Finding the missing honey bee genes: lessons learned from a genome upgrade.
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.
Division of Animal Sciences, Division of Plant Sciences, and MU Informatics Institute, University of Missouri, Columbia, MO 65211, USA. elsikc@missouri.edu.
Christine G
CG
Elsik
Kim C
KC
Worley
Anna K
AK
Bennett
Martin
M
Beye
Francisco
F
Camara
Christopher P
CP
Childers
Dirk C
DC
de Graaf
Griet
G
Debyser
Jixin
J
Deng
Bart
B
Devreese
Eran
E
Elhaik
Jay D
JD
Evans
Leonard J
LJ
Foster
Dan
D
Graur
Roderic
R
Guigo
Katharina Jasmin
KJ
Hoff
Michael E
ME
Holder
Matthew E
ME
Hudson
Greg J
GJ
Hunt
Huaiyang
H
Jiang
Vandita
V
Joshi
Radhika S
RS
Khetani
Peter
P
Kosarev
Christie L
CL
Kovar
Jian
J
Ma
Ryszard
R
Maleszka
Robin F A
RF
Moritz
Monica C
MC
Munoz-Torres
Terence D
TD
Murphy
Donna M
DM
Muzny
Irene F
IF
Newsham
Justin T
JT
Reese
Hugh M
HM
Robertson
Gene E
GE
Robinson
Olav
O
Rueppell
Victor
V
Solovyev
Mario
M
Stanke
Eckart
E
Stolle
Jennifer M
JM
Tsuruda
Matthias Van
MV
Vaerenbergh
Robert M
RM
Waterhouse
Daniel B
DB
Weaver
Charles W
CW
Whitfield
Yuanqing
Y
Wu
Evgeny M
EM
Zdobnov
Lan
L
Zhang
Dianhui
D
Zhu
Richard A
RA
Gibbs
D000818:Animals; D001482:Base Composition; D001516:Bees / Q000235:genetics*; D030541:Databases, Genetic; D017344:Genes, Insect; D020071:Interspersed Repetitive Sequences / Q000235:genetics; D058977:Molecular Sequence Annotation; D016366:Open Reading Frames / Q000235:genetics; D010455:Peptides / Q000032:analysis; D017423:Sequence Analysis, RNA; D017386:Sequence Homology, Amino Acid
D010455:Peptides