{"id":15724,"date":"2022-06-24T13:24:10","date_gmt":"2022-06-24T06:24:10","guid":{"rendered":"https:\/\/bgrssb.icgbio.ru\/2022\/?p=15724"},"modified":"2022-09-20T10:32:31","modified_gmt":"2022-09-20T03:32:31","slug":"genome-assembly-of-colletotrichum-lini-from-long-nanopore-reads","status":"publish","type":"post","link":"https:\/\/bgrssb.icgbio.ru\/2022\/2022\/06\/24\/genome-assembly-of-colletotrichum-lini-from-long-nanopore-reads\/","title":{"rendered":"Genome assembly of Colletotrichum lini from long Nanopore reads"},"content":{"rendered":"<p><em>by Sigova E.A. | Dvorianinova E.M. | Rozhmina T.A. | Kudryavtseva L.P. | Melnikova N.V. | Dmitriev A.A. |<\/em><br \/>\n<em>Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia | Engelhardt<\/em><br \/>\n<em>Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia | Federal Research Center<\/em><br \/>\n<em>for Bast Fiber Crops, Torzhok, Russia<\/em><\/p>\n<p><strong>Motivation and Aim<\/strong>: Colletotrichum lini is the malicious flax anthracnose causative agent.<br \/>\nHowever, the lack of the C. lini whole genome sequence hinders extensive molecular<br \/>\nresearch on the pathogen. Therefore, our aim was to obtain the first genome assembly of C.<br \/>\nlini using the Oxford Nanopore Technologies (ONT) sequencing platform.<br \/>\n<strong>Methods and Algorithms<\/strong>: C. lini highly pathogenic strain #811 was provided by the Institute<br \/>\nfor Flax (Torzhok, Russia). Pure high-molecular DNA was obtained according to our<br \/>\npreviously developed protocol. The spectrophotometry (Nanodrop) and fluorometry (Qubit<br \/>\n4) methods were used to evaluate the quality and quantity of the extracted DNA. DNA<br \/>\nlibraries were prepared and sequenced on the ONT (MinION instrument, FLO-MIN-106<br \/>\nR9.4.1 flow-cell) platform according to the manufacturer\u2019s protocol. The obtained reads<br \/>\nwere bacecalled using Guppy 6.0.1 with different quality filtration thresholds (min_qscore in<br \/>\nrange from 7 to 10). Porechop 0.2.4 was used for adapter removing. Draft assemblies were<br \/>\nperformed using Canu 2.2, Flye 2.8.1, Raven 1.5.1, Shasta 0.8.0, Wtdbg-cns 1.1 (Wtdbg2<br \/>\n0.0), NextDenovo 2.5.0, Miniasm 0.3-r179, Ra 0.2.1, and SmartDenovo tools. BUSCO 5.3.2<br \/>\nand QUAST 5.0.2 were used to analyze the quality of the obtained assemblies.<br \/>\n<strong>Results<\/strong>: We obtained 1.7 Gbases (Gb) of raw ONT reads with an N50 of 15.7 kb. The<br \/>\nassemblers gave better results at lower min qscore values (7-8). The average length of the<br \/>\nassemblies with BUSCO > 80% was 52.2 Mb (48.1-53.5 Mb). Flye produced the most<br \/>\ncontiguous and complete assembly from the ONT data basecalled with min qscore = 7: N50<br \/>\nof 4.4 Mb for a total length of 53.4 Mb, 42 contigs.<br \/>\n<strong>Conclusion<\/strong>: We obtained the first C. lini genome assembly from long ONT reads. This<br \/>\nknowledge is a starting point for further detailed research on C. lini and the flax-pathogen<br \/>\ninteraction.<br \/>\n<strong>Acknowledgements<\/strong>: This work was financially supported by the Russian Science<br \/>\nFoundation, grant 22-16-00169.<\/p>\n<a href=\"https:\/\/bgrssb.icgbio.ru\/2022\/wp-content\/uploads\/sites\/3\/2022\/06\/BGRS-2022_Poster_Sigova_Elizaveta.pdf\" class=\"pdfemb-viewer\" style=\"\" data-width=\"max\" data-height=\"max\"  data-toolbar=\"bottom\" data-toolbar-fixed=\"off\">BGRS-2022_Poster_Sigova_Elizaveta<br\/><\/a>\n","protected":false},"excerpt":{"rendered":"<p>by Sigova E.A. | Dvorianinova E.M. | Rozhmina T.A. | Kudryavtseva L.P. | Melnikova N.V. | Dmitriev A.A. | Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia | Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia | Federal Research Center for Bast Fiber Crops, Torzhok, Russia Motivation and Aim: [&hellip;]<\/p>\n","protected":false},"author":3967,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":[],"categories":[5],"tags":[187,189,190,188],"_links":{"self":[{"href":"https:\/\/bgrssb.icgbio.ru\/2022\/wp-json\/wp\/v2\/posts\/15724"}],"collection":[{"href":"https:\/\/bgrssb.icgbio.ru\/2022\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/bgrssb.icgbio.ru\/2022\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/bgrssb.icgbio.ru\/2022\/wp-json\/wp\/v2\/users\/3967"}],"replies":[{"embeddable":true,"href":"https:\/\/bgrssb.icgbio.ru\/2022\/wp-json\/wp\/v2\/comments?post=15724"}],"version-history":[{"count":1,"href":"https:\/\/bgrssb.icgbio.ru\/2022\/wp-json\/wp\/v2\/posts\/15724\/revisions"}],"predecessor-version":[{"id":15726,"href":"https:\/\/bgrssb.icgbio.ru\/2022\/wp-json\/wp\/v2\/posts\/15724\/revisions\/15726"}],"wp:attachment":[{"href":"https:\/\/bgrssb.icgbio.ru\/2022\/wp-json\/wp\/v2\/media?parent=15724"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/bgrssb.icgbio.ru\/2022\/wp-json\/wp\/v2\/categories?post=15724"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/bgrssb.icgbio.ru\/2022\/wp-json\/wp\/v2\/tags?post=15724"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}