{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,7]],"date-time":"2026-07-07T22:10:10Z","timestamp":1783462210237,"version":"3.55.0"},"reference-count":66,"publisher":"Wiley","issue":"3","license":[{"start":{"date-parts":[[2023,6,6]],"date-time":"2023-06-06T00:00:00Z","timestamp":1686009600000},"content-version":"vor","delay-in-days":36,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["bsapubs.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Appl Plant Sci"],"published-print":{"date-parts":[[2023,5]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Premise<\/jats:title><jats:p>We present approaches used to generate long\u2010read Nanopore sequencing reads for the Liliales and demonstrate how modifications to standard protocols directly impact read length and total output. The goal is to help those interested in generating long\u2010read sequencing data determine which steps may be necessary for optimizing output and results.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>Four species of <jats:italic>Calochortus<\/jats:italic> (Liliaceae) were sequenced. Modifications made to sodium dodecyl sulfate (SDS) extractions and cleanup protocols included grinding with a mortar and pestle, using cut or wide\u2010bore tips, chloroform cleaning, bead cleaning, eliminating short fragments, and using highly purified DNA.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Steps taken to maximize read length can decrease overall output. Notably, the number of pores in a flow cell is correlated with the overall output, yet we did not see an association between the pore number and the read length or the number of reads produced.<\/jats:p><\/jats:sec><jats:sec><jats:title>Discussion<\/jats:title><jats:p>Many factors contribute to the overall success of a Nanopore sequencing run. We showed the direct impact that several modifications to the DNA extraction and cleaning steps have on the total sequencing output, read size, and number of reads generated. We show a tradeoff between read length and the number of reads and, to a lesser extent, the total sequencing output, all of which are important factors for successful de novo genome assembly.<\/jats:p><\/jats:sec>","DOI":"10.1002\/aps3.11524","type":"journal-article","created":{"date-parts":[[2023,6,7]],"date-time":"2023-06-07T21:30:44Z","timestamp":1686173444000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":30,"title":["Balancing read length and sequencing depth: Optimizing Nanopore long\u2010read sequencing for monocots with an emphasis on the Liliales"],"prefix":"10.1002","volume":"11","author":[{"given":"Gisel Y.","family":"De La Cerda","sequence":"first","affiliation":[{"name":"School of Integrative Plant Science, Section of Plant Biology and the L. H. Bailey Hortorium Cornell University  Ithaca New York 14853 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5631-5365","authenticated-orcid":false,"given":"Jacob B.","family":"Landis","sequence":"additional","affiliation":[{"name":"School of Integrative Plant Science, Section of Plant Biology and the L. H. Bailey Hortorium Cornell University  Ithaca New York 14853 USA"},{"name":"BTI Computational Biology Center Boyce Thompson Institute  Ithaca New York 14853 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Evan","family":"Eifler","sequence":"additional","affiliation":[{"name":"Department of Botany University of Wisconsin\u2013Madison  Madison Wisconsin 53706 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7882-3427","authenticated-orcid":false,"given":"Adriana I.","family":"Hernandez","sequence":"additional","affiliation":[{"name":"School of Integrative Plant Science, Section of Plant Biology and the L. H. Bailey Hortorium Cornell University  Ithaca New York 14853 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0076-0152","authenticated-orcid":false,"given":"Fay\u2010Wei","family":"Li","sequence":"additional","affiliation":[{"name":"BTI Computational Biology Center Boyce Thompson Institute  Ithaca New York 14853 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jing","family":"Zhang","sequence":"additional","affiliation":[{"name":"BTI Computational Biology Center Boyce Thompson Institute  Ithaca New York 14853 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7263-7885","authenticated-orcid":false,"given":"Carrie M.","family":"Tribble","sequence":"additional","affiliation":[{"name":"School of Life Sciences University of Hawai\u02bbi, M\u0101noa  Honolulu Hawai\u02bbi 96822 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nisa","family":"Karimi","sequence":"additional","affiliation":[{"name":"Department of Botany University of Wisconsin\u2013Madison  Madison Wisconsin 53706 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patricia","family":"Chan","sequence":"additional","affiliation":[{"name":"Department of Botany University of Wisconsin\u2013Madison  Madison Wisconsin 53706 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas","family":"Givnish","sequence":"additional","affiliation":[{"name":"Department of Botany University of Wisconsin\u2013Madison  Madison Wisconsin 53706 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susan R.","family":"Strickler","sequence":"additional","affiliation":[{"name":"BTI Computational Biology Center Boyce Thompson Institute  Ithaca New York 14853 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7746-512X","authenticated-orcid":false,"given":"Chelsea D.","family":"Specht","sequence":"additional","affiliation":[{"name":"School of Integrative Plant Science, Section of Plant Biology and the L. H. Bailey Hortorium Cornell University  Ithaca New York 14853 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2023,6,6]]},"reference":[{"key":"e_1_2_9_2_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13007-016-0152-4"},{"key":"e_1_2_9_3_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-017-1213-3"},{"key":"e_1_2_9_4_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1469-8137.2005.01433.x"},{"key":"e_1_2_9_5_1","doi-asserted-by":"publisher","DOI":"10.2144\/btn-2021-0050"},{"key":"e_1_2_9_6_1","doi-asserted-by":"publisher","DOI":"10.1086\/334807"},{"key":"e_1_2_9_7_1","doi-asserted-by":"publisher","DOI":"10.1086\/335014"},{"key":"e_1_2_9_8_1","doi-asserted-by":"publisher","DOI":"10.1086\/335169"},{"key":"e_1_2_9_9_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty149"},{"key":"e_1_2_9_10_1","doi-asserted-by":"publisher","DOI":"10.1034\/j.1600-0706.2000.890201.x"},{"key":"e_1_2_9_11_1","doi-asserted-by":"publisher","DOI":"10.1007\/s10592-005-9073-x"},{"key":"e_1_2_9_12_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/19.6.1349"},{"key":"e_1_2_9_13_1","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evab159"},{"key":"e_1_2_9_14_1","first-page":"3","article-title":"Isolation of DNA from plants with large amounts of secondary metabolites","volume":"395","author":"Friar E. A.","year":"2005","journal-title":"Methods in Enzymology"},{"key":"e_1_2_9_15_1","doi-asserted-by":"publisher","DOI":"10.1111\/jbi.14313"},{"key":"e_1_2_9_16_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.pbi.2012.03.006"},{"key":"e_1_2_9_17_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41597-020-00743-4"},{"key":"e_1_2_9_18_1","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.4060"},{"key":"e_1_2_9_19_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0229345"},{"key":"e_1_2_9_20_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0253830"},{"key":"e_1_2_9_21_1","doi-asserted-by":"publisher","DOI":"10.1002\/aps3.11528"},{"key":"e_1_2_9_22_1","doi-asserted-by":"publisher","DOI":"10.1111\/nph.13471"},{"key":"e_1_2_9_23_1","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365-313X.1993.04020403.x"},{"key":"e_1_2_9_24_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2115640118"},{"key":"e_1_2_9_25_1","doi-asserted-by":"publisher","DOI":"10.1002\/ajb2.1060"},{"key":"e_1_2_9_26_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-019-1693-2"},{"key":"e_1_2_9_27_1","doi-asserted-by":"publisher","DOI":"10.1093\/aob\/mcm326"},{"key":"e_1_2_9_28_1","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-7091-1160-4_19"},{"key":"e_1_2_9_29_1","doi-asserted-by":"publisher","DOI":"10.1002\/aps3.1030"},{"key":"e_1_2_9_30_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13007-020-00579-4"},{"key":"e_1_2_9_31_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41596-020-00424-x"},{"key":"e_1_2_9_32_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.032102"},{"key":"e_1_2_9_33_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41477-021-01031-8"},{"key":"e_1_2_9_34_1","doi-asserted-by":"publisher","DOI":"10.2144\/000114460"},{"key":"e_1_2_9_35_1","doi-asserted-by":"publisher","DOI":"10.3835\/plantgenome2013.03.0001in"},{"key":"e_1_2_9_36_1","doi-asserted-by":"publisher","DOI":"10.4238\/vol10-1gmr1030"},{"key":"e_1_2_9_37_1","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giaa146"},{"key":"e_1_2_9_38_1","doi-asserted-by":"publisher","DOI":"10.3390\/mps2040089"},{"key":"e_1_2_9_39_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.abm8127"},{"key":"e_1_2_9_40_1","doi-asserted-by":"publisher","DOI":"10.1046\/j.1469-8137.2003.00951.x"},{"key":"e_1_2_9_41_1","doi-asserted-by":"publisher","DOI":"10.1111\/nph.12617"},{"key":"e_1_2_9_42_1","doi-asserted-by":"publisher","DOI":"10.1111\/nph.16261"},{"key":"e_1_2_9_43_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.mimet.2020.106054"},{"key":"e_1_2_9_44_1","doi-asserted-by":"publisher","DOI":"10.1080\/23311932.2018.1540094"},{"key":"e_1_2_9_45_1","doi-asserted-by":"publisher","DOI":"10.1017\/qpb.2021.18"},{"key":"e_1_2_9_46_1","first-page":"158","article-title":"Extraction of high\u2010molecular\u2010weight DNA from poplar plants for Nanopore sequencing","volume":"2019","author":"Pushkova E. N.","year":"2019","journal-title":"In Current Challenges in Plant Genetics, Genomics, Bioinformatics, and Biotechnology"},{"key":"e_1_2_9_47_1","unstructured":"R Core Team.2021. R: A language and environment for statistical computing. R Foundation for Statistical Computing Vienna Austria. Website:http:\/\/www.R-project.org\/[accessed 24 March 2023]."},{"key":"e_1_2_9_48_1","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4939-6442-0_16"},{"key":"e_1_2_9_49_1","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2022.883897"},{"key":"e_1_2_9_50_1","doi-asserted-by":"crossref","unstructured":"Russo A. B.Mayjonade andG.Potente.2021. HMW DNA extraction from diverse plants species for PacBio and Nanopore sequencing v1. protocols.iohttps:\/\/doi.org\/10.17504\/protocols.io.5t7g6rn","DOI":"10.17504\/protocols.io.5t7g6rn"},{"key":"e_1_2_9_51_1","doi-asserted-by":"publisher","DOI":"10.5402\/2012\/205049"},{"key":"e_1_2_9_52_1","article-title":"Comparison of R9.4.1\/Kit10 and R10\/Kit12 Oxford Nanopore flowcells and chemistries in bacterial genome reconstruction","volume":"9","author":"Sanderson N. D.","year":"2022","journal-title":"Microbial Genomics"},{"key":"e_1_2_9_53_1","doi-asserted-by":"publisher","DOI":"10.1134\/S1022795418050095"},{"key":"e_1_2_9_54_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0163962"},{"key":"e_1_2_9_55_1","doi-asserted-by":"publisher","DOI":"10.3732\/ajb.90.11.1596"},{"key":"e_1_2_9_56_1","first-page":"113","article-title":"A comparison of DNA extraction methods using Petunia hybrida tissues","volume":"24","author":"Tamari F.","year":"2013","journal-title":"Journal of Biomolecular Techniques"},{"key":"e_1_2_9_57_1","doi-asserted-by":"publisher","DOI":"10.1111\/ede.12369"},{"key":"e_1_2_9_58_1","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2022.874322"},{"key":"e_1_2_9_59_1","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2020.01195"},{"key":"e_1_2_9_60_1","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2021.696669"},{"key":"e_1_2_9_61_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-021-01108-x"},{"key":"e_1_2_9_62_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-019-0217-9"},{"key":"e_1_2_9_63_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13100-017-0102-3"},{"key":"e_1_2_9_64_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.yexcr.2016.12.014"},{"key":"e_1_2_9_65_1","doi-asserted-by":"publisher","DOI":"10.1002\/aps3.11526"},{"key":"e_1_2_9_66_1","doi-asserted-by":"publisher","DOI":"10.3732\/apps.1300070"},{"key":"e_1_2_9_67_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.xpro.2021.100343"}],"container-title":["Applications in Plant Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/bsapubs.onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/aps3.11524","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T01:52:55Z","timestamp":1759974775000},"score":1,"resource":{"primary":{"URL":"https:\/\/bsapubs.onlinelibrary.wiley.com\/doi\/10.1002\/aps3.11524"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,5]]},"references-count":66,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2023,5]]}},"alternative-id":["10.1002\/aps3.11524"],"URL":"https:\/\/doi.org\/10.1002\/aps3.11524","archive":["Portico"],"relation":{},"ISSN":["2168-0450","2168-0450"],"issn-type":[{"value":"2168-0450","type":"print"},{"value":"2168-0450","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,5]]},"assertion":[{"value":"2022-09-30","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2023-01-30","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2023-06-06","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e11524"}}