High-quality genome assembly of the silkworm, Bombyx mori

Insect Biochemistry and Molecular Biology
Munetaka KawamotoToru Shimada

Abstract

In 2008, the genome assembly and gene models for the domestic silkworm, Bombyx mori, were published by a Japanese and Chinese collaboration group. However, the genome assembly contains a non-negligible number of misassembled and gap regions due to the presence of many repetitive sequences within the silkworm genome. The erroneous genome assembly occasionally causes incorrect gene prediction. Here we performed hybrid assembly based on 140 × deep sequencing of long (PacBio) and short (Illumina) reads. The remaining gaps in the initial genome assembly were closed using BAC and Fosmid sequences, giving a new total length of 460.3 Mb, with 30 gap regions and an N50 comprising 16.8 Mb in scaffolds and 12.2 Mb in contigs. More RNA-seq and piRNA-seq reads were mapped on the new genome assembly compared with the previous version, indicating that the new genome assembly covers more transcribed regions, including repetitive elements. We performed gene prediction based on the new genome assembly using available mRNA and protein sequence data. The number of gene models was 16,880 with an N50 of 2154 bp. The new gene models reflected more accurate coding sequences and gene sets than old ones. The proportion of repetitive elements was also re...Continue Reading

Citations

Nov 14, 2019·International Journal of Molecular Sciences·Meirong ZhangGuozheng Zhang
Dec 15, 2019·Database : the Journal of Biological Databases and Curation·Zhenglin ZhuZe Zhang
May 24, 2020·Molecular Ecology Resources·Jianping DuanXiangwei Wu
Apr 2, 2020·Scientific Reports·Shou-Min FangZe Zhang
Jan 31, 2020·Nature·Natsuko IzumiYukihide Tomari
Oct 24, 2019·Nucleic Acids Research·Fang LuYi Wang
Oct 31, 2020·Current Biology : CB·Aruni P SenaratneInes A Drinnenberg
Jan 13, 2021·Current Biology : CB·Reto Gassmann
Jan 29, 2021·Database : the Journal of Biological Databases and Curation·X I ChenFei Li
Jan 28, 2021·Molecular Biology and Evolution·Qian CongNick V Grishin
Feb 6, 2021·International Journal of Molecular Sciences·Weizhen SunXiubo Zhao
Feb 10, 2021·G3 : Genes - Genomes - Genetics·Ariel GershmanWinston Timp
Oct 15, 2020·Molecular Ecology Resources·Xianxin ZhaoFei Li
Feb 8, 2020·Current Biology : CB·Nuria Cortes-SilvaInes A Drinnenberg
Mar 2, 2021·Database : the Journal of Biological Databases and Curation·Ching-Chia YangAkiya Jouraku
Feb 20, 2021·PeerJ·Linrong WanUNKNOWN members of the Genefang Research Team: Zi-yan Huang, Cong-fan Bu, Jie Zeng, Zhao-nan Hao, Yan-peng Chen, and Meng-jia Liu
Mar 7, 2021·Journal of Fungi·Yidong YuAndreas Beilhack
Feb 20, 2021·Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics·Chenjie YangQiaoling Zhao
Jun 30, 2021·Virus Genes·Keisuke ShojiSusumu Katsuma
Jul 3, 2021·Insects·Kakeru YokoiHidemasa Bono
Jun 13, 2021·Genome Biology and Evolution·James J LewisStephen H Montgomery
Jul 27, 2021·Acta Biomaterialia·Yutian LeiZhaoming Dong

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