Contact

  • Academic
    jahemker@stanford.edu
    University - Student Department: Department of Developmental Biology Position: Graduate

All Publications

  • Single-fly genome assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life. PLoS biology Kim, B. Y., Gellert, H. R., Church, S. H., Suvorov, A., Anderson, S. S., Barmina, O., Beskid, S. G., Comeault, A. A., Crown, K. N., Diamond, S. E., Dorus, S., Fujichika, T., Hemker, J. A., Hrcek, J., Kankare, M., Katoh, T., Magnacca, K. N., Martin, R. A., Matsunaga, T., Medeiros, M. J., Miller, D. E., Pitnick, S., Schiffer, M., Simoni, S., Steenwinkel, T. E., Syed, Z. A., Takahashi, A., Wei, K. H., Yokoyama, T., Eisen, M. B., Kopp, A., Matute, D., Obbard, D. J., O'Grady, P. M., Price, D. K., Toda, M. J., Werner, T., Petrov, D. A. 2024; 22 (7): e3002697

    Abstract

    Long-read sequencing is driving rapid progress in genome assembly across all major groups of life, including species of the family Drosophilidae, a longtime model system for genetics, genomics, and evolution. We previously developed a cost-effective hybrid Oxford Nanopore (ONT) long-read and Illumina short-read sequencing approach and used it to assemble 101 drosophilid genomes from laboratory cultures, greatly increasing the number of genome assemblies for this taxonomic group. The next major challenge is to address the laboratory culture bias in taxon sampling by sequencing genomes of species that cannot easily be reared in the lab. Here, we build upon our previous methods to perform amplification-free ONT sequencing of single wild flies obtained either directly from the field or from ethanol-preserved specimens in museum collections, greatly improving the representation of lesser studied drosophilid taxa in whole-genome data. Using Illumina Novaseq X Plus and ONT P2 sequencers with R10.4.1 chemistry, we set a new benchmark for inexpensive hybrid genome assembly at US $150 per genome while assembling genomes from as little as 35 ng of genomic DNA from a single fly. We present 183 new genome assemblies for 179 species as a resource for drosophilid systematics, phylogenetics, and comparative genomics. Of these genomes, 62 are from pooled lab strains and 121 from single adult flies. Despite the sample limitations of working with small insects, most single-fly diploid assemblies are comparable in contiguity (>1 Mb contig N50), completeness (>98% complete dipteran BUSCOs), and accuracy (>QV40 genome-wide with ONT R10.4.1) to assemblies from inbred lines. We present a well-resolved multi-locus phylogeny for 360 drosophilid and 4 outgroup species encompassing all publicly available (as of August 2023) genomes for this group. Finally, we present a Progressive Cactus whole-genome, reference-free alignment built from a subset of 298 suitably high-quality drosophilid genomes. The new assemblies and alignment, along with updated laboratory protocols and computational pipelines, are released as an open resource and as a tool for studying evolution at the scale of an entire insect family.

    View details for DOI 10.1371/journal.pbio.3002697

    View details for PubMedID 39024225

  • Single-fly assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life. bioRxiv : the preprint server for biology Kim, B. Y., Gellert, H. R., Church, S. H., Suvorov, A., Anderson, S. S., Barmina, O., Beskid, S. G., Comeault, A. A., Crown, K. N., Diamond, S. E., Dorus, S., Fujichika, T., Hemker, J. A., Hrcek, J., Kankare, M., Katoh, T., Magnacca, K. N., Martin, R. A., Matsunaga, T., Medeiros, M. J., Miller, D. E., Pitnick, S., Simoni, S., Steenwinkel, T. E., Schiffer, M., Syed, Z. A., Takahashi, A., Wei, K. H., Yokoyama, T., Eisen, M. B., Kopp, A., Matute, D., Obbard, D. J., O'Grady, P. M., Price, D. K., Toda, M. J., Werner, T., Petrov, D. A. 2023

    Abstract

    Long-read sequencing is driving rapid progress in genome assembly across all major groups of life, including species of the family Drosophilidae, a longtime model system for genetics, genomics, and evolution. We previously developed a cost-effective hybrid Oxford Nanopore (ONT) long-read and Illumina short-read sequencing approach and used it to assemble 101 drosophilid genomes from laboratory cultures, greatly increasing the number of genome assemblies for this taxonomic group. The next major challenge is to address the laboratory culture bias in taxon sampling by sequencing genomes of species that cannot easily be reared in the lab. Here, we build upon our previous methods to perform amplification-free ONT sequencing of single wild flies obtained either directly from the field or from ethanol-preserved specimens in museum collections, greatly improving the representation of lesser studied drosophilid taxa in whole-genome data. Using Illumina Novaseq X Plus and ONT P2 sequencers with R10.4.1 chemistry, we set a new benchmark for inexpensive hybrid genome assembly at US $150 per genome while assembling genomes from as little as 35 ng of genomic DNA from a single fly. We present 183 new genome assemblies for 179 species as a resource for drosophilid systematics, phylogenetics, and comparative genomics. Of these genomes, 62 are from pooled lab strains and 121 from single adult flies. Despite the sample limitations of working with small insects, most single-fly diploid assemblies are comparable in contiguity (>1Mb contig N50), completeness (>98% complete dipteran BUSCOs), and accuracy (>QV40 genome-wide with ONT R10.4.1) to assemblies from inbred lines. We present a well-resolved multi-locus phylogeny for 360 drosophilid and 4 outgroup species encompassing all publicly available (as of August 2023) genomes for this group. Finally, we present a Progressive Cactus whole-genome, reference-free alignment built from a subset of 298 suitably high-quality drosophilid genomes. The new assemblies and alignment, along with updated laboratory protocols and computational pipelines, are released as an open resource and as a tool for studying evolution at the scale of an entire insect family.

    View details for DOI 10.1101/2023.10.02.560517

    View details for PubMedID 37873137

    View details for PubMedCentralID PMC10592941

  • Champagne: Automated whole-genome phylogenomic character matrix method using large genomic indels for homoplasy-free inference. Genome biology and evolution Schull, J. K., Turakhia, Y., Hemker, J. A., Dally, W. J., Bejerano, G. 2022

    Abstract

    We present Champagne, a whole-genome method for generating character matrices for phylogenomic analysis using large genomic indel events. By rigorously picking orthologous genes and locating large insertion and deletion events, Champagne delivers a character matrix that considerably reduces homoplasy compared to morphological and nucleotide-based matrices, on both established phylogenies and difficult-to-resolve nodes in the mammalian tree. Champagne provides ample evidence in the form of genomic structural variation to support incomplete lineage sorting and possible introgression in Paenungulata and human-chimp-gorilla which were previously inferred primarily through matrices composed of aligned single-nucleotide characters. Champagne also offers further evidence for Myomorpha as sister to Sciuridae and Hystricomorpha in the rodent tree. Champagne harbors distinct theoretical advantages as an automated method that produces nearly homoplasy-free character matrices on the whole-genome scale.

    View details for DOI 10.1093/gbe/evac013

    View details for PubMedID 35171243