiptera: Reduviidae)—kissing bugs. Assembly of whole mitochondrial genome sequences of all 11 specimens along with the results of an ortholog search and BLAST against the NCBI nucleotide database are also presented.

Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations

The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there is therefore still research to be conducted to ensure the reliability of the sedimentary DNA signal. Building on the most recent literature and seven original case studies, we synthesize the state-of-the-art analytical procedures for effective sampling, extraction, amplification, quantification and/or generation of DNA inventories from sedimentary ancient DNA (sedaDNA) via high-throughput sequencing technologies. We provide recommendations based on current knowledge and best practises.

High-throughput methods for efficiently building massive phylogenies from natural history collections

PREMISE

Large phylogenetic data sets have often been restricted to small numbers of loci from GenBank, and a vetted sampling-to-sequencing phylogenomic protocol scaling to thousands of species is not yet available. Here, we report a high-throughput collections-based approach that empowers researchers to explore more branches of the tree of life with numerous loci.

METHODS

We developed an integrated Specimen-to-Laboratory Information Management System (SLIMS), connecting sampling and wet lab efforts with progress tracking at each stage. Using unique identifiers encoded in QR codes and a taxonomic database, a research team can sample herbarium specimens, efficiently record the sampling event, and capture specimen images. After sampling in herbaria, images are uploaded to a citizen science platform for metadata generation, and tissue samples are moved through a simple, high-throughput, plate-based herbarium DNA extraction and sequencing protocol.

RESULTS

We applied this sampling-to-sequencing workflow to ~15,000 species, producing for the first time a data set with ~50% taxonomic representation of the "nitrogen-fixing clade" of angiosperms.

DISCUSSION

The approach we present is appropriate at any taxonomic scale and is extensible to other collection types. The widespread use of large-scale sampling strategies repositions herbaria as accessible but largely untapped resources for broad taxonomic sampling with thousands of species.

The Effects of Herbarium Specimen Characteristics on Short-Read NGS Sequencing Success in Nearly 8000 Specimens: Old, Degraded Samples Have Lower DNA Yields but Consistent Sequencing Success

Phylogenetic datasets are now commonly generated using short-read sequencing technologies unhampered by degraded DNA, such as that often extracted from herbarium specimens. The compatibility of these methods with herbarium specimens has precipitated an increase in broad sampling of herbarium specimens for inclusion in phylogenetic studies. Understanding which sample characteristics are predictive of sequencing success can guide researchers in the selection of tissues and specimens most likely to yield good results. Multiple recent studies have considered the relationship between sample characteristics and DNA yield and sequence capture success. Here we report an analysis of the relationship between sample characteristics and sequencing success for nearly 8,000 herbarium specimens. This study, the largest of its kind, is also the first to include a measure of specimen quality ("greenness") as a predictor of DNA sequencing success. We found that taxonomic group and source herbarium are strong predictors of both DNA yield and sequencing success and that the most important specimen characteristics for predicting success differ for DNA yield and sequencing: greenness was the strongest predictor of DNA yield, and age was the strongest predictor of proportion-on-target reads recovered. Surprisingly, the relationship between age and proportion-on-target reads is the inverse of expectations; older specimens performed slightly better in our capture-based protocols. We also found that DNA yield itself is not a strong predictor of sequencing success. Most literature on DNA sequencing from herbarium specimens considers specimen selection for optimal DNA extraction success, which we find to be an inappropriate metric for predicting success using next-generation sequencing technologies.

Resolving Recalcitrant Clades in the Pantropical Ochnaceae: Insights From Comparative Phylogenomics of Plastome and Nuclear Genomic Data Derived From Targeted Sequencing

Plastid DNA sequence data have been traditionally widely used in plant phylogenetics because of the high copy number of plastids, their uniparental inheritance, and the blend of coding and non-coding regions with divergent substitution rates that allow the reconstruction of phylogenetic relationships at different taxonomic ranks. In the present study, we evaluate the utility of the plastome for the reconstruction of phylogenetic relationships in the pantropical plant family Ochnaceae (Malpighiales). We used the off-target sequence read fraction of a targeted sequencing study (targeting nuclear loci only) to recover more than 100 kb of the plastid genome from the majority of the more than 200 species of Ochnaceae and all but two genera using de novo and reference-based assembly strategies. Most of the recalcitrant nodes in the family's backbone were resolved by our plastome-based phylogenetic inference, corroborating the most recent classification system of Ochnaceae and findings from a phylogenomic study based on nuclear loci. Nonetheless, the phylogenetic relationships within the major clades of tribe Ochnineae, which comprise about two thirds of the family's species diversity, received mostly low support. Generally, the phylogenetic resolution was lowest at the infrageneric level. Overall there was little phylogenetic conflict compared to a recent analysis of nuclear loci. Effects of taxon sampling were invoked as the most likely reason for some of the few well-supported discords. Our study demonstrates the utility of the off-target fraction of a target enrichment study for assembling near-complete plastid genomes for a large proportion of samples.

The Origins of Coca: Museum Genomics Reveals Multiple Independent Domestications from Progenitor Erythroxylum gracilipes

Coca is the natural source of cocaine as well as a sacred and medicinal plant farmed by South American Amerindians and mestizos. The coca crop comprises four closely related varieties classified into two species (Amazonian and Huánuco varieties within Erythroxylum coca Lam., and Colombian and Trujillo varieties within Erythroxylum novogranatense (D. Morris) Hieron.) but our understanding of the domestication and evolutionary history of these taxa is nominal. In this study, we use genomic data from natural history collections to estimate the geographic origins and genetic diversity of this economically and culturally important crop in the context of its wild relatives. Our phylogeographic analyses clearly demonstrate the four varieties of coca comprise two or three exclusive groups nested within the diverse lineages of the widespread, wild species Erythroxylum gracilipes; establishing a new and robust hypothesis of domestication wherein coca originated two or three times from this wild progenitor. The Colombian and Trujillo coca varieties are descended from a single, ancient domestication event in northwestern South America. Huánuco coca was domesticated more recently, possibly in southeastern Peru. Amazonian coca either shares a common domesticated ancestor with Huánuco coca, or it was the product of a third and most recent independent domestication event in the western Amazon basin. This chronology of coca domestication reveals different Holocene peoples in South America were able to independently transform the same natural resource to serve their needs; in this case, a workaday stimulant. [Erythroxylum; Erythroxylaceae; Holocene; Museomics; Neotropics; phylogeography; plant domestication; target-sequence capture.]

New Light on Historical Specimens Reveals a New Species of Ladybird (Coleoptera: Coccinellidae): Morphological, Museomic, and Phylogenetic Analyses

Natural history collections house an important source of genetic data from yet unexplored biological diversity. Molecular data from museum specimens remain underexploited, which is mainly due to the degradation of DNA from specimens over time. However, Next-Generation Sequencing (NGS) technology can now be used to sequence "old" specimens. Indeed, many of these specimens are unique samples of nomenclatural types and can be crucial for resolving systematic or biogeographic scientific questions. Two ladybird beetle specimens from Patagonia corresponding to a new species of the genus Eriopis Mulsant were found in the collections of the Muséum national d'Histoire naturelle (MNHN), Paris. Here, we describe Eriopis patagonia Salazar, sp. nov. Total DNA of one of the two specimens was sequenced by NGS using a paired-end Illumina approach. We reconstruct and characterize the mitochondrial genome of this species (16,194 bp). Then, the protein-coding genes (PCGs) and ribosomal RNAs (rRNAs) were used to infer by maximum likelihood and Bayesian Inference the phylogenetic position of E. patagonia among 27 representatives of Coccinellidae. Phylogenetic analysis confirmed the position of Eriopis as sister group to Cycloneda Crotch. Hence, we highlight the high potential of sequencing technology for extracting molecular information from old specimens, which are used here for the systematic study of a genus, while demonstrating the importance of preserving biological collections.

Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae)

We present a 517-gene phylogenetic framework for the breadfruit genus Artocarpus (ca. 70 spp., Moraceae), making use of silica-dried leaves from recent fieldwork and herbarium specimens (some up to 106 years old) to achieve 96% taxon sampling. We explore issues relating to assembly, paralogous loci, partitions, and analysis method to reconstruct a phylogeny that is robust to variation in data and available tools. While codon partitioning did not result in any substantial topological differences, the inclusion of flanking non-coding sequence in analyses significantly increased the resolution of gene trees. We also found that increasing the size of datasets increased convergence between analysis methods but did not reduce gene tree conflict. We optimized the HybPiper targeted-enrichment sequence assembly pipeline for short sequences derived from degraded DNA extracted from museum specimens. While the subgenera of Artocarpus were monophyletic, revision is required at finer scales, particularly with respect to widespread species. We expect our results to provide a basis for further studies in Artocarpus and provide guidelines for future analyses of datasets based on target enrichment data, particularly those using sequences from both fresh and museum material, counseling careful attention to the potential of off-target sequences to improve resolution.

Digging into the Genomic Past of Swiss Honey Bees by Whole-Genome Sequencing Museum Specimens

Historical specimens in museum collections provide opportunities to gain insights into the genomic past. For the Western honey bee, Apis mellifera L., this is particularly important because its populations are currently under threat worldwide and have experienced many changes in management and environment over the last century. Using Swiss Apis mellifera mellifera as a case study, our research provides important insights into the genetic diversity of native honey bees prior to the industrial-scale introductions and trade of non-native stocks during the 20th century—the onset of intensive commercial breeding and the decline of wild honey bees following the arrival of Varroa destructor. We sequenced whole-genomes of 22 honey bees from the Natural History Museum in Bern collected in Switzerland, including the oldest A. mellifera sample ever sequenced. We identify both, a historic and a recent migrant, natural or human-mediated, which corroborates with the population history of honey bees in Switzerland. Contrary to what we expected, we find no evidence for a significant genetic bottleneck in Swiss honey bees, and find that genetic diversity is not only maintained, but even slightly increased, most probably due to modern apicultural practices. Finally, we identify signals of selection between historic and modern honey bee populations associated with genes enriched in functions linked to xenobiotics, suggesting a possible selective pressure from the increasing use and diversity of chemicals used in agriculture and apiculture over the last century.

Optimized and affordable high-throughput sequencing workflow for preserved and nonpreserved small zooplankton specimens

Genomic analysis of hundreds of individuals is increasingly becoming standard in evolutionary and ecological research. Individual-based sequencing generates large amounts of valuable data from experimental and field studies, while using preserved samples is an invaluable resource for studying biodiversity in remote areas or across time. Yet, small-bodied individuals or specimens from collections are often of limited use for genomic analyses due to a lack of suitable extraction and library preparation protocols for preserved or small amounts of tissues. Currently, high-throughput sequencing in zooplankton is mostly restricted to clonal species, that can be maintained in live cultures to obtain sufficient amounts of tissue, or relies on a whole-genome amplification step that comes with several biases and high costs. Here, we present a workflow for high-throughput sequencing of single small individuals omitting the need for prior whole-genome amplification or live cultures. We establish and demonstrate this method using 27 species of the genus Daphnia, aquatic keystone organisms, and validate it with small-bodied ostracods. Our workflow is applicable to both live and preserved samples at low costs per sample. We first show that a silica-column based DNA extraction method resulted in the highest DNA yields for nonpreserved samples while a precipitation-based technique gave the highest yield for ethanol-preserved samples and provided the longest DNA fragments. We then successfully performed short-read whole genome sequencing from single Daphnia specimens and ostracods. Moreover, we assembled a draft reference genome from a single Daphnia individual (>50× coverage) highlighting the value of the workflow for non-model organisms.

Advantages of an easy-to-use DNA extraction method for minimal-destructive analysis of collection specimens

Here we present and justify an approach for minimal-destructive DNA extraction from historic insect specimens for next generation sequencing applications. An increasing number of studies use insects from museum collections for biodiversity research. However, the availability of specimens for molecular analyses has been limited by the degraded nature of the DNA gained from century-old museum material and the consumptive nature of most DNA extraction procedures. The method described in this manuscript enabled us to successfully extract DNA from specimens as old as 241 years using a minimal-destructive approach. The direct comparison of the DNeasy extraction Kit and the Monarch® PCR & DNA Clean-up Kit showed a significant increase of 17.3-fold higher DNA yield extracted with the Monarch Oligo protocol on average. By using an extraction protocol originally designed for oligonucleotide clean-up, we were able to combine overcoming the restrictions by target fragment size and strand state, with minimising time consumption and labour-intensity. The type specimens used for the minimal-destructive DNA extraction exhibited no significant external change or post-extraction damage, while sufficient DNA was retrieved for analyses.

Museomics for reconstructing historical floristic exchanges: Divergence of stone oaks across Wallacea

Natural history collections and tropical tree diversity are both treasure troves of biological and evolutionary information, but their accessibility for scientific study is impeded by a number of properties. DNA in historical specimens is generally highly fragmented, complicating the recovery of high-grade genetic material. Furthermore, our understanding of hyperdiverse, wide-spread tree assemblages is obstructed by extensive species ranges, fragmented knowledge of tropical tree diversity and phenology, and a widespread lack of species-level diagnostic characters, prohibiting the collecting of readily identifiable specimens which can be used to build, revise or strengthen taxonomic frameworks. This, in turn, delays the application of downstream conservation action. A sizable component of botanical collections are sterile-thus eluding identification and are slowing down progress in systematic treatments of tropical biodiversity. With rapid advances in genomics and bioinformatic approaches to biodiversity research, museomics is emerging as a new field breathing life into natural collections that have been built up over centuries. Using MIGseq (multiplexed ISSR genotyping by sequencing), we generated 10,000s of short loci, for both freshly collected materials and museum specimens (aged >100 years) of Lithocarpus-a widespread tropical tree genus endemic to the Asian tropics. Loci recovery from historical and recently collected samples was not affected by sample age and preservation history of the study material, underscoring the reliability and flexibility of the MIGseq approach. Phylogenomic inference and biogeographic reconstruction across insular Asia, highlights repeated migration and diversification patterns between continental regions and islands. Results indicate that co-occurring insular species at the extremity of the distribution range are not monophyletic, raising the possibility of multiple independent dispersals along the outer edge of Wallacea. This suggests that dispersal of large seeded tree genera throughout Malesia and across Wallacea may have been less affected by large geographic distances and the presence of marine barriers than generally assumed. We demonstrate the utility of MIGseq in museomic studies using non-model taxa, presenting the first range-wide genomic assessment of Lithocarpus and tropical Fagaceae as a proof-of-concept. Our study shows the potential for developing innovative genomic approaches to improve the capture of novel evolutionary signals using valuable natural history collections of hyperdiverse taxa.

A linked-read approach to museomics: Higher quality de novo genome assemblies from degraded tissues

High-throughput sequencing technologies are a proposed solution for accessing the molecular data in historical specimens. However, degraded DNA combined with the computational demands of short-read assemblies has posed significant laboratory and bioinformatics challenges for de novo genome assembly. Linked-read or "synthetic long-read" sequencing technologies, such as 10× Genomics, may provide a cost-effective alternative solution to assemble higher quality de novo genomes from degraded tissue samples. Here, we compare assembly quality (e.g., genome contiguity and completeness, presence of orthogroups) between four new deer mouse (Peromyscus spp.) genomes assembled using linked-read technology and four published genomes assembled from a single shotgun library. At a similar price-point, these approaches produce vastly different assemblies, with linked-read assemblies having overall higher contiguity and completeness, measured by larger N50 values and greater number of genes assembled, respectively. As a proof-of-concept, we used annotated genes from the four Peromyscus linked-read assemblies and eight additional rodent taxa to generate a phylogeny, which reconstructed the expected relationships among species with 100% support. Although not without caveats, our results suggest that linked-read sequencing approaches are a viable option to build de novo genomes from degraded tissues, which may prove particularly valuable for taxa that are extinct, rare or difficult to collect.

Chloroplast genomes of Rubiaceae: Comparative genomics and molecular phylogeny in subfamily Ixoroideae

In Rubiaceae phylogenetics, the number of markers often proved a limitation with authors failing to provide well-supported trees at tribal and generic levels. A robust phylogeny is a prerequisite to study the evolutionary patterns of traits at different taxonomic levels. Advances in next-generation sequencing technologies have revolutionized biology by providing, at reduced cost, huge amounts of data for an increased number of species. Due to their highly conserved structure, generally recombination-free, and mostly uniparental inheritance, chloroplast DNA sequences have long been used as choice markers for plant phylogeny reconstruction. The main objectives of this study are: 1) to gain insight in chloroplast genome evolution in the Rubiaceae (Ixoroideae) through efficient methodology for de novo assembly of plastid genomes; and, 2) to test the efficiency of mining SNPs in the nuclear genome of Ixoroideae based on the use of a coffee reference genome to produce well-supported nuclear trees. We assembled whole chloroplast genome sequences for 27 species of the Rubiaceae subfamily Ixoroideae using next-generation sequences. Analysis of the plastid genome structure reveals a relatively good conservation of gene content and order. Generally, low variation was observed between taxa in the boundary regions with the exception of the inverted repeat at both the large and short single copy junctions for some taxa. An average of 79% of the SNP determined in the Coffea genus are transferable to Ixoroideae, with variation ranging from 35% to 96%. In general, the plastid and the nuclear genome phylogenies are congruent with each other. They are well-resolved with well-supported branches. Generally, the tribes form well-identified clades but the tribe Sherbournieae is shown to be polyphyletic. The results are discussed relative to the methodology used and the chloroplast genome features in Rubiaceae and compared to previous Rubiaceae phylogenies.

The Treasure Vault Can be Opened: Large-Scale Genome Skimming Works Well Using Herbarium and Silica Gel Dried Material

Genome skimming has the potential for generating large data sets for DNA barcoding and wider biodiversity genomic studies, particularly via the assembly and annotation of full chloroplast (cpDNA) and nuclear ribosomal DNA (nrDNA) sequences. We compare the success of genome skims of 2051 herbarium specimens from Norway/Polar regions with 4604 freshly collected, silica gel dried specimens mainly from the European Alps and the Carpathians. Overall, we were able to assemble the full chloroplast genome for 67% of the samples and the full nrDNA cluster for 86%. Average insert length, cover and full cpDNA and rDNA assembly were considerably higher for silica gel dried than herbarium-preserved material. However, complete plastid genomes were still assembled for 54% of herbarium samples compared to 70% of silica dried samples. Moreover, there was comparable recovery of coding genes from both tissue sources (121 for silica gel dried and 118 for herbarium material) and only minor differences in assembly success of standard barcodes between silica dried (89% ITS2, 96% matK and rbcL) and herbarium material (87% ITS2, 98% matK and rbcL). The success rate was > 90% for all three markers in 1034 of 1036 genera in 160 families, and only Boraginaceae worked poorly, with 7 genera failing. Our study shows that large-scale genome skims are feasible and work well across most of the land plant families and genera we tested, independently of material type. It is therefore an efficient method for increasing the availability of plant biodiversity genomic data to support a multitude of downstream applications.

The Global Museum: natural history collections and the future of evolutionary science and public education

Natural history museums are unique spaces for interdisciplinary research and educational innovation. Through extensive exhibits and public programming and by hosting rich communities of amateurs, students, and researchers at all stages of their careers, they can provide a place-based window to focus on integration of science and discovery, as well as a locus for community engagement. At the same time, like a synthesis radio telescope, when joined together through emerging digital resources, the global community of museums (the ‘Global Museum’) is more than the sum of its parts, allowing insights and answers to diverse biological, environmental, and societal questions at the global scale, across eons of time, and spanning vast diversity across the Tree of Life. We argue that, whereas natural history collections and museums began with a focus on describing the diversity and peculiarities of species on Earth, they are now increasingly leveraged in new ways that significantly expand their impact and relevance. These new directions include the possibility to ask new, often interdisciplinary questions in basic and applied science, such as in biomimetic design, and by contributing to solutions to climate change, global health and food security challenges. As institutions, they have long been incubators for cutting-edge research in biology while simultaneously providing core infrastructure for research on present and future societal needs. Here we explore how the intersection between pressing issues in environmental and human health and rapid technological innovation have reinforced the relevance of museum collections. We do this by providing examples as food for thought for both the broader academic community and museum scientists on the evolving role of museums. We also identify challenges to the realization of the full potential of natural history collections and the Global Museum to science and society and discuss the critical need to grow these collections. We then focus on mapping and modelling of museum data (including place-based approaches and discovery), and explore the main projects, platforms and databases enabling this growth. Finally, we aim to improve relevant protocols for the long-term storage of specimens and tissues, ensuring proper connection with tomorrow’s technologies and hence further increasing the relevance of natural history museums.

Large scale genome skimming from herbarium material for accurate plant identification and phylogenomics

BACKGROUND

Herbaria are valuable sources of extensive curated plant material that are now accessible to genetic studies because of advances in high-throughput, next-generation sequencing methods. As an applied assessment of large-scale recovery of plastid and ribosomal genome sequences from herbarium material for plant identification and phylogenomics, we sequenced 672 samples covering 21 families, 142 genera and 530 named and proposed named species. We explored the impact of parameters such as sample age, DNA concentration and quality, read depth and fragment length on plastid assembly error. We also tested the efficacy of DNA sequence information for identifying plant samples using 45 specimens recently collected in the Pilbara.

RESULTS

Genome skimming was effective at producing genomic information at large scale. Substantial sequence information on the chloroplast genome was obtained from 96.1% of samples, and complete or near-complete sequences of the nuclear ribosomal RNA gene repeat were obtained from 93.3% of samples. We were able to extract sequences for the core DNA barcode regions rbcL and matK from 96 to 93.3% of samples, respectively. Read quality and DNA fragment length had significant effects on sequencing outcomes and error correction of reads proved essential. Assembly problems were specific to certain taxa with low GC and high repeat content (Goodenia, Scaevola, Cyperus, Bulbostylis, Fimbristylis) suggesting biological rather than technical explanations. The structure of related genomes was needed to guide the assembly of repeats that exceeded the read length. DNA-based matching proved highly effective and showed that the efficacy for species identification declined in the order cpDNA >> rDNA > matK >> rbcL.

CONCLUSIONS

We showed that a large-scale approach to genome sequencing using herbarium specimens produces high-quality complete cpDNA and rDNA sequences as a source of data for DNA barcoding and phylogenomics.

Molecular digitization of a botanical garden: high-depth whole-genome sequencing of 689 vascular plant species from the Ruili Botanical Garden

Background

Genome sequencing has been widely used in plant research to construct reference genomes and provide evolutionary insights. However, few plant species have had their whole genome sequenced, thus restraining the utility of these data. We collected 1,093 samples of vascular plant species growing in the Ruili Botanical Garden, located in southwest China. Of these, we sequenced 761 samples and collected voucher specimens stored in the Herbarium of China National GeneBank.

Results

The 761 sequenced samples represented 689 vascular plant species from 137 families belonging to 49 orders. Of these, 257 samples were identified to the species level and 504 to the family level, using specimen and chloroplast sequences. In total, we generated 54 Tb of sequencing data, with an average sequencing depth of 60X per species, as estimated from genome sizes. A reference phylogeny was reconstructed with 78 chloroplast genes for molecular identification and other possible applications.

Conclusions

The large dataset of vascular plant genomes generated in this study, which includes both high-depth whole-genome sequencing data and associated voucher specimens, is valuable for plant genome research and other applications. This project also provides insight into the feasibility and technical requirements for “planetary-scale” projects such as the 10,000 Plant Genomes Project and the Earth BioGenome Project.