A telomere to telomere assembly of<i>Oscheius tipulae</i>and the evolution of rhabditid nematode chromosomes

Rosa, Pablo Manuel Gonzalez de la; Thomson, Marian; Trivedi, Urmi; Tracey, Alan S.; Tandonnet, Sophie; Blaxter, Mark

doi:10.1101/2020.09.04.283127

Cited by 13 publications

(41 citation statements)

References 98 publications

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“…Comparison of nematode chromosomes using orthologous proteins (reciprocal best blast hits) indicates that many of the Ascaris germline sex chromosomes are likely derived from recent chromosome fusion events ( Figure 1 ) [ 39 ]. This is further supported by chromosome “painting” analyses using conserved Nigon elements [ 78 ]. These comparative analyses of nematode chromosomes revealed that while extensive intra-chromosomal rearrangements occurred, the karyotypic unit for nematodes remains largely intact except for occasional scission and fusion events [ 78 ].…”

Section: Ascaris Genomesmentioning

confidence: 78%

“…This is further supported by chromosome “painting” analyses using conserved Nigon elements [ 78 ]. These comparative analyses of nematode chromosomes revealed that while extensive intra-chromosomal rearrangements occurred, the karyotypic unit for nematodes remains largely intact except for occasional scission and fusion events [ 78 ]. Interestingly, the fused Ascaris germline sex chromosomes are broken at the sites of these fusions during DNA elimination, resulting in the pre-fusion karyotypes in somatic cells ( Figure 1 ) [ 39 ].…”

Section: Ascaris Genomesmentioning

confidence: 78%

“…In addition, histone modification profiles using ChIP-seq would enable the quantification of epigenetic changes throughout spermatogenesis, oogenesis, fertilization, zygote development, embryogenesis, and larvae development. Finally, comparative genomics using more completed chromosomal assemblies will delineate the evolution of nematode sex chromosomes [ 78 ] as well as the evolutionary developmental biology of embryogenesis and other developmental processes across nematode species.…”

Section: Future Perspectivesmentioning

confidence: 99%

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Genomics of the Parasitic Nematode Ascaris and Its Relatives

Wang

2021

Genes

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Nematodes of the genus Ascaris are important parasites of humans and swine, and the phylogenetically related genera (Parascaris, Toxocara, and Baylisascaris) infect mammals of veterinary interest. Over the last decade, considerable genomic resources have been established for Ascaris, including complete germline and somatic genomes, comprehensive mRNA and small RNA transcriptomes, as well as genome-wide histone and chromatin data. These datasets provide a major resource for studies on the basic biology of these parasites and the host–parasite relationship. Ascaris and its relatives undergo programmed DNA elimination, a highly regulated process where chromosomes are fragmented and portions of the genome are lost in embryonic cells destined to adopt a somatic fate, whereas the genome remains intact in germ cells. Unlike many model organisms, Ascaris transcription drives early development beginning prior to pronuclear fusion. Studies on Ascaris demonstrated a complex small RNA network even in the absence of a piRNA pathway. Comparative genomics of these ascarids has provided perspectives on nematode sex chromosome evolution, programmed DNA elimination, and host–parasite coevolution. The genomic resources enable comparison of proteins across diverse species, revealing many new potential drug targets that could be used to control these parasitic nematodes.

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Section: Ascaris Genomesmentioning

confidence: 78%

Section: Ascaris Genomesmentioning

confidence: 78%

Section: Future Perspectivesmentioning

confidence: 99%

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Genomics of the Parasitic Nematode Ascaris and Its Relatives

Wang

2021

Genes

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“…o Examples: S. mansoni [45], Schistosoma japonicum [51], Schistosoma haematobium [52], Hymenolepis microstoma [46], H. contortus [14], B. malayi/Dirofilaria immitis [53], Heterodera glycines [54], Clonorchis sinensis [55], Ascaris suum [56], Oscheius tipulae [57], P. pacificus [58], Nector americanus [59]. • Community annotation o Engaging school-age/undergraduate students [60].…”

Section: Development and Extension Of Available Resourcesmentioning

confidence: 99%

Improving helminth genome resources in the post-genomic era

Doyle

2022

Trends in Parasitology

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“…Here, we built upon and extended a previous genomic observation 34 and established a genetic and functional model for PDE in the free-living nematode Oscheius tipulae, a member of the Rhabditidae family, which includes Caenorhabditis elegans. 35 We show that DNA elimination occurs during early embryogenesis in O. tipulae.…”

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confidence: 99%

The Nematode Oscheius tipulae as A Genetic Model for Programmed DNA Elimination

Dockendorff

Estrem

Reed

et al. 2022

Preprint

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Programmed DNA elimination (PDE) is a notable exception to the paradigm of genome integrity. In metazoa, PDE often occurs during early embryogenesis, coincident with germline to somatic cell differentiation. During PDE, portions of genomic DNA are lost, resulting in reduced somatic genomes. Recent studies have described the sequences lost and chromosome behavior in metazoa. However, a system for studying the mechanisms and consequences of PDE in metazoa is lacking. Here, we established a functional and genetic model for PDE in the free-living nematode Oscheius tipulae, a member of the Rhabditidae family, which includes Caenorhabditis elegans. O. tipulae was recently suggested to eliminate DNA. Using staged embryos, we show that O. tipulae PDE occurs during embryogenesis at the 2-16 cell stages, similar to the human/pig parasitic nematode Ascaris. We identified a conserved motif, named Sequence For Elimination (SFE), for all 12 break sites on the six chromosomes at the junction of retained and eliminated DNA. SFE mutants exhibit a "fail-to-eliminate" phenotype only at the modified sites. END-seq revealed that breaks can occur at multiple positions within the SFE, with extensive end resection followed by telomere addition to both retained and eliminated ends. We identified through END-seq in the wild-type embryos, genome sequencing of SFE mutants, and comparative genomics of 23 wild isolates a large number of functional SFEs at the chromosome ends. We suggest these alternative SFEs provide flexibility in the sequences eliminated and a fail-safe mechanism for PDE. These studies establish O. tipulae as a new, attractive model to study the mechanisms and consequences of PDE in a metazoan.

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A telomere to telomere assembly ofOscheius tipulaeand the evolution of rhabditid nematode chromosomes

Cited by 13 publications

References 98 publications

Genomics of the Parasitic Nematode Ascaris and Its Relatives

Genomics of the Parasitic Nematode Ascaris and Its Relatives

Improving helminth genome resources in the post-genomic era

The Nematode Oscheius tipulae as A Genetic Model for Programmed DNA Elimination

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