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Article ; Online: Pristionchus pacificus genomics: from genetics to genome sequence.

Dieterich, Christoph / Roeseler, Waltraud / Srinivasan, Jagan

WormBook : the online review of C. elegans biology

2006 , Page(s) 1–14

MeSH term(s)	Animals ; Chromosome Mapping ; Computational Biology ; DNA, Helminth ; Genome, Helminth ; Genomics ; Humans ; Nematoda/genetics ; Sequence Analysis, DNA
Chemical Substances	DNA, Helminth
Language	English
Publishing date	2006-08-14
Publishing country	United States
Document type	Journal Article ; Review
ISSN	1551-8507
ISSN (online)	1551-8507
DOI	10.1895/wormbook.1.116.1
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Article ; Online: Nine new Pristionchus (Nematoda: Diplogastridae) species from China.

Kanzaki, Natsumi / Herrmann, Matthias / Weiler, Christian / Röseler, Waltraud / Theska, Tobias / Berger, Jürgen / Rödelsperger, Christian / Sommer, Ralf J

Zootaxa

2021 Volume 4943, Issue 1, Page(s) zootaxa.4943.1.1

Abstract: ... experiments and genome-wide sequence analysis. ... The model organism Pristionchus pacificus and the genus Pristionchus, Kreis, 1932 have been ... behavior, neurobiology, and genomics of this group of organisms. In particular, mechanistic studies ...

Abstract	The model organism Pristionchus pacificus and the genus Pristionchus, Kreis, 1932 have been intensively studied in the last decade with contemporary work focusing on the development, evolution, ecology, behavior, neurobiology, and genomics of this group of organisms. In particular, mechanistic studies on the development and evolution of mouth-form plasticity, predation and associated self-recognition processes enabled unique insight into life history strategies and the evolution of novelty. These studies include a comparative research agenda making use of the 39 available species of Pristionchus, all of which can be studied in living cultures. Sampling efforts revealed that Asia represents a biodiversity hotspot for Pristionchus worms. However, previous samplings have a bias towards northern and island areas, largely for logistic reasons. Here, we report on two extensive sampling trips to the Yunnan and Shaanxi provinces in Mainland China. We report the isolation of nine new Pristionchus species by morphology, morphometrics, mating experiments and genome-wide sequence analysis.
MeSH term(s)	Animals ; China ; Nematoda/genetics ; Phylogeny ; Rhabditida ; Species Specificity
Language	English
Publishing date	2021-03-17
Publishing country	New Zealand
Document type	Journal Article
ISSN	1175-5334
ISSN (online)	1175-5334
DOI	10.11646/zootaxa.4943.1.1
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Article ; Online: Chromosome fusions repatterned recombination rate and facilitated reproductive isolation during Pristionchus nematode speciation.

Yoshida, Kohta / Rödelsperger, Christian / Röseler, Waltraud / Riebesell, Metta / Sun, Simo / Kikuchi, Taisei / Sommer, Ralf J

Nature ecology & evolution

2023 Volume 7, Issue 3, Page(s) 424–439

Abstract: ... in speciation genomics revealed the importance of inversions, whereas the role of other genome-structural ... reproductive isolation of closely related nematodes: the androdioecious (hermaphroditic) model Pristionchus pacificus and ... its dioecious sister species Pristionchus exspectatus. A chromosome-level genome assembly of P. exspectatus ...

Abstract	Large-scale genome-structural evolution is common in various organisms. Recent developments in speciation genomics revealed the importance of inversions, whereas the role of other genome-structural rearrangements, including chromosome fusions, have not been well characterized. We study genomic divergence and reproductive isolation of closely related nematodes: the androdioecious (hermaphroditic) model Pristionchus pacificus and its dioecious sister species Pristionchus exspectatus. A chromosome-level genome assembly of P. exspectatus using single-molecule and Hi-C sequencing revealed a chromosome-wide rearrangement relative to P. pacificus. Strikingly, genomic characterization and cytogenetic studies including outgroup species Pristionchus occultus indicated two independent fusions involving the same chromosome, ChrIR, between these related species. Genetic linkage analysis indicated that these fusions altered the chromosome-wide pattern of recombination, resulting in large low-recombination regions that probably facilitated the coevolution between some of the ~14.8% of genes across the entire genomes. Quantitative trait locus analyses for hybrid sterility in all three sexes revealed that major quantitative trait loci mapped to the fused chromosome ChrIR. While abnormal chromosome segregations of the fused chromosome partially explain hybrid female sterility, hybrid-specific recombination that breaks linkage of genes in the low-recombination region was associated with hybrid male sterility. Thus, recent chromosome fusions repatterned recombination rate and drove reproductive isolation during Pristionchus speciation.
MeSH term(s)	Animals ; Female ; Male ; Reproductive Isolation ; Nematoda/genetics ; Chromosomes ; Genome ; Recombination, Genetic
Language	English
Publishing date	2023-01-30
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2397-334X
ISSN (online)	2397-334X
DOI	10.1038/s41559-022-01980-z
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Article ; Online: Analysis of repeat elements in the Pristionchus pacificus genome reveals an ancient invasion by horizontally transferred transposons.

Athanasouli, Marina / Rödelsperger, Christian

BMC genomics

2022 Volume 23, Issue 1, Page(s) 523

Abstract: ... to the annotation of the Pristionchus pacificus genome and assess their impact on novel gene formation.: Results ... Different computational approaches define up to 24% of the P. pacificus genome as repetitive sequences ... pacificus lineage.: Conclusions: The comprehensive annotation of repetitive elements in the P. pacificus ...

Abstract	Background: Repetitive sequences and mobile elements make up considerable fractions of individual genomes. While transposition events can be detrimental for organismal fitness, repetitive sequences form an enormous reservoir for molecular innovation. In this study, we aim to add repetitive elements to the annotation of the Pristionchus pacificus genome and assess their impact on novel gene formation. Results: Different computational approaches define up to 24% of the P. pacificus genome as repetitive sequences. While retroelements are more frequently found at the chromosome arms, DNA transposons are distributed more evenly. We found multiple DNA transposons, as well as LTR and LINE elements with abundant evidence of expression as single-exon transcripts. When testing whether transposons disproportionately contribute towards new gene formation, we found that roughly 10-20% of genes across all age classes overlap transposable elements with the strongest trend being an enrichment of low complexity regions among the oldest genes. Finally, we characterized a horizontal gene transfer of Zisupton elements into diplogastrid nematodes. These DNA transposons invaded nematodes from eukaryotic donor species and experienced a recent burst of activity in the P. pacificus lineage. Conclusions: The comprehensive annotation of repetitive elements in the P. pacificus genome builds a resource for future functional genomic analyses as well as for more detailed investigations of molecular innovations.
MeSH term(s)	Animals ; DNA Transposable Elements/genetics ; Gene Transfer, Horizontal ; Genomics ; Retroelements/genetics ; Rhabditida/genetics
Chemical Substances	DNA Transposable Elements ; Retroelements
Language	English
Publishing date	2022-07-19
Publishing country	England
Document type	Journal Article
ZDB-ID	2041499-7
ISSN	1471-2164 ; 1471-2164
ISSN (online)	1471-2164
ISSN	1471-2164
DOI	10.1186/s12864-022-08731-1
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Article ; Online: Robust, versatile DNA FISH probes for chromosome-specific repeats in Caenorhabditis elegans and Pristionchus pacificus.

Adilardi, Renzo S / Dernburg, Abby F

G3 (Bethesda, Md.)

2022 Volume 12, Issue 7

Abstract: ... We analyzed recent genome assemblies of Caenorhabditis elegans and Pristionchus pacificus to identify ... The methods presented here can be easily applied in other model and nonmodel organisms with a sequenced genome. ... tandem repeats with a unique genomic localization. Based on these findings, we designed and validated sets ...

Abstract	Repetitive DNA sequences are useful targets for chromosomal fluorescence in situ hybridization. We analyzed recent genome assemblies of Caenorhabditis elegans and Pristionchus pacificus to identify tandem repeats with a unique genomic localization. Based on these findings, we designed and validated sets of oligonucleotide probes for each species targeting at least 1 locus per chromosome. These probes yielded reliable fluorescent signals in different tissues and can easily be combined with the immunolocalization of cellular proteins. Synthesis and labeling of these probes are highly cost-effective and require no hands-on labor. The methods presented here can be easily applied in other model and nonmodel organisms with a sequenced genome.
MeSH term(s)	Animals ; Caenorhabditis elegans/genetics ; Chromosomes/genetics ; DNA ; DNA Probes ; In Situ Hybridization, Fluorescence ; Nematoda/genetics
Chemical Substances	DNA Probes ; DNA (9007-49-2)
Language	English
Publishing date	2022-05-14
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2629978-1
ISSN	2160-1836 ; 2160-1836
ISSN (online)	2160-1836
ISSN	2160-1836
DOI	10.1093/g3journal/jkac121
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Article ; Online: Two new Species of Pristionchus (Nematoda

Herrmann Matthias / Kanzaki Natsumi / Weiler Christian / Yoshida Kohta / RÖdelsperger Christian / Sommer Ralf J.

Journal of Nematology, Vol 51, Iss 1, Pp 1-

Diplogastridae) include the Gonochoristic Sister Species of P. fissidentatus

2019 Volume 14

Abstract: ... transcriptome sequence analysis. Previous phylotranscriptomic analysis of the complete Pristionchus genus ... group” in America, the “pacificus species group” in Asia, and the “lheritieri species group ... from Taiwan and P. yamagatae sp. n. from Japan by means of morphology, morphometrics and genome-wide ...

Abstract	The genus Pristionchus (Kreis, 1932) consists of more than 30 soil nematode species that are often found in association with scarab beetles. Three major radiations have resulted in the “maupasi species group” in America, the “pacificus species group” in Asia, and the “lheritieri species group,” which contains species from Europe and Asia. Phylogenetic analysis indicates that a group of three species, including the gonochorists P. elegans and P. bucculentus and the hermaphrodite P. fissidentatus, is basal to the above-mentioned radiations. Two novel species are described here: Pristionchus paulseni sp. n. from Taiwan and P. yamagatae sp. n. from Japan by means of morphology, morphometrics and genome-wide transcriptome sequence analysis. Previous phylotranscriptomic analysis of the complete Pristionchus genus recognized P. paulseni sp. n. as the sister species of P. fissidentatus, and thus its importance for macro-evolutionary studies. Specifically, the gonochorist P. paulseni sp. n. and the hermaphrodite P. fissidentatus form a species pair that is the sister group to all other described Pristionchus species. P. paulseni sp. n. has two distinct mouth forms, supporting the notion that the mouth dimorphism is ancestral in the genus Pristionchus.
Keywords	pristionchus pacificus ; p. fissidentatus ; taiwan ; japan ; scarab beetles ; Biology (General) ; QH301-705.5
Subject code	590 ; 580
Language	English
Publishing date	2019-01-01T00:00:00Z
Publisher	Sciendo
Document type	Article ; Online
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Article ; Online: The community-curated Pristionchus pacificus genome facilitates automated gene annotation improvement in related nematodes.

Rödelsperger, Christian

BMC genomics

2021 Volume 22, Issue 1, Page(s) 216

Abstract: Background: The nematode Pristionchus pacificus is an established model organism ... that the reannotation of phylogenomic data from nine related nematode species using the community-curated P. pacificus ... employed recently to improve the quality of gene annotations of P. pacificus and to more easily facilitate ...

Abstract	Background: The nematode Pristionchus pacificus is an established model organism for comparative studies with Caenorhabditis elegans. Over the past years, it developed into an independent animal model organism for elucidating the genetic basis of phenotypic plasticity. Community-based curations were employed recently to improve the quality of gene annotations of P. pacificus and to more easily facilitate reverse genetic studies using candidate genes from C. elegans. Results: Here, I demonstrate that the reannotation of phylogenomic data from nine related nematode species using the community-curated P. pacificus gene set as homology data substantially improves the quality of gene annotations. Benchmarking of universal single copy orthologs (BUSCO) estimates a median completeness of 84% which corresponds to a 9% increase over previous annotations. Nevertheless, the ability to infer gene models based on homology already drops beyond the genus level reflecting the rapid evolution of nematode lineages. This also indicates that the highly curated C. elegans genome is not optimally suited for annotating non-Caenorhabditis genomes based on homology. Furthermore, comparative genomic analysis of apparently missing BUSCO genes indicates a failure of ortholog detection by the BUSCO pipeline due to the insufficient sample size and phylogenetic breadth of the underlying OrthoDB data set. As a consequence, the quality of multiple divergent nematode genomes might be underestimated. Conclusions: This study highlights the need for optimizing gene annotation protocols and it demonstrates the benefit of a high quality genome for phylogenomic data of related species.
MeSH term(s)	Animals ; Caenorhabditis elegans/genetics ; Genome ; Molecular Sequence Annotation ; Nematoda/genetics ; Phylogeny ; Rhabditida/genetics
Language	English
Publishing date	2021-03-25
Publishing country	England
Document type	Journal Article
ISSN	1471-2164
ISSN (online)	1471-2164
DOI	10.1186/s12864-021-07529-x
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Article ; Online: Pristionchus pacificus protocols.

Pires-daSilva, Andre

WormBook : the online review of C. elegans biology

2013 , Page(s) 1–20

MeSH term(s)	Animals ; Chromosome Mapping ; DNA, Helminth ; Freezing ; Gene Library ; Genes, Helminth ; Genome, Helminth ; In Situ Hybridization ; Morpholinos ; Mutagenesis ; Nematoda/genetics ; Nematoda/physiology ; Parasitology/methods ; RNA Interference ; RNA, Helminth ; Sequence Analysis, DNA ; Transgenes
Chemical Substances	DNA, Helminth ; Morpholinos ; RNA, Helminth
Language	English
Publishing date	2013-03-14
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ISSN	1551-8507
ISSN (online)	1551-8507
DOI	10.1895/wormbook.1.114.2
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Article ; Online: Comparative genomics and community curation further improve gene annotations in the nematode Pristionchus pacificus.

Athanasouli, Marina / Witte, Hanh / Weiler, Christian / Loschko, Tobias / Eberhardt, Gabi / Sommer, Ralf J / Rödelsperger, Christian

BMC genomics

2020 Volume 21, Issue 1, Page(s) 708

Abstract: Background: Nematode model organisms such as Caenorhabditis elegans and Pristionchus pacificus are ... by the discrepancy in the quality of gene annotations, a common problem in nematode and invertebrate genomics ... However, the identification of P. pacificus orthologs of candidate genes known from C. elegans is complicated ...

Abstract	Background: Nematode model organisms such as Caenorhabditis elegans and Pristionchus pacificus are powerful systems for studying the evolution of gene function at a mechanistic level. However, the identification of P. pacificus orthologs of candidate genes known from C. elegans is complicated by the discrepancy in the quality of gene annotations, a common problem in nematode and invertebrate genomics. Results: Here, we combine comparative genomic screens for suspicious gene models with community-based curation to further improve the quality of gene annotations in P. pacificus. We extend previous curations of one-to-one orthologs to larger gene families and also orphan genes. Cross-species comparisons of protein lengths, screens for atypical domain combinations and species-specific orphan genes resulted in 4311 candidate genes that were subject to community-based curation. Corrections for 2946 gene models were implemented in a new version of the P. pacificus gene annotations. The new set of gene annotations contains 28,896 genes and has a single copy ortholog completeness level of 97.6%. Conclusions: Our work demonstrates the effectiveness of comparative genomic screens to identify suspicious gene models and the scalability of community-based approaches to improve the quality of thousands of gene models. Similar community-based approaches can help to improve the quality of gene annotations in other invertebrate species, including parasitic nematodes.
MeSH term(s)	Animals ; Caenorhabditis elegans/genetics ; Genomics ; Molecular Sequence Annotation/methods ; Molecular Sequence Annotation/standards ; Rhabditida/genetics ; Species Specificity
Language	English
Publishing date	2020-10-12
Publishing country	England
Document type	Journal Article
ISSN	1471-2164
ISSN (online)	1471-2164
DOI	10.1186/s12864-020-07100-0
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Article ; Online: Screening for CRISPR/Cas9-induced mutations using a co-injection marker in the nematode Pristionchus pacificus.

Nakayama, Ken-Ichi / Ishita, Yuuki / Chihara, Takahiro / Okumura, Misako

Development genes and evolution

2020 Volume 230, Issue 3, Page(s) 257–264

Abstract: ... editing events and will facilitate the development of new genome-editing methods in P. pacificus. ... Pristionchus pacificus is a satellite model and has been used to understand interesting phenomena ... CRISPR/Cas9 genome-editing methods are used to reveal functions of genes and molecular mechanisms ...

Abstract	CRISPR/Cas9 genome-editing methods are used to reveal functions of genes and molecular mechanisms underlying biological processes in many species, including nematodes. In evolutionary biology, the nematode Pristionchus pacificus is a satellite model and has been used to understand interesting phenomena such as phenotypic plasticity and self-recognition. In P. pacificus, CRISPR/Cas9-mediated mutations are induced by microinjecting a guide RNA (gRNA) and Cas9 protein into the gonads. However, mutant screening is laborious and time-consuming due to the absence of visual markers. In this study, we established a Co-CRISPR strategy by using a dominant roller marker in P. pacificus. We found that heterozygous mutations in Ppa-prl-1 induced the roller phenotype, which can be used as an injection marker. After the co-injection of Ppa-prl-1 gRNA, target gRNA, and the Cas9 protein, roller progeny and their siblings were examined using the heteroduplex mobility assay and DNA sequencing. We found that some of the roller and non-roller siblings had mutations at the target site. We used varying Cas9 concentrations and found that a higher concentration of Cas9 did not increase genome-editing events. The Co-CRISPR strategy promotes the screening for genome-editing events and will facilitate the development of new genome-editing methods in P. pacificus.
MeSH term(s)	Animals ; CRISPR-Cas Systems ; Chemotaxis ; Electrophoresis, Microchip/methods ; Gene Editing/methods ; Genetic Markers ; Genome, Helminth ; Heterozygote ; Microinjections/methods ; Models, Animal ; Mutation ; Nematoda/genetics ; Phenotype ; RNA, Guide, CRISPR-Cas Systems
Chemical Substances	Genetic Markers ; RNA, Guide, CRISPR-Cas Systems
Language	English
Publishing date	2020-02-06
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1327962-2
ISSN	1432-041X ; 0949-944X
ISSN (online)	1432-041X
ISSN	0949-944X
DOI	10.1007/s00427-020-00651-y
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