Nanopore sequencing reads improve assembly and gene annotation of the Parochlus steinenii genome
Parochlus steinenii is a winged midge from King George Island. It is cold-tolerant and endures the harsh Antarctic winter. Previously, we reported the genome of this midge, but the genome assembly with short reads had limited contig contiguity, which reduced the completeness of the genome assembly a...
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ftpubmed:oai:pubmedcentral.nih.gov:6434015 2023-05-15T13:34:38+02:00 Nanopore sequencing reads improve assembly and gene annotation of the Parochlus steinenii genome Shin, Seung Chul Kim, Hyun Lee, Jun Hyuck Kim, Han-Woo Park, Joonho Choi, Beom-Soon Lee, Sang-Choon Kim, Ji Hee Lee, Hyoungseok Kim, Sanghee 2019-03-25 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6434015/ http://www.ncbi.nlm.nih.gov/pubmed/30911035 https://doi.org/10.1038/s41598-019-41549-8 en eng Nature Publishing Group UK http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6434015/ http://www.ncbi.nlm.nih.gov/pubmed/30911035 http://dx.doi.org/10.1038/s41598-019-41549-8 © The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. CC-BY Article Text 2019 ftpubmed https://doi.org/10.1038/s41598-019-41549-8 2019-04-07T00:41:04Z Parochlus steinenii is a winged midge from King George Island. It is cold-tolerant and endures the harsh Antarctic winter. Previously, we reported the genome of this midge, but the genome assembly with short reads had limited contig contiguity, which reduced the completeness of the genome assembly and the annotated gene sets. Recently, assembly contiguity has been increased using nanopore technology. A number of methods for enhancing the low base quality of the assembly have been reported, including long-read (e.g. Nanopolish) or short-read (e.g. Pilon) based methods. Based on these advances, we used nanopore technologies to upgrade the draft genome sequence of P. steinenii. The final assembled genome was 145,366,448 bases in length. The contig number decreased from 9,132 to 162, and the N50 contig size increased from 36,946 to 1,989,550 bases. The BUSCO completeness of the assembly increased from 87.8 to 98.7%. Improved assembly statistics helped predict more genes from the draft genome of P. steinenii. The completeness of the predicted gene model increased from 79.5 to 92.1%, but the numbers and types of the predicted repeats were similar to those observed in the short read assembly, with the exception of long interspersed nuclear elements. In the present study, we markedly improved the P. steinenii genome assembly statistics using nanopore sequencing, but found that genome polishing with high-quality reads was essential for improving genome annotation. The number of genes predicted and the lengths of the genes were greater than before, and nanopore technology readily improved genome information. Text Antarc* Antarctic King George Island PubMed Central (PMC) Antarctic King George Island Scientific Reports 9 1 |
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Article Shin, Seung Chul Kim, Hyun Lee, Jun Hyuck Kim, Han-Woo Park, Joonho Choi, Beom-Soon Lee, Sang-Choon Kim, Ji Hee Lee, Hyoungseok Kim, Sanghee Nanopore sequencing reads improve assembly and gene annotation of the Parochlus steinenii genome |
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Article |
description |
Parochlus steinenii is a winged midge from King George Island. It is cold-tolerant and endures the harsh Antarctic winter. Previously, we reported the genome of this midge, but the genome assembly with short reads had limited contig contiguity, which reduced the completeness of the genome assembly and the annotated gene sets. Recently, assembly contiguity has been increased using nanopore technology. A number of methods for enhancing the low base quality of the assembly have been reported, including long-read (e.g. Nanopolish) or short-read (e.g. Pilon) based methods. Based on these advances, we used nanopore technologies to upgrade the draft genome sequence of P. steinenii. The final assembled genome was 145,366,448 bases in length. The contig number decreased from 9,132 to 162, and the N50 contig size increased from 36,946 to 1,989,550 bases. The BUSCO completeness of the assembly increased from 87.8 to 98.7%. Improved assembly statistics helped predict more genes from the draft genome of P. steinenii. The completeness of the predicted gene model increased from 79.5 to 92.1%, but the numbers and types of the predicted repeats were similar to those observed in the short read assembly, with the exception of long interspersed nuclear elements. In the present study, we markedly improved the P. steinenii genome assembly statistics using nanopore sequencing, but found that genome polishing with high-quality reads was essential for improving genome annotation. The number of genes predicted and the lengths of the genes were greater than before, and nanopore technology readily improved genome information. |
format |
Text |
author |
Shin, Seung Chul Kim, Hyun Lee, Jun Hyuck Kim, Han-Woo Park, Joonho Choi, Beom-Soon Lee, Sang-Choon Kim, Ji Hee Lee, Hyoungseok Kim, Sanghee |
author_facet |
Shin, Seung Chul Kim, Hyun Lee, Jun Hyuck Kim, Han-Woo Park, Joonho Choi, Beom-Soon Lee, Sang-Choon Kim, Ji Hee Lee, Hyoungseok Kim, Sanghee |
author_sort |
Shin, Seung Chul |
title |
Nanopore sequencing reads improve assembly and gene annotation of the Parochlus steinenii genome |
title_short |
Nanopore sequencing reads improve assembly and gene annotation of the Parochlus steinenii genome |
title_full |
Nanopore sequencing reads improve assembly and gene annotation of the Parochlus steinenii genome |
title_fullStr |
Nanopore sequencing reads improve assembly and gene annotation of the Parochlus steinenii genome |
title_full_unstemmed |
Nanopore sequencing reads improve assembly and gene annotation of the Parochlus steinenii genome |
title_sort |
nanopore sequencing reads improve assembly and gene annotation of the parochlus steinenii genome |
publisher |
Nature Publishing Group UK |
publishDate |
2019 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6434015/ http://www.ncbi.nlm.nih.gov/pubmed/30911035 https://doi.org/10.1038/s41598-019-41549-8 |
geographic |
Antarctic King George Island |
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Antarctic King George Island |
genre |
Antarc* Antarctic King George Island |
genre_facet |
Antarc* Antarctic King George Island |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6434015/ http://www.ncbi.nlm.nih.gov/pubmed/30911035 http://dx.doi.org/10.1038/s41598-019-41549-8 |
op_rights |
© The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
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CC-BY |
op_doi |
https://doi.org/10.1038/s41598-019-41549-8 |
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Scientific Reports |
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