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Genes 2018, 9(1), 6; doi:10.3390/genes9010006

Genome Sequencing and Assembly by Long Reads in Plants

1
College of Agronomy, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
2
College of Bioscience and Biotechnology, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
3
School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, China
*
Authors to whom correspondence should be addressed.
Received: 20 November 2017 / Revised: 18 December 2017 / Accepted: 18 December 2017 / Published: 28 December 2017
(This article belongs to the Special Issue Plant Genomics and Epigenomics for Trait Improvement)
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Abstract

Plant genomes generated by Sanger and Next Generation Sequencing (NGS) have provided insight into species diversity and evolution. However, Sanger sequencing is limited in its applications due to high cost, labor intensity, and low throughput, while NGS reads are too short to resolve abundant repeats and polyploidy, leading to incomplete or ambiguous assemblies. The advent and improvement of long-read sequencing by Third Generation Sequencing (TGS) methods such as PacBio and Nanopore have shown promise in producing high-quality assemblies for complex genomes. Here, we review the development of sequencing, introducing the application as well as considerations of experimental design in TGS of plant genomes. We also introduce recent revolutionary scaffolding technologies including BioNano, Hi-C, and 10× Genomics. We expect that the informative guidance for genome sequencing and assembly by long reads will benefit the initiation of scientists’ projects. View Full-Text
Keywords: genome assembly; long reads; Sanger sequencing; Next Generation Sequencing; Third Generation Sequencing genome assembly; long reads; Sanger sequencing; Next Generation Sequencing; Third Generation Sequencing
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Li, C.; Lin, F.; An, D.; Wang, W.; Huang, R. Genome Sequencing and Assembly by Long Reads in Plants. Genes 2018, 9, 6.

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