Rapid construction of genome map for large yellow croaker Larimichthys crocea by the whole-genome mapping in BioNano Genomics Irys systemReport as inadecuate




Rapid construction of genome map for large yellow croaker Larimichthys crocea by the whole-genome mapping in BioNano Genomics Irys system - Download this document for free, or read online. Document in PDF available to download.

BMC Genomics

, 16:670

Non-human and non-rodent vertebrate genomics

Abstract

BackgroundLarge 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.

ResultsFor 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 Mb. The excellent hybrid alignment with large yellow croaker draft genome validated the consensus genome map assembly and highlighted a promising application of whole-genome mapping on draft genome sequence super-scaffolding. The genome map data of large yellow croaker are accessible on lycgenomics.jmu.edu.cn-pm.

ConclusionUsing the state-of-the-art whole-genome mapping technique in Irys system, the first whole-genome map for large yellow croaker has been constructed and thus highly facilitates the ongoing genomic and evolutionary studies for the species. To our knowledge, this is the first public report on genome map construction by the whole-genome mapping for aquatic-organisms. Our study demonstrates a promising application of the whole-genome mapping on genome maps construction for other non-model organisms in a fast and reliable manner.

KeywordsLarge yellow croaker Gene map Whole-genome mapping Genome assembly AbbreviationsAFLPAmplified fragment length polymorphism

GWASGenome-wide association studies

NGSNext Generation Sequencing

BPPBases per pixel

PMBCsPeripheral mononuclear cells

CVCoefficient of variation

PFGEPulsed field gel electrophoresis

FPFalse positive

FNFalse negative

Electronic supplementary materialThe online version of this article doi:10.1186-s12864-015-1871-z contains supplementary material, which is available to authorized users.

Download fulltext PDF



Author: Shijun Xiao - Jiongtang Li - Fengshou Ma - Lujing Fang - Shuangbin Xu - Wei Chen - Zhi Yong Wang

Source: https://link.springer.com/



DOWNLOAD PDF




Related documents