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

Research output: Contribution to journalArticle

Standard

Finding the missing honey bee genes : lessons learned from a genome upgrade. / Honeybee Genome Sequencing Consortium.

In: BMC Genomics, Vol. 15, 86, 30.01.2014.

Research output: Contribution to journalArticle

Harvard

APA

CBE

MLA

Vancouver

Author

Honeybee Genome Sequencing Consortium. / Finding the missing honey bee genes : lessons learned from a genome upgrade. In: BMC Genomics. 2014 ; Vol. 15.

RIS

TY - JOUR

T1 - Finding the missing honey bee genes

T2 - lessons learned from a genome upgrade

AU - Elsik, Christine G

AU - Worley, Kim C

AU - Bennett, Anna K

AU - Beye, Martin

AU - Camara, Francisco

AU - Childers, Christopher P

AU - de Graaf, Dirk C

AU - Debyser, Griet

AU - Deng, Jixin

AU - Devreese, Bart

AU - Elhaik, Eran

AU - Evans, Jay D

AU - Foster, Leonard J

AU - Graur, Dan

AU - Guigo, Roderic

AU - Hoff, Katharina Jasmin

AU - Holder, Michael E

AU - Hudson, Matthew E

AU - Hunt, Greg J

AU - Jiang, Huaiyang

AU - Joshi, Vandita

AU - Khetani, Radhika S

AU - Kosarev, Peter

AU - Kovar, Christie L

AU - Ma, Jian

AU - Maleszka, Ryszard

AU - Moritz, Robin F A

AU - Munoz-Torres, Monica C

AU - Murphy, Terence D

AU - Muzny, Donna M

AU - Newsham, Irene F

AU - Reese, Justin T

AU - Robertson, Hugh M

AU - Robinson, Gene E

AU - Rueppell, Olav

AU - Solovyev, Victor

AU - Stanke, Mario

AU - Stolle, Eckart

AU - Tsuruda, Jennifer M

AU - Vaerenbergh, Matthias Van

AU - Waterhouse, Robert M

AU - Weaver, Daniel B

AU - Whitfield, Charles W

AU - Wu, Yuanqing

AU - Zdobnov, Evgeny M

AU - Zhang, Lan

AU - Zhu, Dianhui

AU - Gibbs, Richard A

AU - Honeybee Genome Sequencing Consortium

PY - 2014/1/30

Y1 - 2014/1/30

N2 - BACKGROUND: 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.RESULTS: 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.CONCLUSIONS: 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.

AB - BACKGROUND: 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.RESULTS: 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.CONCLUSIONS: 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.

KW - Animals

KW - Base Composition

KW - Bees/genetics

KW - Databases, Genetic

KW - Genes, Insect

KW - Interspersed Repetitive Sequences/genetics

KW - Molecular Sequence Annotation

KW - Open Reading Frames/genetics

KW - Peptides/analysis

KW - Sequence Analysis, RNA

KW - Sequence Homology, Amino Acid

U2 - 10.1186/1471-2164-15-86

DO - 10.1186/1471-2164-15-86

M3 - Article

VL - 15

JO - BMC Genomics

JF - BMC Genomics

SN - 1471-2164

M1 - 86

ER -