Julie C Dunning Hotopp

University of Maryland, Baltimore | UMB · Institute for Genome Sciences

RNA modifications, such as methylation, can be detected with Oxford Nanopore Technologies direct RNA sequencing. One commonly used tool for detecting 5-methylcytosine (m ⁵ C) modifications is Tombo, which uses an “Alternative Model” to detect putative modifications from a single sample. We examined direct RNA sequencing data from diverse taxa inclu...

RNA modifications, such as methylation, can be detected with Oxford Nanopore Technologies direct RNA sequencing. One commonly used tool for detecting 5-methylcytosine (m ⁵ C) modifications is Tombo, which uses an “Alternative Model” to detect putative modifications from a single sample. We examined direct RNA sequencing data from diverse taxa inclu...

Eukaryotic genomes can acquire bacterial DNA via lateral gene transfer (LGT).¹ A prominent source of LGT is Wolbachia,² a widespread endosymbiont of arthropods and nematodes that is transmitted maternally through female germline cells.³,⁴ The DNA transfer from the Wolbachia endosymbiont wAna to Drosophila ananassae is extensive5, 6, 7 and has been...

The sequence diversity of natural and laboratory populations of Brugia pahangi and Brugia malayi was assessed with Illumina resequencing followed by mapping to identify single nucleotide variants and insertions/deletions. In natural and laboratory Brugia populations, there is a lack of sequence diversity on chromosome X relative to the autosomes (π...

Acute myeloid leukemia (AML) with fms-like tyrosine kinase 3 internal tandem duplication (FLT3-ITD) relapses with new chromosome abnormalities following chemotherapy, implicating genomic instability. Error-prone alternative non-homologous end-joining (Alt-NHEJ) DNA double-strand break (DSB) repair is upregulated in FLT3-ITD-expresssing cells, drive...

Library preparation for high-throughput sequencing applications is a critical step in producing representative, unbiased sequencing data. The iGenomX Riptide High Throughput Rapid Library Prep Kit purports to provide high-quality sequencing data with lower costs compared to other Illumina library kits. To test these claims, we compared sequence dat...

Advances in transcriptome sequencing allow for simultaneous interrogation of differentially expressed genes from multiple species originating from a single RNA sample, termed dual or multi-species transcriptomics. Compared to single-species differential expression analysis, the design of multi-species differential expression experiments must accoun...

The newest generation of DNA sequencing technology is highlighted by the ability to generate sequence reads hundreds of kilobases in length. Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have pioneered competitive long read platforms, with more recent work focused on improving sequencing throughput and per-base accuracy. We us...

Fungi of the order Mucorales cause mucormycosis, a lethal infection with an incompletely understood pathogenesis. We demonstrate that Mucorales fungi produce a toxin, which plays a central role in virulence. Polyclonal antibodies against this toxin inhibit its ability to damage human cells in vitro and prevent hypovolemic shock, organ necrosis and...

To the Editor I have concerns about the methodology, which influences the results and conclusions, reported in a recent article on coronavirus disease 2019 samples that has garnered attention because of its implications for important public health decisions. In “Age-Related Differences in Nasopharyngeal Severe Acute Respiratory Syndrome Coronavirus...

Fungi of the order Mucorales cause mucormycosis, a lethal infection with an incompletely understood pathogenesis. We now demonstrate that Mucorales fungi produce a toxin that plays a central role in virulence. Polyclonal antibodies against this toxin inhibit its ability to damage human cells in vitro, and prevent hypovolemic shock, organ necrosis,...

Quantification tools for RNA sequencing (RNA-Seq) analyses are often designed and tested using human transcriptomics data sets, in which full-length transcript sequences are well annotated. For prokaryotic transcriptomics experiments, full-length transcript sequences are seldom known, and coding sequences must instead be used for quantification ste...

Background The genus Ehrlichia consists of tick-borne obligatory intracellular bacteria that can cause deadly diseases of medical and agricultural importance. Ehrlichia sp. HF, isolated from Ixodes ovatus ticks in Japan [also referred to as I. ovatus Ehrlichia (IOE) agent], causes acute fatal infection in laboratory mice that resembles acute fatal...

Microbiology Resource Announcements (MRA) provides peer-reviewed announcements of scientific resources for the microbial research community. We describe the best practices for writing an announcement that ensures that these publications are truly useful resources. Adhering to these best practices can lead to successful publication without the need...

Wolbachia is a genus containing obligate, intracellular endosymbionts with arthropod and nematode hosts. Numerous studies have identified differentially expressed transcripts in Wolbachia endosymbionts that potentially inform the biological interplay between these endosymbionts and their hosts, albeit with discordant results. Here, we re-analyze al...

The 13,647-bp complete mitochondrial genome of Mansonella perstans was sequenced and is syntenic to the mitochondrial genome of Mansonella ozzardi . Phylogenetic analysis of the mitochondrial genome is consistent with the known phylogeny of ONC5 group filarial nematodes.

Background The newest generation of DNA sequencing technology is highlighted by the ability to sequence reads hundreds of kilobases in length, and the increased availability of long read data has democratized the genome sequencing and assembly process. PacBio and Oxford Nanopore Technologies (ONT) have pioneered competitive long read platforms, wit...

Lymphatic filariasis is a devastating disease caused by filarial nematode roundworms, which contain obligate Wolbachia endosymbionts. Here, we assembled the genome of w Bp, the Wolbachia endosymbiont of the filarial nematode Brugia pahangi , from Illumina, Pacific Biosciences, and Oxford Nanopore data. The complete, circular genome is 1,072,967 bp.

Brugia pahangi is a zoonotic parasite that is closely related to human-infecting filarial nematodes. Here, we report the nearly complete genome of Brugia pahangi , including assemblies of four autosomes and an X chromosome, with only seven gaps. The Y chromosome is still not completely assembled.

Lymphatic filariasis affects ∼120 million people and can result in elephantiasis and hydrocele. Here, we report the nearly complete genome sequence of the best-studied causative agent of lymphatic filariasis, Brugia malayi . The assembly contains four autosomes, an X chromosome, and only eight gaps but lacks a contiguous sequence for the known Y ch...

Sex determination mechanisms often differ even between related species yet the evolution of sex chromosomes remains poorly understood in all but a few model organisms. Some nematodes such as Caenorhabditis elegans have an XO sex determination system while others, such as the filarial parasite Brugia malayi, have an XY mechanism. We present a comple...

Background: Plasmodium falciparum (Pf) whole-organism sporozoite vaccines have been shown to provide significant protection against controlled human malaria infection (CHMI) in clinical trials. Initial CHMI studies showed significantly higher durable protection against homologous than heterologous strains, suggesting the presence of strain-specifi...

As sequencing read length has increased, researchers have quickly adopted longer reads for their experiments. Here, we examine 14 pathogen or host-pathogen differential gene expression data sets to assess whether using longer reads is warranted. A variety of data sets was used to assess what genomic attributes might affect the outcome of differenti...

To better understand the transcriptomic interplay of organisms associated with lymphatic filariasis, we conducted multispecies transcriptome sequencing (RNA-Seq) on the filarial nematode Brugia malayi , its Wolbachia endosymbiont w Bm, and its laboratory vector Aedes aegypti across the entire B. malayi life cycle. In w Bm, transcription of the nonc...

Here, we present the complete genome sequence of the Wolbachia endosymbiont w Ana, isolated from Drosophila ananassae and derived from Oxford Nanopore and Illumina sequencing. We anticipate that this will aid in Wolbachia comparative genomics and the assembly of D. ananassae specifically in regions containing extensive lateral gene transfer events.

Descriptions of resources, like the genome assemblies reported in Microbiology Resource Announcements , are often frozen at their time of publication, yet they will need to be interpreted in the midst of continually evolving technologies. It is therefore important to ensure that researchers accessing published resources have access to all of the in...

Analysis of sequence read pairs can be essential for characterizing structural variation, including junction-spanning pairs of reads (JSPRs) suggesting recent lateral/horizontal gene transfer. TwinBLAST can be used to facilitate this analysis of JSPRs by enabling the visualization and curation of two BLAST reports side by side in a single interface...

Background Although cell lines are an essential resource for studying cancer biology, many are of unknown ancestral origin, and their use may not be optimal for evaluating the biology of all patient populations. Methods An admixture analysis was performed using genome‐wide chip data from the Catalogue of Somatic Mutations in Cancer (COSMIC) Cell L...

With the exponential increase in the number of bacterial taxa with ge-nome sequence data, a new standardized method to assign species designations is needed that is consistent with classically obtained taxonomic analyses. This is particularly acute for unculturable, obligate intracellular bacteria with which classically defined methods, like DNA-DN...

With the increasing availability of genome sequences, we sought to develop and apply a robust, portable, and high-resolution method for the assignment of genera and species designations that can recapitulate classically defined taxonomic designations. Using cutoffs derived from the lengths and sequence identities of core genome alignments along wit...

Here, we present a comprehensive transcriptomics data set of Brugia malayi , its Wolbachia endosymbiont w Bm, and its vector host. This study samples from 16 stages across the entire B. malayi life cycle, including stage 1 through 4 larvae, adult males and females, embryos, immature microfilariae, and mature microfilariae.

The pestivorous tephritid olive fly has long been known as a frequent host of the obligately host-associated bacterial endosymbiont, Erwinia dacicola, as well as other facultative endosymbionts. The genomes of Erwinia dacicola and Enterobacter sp. OLF, isolated from a California olive fly, encode the ability to supplement amino acids and vitamins m...

Erwinia dacicola is a dominant endosymbiont of the pestiferous olive fly. Its genome is similar in size and GC content to those of free-living Erwinia species, including the plant pathogen Erwinia amylovora . The E. dacicola genome encodes the metabolic capability to supplement and detoxify the olive fly’s diet in larval and adult stages.

Enrichment methodologies enable the analysis of minor members in multi-species transcriptomic data. We compared the standard enrichment of bacterial and eukaryotic mRNA to a targeted enrichment using an Agilent SureSelect (AgSS) capture for Brugia malayi, Aspergillus fumigatus, and the Wolbachia endosymbiont of B. malayi (wBm). Without introducing...

Enterobacter sp. strain OLF colonizes laboratory-reared and wild individuals of the olive fruit fly Bactrocera oleae . The 5.07-kbp genome sequence of Enterobacter sp. strain OLF encodes metabolic pathways that allow the bacterium to partially supplement the diet of the olive fly when its dominant endosymbiont, Erwinia dacicola , is absent.

A divergent strain of Rickettsia japonica was isolated from a Dew's Australian bat argasid tick, Argas (Carios) dewae, collected in southern Victoria, Australia and a full-genome analysis along with sequencing of 5 core gene fragments was undertaken. This isolate was designated Rickettsia japonica str. argasii (ATCC VR-1665, CSUR R179).

Background: Lateral gene transfer (LGT), also known as horizontal gene transfer, into multicellular eukaryotes with differentiated tissues, particularly gonads, continues to be met with skepticism by many prominent evolutionary and genomic biologists. A detailed examination of 26 animal genomes identified putative LGTs in invertebrate and vertebra...

Motivation The major algorithms for quantifying transcriptomics data for differential gene expression analysis were designed for analyzing data from human or human-like genomes, specifically those with single gene transcripts and distinct transcriptional boundaries that extend beyond the coding sequence (CDS) as identified through expressed sequenc...

As sequencing read length has increased, researchers have quickly adopted longer reads for their experiments. Here, we examine host-pathogen interaction studies to assess if using longer reads is warranted. Six diverse datasets encountered in studies of host-pathogen interactions were used to assess what genomic attributes might affect the outcome...

With the exponential increase in the number of bacterial taxa with genome sequence data, a new standardized method is needed to assign bacterial species designations using genomic data that is consistent with the classically-obtained taxonomy. This is particularly acute for unculturable obligate intracellular bacteria like those in the Rickettsiale...

Resistance to ceftriaxone in Neisseria gonorrhoeae is mainly conferred by mosaic penA alleles that encode penicillin-binding protein 2 (PBP2) variants with markedly lower rates of acylation by ceftriaxone. To assess the impact of these mosaic penA alleles on gonococcal fitness, we introduced the mosaic penA alleles from two ceftriaxone-resistant (C...

Enrichment methodologies enable analysis of minor members in multi-species transcriptomic analyses. We compared standard enrichment of bacterial and eukaryotic mRNA to targeted enrichment with Agilent SureSelect (AgSS) capture for Brugia malayi , Aspergillus fumigatus , and the Wolbachia endosymbiont of B. malayi (wBm). Without introducing signific...

Aspergillus fumigatus is an opportunistic, ubiquitous, saprophytic mould that can cause severe allergic responses in atopic individuals as well as life-threatening infections in immunocompromised patients. A critical step in the establishment of infection is the invasion of airway epithelial cells by the inhaled fungi. Understanding how A. fumigatu...

In "Retrotransposons Are the Major Contributors to the Expansion of the Drosophila ananassae Muller F Element," Leung et al. (2017) improved contigs attributed to the Muller F element from the original CAF1 assembly, and used them to conclude that most of the sequence expansion of the fourth chromosome of D. ananassae is due to a higher transposon...

Lateral gene transfer (LGT) into multicellular eukaryotes with differentiated tissues, particularly gonads, continues to be met with skepticism by many prominent evolutionary and genomic biologists. A detailed examination of 26 animal genomes identifed putative LGTs in invertebrate and vertebrate genomes, concluding that there are fewer predicted L...

Lateral gene transfer (LGT) from microbial symbionts to invertebrate animals is described at an increasing rate, particularly between Wolbachia endosymbionts and their diverse invertebrate hosts. We sought to assess the use of a capture system to cost-effectively sequence such LGT from the host genome. The sequencing depth of Illumina paired end da...

The draft genome assembly of the Wolbachia endosymbiont of Wuchereria bancrofti (wWb) genome consists of 1,060,850 bp in 100 contigs and contains 961 ORFs, with a single copy of the 5S rRNA, 16S rRNA, and 23S rRNA and each of the 34 tRNA genes. Phylogenetic core genome analyses show wWb to cluster with other strains in supergroup D of the Wolbachia...

As sequencing technologies have evolved, the tools to analyze these sequences have made similar advances. However, for multi-species samples, we observed important and adverse differences in alignment specificity and computation time for bwa-mem (Burrows–Wheeler aligner-maximum exact matches) relative to bwa-aln. Therefore, we sought to optimize bw...

Neorickettsia helminthoeca, a type species of the genus Neorickettsia, is an endosymbiont of digenetic trematodes of veterinary importance. Upon ingestion of salmonid fish parasitized with infected trematodes, canids develop salmon poisoning disease (SPD), an acute febrile illness that is particularly severe and often fatal in dogs without adequate...

Fig. S4. One‐component regulatory systems of N. helminthoeca.

Table S1. Ortholog clusters conserved among N. helminthoeca, N. risticii and N. sennetsu based on three‐way comparison analysis

Table S2. N. helminthoeca‐specific proteins compared to N. sennetsu and N. risticii

Table S3. N. risticii‐specific proteins compared to N. helminthoeca and N. sennetsu

Table S5. Amino acid and cofactor biosynthesis in Family Anaplasmataceae

Fig. S5. Phylogenetic analysis of AnkA or Ank200 homologous proteins in the family Anaplasmataceae.

Table S6. Potential pathogenic genes in Neorickettsia species

Table S8. Genes involved in DNA repair and homologous recombination

Table S11. Oligonucleotide primers used for cloning N. helminthoeca outer membrane proteins

Fig. S2. Secondary Structure of N. helminthoeca P51 Protein.