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Nematode genome announcement: A chromosome-scale genome assembly for the Pristionchus pacificus reference mapping strain PS1843

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11. Sept. 2024

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Alonge M., Lebeigle L., Kirsche M., Jenike K., Ou S., Aganezov S., Wang X., Lippman Z. B., Schatz M. C., Soyk S. Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing. Genome Biol. 2022;23(1):258. AlongeM. LebeigleL. KirscheM. JenikeK. OuS. AganezovS. WangX. LippmanZ. B. SchatzM. C. SoykS. Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing Genome Biol 2022 23 1 258 Search in Google Scholar

Athanasouli M., Witte H., Weiler C., Loschko T., Eberhardt G., Sommer R. J., Rödelsperger C. Comparative genomics and community curation further improve gene annotations in the nematode Pristionchus pacificus. BMC Genomics. 2020;21(1):708. AthanasouliM. WitteH. WeilerC. LoschkoT. EberhardtG. SommerR. J. RödelspergerC. Comparative genomics and community curation further improve gene annotations in the nematode Pristionchus pacificus BMC Genomics 2020 21 1 708 Search in Google Scholar

Dardiry M., Eberhardt G., Witte H., Rödelsperger C., Lightfoot J. W., Sommer R. J. Divergent combinations of cis-regulatory elements control the evolution of phenotypic plasticity. PLoS Biol. 2023;21(8). DardiryM. EberhardtG. WitteH. RödelspergerC. LightfootJ. W. SommerR. J. Divergent combinations of cis-regulatory elements control the evolution of phenotypic plasticity PLoS Biol 2023 21 8 Search in Google Scholar

Dieterich C., Clifton S. W., Schuster L. N., Chinwalla A., Delehaunty K., Dinkelacker I., Fulton L., Fulton R., Godfrey J., Minx P., Mitreva M., Roeseler W., et al. The Pristionchus pacificus genome provides a unique perspective on nematode lifestyle and parasitism. Nat Genet. 2008;40(10):1193–1198. DieterichC. CliftonS. W. SchusterL. N. ChinwallaA. DelehauntyK. DinkelackerI. FultonL. FultonR. GodfreyJ. MinxP. MitrevaM. RoeselerW. The Pristionchus pacificus genome provides a unique perspective on nematode lifestyle and parasitism Nat Genet 2008 40 10 1193 1198 Search in Google Scholar

Han Z., Lo W.-S., Lightfoot J. W., Witte H., Sun S., Sommer R. J. Improving transgenesis efficiency and CRISPR-associated tools through codon optimization and native intron addition in nematodes. Genetics. 2020;216(4):947–956. HanZ. LoW.-S. LightfootJ. W. WitteH. SunS. SommerR. J. Improving transgenesis efficiency and CRISPR-associated tools through codon optimization and native intron addition in nematodes Genetics 2020 216 4 947 956 Search in Google Scholar

Hiraga H., Ishita Y., Chihara T., Okumura M. Efficient visual screening of CRISPR/Cas9 genome editing in the nematode Pristionchus pacificus. Dev Growth Differ. 2021;63(9):488–500. HiragaH. IshitaY. ChiharaT. OkumuraM. Efficient visual screening of CRISPR/Cas9 genome editing in the nematode Pristionchus pacificus Dev Growth Differ 2021 63 9 488 500 Search in Google Scholar

Igreja C., Loschko T., Schäfer A., Sharma D. R., Quiobe S. P., Aloshy E., Witte H., Sommer R. J. Application of ALFA-Tagging in the nematode model organisms and. Cells. 2022;11(23):3875. IgrejaC. LoschkoT. SchäferA. SharmaD. R. QuiobeS. P. AloshyE. WitteH. SommerR. J. Application of ALFA-Tagging in the nematode model organisms and Cells 2022 11 23 3875 Search in Google Scholar

Koren S., Walenz B. P., Berlin K., Miller J. R., Bergman N. H., Phillippy A. M. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 2017;27(5):722–736. KorenS. WalenzB. P. BerlinK. MillerJ. R. BergmanN. H. PhillippyA. M. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation Genome Res 2017 27 5 722 736 Search in Google Scholar

Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018;34(18):3094–3100. LiH. Minimap2: pairwise alignment for nucleotide sequences Bioinformatics 2018 34 18 3094 3100 Search in Google Scholar

Mayer M. G., Rödelsperger C., Witte H., Riebesell M., Sommer R. J. The orphan gene dauerless regulates dauer development and intraspecific competition in nematodes by copy number variation. PLoS Genet. 2015;11(6). MayerM. G. RödelspergerC. WitteH. RiebesellM. SommerR. J. The orphan gene dauerless regulates dauer development and intraspecific competition in nematodes by copy number variation PLoS Genet 2015 11 6 Search in Google Scholar

McGaughran A., Rödelsperger C., Grimm D. G., Meyer J. M., Moreno E., Morgan K., Leaver M., Serobyan V., Rakitsch B., Borgwardt K. M., Sommer R. J. Genomic profiles of diversification and genotype-phenotype association in island nematode lineages. Mol Biol Evol. 2016;33(9):2257–2272. McGaughranA. RödelspergerC. GrimmD. G. MeyerJ. M. MorenoE. MorganK. LeaverM. SerobyanV. RakitschB. BorgwardtK. M. SommerR. J. Genomic profiles of diversification and genotype-phenotype association in island nematode lineages Mol Biol Evol 2016 33 9 2257 2272 Search in Google Scholar

Moreno E., McGaughran A., Rödelsperger C., Zimmer M., Sommer R. J. Oxygen-induced social behaviours in Pristionchus pacificus have a distinct evolutionary history and genetic regulation from Caenorhabditis elegans. Proc Biol Sci. 2016;283(1825):20152263. MorenoE. McGaughranA. RödelspergerC. ZimmerM. SommerR. J. Oxygen-induced social behaviours in Pristionchus pacificus have a distinct evolutionary history and genetic regulation from Caenorhabditis elegans Proc Biol Sci 2016 283 1825 20152263 Search in Google Scholar

Prabh N., Rödelsperger C. Multiple Pristionchus pacificus genomes reveal distinct evolutionary dynamics between de novo candidates and duplicated genes. Genome Res. 2022;32(7):1315–1327. PrabhN. RödelspergerC. Multiple Pristionchus pacificus genomes reveal distinct evolutionary dynamics between de novo candidates and duplicated genes Genome Res 2022 32 7 1315 1327 Search in Google Scholar

Rillo-Bohn R., Adilardi R., Mitros T., Avşaroğlu B., Stevens L., Köhler S., Bayes J., Wang C., Lin S., Baskevitch K. A., Rokhsar D. S., Dernburg A. F. Analysis of meiosis in Pristionchus pacificus reveals plasticity in homolog pairing and synapsis in the nematode lineage. Elife. 2021;10. Rillo-BohnR. AdilardiR. MitrosT. AvşaroğluB. StevensL. KöhlerS. BayesJ. WangC. LinS. BaskevitchK. A. RokhsarD. S. DernburgA. F. Analysis of meiosis in Pristionchus pacificus reveals plasticity in homolog pairing and synapsis in the nematode lineage Elife 2021 10 Search in Google Scholar

Rödelsperger C. The community-curated Pristionchus pacificus genome facilitates automated gene annotation improvement in related nematodes. BMC Genomics. 2021;22(1):216. RödelspergerC. The community-curated Pristionchus pacificus genome facilitates automated gene annotation improvement in related nematodes BMC Genomics 2021 22 1 216 Search in Google Scholar

Rödelsperger C., Meyer J. M., Prabh N., Lanz C., Bemm F., Sommer R. J. Single-molecule sequencing reveals the chromosome-scale genomic architecture of the nematode model organism Pristionchus pacificus. Cell Rep. 2017;21(3):834–844. RödelspergerC. MeyerJ. M. PrabhN. LanzC. BemmF. SommerR. J. Single-molecule sequencing reveals the chromosome-scale genomic architecture of the nematode model organism Pristionchus pacificus Cell Rep 2017 21 3 834 844 Search in Google Scholar

Rödelsperger C., Neher R. A., Weller A. M., Eberhardt G., Witte H., Mayer W. E., Dieterich C., Sommer R. J. Characterization of genetic diversity in the nematode Pristionchus pacificus from population-scale resequencing data. Genetics. 2014;196(4):1153–1165. RödelspergerC. NeherR. A. WellerA. M. EberhardtG. WitteH. MayerW. E. DieterichC. SommerR. J. Characterization of genetic diversity in the nematode Pristionchus pacificus from population-scale resequencing data Genetics 2014 196 4 1153 1165 Search in Google Scholar

Rödelsperger C., Röseler W., Prabh N., Yoshida K., Weiler C., Herrmann M., Sommer R. J. Phylotranscriptomics of Pristionchus nematodes reveals parallel gene loss in six hermaphroditic lineages. Curr Biol. 2018;28(19):3123–3127.e5. RödelspergerC. RöselerW. PrabhN. YoshidaK. WeilerC. HerrmannM. SommerR. J. Phylotranscriptomics of Pristionchus nematodes reveals parallel gene loss in six hermaphroditic lineages Curr Biol 2018 28 19 3123 3127.e5 Search in Google Scholar

Sieriebriennikov B., Sun S., Lightfoot J. W., Witte H., Moreno E., Rödelsperger C., Sommer R. J. Conserved nuclear hormone receptors controlling a novel plastic trait target fast-evolving genes expressed in a single cell. PLoS Genet. 2020;16(4). SieriebriennikovB. SunS. LightfootJ. W. WitteH. MorenoE. RödelspergerC. SommerR. J. Conserved nuclear hormone receptors controlling a novel plastic trait target fast-evolving genes expressed in a single cell PLoS Genet 2020 16 4 Search in Google Scholar

Simão F. A., Waterhouse R. M., Ioannidis P., Kriventseva E. V., Zdobnov E. M. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015;31(19):3210–3212. SimãoF. A. WaterhouseR. M. IoannidisP. KriventsevaE. V. ZdobnovE. M. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs Bioinformatics 2015 31 19 3210 3212 Search in Google Scholar

Sommer R. J., Dardiry M., Lenuzzi M., Namdeo S., Renahan T., Sieriebriennikov B., Werner M. S. The genetics of phenotypic plasticity in nematode feeding structures. Open Biol. 2017;7(3):160332. SommerR. J. DardiryM. LenuzziM. NamdeoS. RenahanT. SieriebriennikovB. WernerM. S. The genetics of phenotypic plasticity in nematode feeding structures Open Biol 2017 7 3 160332 Search in Google Scholar

Sommer R. J., McGaughran A. The nematode Pristionchus pacificus as a model system for integrative studies in evolutionary biology. Mol Ecol. 2013;22(9):2380–2393. SommerR. J. McGaughranA. The nematode Pristionchus pacificus as a model system for integrative studies in evolutionary biology Mol Ecol 2013 22 9 2380 2393 Search in Google Scholar

Srinivasan J., Sinz W., Lanz C., Brand A., Nandakumar R., Raddatz G., Witte H., Keller H., Kipping I., Pires-daSilva A., Jesse T., Millare J., et al. A bacterial artificial chromosome-based genetic linkage map of the nematode Pristionchus pacificus. Genetics. 2002;162(1):129–134. SrinivasanJ. SinzW. LanzC. BrandA. NandakumarR. RaddatzG. WitteH. KellerH. KippingI. Pires-daSilvaA. JesseT. MillareJ. A bacterial artificial chromosome-based genetic linkage map of the nematode Pristionchus pacificus Genetics 2002 162 1 129 134 Search in Google Scholar

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