Extensively duplicated and transcriptionally active recent lateral gene transfer from a bacterial Wolbachia endosymbiont to its host filarial nematode Brugia malayi

Ioannidis, Panagiotis; Johnston, Kelly L.; Riley, David R.; Kumar, Nikhil; White, James R.; Olarte, Karen T; Ott, Sandra; Tallon, Luke J.; Foster, Jeremy M.; Taylor, Mark J.; Hotopp, Julie C. Dunning

doi:10.1186/1471-2164-14-639

Cited by 37 publications

(47 citation statements)

References 41 publications

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“…31 . In panel A, the previously established 17 threshold for predicting a nuwt in the depletion data is shown with a dashed black line. In panel B, the second and third standard deviations from the mean are shown with dashed green and blue lines, respectively. …”

Section: Resultsmentioning

confidence: 99%

“…Validation was conducted by using qPCR to measure the copy number of nuwts for comparison to the sequencing depth, which should also reflect the copy number 17 . A comparison of this previous qPCR data with the capture data presented here reveals similar R 2 values for both data sets, suggesting that at least a subset of nuwts can be predicted accurately (Fig.…”

Section: Resultsmentioning

confidence: 99%

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Targeted Enrichment and Sequencing of Recent Endosymbiont-Host Lateral Gene Transfers

Hotopp

Slatko

Foster

2017

Sci Rep

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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 data obtained with a Wolbachia capture system correlated well with that for an Illumina paired end data set used to detect LGT in Wolbachia-depleted B. malayi (p-value: <2e-16). Using a sequencing depth threshold of two or three standard deviations above the mean, 96.9% or 96.7% of positions, respectively, are predicted in the same manner between the two datasets, with 24.7% or 42.5% of the known 49.0 kbp of LGT sequence predicted correctly, respectively. Prior qPCR results for nuwts showed similar correlations for both datasets supporting our conclusion that oligonucleotide-based capture methods can be used to obtain sequences from Wolbachia-host LGT. However, at least 121 positions had a minority of the reads supporting the endosymbiont reference base call using the capture data, illustrating that sequence reads from endosymbiont-host LGTs can confound endosymbiont genome projects, erroneously altering the called consensus genome, a problem that is irrespective to the sequencing technology or platform.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Targeted Enrichment and Sequencing of Recent Endosymbiont-Host Lateral Gene Transfers

Hotopp

Slatko

Foster

2017

Sci Rep

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“…Hotopp et al (2007) found traces of Wolbachia DNA fragments in six of 21 published genomes of various invertebrate taxa. Another study found that some transferred genes from wBm into the B. malayi genome seem to be transcribed in a way that is stagespecific during the development of the worm (Ioannidis et al, 2013). These results suggest that Wolbachia may indeed represent an important source of genomic innovation for their hosts.…”

Section: Genomic Reduction and Lateral Gene Transfermentioning

confidence: 86%

Wolbachia Associations with Insects: Winning or Losing Against a Master Manipulator

2016

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Wolbachia are intracellular, maternally inherited bacteria with an impressive history of adaptation to intracellular lifestyles. Instead of adapting to a single host lineage, Wolbachia evolved ways to jump across host species and establish relatively stable associations maintained through vertical transmission. Wolbachia are capable of manipulating the reproduction of infected hosts in a remarkable way. Traditionally, such reproductive manipulations have been regarded as the general mechanism by which Wolbachia spread through host populations. Recent evidence suggests that Wolbachia-host interactions are more complex than previously thought and may be driven by the onset and resolution of conflicts of interest. Here, we discuss how reproductive manipulation phenotypes may be transient. As the host adapts to infection, manipulation phenotypes attenuate and the continuity of the symbioses may rely on the physiological advantages Wolbachia may confer to their host. For facultative symbionts, such benefits are likely to be dependent on the environment. Here, we also review evidence that supports the view of environment-dependent facultative mutualism as a stable evolutionary outcome of Wolbachia infections beside extinction and obligate symbioses. Finally, our current understanding of the biology of mitochondria and Wolbachia unravels remarkable parallels in the way they interact with the nuclear genome. Great insights into both the Wolbachia and mitochondrial research fields can be revealed if such fields are considered to be overlapping, rather than independent from each other.

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“…malayi genome assembly and improvement. An unpublished B. malayi assembly in Wormbase WS242 (9827 contigs with an assembled size of 94,136,248 bp and a contig N50 of 191,089 bp) was generated from a mixture of capillary 6 , 454 (3, 8, and 20 kb mate pair libraries) and Illumina (500 bp paired end and 3 kb mate pair libraries) sequence data 42 . In this study a total of 11.3 Gb of long read data produced on the PacBio RSII instrument passed the 0.75 quality filter.…”

Section: Methodsmentioning

confidence: 99%

Sex chromosome evolution in parasitic nematodes of humans

et al. 2020

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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 complete B. malayi genome assembly and define Nigon elements shared with C. elegans, which we then map to the genomes of other filarial species and more distantly related nematodes. We find a remarkable plasticity in sex chromosome evolution with several distinct cases of neo-X and neo-Y formation, X-added regions, and conversion of autosomes to sex chromosomes from which we propose a model of chromosome evolution across different nematode clades. The phylum Nematoda offers a new and innovative system for gaining a deeper understanding of sex chromosome evolution.

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Extensively duplicated and transcriptionally active recent lateral gene transfer from a bacterial Wolbachia endosymbiont to its host filarial nematode Brugia malayi

Cited by 37 publications

References 41 publications

Targeted Enrichment and Sequencing of Recent Endosymbiont-Host Lateral Gene Transfers

Targeted Enrichment and Sequencing of Recent Endosymbiont-Host Lateral Gene Transfers

Wolbachia Associations with Insects: Winning or Losing Against a Master Manipulator

Sex chromosome evolution in parasitic nematodes of humans

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