Comparative analysis of grapevine whole-genome gene predictions, functional annotation, categorization and integration of the predicted gene sequences.

BMC Research Notes
Jérôme GrimpletJosé M Martínez-Zapater

Abstract

The first draft assembly and gene prediction of the grapevine genome (8X base coverage) was made available to the scientific community in 2007, and functional annotation was developed on this gene prediction. Since then additional Sanger sequences were added to the 8X sequences pool and a new version of the genomic sequence with superior base coverage (12X) was produced. In order to more efficiently annotate the function of the genes predicted in the new assembly, it is important to build on as much of the previous work as possible, by transferring 8X annotation of the genome to the 12X version. The 8X and 12X assemblies and gene predictions of the grapevine genome were compared to answer the question, "Can we uniquely map 8X predicted genes to 12X predicted genes?" The results show that while the assemblies and gene structure predictions are too different to make a complete mapping between them, most genes (18,725) showed a one-to-one relationship between 8X predicted genes and the last version of 12X predicted genes. In addition, reshuffled genomic sequence structures appeared. These highlight regions of the genome where the gene predictions need to be taken with caution. Based on the new grapevine gene functional annotation ...Continue Reading

References

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Citations

Aug 7, 2013·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Lukasz GrzeskowiakM Stella Grando
May 11, 2013·Plant & Cell Physiology·Pablo Carbonell-BejeranoJosé M Martínez-Zapater
Oct 6, 2012·BMC Plant Biology·José Díaz-RiquelmeMaría J Carmona
Mar 29, 2014·BMC Plant Biology·Pablo Carbonell-BejeranoJosé Miguel Martínez-Zapater
Dec 18, 2013·BMC Genomics·Darren C J WongChristopher M Ford
Dec 4, 2013·Plant Physiology and Biochemistry : PPB·Patricia Agudelo-RomeroAna M Fortes
Nov 6, 2015·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Javier TelloJavier Ibáñez
Jan 29, 2016·BMC Genomics·Jérôme GrimpletMaría José Carmona
Nov 20, 2015·Frontiers in Plant Science·Anne Y FennellKatherine L Mathiason
Nov 28, 2012·The Plant Journal : for Cell and Molecular Biology·Lucie FernandezLaurent Torregrosa
Jun 14, 2015·Journal of Experimental Botany·Laura CostantiniMaria Stella Grando
Dec 17, 2014·BMC Genomics·Miguel Jesus Nunes RamosMargarida Rocheta
Dec 17, 2014·BMC Genomics·Simona AbbàCristina Marzachì
Dec 8, 2014·BMC Genomics·Jérôme GrimpletGrant R Cramer
Mar 26, 2015·Plant Science : an International Journal of Experimental Plant Biology·Michaela GriesserAstrid Forneck
Feb 14, 2015·Journal of Experimental Botany·Patricia Agudelo-RomeroAna Margarida Fortes
Dec 3, 2014·Plant Science : an International Journal of Experimental Plant Biology·Dennis J GraySadanand A Dhekney
Dec 30, 2014·Frontiers in Plant Science·Iniga S George, Paul A Haynes
Dec 30, 2014·Frontiers in Plant Science·Sushma NaithaniPankaj Jaiswal
Oct 15, 2014·PloS One·Lorena AlmagroMaría A Pedreño
Jun 1, 2016·Frontiers in Plant Science·Marco MorettoKristof Engelen
Jul 16, 2016·The Plant Journal : for Cell and Molecular Biology·Maria Francesca CardoneDonato Antonacci
Feb 3, 2016·Scientific Reports·Vitantonio PantaleoGiorgio Gambino
Jan 18, 2018·Plant, Cell & Environment·Karlia MeithaMichael J Considine

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Software Mentioned

GAZE
Megablast
BLAST
JIGSAW
VitisNet
Funcat

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