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Nanopore sequencing reads improve assembly and gene annotation of the Parochlus steinenii genome

Cited 4 time in wos
Cited 5 time in scopus
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Title
Nanopore sequencing reads improve assembly and gene annotation of the Parochlus steinenii genome
Other Titles
남극 곤충 Parochlus steinenii 유전체 지도의 정밀도 향상
Authors
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
Subject
Science & Technology - Other Topics
Issue Date
2019-03
Citation
Shin, Seung Chul, et al. 2019. "Nanopore sequencing reads improve assembly and gene annotation of the Parochlus steinenii genome". SCIENTIFIC REPORTS, 9(5095): 1-10.
Abstract
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.
URI
https://repository.kopri.re.kr/handle/201206/10891
DOI
http://dx.doi.org/10.1038/s41598-019-41549-8
Appears in Collections  
2019-2019, Application study on the Arctic cold-active enzyme degrading organic carbon compounds (19-19) / Kim, Han-Woo (PN19082)
2018-2018, Modeling responses of terrestrial organisms to environmental changes on King George Island (18-18) / Lee, Hyoungseok (PE18090)
2018-2018, Application study on the Arctic cold-active enzyme degrading organic carbon compounds (18-18) / Kim, Han-Woo (PN18082)
2017-2018, Application study on the Arctic cold-active enzyme degrading organic carbon compounds (17-18) / Lee, Jun Hyuck; Kim, Han-Woo (PN17083; PN18082)
2019-2019, Modeling responses of terrestrial organisms to environmental changes on King George Island (19-19) / Lee, Hyoungseok (PE19090)
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