All Publications


  • Long live the king: chromosome-level assembly of the lion (Panthera leo) using linked-read, Hi-C, and long-read data. BMC biology Armstrong, E. E., Taylor, R. W., Miller, D. E., Kaelin, C. B., Barsh, G. S., Hadly, E. A., Petrov, D. 2020; 18 (1): 3

    Abstract

    BACKGROUND: The lion (Panthera leo) is one of the most popular and iconic feline species on the planet, yet in spite of its popularity, the last century has seen massive declines for lion populations worldwide. Genomic resources for endangered species represent an important way forward for the field of conservation, enabling high-resolution studies of demography, disease, and population dynamics. Here, we present a chromosome-level assembly from a captive African lion from the Exotic Feline Rescue Center (Center Point, IN) as a resource for current and subsequent genetic work of the sole social species of the Panthera clade.RESULTS: Our assembly is composed of 10x Genomics Chromium data, Dovetail Hi-C, and Oxford Nanopore long-read data. Synteny is highly conserved between the lion, other Panthera genomes, and the domestic cat. We find variability in the length of runs of homozygosity across lion genomes, indicating contrasting histories of recent and possibly intense inbreeding and bottleneck events. Demographic analyses reveal similar ancient histories across all individuals during the Pleistocene except the Asiatic lion, which shows a more rapid decline in population size. We show a substantial influence on the reference genome choice in the inference of demographic history and heterozygosity.CONCLUSIONS: We demonstrate that the choice of reference genome is important when comparing heterozygosity estimates across species and those inferred from different references should not be compared to each other. In addition, estimates of heterozygosity or the amount or length of runs of homozygosity should not be taken as reflective of a species, as these can differ substantially among individuals. This high-quality genome will greatly aid in the continuing research and conservation efforts for the lion, which is rapidly moving towards becoming a species in danger of extinction.

    View details for DOI 10.1186/s12915-019-0734-5

    View details for PubMedID 31915011

  • Horizontal transfer of bacterial cytolethal distending toxin B genes to insects. Molecular biology and evolution Verster, K. I., Wisecaver, J. H., Karageorgi, M., Duncan, R. P., Gloss, A. D., Armstrong, E., Price, D. K., Menon, A. R., Ali, Z. M., Whiteman, N. K. 2019

    Abstract

    Horizontal gene transfer (HGT) events have played a major role in the evolution of microbial species, but their importance in animals is less clear. Here we report HGT of cytolethal distending toxin B (cdtB), prokaryotic genes encoding eukaryote-targeting DNase I toxins, into the genomes of vinegar flies (Diptera: Drosophilidae) and aphids (Hemiptera: Aphididae). We found insect-encoded cdtB genes are most closely related to orthologs from bacteriophage that infect Candidatus Hamiltonella defensa, a bacterial mutualistic symbiont of aphids that may confer resistance to parasitoid wasps. In drosophilids, cdtB orthologs are highly expressed during the parasitoid-prone larval stage and encode a protein with ancestral DNase activity. We show that cdtB has been domesticated by diverse insects and hypothesize that it functions in defense against their natural enemies.

    View details for DOI 10.1093/molbev/msz146

    View details for PubMedID 31236589

  • Comparative analyses identify genomic features potentially involved in the evolution of birds-of-paradise GIGASCIENCE Prost, S., Armstrong, E. E., Nylander, J., Thomas, G. C., Suh, A., Petersen, B., Dalen, L., Benz, B. W., Blom, M. K., Palkopoulou, E., Ericson, P. P., Irestedt, M. 2019; 8 (5)
  • Cost-effective assembly of the African wild dog (Lycaon pictus) genome using linked reads GIGASCIENCE Armstrong, E. E., Taylor, R. W., Prost, S., Blinston, P., van der Meer, E., Madzikanda, H., Mufute, O., Mandisodza-Chikerema, R., Stuelpnagel, J., Sillero-Zubiri, C., Petrov, D. 2019; 8 (2)
  • Comparative analyses identify genomic features potentially involved in the evolution of birds-of-paradise. GigaScience Prost, S., Armstrong, E. E., Nylander, J., Thomas, G. W., Suh, A., Petersen, B., Dalen, L., Benz, B. W., Blom, M. P., Palkopoulou, E., Ericson, P. G., Irestedt, M. 2019

    Abstract

    The diverse array of phenotypes and courtship displays exhibited by birds-of-paradise have long fascinated scientists and laymen alike. Remarkably, almost nothing is known about the genomics of this iconic radiation. There are 41 species in 16 genera currently recognized within the birds-of-paradise family (Paradisaeidae), most of which are endemic to the island of New Guinea. In this study, we sequenced genomes of representatives from all five major clades within this family to characterize genomic changes that may have played a role in the evolution of the group's extensive phenotypic diversity. We found genes important for coloration, morphology, feather and eye development to be under positive selection. In birds-of-paradise with complex lekking systems and strong sexual dimorphism, the core birds-of-paradise, we found GO categories for "startle response" and "olfactory receptor activity" to be enriched among the gene families expanding significantly faster compared to the other birds in our study. Furthermore, we found novel families of retrovirus-like retrotransposons active in all three de novo genomes since the early diversification of the birds-of-paradise group, which might have played a role in the evolution of this fascinating group of birds.

    View details for PubMedID 30689847

  • Cost-effective assembly of the African wild dog (Lycaon pictus) genome using linked reads. GigaScience Armstrong, E. E., Taylor, R. W., Prost, S., Blinston, P., van der Meer, E., Madzikanda, H., Mufute, O., Mandisodza-Chikerema, R., Stuelpnagel, J., Sillero-Zubiri, C., Petrov, D. 2018

    Abstract

    Background: A high-quality reference genome assembly is a valuable tool for the study of non-model organisms. Genomic techniques can provide important insights about past population sizes, local adaptation, and aid in the development of breeding management plans. This information is important for fields like conservation genetics, where endangered species require critical and immediate attention. However, funding for genomic-based methods can be sparse for conservation projects, as costs for general species management can consume budgets.Findings: Here we report the generation of high-quality reference genomes for the African wild dog (Lycaon pictus) at a low cost (< $3000), thereby facilitating future studies of this endangered canid. We generated assemblies for three individuals using the linked-read 10x Genomics Chromium system. The most continuous assembly had a scaffold and contig N50 of 21 Mb and 83 Kb, respectively, and completely reconstructed 95% of a set of conserved mammalian genes. Additionally, we estimate the heterozygosity and demographic history of African wild dogs, revealing that although they have historically low effective population sizes, heterozygosity remains high.Conclusions: We show that 10x Genomics Chromium data can be used to effectively generate high-quality genomes from Illumina short-read data of intermediate coverage (25-50x). Interestingly, the wild dog shows higher heterozygosity than other species of conservation concern, possibly due to its behavioral ecology. The availability of reference genomes for non-model organisms will facilitate better genetic monitoring of threatened species such as the African wild dog and help conservationists to better understand the ecology and adaptability of those species in a changing environment.

    View details for PubMedID 30346553

  • Draft Genome Sequence and Annotation of the Lichen-Forming Fungus Arthonia radiata. Genome announcements Armstrong, E. E., Prost, S., Ertz, D., Westberg, M., Frisch, A., Bendiksby, M. 2018; 6 (14)

    Abstract

    We report here the draft de novo genome assembly, transcriptome assembly, and annotation of the lichen-forming fungus Arthonia radiata (Pers.) Ach., the type species for Arthoniomycetes, a class of lichen-forming, lichenicolous, and saprobic Ascomycota. The genome was assembled using overlapping paired-end and mate pair libraries and sequenced on an Illumina HiSeq 2500 instrument.

    View details for PubMedID 29622619

  • Rapid divergence of mussel populations despite incomplete barriers to dispersal MOLECULAR ECOLOGY Maas, D. L., Prost, S., Bi, K., Smith, L. L., Armstrong, E. E., Aji, L. P., Toha, A. A., Gillespie, R. G., Becking, L. E. 2018; 27 (7): 1556–71

    Abstract

    Striking genetic structure among marine populations at small spatial scales is becoming evident with extensive molecular studies. Such observations suggest isolation at small scales may play an important role in forming patterns of genetic diversity within species. Isolation-by-distance, isolation-by-environment and historical priority effects are umbrella terms for a suite of processes that underlie genetic structure, but their relative importance at different spatial and temporal scales remains elusive. Here, we use marine lakes in Indonesia to assess genetic structure and assess the relative roles of the processes in shaping genetic differentiation in populations of a bivalve mussel (Brachidontes sp.). Marine lakes are landlocked waterbodies of similar age (6,000-10,000 years), but with heterogeneous environments and varying degrees of connection to the sea. Using a population genomic approach (double-digest restriction-site-associated DNA sequencing), we show strong genetic structuring across populations (range FST : 0.07-0.24) and find limited gene flow through admixture plots. At large spatial scales (>1,400 km), a clear isolation-by-distance pattern was detected. At smaller spatial scales (<200 km), this pattern is maintained, but accompanied by an association of genetic divergence with degree of connection. We hypothesize that (incomplete) dispersal barriers can cause initial isolation, allowing priority effects to give the numerical advantage necessary to initiate strong genetic structure. Priority effects may be strengthened by local adaptation, which the data may corroborate by showing a high correlation between mussel genotypes and temperature. Our study indicates an often-neglected role of (evolution-mediated) priority effects in shaping population divergence.

    View details for PubMedID 29575349