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Draft Genome Assembly of Root Knot Nematode, Meloidogyne fallax

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16 kwi 2025

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Adrian, S. R., & Hubley, R. (2023). RepeatMasker [Online]. https://www.repeatmasker.org/ AdrianS. R. HubleyR. 2023 RepeatMasker [Online] https://www.repeatmasker.org/ Search in Google Scholar

Alford, D. V. (2012). Chapter 4 - Miscellaneous Pests. In D. V. Alford (Ed.), Pests of Ornamental Trees, Shrubs and Flowers (2nd ed., pp. 87–112). Academic Press. AlfordD. V. 2012 Chapter 4 - Miscellaneous Pests In AlfordD. V. (Ed.), Pests of Ornamental Trees, Shrubs and Flowers 2nd ed. 87 112 Academic Press Search in Google Scholar

Alonge, M., Lebeigle, L., Kirsche, M., Jenike, K., Ou, S., Aganezov, S., Wang, X., Lippman, Z. B., Schatz, M. C., & Soyk, S. (2022). Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing. Genome Biology, 23(1), 258. https://doi.org/10.1186/s13059-022-02758-2 AlongeM. LebeigleL. KirscheM. JenikeK. OuS. AganezovS. WangX. LippmanZ. B. SchatzM. C. SoykS. 2022 Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing Genome Biology 23 1 258 https://doi.org/10.1186/s13059-022-02758-2 Search in Google Scholar

Álvarez-Ortega, S., Brito, J. A., & Subbotin, S. A. (2019). Multigene phylogeny of root-knot nematodes and molecular characterization of Meloidogyne nataliei Golden, Rose & Bird, 1981 (Nematoda: Tylenchida). Scientific Reports, 9(1), 11788. https://doi.org/10.1038/s41598-019-48283-9 Álvarez-OrtegaS. BritoJ. A. SubbotinS. A. 2019 Multigene phylogeny of root-knot nematodes and molecular characterization of Meloidogyne nataliei Golden, Rose & Bird, 1981 (Nematoda: Tylenchida) Scientific Reports 9 1 11788 https://doi.org/10.1038/s41598-019-48283-9 Search in Google Scholar

Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M., Kulikov, A. S., Lesin, V. M., Nikolenko, S. I., Pham, S., Prjibelski, A. D., Pyshkin, A. V., Sirotkin, A. V., Vyahhi, N., Tesler, G., Alekseyev, M. A., & Pevzner, P. A. (2012). SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology, 19(5), 455–477. https://doi.org/10.1089/cmb.2012.0042 BankevichA. NurkS. AntipovD. GurevichA. A. DvorkinM. KulikovA. S. LesinV. M. NikolenkoS. I. PhamS. PrjibelskiA. D. PyshkinA. V. SirotkinA. V. VyahhiN. TeslerG. AlekseyevM. A. PevznerP. A. 2012 SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing Journal of Computational Biology 19 5 455 477 https://doi.org/10.1089/cmb.2012.0042 Search in Google Scholar

Brinkman, H., Goossens, J. J. M., & Van Riel, H. R. (1996). Comparative host suitability of selected crop plants to Meloidogyne chitwoodi. Anzeiger für Schädlingskunde, Pflanzenschutz, Umweltschutz, 69(5), 127–129. BrinkmanH. GoossensJ. J. M. Van RielH. R. 1996 Comparative host suitability of selected crop plants to Meloidogyne chitwoodi Anzeiger für Schädlingskunde, Pflanzenschutz, Umweltschutz 69 5 127 129 Search in Google Scholar

Castagnone-Sereno, P., Danchin, E. G. J., Perfus-Barbeoch, L., & Abad, P. (2013). Diversity and evolution of root-knot nematodes, genus Meloidogyne: New insights from the genomic era. Annual Review of Phytopathology, 51, 203–220. https://doi.org/10.1146/annurev-phyto-082712-102316 Castagnone-SerenoP. DanchinE. G. J. Perfus-BarbeochL. AbadP. 2013 Diversity and evolution of root-knot nematodes, genus Meloidogyne: New insights from the genomic era Annual Review of Phytopathology 51 203 220 https://doi.org/10.1146/annurev-phyto-082712-102316 Search in Google Scholar

Challis, R. B., Mark, R., Richards, E., Rajan, J., & Cochrane, G. (2023). Filtering a Dataset [Online]. https://blobtoolkit.genomehubs.org/blobtools2/blobtools2-tutorials/filtering-a-dataset/ ChallisR. B. MarkR. RichardsE. RajanJ. CochraneG. 2023 Filtering a Dataset [Online] https://blobtoolkit.genomehubs.org/blobtools2/blobtools2-tutorials/filtering-a-dataset/ Search in Google Scholar

Dai, D., Xie, C., Zhou, Y., Bo, D., Zhang, S., Mao, S., Liao, Y., Cui, S., Zhu, Z., Wang, X., Li, F., Peng, D., Zheng, J., & Sun, M. (2023). Unzipped chromo-some-level genomes reveal allopolyploid nematode origin pattern as unreduced gamete hybridization. Nature Communications, 14(1), 7156. https://doi.org/10.1038/s41467-023-42861-5 DaiD. XieC. ZhouY. BoD. ZhangS. MaoS. LiaoY. CuiS. ZhuZ. WangX. LiF. PengD. ZhengJ. SunM. 2023 Unzipped chromo-some-level genomes reveal allopolyploid nematode origin pattern as unreduced gamete hybridization Nature Communications 14 1 7156 https://doi.org/10.1038/s41467-023-42861-5 Search in Google Scholar

Elling, A. A. (2013). Major emerging problems with minor Meloidogyne species. Phytopathology, 103(10), 1092–1102. https://doi.org/10.1094/PHYTO-03-13-0081-R EllingA. A. 2013 Major emerging problems with minor Meloidogyne species Phytopathology 103 10 1092 1102 https://doi.org/10.1094/PHYTO-03-13-0081-R Search in Google Scholar

EPPO. (2023). Meloidogyne fallax Distribution [Online]. https://gd.eppo.int/taxon/MELGFA/distribution EPPO 2023 Meloidogyne fallax Distribution [Online] https://gd.eppo.int/taxon/MELGFA/distribution Search in Google Scholar

Flynn, J. M., Hubley, R., Goubert, C., Rosen, J., Clark, A. G., Feschotte, C., & Smit, A. F. (2020). RepeatModeler2 for automated genomic discovery of transposable element families. Proceedings of the National Academy of Sciences, 117(17), 9451–9457. https://doi.org/10.1073/pnas.1921008117 FlynnJ. M. HubleyR. GoubertC. RosenJ. ClarkA. G. FeschotteC. SmitA. F. 2020 RepeatModeler2 for automated genomic discovery of transposable element families Proceedings of the National Academy of Sciences 117 17 9451 9457 https://doi.org/10.1073/pnas.1921008117 Search in Google Scholar

Gurevich, A., Saveliev, V., Vyahhi, N., & Tesler, G. (2013). QUAST: Quality assessment tool for genome assemblies. Bioinformatics, 29(8), 1072–1075. https://doi.org/10.1093/bioinformatics/btt089 GurevichA. SavelievV. VyahhiN. TeslerG. 2013 QUAST: Quality assessment tool for genome assemblies Bioinformatics 29 8 1072 1075 https://doi.org/10.1093/bioinformatics/btt089 Search in Google Scholar

Illumina. (2023). Illumina NovaSeq 6000 [Online]. https://emea.illumina.com/systems/sequencing-platforms/novaseq.html Illumina 2023 Illumina NovaSeq 6000 [Online] https://emea.illumina.com/systems/sequencing-platforms/novaseq.html Search in Google Scholar

Krueger, F. (2012). Trim Galore [Online]. https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ KruegerF. 2012 Trim Galore [Online] https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ Search in Google Scholar

Laetsch, D., & Blaxter, M. (2017). BlobTools: Interrogation of genome assemblies [version 1; peer review: 2 approved with reservations]. F1000Research, 6, 1504. https://doi.org/10.12688/f1000research.12609.1 LaetschD. BlaxterM. 2017 BlobTools: Interrogation of genome assemblies [version 1; peer review: 2 approved with reservations] F1000Research 6 1504 https://doi.org/10.12688/f1000research.12609.1 Search in Google Scholar

Lee, S., Nguyen, L. T., Hayes, B. J., & Ross, E. (2021). Prowler: A novel trimming algorithm for Oxford Nanopore sequence data. Bioinformatics. https://doi.org/10.1093/bioinformatics/btab744 LeeS. NguyenL. T. HayesB. J. RossE. 2021 Prowler: A novel trimming algorithm for Oxford Nanopore sequence data Bioinformatics https://doi.org/10.1093/bioinformatics/btab744 Search in Google Scholar

Manni, M., Berkeley, M. R., Seppey, M., & Zdobnov, E. M. (2021). BUSCO: Assessing genomic data quality and beyond. Current Protocols, 1(11), e243. https://doi.org/10.1002/cphc.243 ManniM. BerkeleyM. R. SeppeyM. ZdobnovE. M. 2021 BUSCO: Assessing genomic data quality and beyond Current Protocols 1 11 e243 https://doi.org/10.1002/cphc.243 Search in Google Scholar

Nischwitz, C., Skantar, A., Handoo, Z. A., Hult, M. N., Schmitt, M. E., & McClure, M. A. (2013). Occurrence of Meloidogyne fallax in North America, and molecular characterization of M. fallax and M. minor from U.S. Golf Course Greens. Plant Disease, 97(11), 1438–1444. https://doi.org/10.1094/PDIS-04-13-0361-RE NischwitzC. SkantarA. HandooZ. A. HultM. N. SchmittM. E. McClureM. A. 2013 Occurrence of Meloidogyne fallax in North America, and molecular characterization of M. fallax and M. minor from U.S. Golf Course Greens Plant Disease 97 11 1438 1444 https://doi.org/10.1094/PDIS-04-13-0361-RE Search in Google Scholar

Oxford Nanopore Technologies. (2023). PromethION [Online]. https://nanoporetech.com/products/promethion Oxford Nanopore Technologies 2023 PromethION [Online] https://nanoporetech.com/products/promethion Search in Google Scholar

QIAGEN. (2015). QIAGEN Genomic DNA Handbook [Online]. https://www.qiagen.com/us/resources/download.aspx?id=d2b85b26-16dd-4259-a3a7-a08cbd2a08a3&lang=en QIAGEN 2015 QIAGEN Genomic DNA Handbook [Online] https://www.qiagen.com/us/resources/download.aspx?id=d2b85b26-16dd-4259-a3a7-a08cbd2a08a3&lang=en Search in Google Scholar

Santo, G., O’Bannon, J., Finley, A., & Golden, A. (1981). Occurrence and host range of a new root-knot nematode (Meloidogyne chitwoodi) in the Pacific Northwest. Plant Disease, 64(10), 951–952. https://doi.org/10.1094/PD-64-951 SantoG. O’BannonJ. FinleyA. GoldenA. 1981 Occurrence and host range of a new root-knot nematode (Meloidogyne chitwoodi) in the Pacific Northwest Plant Disease 64 10 951 952 https://doi.org/10.1094/PD-64-951 Search in Google Scholar

Shen, W., Le, S., Li, Y., & Hu, F. (2016). SeqKit: A cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PLOS ONE, 11(8), e0163962. https://doi.org/10.1371/journal.pone.0163962 ShenW. LeS. LiY. HuF. 2016 SeqKit: A cross-platform and ultrafast toolkit for FASTA/Q file manipulation PLOS ONE 11 8 e0163962 https://doi.org/10.1371/journal.pone.0163962 Search in Google Scholar

Shen, W., Sipos, B., & Zhao, L. (2024). SeqKit2: A Swiss army knife for sequence and alignment processing. iMeta, e191. https://doi.org/10.1002/imt2.191 ShenW. SiposB. ZhaoL. 2024 SeqKit2: A Swiss army knife for sequence and alignment processing iMeta e191 https://doi.org/10.1002/imt2.191 Search in Google Scholar

Van Der Beek, J. G., & Karssen, G. (1997). Interspecific hybridization of meiotic parthenogenetic Meloidogyne chitwoodi and M. fallax. Phytopathology, 87(10), 1061–1066. https://doi.org/10.1094/PHYTO.1997.87.10.1061 Van Der BeekJ. G. KarssenG. 1997 Interspecific hybridization of meiotic parthenogenetic Meloidogyne chitwoodi and M. fallax Phytopathology 87 10 1061 1066 https://doi.org/10.1094/PHYTO.1997.87.10.1061 Search in Google Scholar

Waeyenberge, L., & Moens, M. (2001). Meloidogyne chitwoodi and M. fallax in Belgium. Nematologia Mediterranea, 29(1), 91–97. WaeyenbergeL. MoensM. 2001 Meloidogyne chitwoodi and M. fallax in Belgium Nematologia Mediterranea 29 1 91 97 Search in Google Scholar

Wood, D. E., Lu, J., & Langmead, B. (2019). Improved metagenomic analysis with Kraken 2. Genome Biology, 20(1), 257. https://doi.org/10.1186/s13059-019-1891-0 WoodD. E. LuJ. LangmeadB. 2019 Improved metagenomic analysis with Kraken 2 Genome Biology 20 1 257 https://doi.org/10.1186/s13059-019-1891-0 Search in Google Scholar

Xu, M., Guo, L., Gu, S., Wang, O., Zhang, R., Peters, B. A., Fan, G., Liu, X., Xu, X., Deng, L., & Zhang, Y. (2020). TGS-GapCloser: A fast and accurate gap closer for large genomes with low coverage of error-prone long reads. GigaScience, 9(12), giaa144. https://doi.org/10.1093/gigascience/giaa144 XuM. GuoL. GuS. WangO. ZhangR. PetersB. A. FanG. LiuX. XuX. DengL. ZhangY. 2020 TGS-GapCloser: A fast and accurate gap closer for large genomes with low coverage of error-prone long reads GigaScience 9 12 giaa144 https://doi.org/10.1093/gigascience/giaa144 Search in Google Scholar

Język:
Angielski
Częstotliwość wydawania:
1 razy w roku
Dziedziny czasopisma:
Nauki biologiczne, Nauki biologiczne, inne