Rapid construction of genome map for large yellow croaker (Larimichthys crocea) by the whole-genome mapping in BioNano Genomics Irys system

BMC Genomics
Shijun XiaoZhi Yong Wang

Abstract

Large yellow croaker (Larimichthys crocea) is an important commercial fish in China and East-Asia. The annual product of the species from the aqua-farming industry is about 90 thousand tons. In spite of its economic importance, genetic studies of economic traits and genomic selections of the species are hindered by the lack of genomic resources. Specifically, a whole-genome physical map of large yellow croaker is still missing. The traditional BAC-based fingerprint method is extremely time- and labour-consuming. Here we report the first genome map construction using the high-throughput whole-genome mapping technique by nanochannel arrays in BioNano Genomics Irys system. For an optimal marker density of ~10 per 100 kb, the nicking endonuclease Nt.BspQ1 was chosen for the genome map generation. 645,305 DNA molecules with a total length of ~112 Gb were labelled and detected, covering more than 160X of the large yellow croaker genome. Employing IrysView package and signature patterns in raw DNA molecules, a whole-genome map of large yellow croaker was assembled into 686 maps with a total length of 727 Mb, which was consistent with the estimated genome size. The N50 length of the whole-genome map, including 126 maps, was up to 1.7 M...Continue Reading

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Citations

Apr 27, 2016·Genomics Data·Christopher P JenkinsonRalph A DeFronzo
Jan 18, 2017·Lab on a Chip·Vilhelm Müller, Fredrik Westerlund
Jun 13, 2017·Bioinformatics·Yuxuan YuanDavid Edwards
Dec 14, 2017·Botanical Studies·Wen-Chieh TsaiHong-Hwa Chen
Dec 24, 2019·Algorithms for Molecular Biology : AMB·Martin D MuggliChristina Boucher
Aug 18, 2020·Computational and Structural Biotechnology Journal·Yuxuan YuanTing-Fung Chan

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Methods Mentioned

BETA
flow cytometry
PCR
density gradient centrifugation
electrophoresis
chips

Software Mentioned

Irys system
R package of fastcluster
Assembler
IrysView
IrysView package
BioNano Genomics Irys
Irys
RefAligner

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