Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2017 May 17:8:826.
doi: 10.3389/fpls.2017.00826. eCollection 2017.

How Single Molecule Real-Time Sequencing and Haplotype Phasing Have Enabled Reference-Grade Diploid Genome Assembly of Wine Grapes

Andrea Minio  1 , Jerry Lin  1 , Brandon S Gaut  2 , Dario Cantu  1
Affiliations

How Single Molecule Real-Time Sequencing and Haplotype Phasing Have Enabled Reference-Grade Diploid Genome Assembly of Wine Grapes

Andrea Minio et al. Front Plant Sci. .
No abstract available

Keywords: cabernet sauvignon; comparative genomics; grape pan-genome; heterozygosity; inbreeding depression.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Comparison of conventional assemblers and their application to the grapevine genome using FALCON-Unzip and its results on Cabernet Sauvignon. (A) A diagram comparing how conventional assemblers and FALCON-Unzip resolve homozygous and heterozygous regions of diploid genomes. (B) Comparison of sequence length distribution between the primary contigs of Cabernet Sauvignon assembled with FALCON-Unzip and other Vitis vinifera genome contig and scaffold assemblies. (C) Distribution of sequence identity between RNAseq reads and reference when mapping is done only on primary contigs or on a combination of primary contigs and haplotigs. (D) Shared coding genes sequences between Cabernet Sauvignon haplotypes and PN40024. Predicted coding sequences from the Cabernet Sauvignon primary contigs were aligned using GMAP (Wu and Watanabe, 2005) to the Cabernet Sauvignon haplotigs and the PN40024 chromosomes to identify the shared part of the represented gene space. Only alignments with identity ≥80% and coverage ≥66% were considered. In similar fashion, coding sequences from the Cabernet Sauvignon haplotigs were aligned against the primary contigs and the PN40024 chromosomes, and coding sequences from PN40024 were aligned against both primary contigs and haplotigs of Cabernet Sauvignon.
See this image and copyright information in PMC

References

    1. Alonso-Blanco C., Andrade J., Becker C., Bemm F., Bergelson J., Borgwardt K. M. M., et al. (2016). 1,135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana. Cell 166, 481–491. 10.1016/j.cell.2016.05.063 - DOI - PMC - PubMed
    1. Argout X., Salse J., Aury J.-M., Guiltinan M. J., Droc G., Gouzy J., et al. (2011). The genome of Theobroma cacao. Nat. Genet. 43, 101–108. 10.1038/ng.736 - DOI - PubMed
    1. Auton A., Abecasis G. R., Altshuler D. M., Durbin R. M., Abecasis G. R., Bentley D. R., et al. (2015). A global reference for human genetic variation. Nature 526, 68–74. 10.1038/nature15393 - DOI - PMC - PubMed
    1. Boursiquot J. M., Lacombe T., Laucou V., Julliard S., Perrin F. X., Lanier N., et al. (2009). Parentage of merlot and related winegrape cultivars of southwestern france: discovery of the missing link. Aust. J. Grape Wine Res. 15, 144–155. 10.1111/j.1755-0238.2008.00041.x - DOI
    1. Bowers J. E., Meredith C. P. (1997). The parentage of a classic wine grape, Cabernet Sauvignon. Nat. Genet. 16, 84–87. 10.1038/ng0597-84 - DOI - PubMed