Finding the missing honey bee genes: lessons learned from a genome upgrade.

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Etat: Public
Version: Final published version
Licence: Non spécifiée
ID Serval
serval:BIB_F59D49CE5B0E
Type
Article: article d'un périodique ou d'un magazine.
Sous-type
Compte-rendu: analyse d'une oeuvre publiée.
Collection
Publications
Titre
Finding the missing honey bee genes: lessons learned from a genome upgrade.
Périodique
BMC Genomics
Auteur⸱e⸱s
Elsik C.G., Worley K.C., Bennett A.K., Beye M., Camara F., Childers C.P., de Graaf D.C., Debyser G., Deng J., Devreese B., Elhaik E., Evans J.D., Foster L.J., Graur D., Guigo R., Hoff K.J., Holder M.E., Hudson M.E., Hunt G.J., Jiang H., Joshi V., Khetani R.S., Kosarev P., Kovar C.L., Ma J., Maleszka R., Moritz R.F., Munoz-Torres M.C., Murphy T.D., Muzny D.M., Newsham I.F., Reese J.T., Robertson H.M., Robinson G.E., Rueppell O., Solovyev V., Stanke M., Stolle E., Tsuruda J.M., Vaerenbergh M.V., Waterhouse R.M., Weaver D.B., Whitfield C.W., Wu Y., Zdobnov E.M., Zhang L., Zhu D., Gibbs R.A.
Collaborateur⸱rice⸱s
HGSC production teams, Honey Bee Genome Sequencing Consortium
ISSN
1471-2164 (Electronic)
ISSN-L
1471-2164
Statut éditorial
Publié
Date de publication
2014
Peer-reviewed
Oui
Volume
15
Pages
86
Langue
anglais
Résumé
The first generation of genome sequence assemblies and annotations have had a significant impact upon our understanding of the biology of the sequenced species, the phylogenetic relationships among species, the study of populations within and across species, and have informed the biology of humans. As only a few Metazoan genomes are approaching finished quality (human, mouse, fly and worm), there is room for improvement of most genome assemblies. The honey bee (Apis mellifera) genome, published in 2006, was noted for its bimodal GC content distribution that affected the quality of the assembly in some regions and for fewer genes in the initial gene set (OGSv1.0) compared to what would be expected based on other sequenced insect genomes.
Here, we report an improved honey bee genome assembly (Amel_4.5) with a new gene annotation set (OGSv3.2), and show that the honey bee genome contains a number of genes similar to that of other insect genomes, contrary to what was suggested in OGSv1.0. The new genome assembly is more contiguous and complete and the new gene set includes ~5000 more protein-coding genes, 50% more than previously reported. About 1/6 of the additional genes were due to improvements to the assembly, and the remaining were inferred based on new RNAseq and protein data.
Lessons learned from this genome upgrade have important implications for future genome sequencing projects. Furthermore, the improvements significantly enhance genomic resources for the honey bee, a key model for social behavior and essential to global ecology through pollination.
Mots-clé
Animals, Base Composition, Bees/genetics, Databases, Genetic, Genes, Insect, Interspersed Repetitive Sequences/genetics, Molecular Sequence Annotation, Open Reading Frames/genetics, Peptides/analysis, Sequence Analysis, RNA, Sequence Homology, Amino Acid
Pubmed
Web of science
Open Access
Oui
Création de la notice
20/09/2017 11:01
Dernière modification de la notice
03/01/2020 19:06
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