Browsing by Author "Dudchenko, Olga"
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Item A Chromosome-length Assembly of the Black Petaltail (Tanypteryx hageni) Dragonfly(Oxford University Press, 2023) Tolman, Ethan R; Beatty, Christopher D; Bush, Jonas; Kohli, Manpreet; Moreno, Carlos M; Ware, Jessica L; Weber, K Scott; Khan, Ruqayya; Maheshwari, Chirag; Weisz, David; Dudchenko, Olga; Aiden, Erez Lieberman; Frandsen, Paul B; Center for Theoretical Biological PhysicsWe present a chromosome-length genome assembly and annotation of the Black Petaltail dragonfly (Tanypteryx hageni). This habitat specialist diverged from its sister species over 70 million years ago, and separated from the most closely related Odonata with a reference genome 150 million years ago. Using PacBio HiFi reads and Hi-C data for scaffolding we produce one of the most high-quality Odonata genomes to date. A scaffold N50 of 206.6 Mb and a single copy BUSCO score of 96.2% indicate high contiguity and completeness.Item A Chromosome-Length Assembly of the Hawaiian Monk Seal (Neomonachus schauinslandi): A History of “Genetic Purging” and Genomic Stability(MDPI, 2022) Mohr, David W.; Gaughran, Stephen J.; Paschall, Justin; Naguib, Ahmed; Pang, Andy Wing Chun; Dudchenko, Olga; Aiden, Erez Lieberman; Church, Deanna M.; Scott, Alan F.; Center for Theoretical Biological PhysicsThe Hawaiian monk seal (HMS) is the single extant species of tropical earless seals of the genus Neomonachus. The species survived a severe bottleneck in the late 19th century and experienced subsequent population declines until becoming the subject of a NOAA-led species recovery effort beginning in 1976 when the population was fewer than 1000 animals. Like other recovering species, the Hawaiian monk seal has been reported to have reduced genetic heterogeneity due to the bottleneck and subsequent inbreeding. Here, we report a chromosomal reference assembly for a male animal produced using a variety of methods. The final assembly consisted of 16 autosomes, an X, and portions of the Y chromosomes. We compared variants in this animal to other HMS and to a frequently sequenced human sample, confirming about 12% of the variation seen in man. To confirm that the reference animal was representative of the HMS, we compared his sequence to that of 10 other individuals and noted similarly low variation in all. Variation in the major histocompatibility (MHC) genes was nearly absent compared to the orthologous human loci. Demographic analysis predicts that Hawaiian monk seals have had a long history of small populations preceding the bottleneck, and their current low levels of heterozygosity may indicate specialization to a stable environment. When we compared our reference assembly to that of other species, we observed significant conservation of chromosomal architecture with other pinnipeds, especially other phocids. This reference should be a useful tool for future evolutionary studies as well as the long-term management of this species.Item A Chromosome-Length Reference Genome for the Endangered Pacific Pocket Mouse Reveals Recent Inbreeding in a Historically Large Population(Oxford University Press, 2022) Wilder, Aryn P; Dudchenko, Olga; Curry, Caitlin; Korody, Marisa; Turbek, Sheela P; Daly, Mark; Misuraca, Ann; Wang, Gaojianyong; Khan, Ruqayya; Weisz, David; Fronczek, Julie; Aiden, Erez Lieberman; Houck, Marlys L; Shier, Debra M; Ryder, Oliver A; Steiner, Cynthia C; Center for Theoretical Biological PhysicsHigh-quality reference genomes are fundamental tools for understanding population history, and can provide estimates of genetic and demographic parameters relevant to the conservation of biodiversity. The federally endangered Pacific pocket mouse (PPM), which persists in three small, isolated populations in southern California, is a promising model for studying how demographic history shapes genetic diversity, and how diversity in turn may influence extinction risk. To facilitate these studies in PPM, we combined PacBio HiFi long reads with Omni-C and Hi-C data to generate a de novo genome assembly, and annotated the genome using RNAseq. The assembly comprised 28 chromosome-length scaffolds (N50 = 72.6 MB) and the complete mitochondrial genome, and included a long heterochromatic region on chromosome 18 not represented in the previously available short-read assembly. Heterozygosity was highly variable across the genome of the reference individual, with 18% of windows falling in runs of homozygosity (ROH) >1 MB, and nearly 9% in tracts spanning >5 MB. Yet outside of ROH, heterozygosity was relatively high (0.0027), and historical Ne estimates were large. These patterns of genetic variation suggest recent inbreeding in a formerly large population. Currently the most contiguous assembly for a heteromyid rodent, this reference genome provides insight into the past and recent demographic history of the population, and will be a critical tool for management and future studies of outbreeding depression, inbreeding depression, and genetic load.Item A pan-genome and chromosome-length reference genome of narrow-leafed lupin (Lupinus angustifolius) reveals genomic diversity and insights into key industry and biological traits(Wiley, 2022) Garg, Gagan; Kamphuis, Lars G.; Bayer, Philipp E.; Kaur, Parwinder; Dudchenko, Olga; Taylor, Candy M.; Frick, Karen M.; Foley, Rhonda C.; Gao, Ling-Ling; Aiden, Erez Lieberman; Edwards, David; Singh, Karam B.; Center for Theoretical Biological PhysicsNarrow-leafed lupin (NLL; Lupinus angustifolius) is a key rotational crop for sustainable farming systems, whose grain is high in protein content. It is a gluten-free, non-genetically modified, alternative protein source to soybean (Glycine max) and as such has gained interest as a human food ingredient. Here, we present a chromosome-length reference genome for the species and a pan-genome assembly comprising 55 NLL lines, including Australian and European cultivars, breeding lines and wild accessions. We present the core and variable genes for the species and report on the absence of essential mycorrhizal associated genes. The genome and pan-genomes of NLL and its close relative white lupin (Lupinus albus) are compared. Furthermore, we provide additional evidence supporting LaRAP2-7 as the key alkaloid regulatory gene for NLL and demonstrate the NLL genome is underrepresented in classical NLR disease resistance genes compared to other sequenced legume species. The NLL genomic resources generated here coupled with previously generated RNA sequencing datasets provide new opportunities to fast-track lupin crop improvement.Item A rapid, low-cost, and highly sensitive SARS-CoV-2 diagnostic based on whole-genome sequencing(Public Library of Science, 2023) Adastra, Per A.; Durand, Neva C.; Mitra, Namita; Pulido, Saul Godinez; Mahajan, Ragini; Blackburn, Alyssa; Colaric, Zane L.; Theisen, Joshua W. M.; Weisz, David; Dudchenko, Olga; Gnirke, Andreas; Rao, Suhas S. P.; Kaur, Parwinder; Aiden, Erez Lieberman; Aiden, Aviva Presser; Center for Theoretical Biological PhysicsEarly detection of SARS-CoV-2 infection is key to managing the current global pandemic, as evidence shows the virus is most contagious on or before symptom onset. Here, we introduce a low-cost, high-throughput method for diagnosing and studying SARS-CoV-2 infection. Dubbed Pathogen-Oriented Low-Cost Assembly & Re-Sequencing (POLAR), this method amplifies the entirety of the SARS-CoV-2 genome. This contrasts with typical RT-PCR-based diagnostic tests, which amplify only a few loci. To achieve this goal, we combine a SARS-CoV-2 enrichment method developed by the ARTIC Network (https://artic.network/) with short-read DNA sequencing and de novo genome assembly. Using this method, we can reliably (>95% accuracy) detect SARS-CoV-2 at a concentration of 84 genome equivalents per milliliter (GE/mL). The vast majority of diagnostic methods meeting our analytical criteria that are currently authorized for use by the United States Food and Drug Administration with the Coronavirus Disease 2019 (COVID-19) Emergency Use Authorization require higher concentrations of the virus to achieve this degree of sensitivity and specificity. In addition, we can reliably assemble the SARS-CoV-2 genome in the sample, often with no gaps and perfect accuracy given sufficient viral load. The genotypic data in these genome assemblies enable the more effective analysis of disease spread than is possible with an ordinary binary diagnostic. These data can also help identify vaccine and drug targets. Finally, we show that the diagnoses obtained using POLAR of positive and negative clinical nasal mid-turbinate swab samples 100% match those obtained in a clinical diagnostic lab using the Center for Disease Control’s 2019-Novel Coronavirus test. Using POLAR, a single person can manually process 192 samples over an 8-hour experiment at the cost of ~$36 per patient (as of December 7th, 2022), enabling a 24-hour turnaround with sequencing and data analysis time. We anticipate that further testing and refinement will allow greater sensitivity using this approach.Item Chromatin alternates between A and B compartments at kilobase scale for subgenic organization(Springer Nature, 2023) Harris, Hannah L.; Gu, Huiya; Olshansky, Moshe; Wang, Ailun; Farabella, Irene; Eliaz, Yossi; Kalluchi, Achyuth; Krishna, Akshay; Jacobs, Mozes; Cauer, Gesine; Pham, Melanie; Rao, Suhas S. P.; Dudchenko, Olga; Omer, Arina; Mohajeri, Kiana; Kim, Sungjae; Nichols, Michael H.; Davis, Eric S.; Gkountaroulis, Dimos; Udupa, Devika; Aiden, Aviva Presser; Corces, Victor G.; Phanstiel, Douglas H.; Noble, William Stafford; Nir, Guy; Di Pierro, Michele; Seo, Jeong-Sun; Talkowski, Michael E.; Aiden, Erez Lieberman; Rowley, M. Jordan; Center for Theoretical Biological PhysicsNuclear compartments are prominent features of 3D chromatin organization, but sequencing depth limitations have impeded investigation at ultra fine-scale. CTCF loops are generally studied at a finer scale, but the impact of looping on proximal interactions remains enigmatic. Here, we critically examine nuclear compartments and CTCF loop-proximal interactions using a combination of in situ Hi-C at unparalleled depth, algorithm development, and biophysical modeling. Producing a large Hi-C map with 33 billion contacts in conjunction with an algorithm for performing principal component analysis on sparse, super massive matrices (POSSUMM), we resolve compartments to 500 bp. Our results demonstrate that essentially all active promoters and distal enhancers localize in the A compartment, even when flanking sequences do not. Furthermore, we find that the TSS and TTS of paused genes are often segregated into separate compartments. We then identify diffuse interactions that radiate from CTCF loop anchors, which correlate with strong enhancer-promoter interactions and proximal transcription. We also find that these diffuse interactions depend on CTCF’s RNA binding domains. In this work, we demonstrate features of fine-scale chromatin organization consistent with a revised model in which compartments are more precise than commonly thought while CTCF loops are more protracted.Item Chromosome size affects sequence divergence between species through the interplay of recombination and selection(Wiley, 2022) Tigano, Anna; Khan, Ruqayya; Omer, Arina D.; Weisz, David; Dudchenko, Olga; Multani, Asha S.; Pathak, Sen; Behringer, Richard R.; Aiden, Erez L.; Fisher, Heidi; MacManes, Matthew D.; Center for Theoretical and Biological PhysicsThe structure of the genome shapes the distribution of genetic diversity and sequence divergence. To investigate how the relationship between chromosome size and recombination rate affects sequence divergence between species, we combined empirical analyses and evolutionary simulations. We estimated pairwise sequence divergence among 15 species from three different mammalian clades—Peromyscus rodents, Mus mice, and great apes—from chromosome-level genome assemblies. We found a strong significant negative correlation between chromosome size and sequence divergence in all species comparisons within the Peromyscus and great apes clades but not the Mus clade, suggesting that the dramatic chromosomal rearrangements among Mus species may have masked the ancestral genomic landscape of divergence in many comparisons. Our evolutionary simulations showed that the main factor determining differences in divergence among chromosomes of different sizes is the interplay of recombination rate and selection, with greater variation in larger populations than in smaller ones. In ancestral populations, shorter chromosomes harbor greater nucleotide diversity. As ancestral populations diverge, diversity present at the onset of the split contributes to greater sequence divergence in shorter chromosomes among daughter species. The combination of empirical data and evolutionary simulations revealed that chromosomal rearrangements, demography, and divergence times may also affect the relationship between chromosome size and divergence, thus deepening our understanding of the role of genome structure in the evolution of species divergence.Item Chromosome-length genome assembly and linkage map of a critically endangered Australian bird: the helmeted honeyeater(Oxford University Press, 2022) Robledo-Ruiz, Diana A.; Gan, Han Ming; Kaur, Parwinder; Dudchenko, Olga; Weisz, David; Khan, Ruqayya; Aiden, Erez Lieberman; Osipova, Ekaterina; Hiller, Michael; Morales, Hernán E.; Magrath, Michael J.L.; Clarke, Rohan H.; Sunnucks, Paul; Pavlova, Alexandra; Center for Theoretical Biological PhysicsThe helmeted honeyeater (Lichenostomus melanops cassidix) is a Critically Endangered bird endemic to Victoria, Australia. To aid its conservation, the population is the subject of genetic rescue. To understand, monitor, and modulate the effects of genetic rescue on the helmeted honeyeater genome, a chromosome-length genome and a high-density linkage map are required.We used a combination of Illumina, Oxford Nanopore, and Hi-C sequencing technologies to assemble a chromosome-length genome of the helmeted honeyeater, comprising 906 scaffolds, with length of 1.1 Gb and scaffold N50 of 63.8 Mb. Annotation comprised 57,181 gene models. Using a pedigree of 257 birds and 53,111 single-nucleotide polymorphisms, we obtained high-density linkage and recombination maps for 25 autosomes and Z chromosome. The total sex-averaged linkage map was 1,347 cM long, with the male map being 6.7% longer than the female map. Recombination maps revealed sexually dimorphic recombination rates (overall higher in males), with average recombination rate of 1.8 cM/Mb. Comparative analyses revealed high synteny of the helmeted honeyeater genome with that of 3 passerine species (e.g., 32 Hi-C scaffolds mapped to 30 zebra finch autosomes and Z chromosome). The genome assembly and linkage map suggest that the helmeted honeyeater exhibits a fission of chromosome 1A into 2 chromosomes relative to zebra finch. PSMC analysis showed a ∼15-fold decline in effective population size to ∼60,000 from mid- to late Pleistocene.The annotated chromosome-length genome and high-density linkage map provide rich resources for evolutionary studies and will be fundamental in guiding conservation efforts for the helmeted honeyeater.Item Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome(Springer Nature, 2021) Edwards, Richard J.; Field, Matt A.; Ferguson, James M.; Dudchenko, Olga; Keilwagen, Jens; Rosen, Benjamin D.; Johnson, Gary S.; Rice, Edward S.; Hillier, La Deanna; Hammond, Jillian M.; Towarnicki, Samuel G.; Omer, Arina; Khan, Ruqayya; Skvortsova, Ksenia; Bogdanovic, Ozren; Zammit, Robert A.; Aiden, Erez Lieberman; Warren, Wesley C.; Ballard, J. William O.; Center for Theoretical and Biological PhysicsBasenjis are considered an ancient dog breed of central African origins that still live and hunt with tribesmen in the African Congo. Nicknamed the barkless dog, Basenjis possess unique phylogeny, geographical origins and traits, making their genome structure of great interest. The increasing number of available canid reference genomes allows us to examine the impact the choice of reference genome makes with regard to reference genome quality and breed relatedness.Item Chromosome-length genome assembly of Teladorsagia circumcincta – a globally important helminth parasite in livestock(Springer Nature, 2023) Hassan, Shamshad Ul; Chua, Eng Guan; Paz, Erwin A.; Tay, Chin Yen; Greeff, Johan C.; Palmer, Dieter G.; Dudchenko, Olga; Aiden, Erez Lieberman; Martin, Graeme B.; Kaur, Parwinder; Center for Theoretical Biological PhysicsGastrointestinal (GIT) helminthiasis is a global problem that affects livestock health, especially in small ruminants. One of the major helminth parasites of sheep and goats, Teladorsagia circumcincta, infects the abomasum and causes production losses, reductions in weight gain, diarrhoea and, in some cases, death in young animals. Control strategies have relied heavily on the use of anthelmintic medication but, unfortunately, T. circumcincta has developed resistance, as have many helminths. Vaccination offers a sustainable and practical solution, but there is no commercially available vaccine to prevent Teladorsagiosis. The discovery of new strategies for controlling T. circumcincta, such as novel vaccine targets and drug candidates, would be greatly accelerated by the availability of better quality, chromosome-length, genome assembly because it would allow the identification of key genetic determinants of the pathophysiology of infection and host-parasite interaction. The available draft genome assembly of T. circumcincta (GCA_002352805.1) is highly fragmented and thus impedes large-scale investigations of population and functional genomics.Item Chromosome-level genome of Schistosoma haematobium underpins genome-wide explorations of molecular variation(Public Library of Science, 2022) Stroehlein, Andreas J.; Korhonen, Pasi K.; Lee, V. Vern; Ralph, Stuart A.; Mentink-Kane, Margaret; You, Hong; McManus, Donald P.; Tchuenté, Louis-Albert Tchuem; Stothard, J. Russell; Kaur, Parwinder; Dudchenko, Olga; Aiden, Erez Lieberman; Yang, Bicheng; Yang, Huanming; Emery, Aidan M.; Webster, Bonnie L.; Brindley, Paul J.; Rollinson, David; Chang, Bill C.H.; Gasser, Robin B.; Young, Neil D.; Center for Theoretical Biological PhysicsUrogenital schistosomiasis is caused by the blood fluke Schistosoma haematobium and is one of the most neglected tropical diseases worldwide, afflicting > 100 million people. It is characterised by granulomata, fibrosis and calcification in urogenital tissues, and can lead to increased susceptibility to HIV/AIDS and squamous cell carcinoma of the bladder. To complement available treatment programs and break the transmission of disease, sound knowledge and understanding of the biology and ecology of S. haematobium is required. Hybridisation/introgression events and molecular variation among members of the S. haematobium-group might effect important biological and/or disease traits as well as the morbidity of disease and the effectiveness of control programs including mass drug administration. Here we report the first chromosome-contiguous genome for a well-defined laboratory line of this blood fluke. An exploration of this genome using transcriptomic data for all key developmental stages allowed us to refine gene models (including non-coding elements) and annotations, discover ‘new’ genes and transcription profiles for these stages, likely linked to development and/or pathogenesis. Molecular variation within S. haematobium among some geographical locations in Africa revealed unique genomic ‘signatures’ that matched species other than S. haematobium, indicating the occurrence of introgression events. The present reference genome (designated Shae.V3) and the findings from this study solidly underpin future functional genomic and molecular investigations of S. haematobium and accelerate systematic, large-scale population genomics investigations, with a focus on improved and sustained control of urogenital schistosomiasis.Item Emx2 underlies the development and evolution of marsupial gliding membranes(Springer Nature, 2024) Moreno, Jorge A.; Dudchenko, Olga; Feigin, Charles Y.; Mereby, Sarah A.; Chen, Zhuoxin; Ramos, Raul; Almet, Axel A.; Sen, Harsha; Brack, Benjamin J.; Johnson, Matthew R.; Li, Sha; Wang, Wei; Gaska, Jenna M.; Ploss, Alexander; Weisz, David; Omer, Arina D.; Yao, Weijie; Colaric, Zane; Kaur, Parwinder; Leger, Judy St; Nie, Qing; Mena, Alexandria; Flanagan, Joseph P.; Keller, Greta; Sanger, Thomas; Ostrow, Bruce; Plikus, Maksim V.; Kvon, Evgeny Z.; Aiden, Erez Lieberman; Mallarino, Ricardo; Center for Theoretical Biological PhysicsPhenotypic variation among species is a product of evolutionary changes to developmental programs1,2. However, how these changes generate novel morphological traits remains largely unclear. Here we studied the genomic and developmental basis of the mammalian gliding membrane, or patagium—an adaptative trait that has repeatedly evolved in different lineages, including in closely related marsupial species. Through comparative genomic analysis of 15 marsupial genomes, both from gliding and non-gliding species, we find that the Emx2 locus experienced lineage-specific patterns of accelerated cis-regulatory evolution in gliding species. By combining epigenomics, transcriptomics and in-pouch marsupial transgenics, we show that Emx2 is a critical upstream regulator of patagium development. Moreover, we identify different cis-regulatory elements that may be responsible for driving increased Emx2 expression levels in gliding species. Lastly, using mouse functional experiments, we find evidence that Emx2 expression patterns in gliders may have been modified from a pre-existing program found in all mammals. Together, our results suggest that patagia repeatedly originated through a process of convergent genomic evolution, whereby regulation of Emx2 was altered by distinct cis-regulatory elements in independently evolved species. Thus, different regulatory elements targeting the same key developmental gene may constitute an effective strategy by which natural selection has harnessed regulatory evolution in marsupial genomes to generate phenotypic novelty.Item Genome-wide diversity in the California condor tracks its prehistoric abundance and decline(Elsevier, 2021) Robinson, Jacqueline A.; Bowie, Rauri C. K.; Dudchenko, Olga; Aiden, Erez Lieberman; Hendrickson, Sher L.; Steiner, Cynthia C.; Ryder, Oliver A.; Mindell, David P.; Wall, Jeffrey D.; Center for Theoretical and Biological PhysicsDue to their small population sizes, threatened and endangered species frequently suffer from a lack of genetic diversity, potentially leading to inbreeding depression and reduced adaptability.1 During the latter half of the twentieth century, North America’s largest soaring bird,2 the California condor (Gymnogyps californianus; Critically Endangered3), briefly went extinct in the wild. Though condors once ranged throughout North America, by 1982 only 22 individuals remained. Following decades of captive breeding and release efforts, there are now >300 free-flying wild condors and ∼200 in captivity. The condor’s recent near-extinction from lead poisoning, poaching, and loss of habitat is well documented,4 but much about its history remains obscure. To fill this gap and aid future management of the species, we produced a high-quality chromosome-length genome assembly for the California condor and analyzed its genome-wide diversity. For comparison, we also examined the genomes of two close relatives: the Andean condor (Vultur gryphus; Vulnerable3) and the turkey vulture (Cathartes aura; Least Concern3). The genomes of all three species show evidence of historic population declines. Interestingly, the California condor genome retains a high degree of variation, which our analyses reveal is a legacy of its historically high abundance. Correlations between genome-wide diversity and recombination rate further suggest a history of purifying selection against linked deleterious alleles, boding well for future restoration. We show how both long-term evolutionary forces and recent inbreeding have shaped the genome of the California condor, and provide crucial genomic resources to enable future research and conservation.Item Genomic signatures of barley breeding for environmental adaptation to the new continents(Wiley, 2023) Hu, Haifei; Wang, Penghao; Angessa, Tefera Tolera; Zhang, Xiao-Qi; Chalmers, Kenneth J.; Zhou, Gaofeng; Hill, Camilla Beate; Jia, Yong; Simpson, Craig; Fuller, John; Saxena, Alka; Al Shamaileh, Hadi; Iqbal, Munir; Chapman, Brett; Kaur, Parwinder; Dudchenko, Olga; Aiden, Erez Lieberman; Keeble-Gagnere, Gabriel; Westcott, Sharon; Leah, David; Tibbits, Josquin F.; Waugh, Robbie; Langridge, Peter; Varshney, Rajeev; He, Tianhua; Li, Chengdao; Center for Theoretical Biological PhysicsItem Improved high quality sand fly assemblies enabled by ultra low input long read sequencing(Springer Nature, 2024) Huang, Michelle; Kingan, Sarah; Shoue, Douglas; Nguyen, Oanh; Froenicke, Lutz; Galvin, Brendan; Lambert, Christine; Khan, Ruqayya; Maheshwari, Chirag; Weisz, David; Maslen, Gareth; Davison, Helen; Aiden, Erez Lieberman; Korlach, Jonas; Dudchenko, Olga; McDowell, Mary Ann; Richards, Stephen; Center for Theoretical Biological PhysicsPhlebotomine sand flies are the vectors of leishmaniasis, a neglected tropical disease. High-quality reference genomes are an important tool for understanding the biology and eco-evolutionary dynamics underpinning disease epidemiology. Previous leishmaniasis vector reference sequences were limited by sequencing technologies available at the time and inadequate for high-resolution genomic inquiry. Here, we present updated reference assemblies of two sand flies, Phlebotomus papatasi and Lutzomyia longipalpis. These chromosome-level assemblies were generated using an ultra-low input library protocol, PacBio HiFi long reads, and Hi-C technology. The new P. papatasi reference has a final assembly span of 351.6 Mb and contig and scaffold N50s of 926 kb and 111.8 Mb, respectively. The new Lu. longipalpis reference has a final assembly span of 147.8 Mb and contig and scaffold N50s of 1.09 Mb and 40.6 Mb, respectively. Benchmarking Universal Single-Copy Orthologue (BUSCO) assessments indicated 94.5% and 95.6% complete single copy insecta orthologs for P. papatasi and Lu. longipalpis. These improved assemblies will serve as an invaluable resource for future genomic work on phlebotomine sandflies.Item The Australasian dingo archetype: de novo chromosome-length genome assembly, DNA methylome, and cranial morphology(Oxford University Press, 2023) Ballard, J. William O.; Field, Matt A.; Edwards, Richard J.; Wilson, Laura A.B.; Koungoulos, Loukas G.; Rosen, Benjamin D.; Chernoff, Barry; Dudchenko, Olga; Omer, Arina; Keilwagen, Jens; Skvortsova, Ksenia; Bogdanovic, Ozren; Chan, Eva; Zammit, Robert; Hayes, Vanessa; Aiden, Erez Lieberman; Center for Theoretical and Biological PhysicsOne difficulty in testing the hypothesis that the Australasian dingo is a functional intermediate between wild wolves and domesticated breed dogs is that there is no reference specimen. Here we link a high-quality de novo long-read chromosomal assembly with epigenetic footprints and morphology to describe the Alpine dingo female named Cooinda. It was critical to establish an Alpine dingo reference because this ecotype occurs throughout coastal eastern Australia where the first drawings and descriptions were completed.We generated a high-quality chromosome-level reference genome assembly (Canfam_ADS) using a combination of Pacific Bioscience, Oxford Nanopore, 10X Genomics, Bionano, and Hi-C technologies. Compared to the previously published Desert dingo assembly, there are large structural rearrangements on chromosomes 11, 16, 25, and 26. Phylogenetic analyses of chromosomal data from Cooinda the Alpine dingo and 9 previously published de novo canine assemblies show dingoes are monophyletic and basal to domestic dogs. Network analyses show that the mitochondrial DNA genome clusters within the southeastern lineage, as expected for an Alpine dingo. Comparison of regulatory regions identified 2 differentially methylated regions within glucagon receptor GCGR and histone deacetylase HDAC4 genes that are unmethylated in the Alpine dingo genome but hypermethylated in the Desert dingo. Morphologic data, comprising geometric morphometric assessment of cranial morphology, place dingo Cooinda within population-level variation for Alpine dingoes. Magnetic resonance imaging of brain tissue shows she had a larger cranial capacity than a similar-sized domestic dog.These combined data support the hypothesis that the dingo Cooinda fits the spectrum of genetic and morphologic characteristics typical of the Alpine ecotype. We propose that she be considered the archetype specimen for future research investigating the evolutionary history, morphology, physiology, and ecology of dingoes. The female has been taxidermically prepared and is now at the Australian Museum, Sydney.Item The Australian dingo is an early offshoot of modern breed dogs(AAAS, 2022) Field, Matt A.; Yadav, Sonu; Dudchenko, Olga; Esvaran, Meera; Rosen, Benjamin D.; Skvortsova, Ksenia; Edwards, Richard J.; Keilwagen, Jens; Cochran, Blake J.; Manandhar, Bikash; Bustamante, Sonia; Rasmussen, Jacob Agerbo; Melvin, Richard G.; Chernoff, Barry; Omer, Arina; Colaric, Zane; Chan, Eva K. F.; Minoche, Andre E.; Smith, Timothy P. L.; Gilbert, M. Thomas P.; Bogdanovic, Ozren; Zammit, Robert A.; Thomas, Torsten; Aiden, Erez L.; Ballard, J. William O.; Center for Theoretical Biological PhysicsDogs are uniquely associated with human dispersal and bring transformational insight into the domestication process. Dingoes represent an intriguing case within canine evolution being geographically isolated for thousands of years. Here, we present a high-quality de novo assembly of a pure dingo (CanFam_DDS). We identified large chromosomal differences relative to the current dog reference (CanFam3.1) and confirmed no expanded pancreatic amylase gene as found in breed dogs. Phylogenetic analyses using variant pairwise matrices show that the dingo is distinct from five breed dogs with 100% bootstrap support when using Greenland wolf as the outgroup. Functionally, we observe differences in methylation patterns between the dingo and German shepherd dog genomes and differences in serum biochemistry and microbiome makeup. Our results suggest that distinct demographic and environmental conditions have shaped the dingo genome. In contrast, artificial human selection has likely shaped the genomes of domestic breed dogs after divergence from the dingo.Item The swan genome and transcriptome, it is not all black and white(Springer Nature, 2023) Karawita, Anjana C.; Cheng, Yuanyuan; Chew, Keng Yih; Challagulla, Arjun; Kraus, Robert; Mueller, Ralf C.; Tong, Marcus Z. W.; Hulme, Katina D.; Bielefeldt-Ohmann, Helle; Steele, Lauren E.; Wu, Melanie; Sng, Julian; Noye, Ellesandra; Bruxner, Timothy J.; Au, Gough G.; Lowther, Suzanne; Blommaert, Julie; Suh, Alexander; McCauley, Alexander J.; Kaur, Parwinder; Dudchenko, Olga; Aiden, Erez; Fedrigo, Olivier; Formenti, Giulio; Mountcastle, Jacquelyn; Chow, William; Martin, Fergal J.; Ogeh, Denye N.; Thiaud-Nissen, Françoise; Howe, Kerstin; Tracey, Alan; Smith, Jacqueline; Kuo, Richard I.; Renfree, Marilyn B.; Kimura, Takashi; Sakoda, Yoshihiro; McDougall, Mathew; Spencer, Hamish G.; Pyne, Michael; Tolf, Conny; Waldenström, Jonas; Jarvis, Erich D.; Baker, Michelle L.; Burt, David W.; Short, Kirsty R.; Centre for Theoretical Biological PhysicsBackground: The Australian black swan (Cygnus atratus) is an iconic species with contrasting plumage to that of the closely related northern hemisphere white swans. The relative geographic isolation of the black swan may have resulted in a limited immune repertoire and increased susceptibility to infectious diseases, notably infectious diseases from which Australia has been largely shielded. Unlike mallard ducks and the mute swan (Cygnus olor), the black swan is extremely sensitive to highly pathogenic avian influenza. Understanding this susceptibility has been impaired by the absence of any available swan genome and transcriptome information. Results: Here, we generate the first chromosome-length black and mute swan genomes annotated with transcriptome data, all using long-read based pipelines generated for vertebrate species. We use these genomes and transcriptomes to show that unlike other wild waterfowl, black swans lack an expanded immune gene repertoire, lack a key viral pattern-recognition receptor in endothelial cells and mount a poorly controlled inflammatory response to highly pathogenic avian influenza. We also implicate genetic differences in SLC45A2 gene in the iconic plumage of the black swan. Conclusion: Together, these data suggest that the immune system of the black swan is such that should any avian viral infection become established in its native habitat, the black swan would be in a significant peril.Item Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample(Elsevier, 2024) Sandoval-Velasco, Marcela; Dudchenko, Olga; Rodríguez, Juan Antonio; Pérez Estrada, Cynthia; Dehasque, Marianne; Fontsere, Claudia; Mak, Sarah S. T.; Khan, Ruqayya; Contessoto, Vinícius G.; Oliveira Junior, Antonio B.; Kalluchi, Achyuth; Zubillaga Herrera, Bernardo J.; Jeong, Jiyun; Roy, Renata P.; Christopher, Ishawnia; Weisz, David; Omer, Arina D.; Batra, Sanjit S.; Shamim, Muhammad S.; Durand, Neva C.; O’Connell, Brendan; Roca, Alfred L.; Plikus, Maksim V.; Kusliy, Mariya A.; Romanenko, Svetlana A.; Lemskaya, Natalya A.; Serdyukova, Natalya A.; Modina, Svetlana A.; Perelman, Polina L.; Kizilova, Elena A.; Baiborodin, Sergei I.; Rubtsov, Nikolai B.; Machol, Gur; Rath, Krisha; Mahajan, Ragini; Kaur, Parwinder; Gnirke, Andreas; Garcia-Treviño, Isabel; Coke, Rob; Flanagan, Joseph P.; Pletch, Kelcie; Ruiz-Herrera, Aurora; Plotnikov, Valerii; Pavlov, Innokentiy S.; Pavlova, Naryya I.; Protopopov, Albert V.; Di Pierro, Michele; Graphodatsky, Alexander S.; Lander, Eric S.; Rowley, M. Jordan; Wolynes, Peter G.; Onuchic, José N.; Dalén, Love; Marti-Renom, Marc A.; Gilbert, M. Thomas P.; Aiden, Erez Lieberman; Center for Theoretical Biological PhysicsAnalyses of ancient DNA typically involve sequencing the surviving short oligonucleotides and aligning to genome assemblies from related, modern species. Here, we report that skin from a female woolly mammoth (†Mammuthus primigenius) that died 52,000 years ago retained its ancient genome architecture. We use PaleoHi-C to map chromatin contacts and assemble its genome, yielding 28 chromosome-length scaffolds. Chromosome territories, compartments, loops, Barr bodies, and inactive X chromosome (Xi) superdomains persist. The active and inactive genome compartments in mammoth skin more closely resemble Asian elephant skin than other elephant tissues. Our analyses uncover new biology. Differences in compartmentalization reveal genes whose transcription was potentially altered in mammoths vs. elephants. Mammoth Xi has a tetradic architecture, not bipartite like human and mouse. We hypothesize that, shortly after this mammoth’s death, the sample spontaneously freeze-dried in the Siberian cold, leading to a glass transition that preserved subfossils of ancient chromosomes at nanometer scale.Item Whole genome analysis of clouded leopard species reveals an ancient divergence and distinct demographic histories(Cell Press, 2022) Bursell, Madeline G.; Dikow, Rebecca B.; Figueiró, Henrique V.; Dudchenko, Olga; Flanagan, Joseph P.; Aiden, Erez Lieberman; Goossens, Benoit; Nathan, Senthilvel K. S. S.; Johnson, Warren E.; Koepfli, Klaus-Peter; Frandsen, Paul B.; Center for Theoretical Biological PhysicsSimilar to other apex predator species, populations of mainland (Neofelis nebulosa) and Sunda (Neofelis diardi) clouded leopards are declining. Understanding their patterns of genetic variation can provide critical insights on past genetic erosion and a baseline for understanding their long-term conservation needs. As a step toward this goal, we present draft genome assemblies for the two clouded leopard species to quantify their phylogenetic divergence, genome-wide diversity, and historical population trends. We estimate that the two species diverged 5.1 Mya, much earlier than previous estimates of 1.41 Mya and 2.86 Mya, suggesting they separated when Sundaland was becoming increasingly isolated from mainland Southeast Asia. The Sunda clouded leopard displays a distinct and reduced effective population size trajectory, consistent with a lower genome-wide heterozygosity and SNP density, relative to the mainland clouded leopard. Our results provide new insights into the evolutionary history and genetic health of this unique lineage of felids.