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Review
. 2017 Dec 28;9(1):6.
doi: 10.3390/genes9010006.

Genome Sequencing and Assembly by Long Reads in Plants

Changsheng Li  1 , Feng Lin  2 , Dong An  3 , Wenqin Wang  4 , Ruidong Huang  5
Affiliations
Review

Genome Sequencing and Assembly by Long Reads in Plants

Changsheng Li et al. Genes (Basel). .

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.

Keywords: Next Generation Sequencing; Sanger sequencing; Third Generation Sequencing; genome assembly; long reads.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
The pipeline of genome assembly and annotation by long reads. gDNA: genomic DNA; cDNA: complementary DNA.
See this image and copyright information in PMC

References

    1. Yuan Y., Bayer P.E., Batley J., Edwards D. Improvements in genomic technologies: Application to crop genomics. Trends Biotechnol. 2017;35:547–558. doi: 10.1016/j.tibtech.2017.02.009. - DOI - PubMed
    1. Velasco R., Zharkikh A., Affourtit J., Dhingra A., Cestaro A., Kalyanaraman A., Fontana P., Bhatnagar S.K., Troggio M., Pruss D., et al. The genome of the domesticated apple (Malus × domestica Borkh.) Nat. Genet. 2010;42:833–839. doi: 10.1038/ng.654. - DOI - PubMed
    1. Argout X., Salse J., Aury J.M., Guiltinan M.J., Droc G., Gouzy J., Allegre M., Chaparro C., Legavre T., Maximova S.N., et al. The genome of Theobroma cacao. Nat. Genet. 2011;43:101–108. doi: 10.1038/ng.736. - DOI - PubMed
    1. Dong J., Feng Y., Kumar D., Zhang W., Zhu T., Luo M.-C., Messing J. Analysis of tandem gene copies in maize chromosomal regions reconstructed from long sequence reads. Proc. Natl. Acad. Sci. USA. 2016;113:7949–7956. doi: 10.1073/pnas.1608775113. - DOI - PMC - PubMed
    1. Paterson A.H., Bowers J.E., Bruggmann R., Dubchak I., Grimwood J., Gundlach H., Haberer G., Hellsten U., Mitros T., Poliakov A., et al. The Sorghum bicolor genome and the diversification of grasses. Nature. 2009;457:551–556. doi: 10.1038/nature07723. - DOI - PubMed

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