Chromosome-wide evolution and sex determination in a nematode with three sexes

Tandonnet, Sophie; Koutsovoulos, Georgios; Adams, Sally; Cloarec, Delphine; Parihar, Manish; Blaxter, Mark; Pires-daSilva, André

doi:10.1101/466961

Cited by 6 publications

(4 citation statements)

References 82 publications

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“…The small 3 Mb of S. carpocapsae chromosome X section is the only section orthologous to P. pacificus chromosome X, while most of the scaffolds are orthologous to P. pacificus chromosome I. This small segment of chromosome X orthologous among S. carpocapsae , C. elegans and P. pacificus might represent a Nigon unit, which are proposed to be deeply conserved linkage groups found conserved between nematodes (Tandonnet et al , 2018). A comparison of A. rhodensis chromosomes to four Caenorhabditis species including C. elegans pinpointed these Nigon units, one of which (NX) was found as a sole component of chromosome X or found combined with other Nigon units (Tandonnet et al , 2018).…”

Section: Discussionmentioning

confidence: 99%

“…This small segment of chromosome X orthologous among S. carpocapsae , C. elegans and P. pacificus might represent a Nigon unit, which are proposed to be deeply conserved linkage groups found conserved between nematodes (Tandonnet et al , 2018). A comparison of A. rhodensis chromosomes to four Caenorhabditis species including C. elegans pinpointed these Nigon units, one of which (NX) was found as a sole component of chromosome X or found combined with other Nigon units (Tandonnet et al , 2018). Interestingly, S. carpocapsae scaffolds are orthologous to single C. elegans chromosomes, which is reminiscent of a macrosynteny analysis in other nematode clades that also found conservation of orthologous chromosomal parts (Fradin et al , 2017).…”

Section: Discussionmentioning

confidence: 99%

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Hybrid Assembly of the Genome of the Entomopathogenic Nematode Steinernema carpocapsae Identifies the X-Chromosome

Serra

Macchietto

Macias-Muñoz

et al. 2019

G3 Genes|Genomes|Genetics

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Entomopathogenic nematodes from the genus Steinernema are lethal insect parasites that quickly kill their insect hosts with the help of their symbiotic bacteria. Steinernema carpocapsae is one of the most studied entomopathogens due to its broad lethality to diverse insect species and its effective commercial use as a biological control agent for insect pests, as well as a genetic model for studying parasitism, pathogenesis, and symbiosis. In this study, we used long-reads from the Pacific Biosciences platform and BioNano Genomics Irys system to assemble the most complete genome of the S. carpocapsae ALL strain to date, comprising 84.5 Mb in 16 scaffolds, with an N50 of 7.36 Mb. The largest scaffold, with 20.9 Mb, was identified as chromosome X based on sex-specific genome sequencing. The high level of contiguity allowed us to characterize gene density, repeat content, and GC content. RNA-seq data from 17 developmental stages, spanning from embryo to adult, were used to predict 30,957 gene models. Using this improved genome, we performed a macrosyntenic analysis to Caenorhabditis elegans and Pristionchus pacificus and found S. carpocapsae’s chromosome X to be primarily orthologous to C. elegans ’ and P. pacificus ’ chromosome II and IV. We also investigated the expansion of protein families and gene expression differences between adult male and female stage nematodes. This new genome and more accurate set of annotations provide a foundation for additional comparative genomic and gene expression studies within the Steinernema clade and across the Nematoda phylum.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Hybrid Assembly of the Genome of the Entomopathogenic Nematode Steinernema carpocapsae Identifies the X-Chromosome

Serra

Macchietto

Macias-Muñoz

et al. 2019

G3 Genes|Genomes|Genetics

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“…Chr1 to Chr5 of R. diutinus can be divided into two S. ratti syntenic groups; Chr2 and Chr3 of R. diutinus were mixed up and correspond to S. ratti Chr1 right hand and Chr2 left hand, whereas R. diutinus Chr1, 4 and 5 correspond to S. ratti Chr2 right hand and Chr1 left hand (figure 3a). Nigon elements, proposed as seven ancestral chromosome elements in rhabditine nematodes, have been used to reconstruct evolutionary history in other nematodes [41]. However, the Nigon elements are not conserved in S. ratti [25], which means that they are not useful for investigating chromosomal relationships in the Strongyloides clade.…”

Section: (B) Syntenic Relationship Of Chromosomes In the Strongyloide...mentioning

confidence: 99%

Syntenic relationship of chromosomes in Strongyloides species and Rhabditophanes diutinus based on the chromosome-level genome assemblies

Kounosu,

Sun,

Maeda

et al. 2023

Phil. Trans. R. Soc. B

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The Strongyloides clade, to which the parasitic nematode genus Strongyloides belongs, contains taxa with diverse lifestyles, ranging from free-living to obligate vertebrate parasites. Reproductive strategies are also diverse in this group of nematodes, employing not only sexual reproduction but also parthenogenesis, making it an attractive group to study genome adaptation to specific conditions. An in-depth understanding of genome evolution, however, has been hampered by fragmented genome assemblies. In this study, we generated chromosome-level genome assemblies for two Strongyloides species and the outgroup species Rhabditophanes diutinus using long-read sequencing and high‐throughput chromosome conformation capture (Hi-C). Our synteny analyses revealed a clearer picture of chromosome evolution in this group, suggesting that a functional sex chromosome has been maintained throughout the group. We further investigated sex chromosome dynamics in the lifecycle of Strongyloides ratti and found that bivalent formation in oocytes appears to be important for male production in the mitotic parthenogenesis. This article is part of the Theo Murphy meeting issue ‘ Strongyloides : omics to worm-free populations’.

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“…PS1159 and Propanagrolaimus sp. JU765, in relation to the nematode model organisms C. elegans and P. pacificus, as well as A. rhodensis and S. ratti, species with reportedly successful use of the CRISPR system (modified fromBlaxter and Koutsovoulos, 2015;Tandonnet et al, 2018) XbaI cleavage site (orange). Asterisk shows in frame stop codon after successful incorporation of desired bases.…”

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confidence: 99%

CRISPR/Cas9 mediated gene editing in non-model nematodePanagrolaimussp. PS1159

Hellekes

Claus

Seiler

et al. 2022

Preprint

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The phylum Nematoda consists of a huge diversity of species in a broad range of ecosystems and habitats. Nematodes share a largely conserved Bauplan but major differences have been found in early developmental processes. The development of the nematode model organism Caenorhabditis elegans has been studied in great detail for decades. These efforts have provided the community with a large number of protocols and methods. Unfortunately, many of these tools are not easily applicable in non-Caenorhabditis nematodes. In recent years it has become clear that many crucial genes in the C. elegans developmental toolkit are absent in other nematode species. It is thus necessary to study the developmental program of other nematode species in detail to understand evolutionary conservation and novelty in the phylum. Panagrolaimus sp. PS1159 is a non-parasitic nematode exhibiting parthenogenetic reproduction and we are establishing the species to comparatively study evolution, biodiversity and alternative reproduction and survival strategies. Here, we demonstrate the first successful application of the CRISPR/Cas9 system for genome editing in Panagrolaimus sp. PS1159 and its closely related hermaphroditic species Propanagrolaimus sp. JU765 with both the non-homologous end joining and the homology-directed repair mechanism. Using microinjections and modifying published protocols from C. elegans and P. pacificus we induced mutations in the orthologue of unc-22, which resulted in a visible uncoordinated twitching phenotype. We also compared the HDR efficiency following the delivery of different repair templates. This work will expand the applicability for a wide range of non-model nematodes from across the tree and facilitate functional analysis into the evolution of parthenogenesis, changes in the developmental program of Nematoda, and cryptobiosis.

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Chromosome-wide evolution and sex determination in a nematode with three sexes

Cited by 6 publications

References 82 publications

Hybrid Assembly of the Genome of the Entomopathogenic Nematode Steinernema carpocapsae Identifies the X-Chromosome

Hybrid Assembly of the Genome of the Entomopathogenic Nematode Steinernema carpocapsae Identifies the X-Chromosome

Syntenic relationship of chromosomes in Strongyloides species and Rhabditophanes diutinus based on the chromosome-level genome assemblies

CRISPR/Cas9 mediated gene editing in non-model nematodePanagrolaimussp. PS1159

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