publication . Article . Other literature type . 2014

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

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.; ...
Closed Access
  • Published: 30 Jan 2014 Journal: BMC genomics, volume 15, pages 86-86
Abstract
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 s...
Subjects
free text keywords: 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, Biology and Life Sciences, OPEN READING FRAMES, APIS-MELLIFERA, TRANSPOSABLE ELEMENTS, CLASSIFICATION-SYSTEM, PROTEIN FAMILIES, DOMAIN DATABASE, TANDEM REPEATS, DNA-SEQUENCES, SOCIAL INSECT, DRAFT GENOME, Abelles, Genètica molecular, Seqüència d'aminoàcids, ddc:576.5, Research Article, Apis mellifera, GC content, Gene annotation, Gene prediction, Genome assembly, Genome improvement, Genome sequencing, Repetitive DNA, Transcriptome, Apis mellifera; GC content; Gene annotation; Gene prediction; Genome assembly; Genome improvement; Genome sequencing; Repetitive DNA; Transcriptome, Biotechnology, Genetics
Funded by
NIH| Genomes and Genetics at the BCM-HGSC
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 3U54HG003273-04S1
  • Funding stream: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
,
SNSF| Insect (meta)genomics
Project
  • Funder: Swiss National Science Foundation (SNSF)
  • Project Code: 31003A_143936
  • Funding stream: Project funding | Project funding (Div. I-III)
121 references, page 1 of 9

1. Honey Bee Genome Sequencing Consortium: Insights into social insects from the genome of the honeybee Apis mellifera. Nature 2006, 443:931-949. [OpenAIRE]

2. Zayed A, Robinson GE: Understanding the relationship between brain gene expression and social behavior: lessons from the honey bee. Annu Rev Genet 2012, 46:591-615.

3. Begna D, Han B, Feng M, Fang Y, Li J: Differential expressions of nuclear proteomes between honeybee (Apis mellifera L.) queen and worker larvae: a deep insight into caste pathway decisions. J Proteome Res 2012, 11:1317-1329.

4. Cornman RS, Tarpy DR, Chen Y, Jeffreys L, Lopez D, Pettis JS, vanEngelsdorp D, Evans JD: Pathogen webs in collapsing honey bee colonies. PLoS ONE 2012, 7:e43562.

5. Foret S, Kucharski R, Pellegrini M, Feng S, Jacobsen SE, Robinson GE, Maleszka R: DNA methylation dynamics, metabolic fluxes, gene splicing, and alternative phenotypes in honey bees. Proc Natl Acad Sci USA 2012, 109:4968-4973. [OpenAIRE]

6. Li-Byarlay H, Li Y, Stroud H, Feng S, Newman TC, Kaneda M, Hou KK, Worley KC, Elsik CG, Wickline SA, et al: RNA interference knockdown of DNA methyltransferase 3 affects gene alternative splicing in the honey bee. Proc Nat Aca Sci USA 2013, 110:12750-12755.

7. Calderone NW: Insect pollinated crops, insect pollinators and US agriculture: trend analysis of aggregate data for the period 1992-2009. PLos One 2012, 7:e37235.

8. Gallai N, Salles JM, Settele J, Vaissière BE: Economic valuation of the vulnerability of world agriculture confronted with pollinator decline. Ecol Econ 2009, 68:810-821. [OpenAIRE]

9. Alaux C, Dantec C, Parrinello H, Le Conte Y: Nutrigenomics in honey bees: digital gene expression analysis of pollen's nutritive effects on healthy and varroa-parasitized bees. BMC Genomics 2011, 12:496. [OpenAIRE]

10. Johnson RM, Mao W, Pollock HS, Niu G, Schuler MA, Berenbaum MR: Ecologically appropriate xenobiotics induce cytochrome P450s in Apis Mellifera. PLoS ONE 2012, 7:e31051.

11. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, et al: Initial sequencing and analysis of the human genome. Nature 2001, 409:860-921. [OpenAIRE]

12. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, et al: The sequence of the human genome. Science 2001, 291:1304-1351.

13. Church DM, Goodstadt L, Hillier LW, Zody MC, Goldstein S, She X, Bult CJ, Agarwala R, Cherry JL, DiCuccio M, et al: Lineage-specific biology revealed by a finished genome assembly of the mouse. PLoS Biol 2009, 7:e1000112. [OpenAIRE]

14. International Human Genome Sequencing Consortium: Finishing the euchromatic sequence of the human genome. Nature 2004, 431:931-945.

15. Celniker SE, Wheeler DA, Kronmiller B, Carlson JW, Halpern A, Patel S, Adams M, Champe M, Dugan SP, Frise E, et al: Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence. Genome Biol 2002, 3:RESEARCH0079.

121 references, page 1 of 9
Abstract
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 s...
Subjects
free text keywords: 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, Biology and Life Sciences, OPEN READING FRAMES, APIS-MELLIFERA, TRANSPOSABLE ELEMENTS, CLASSIFICATION-SYSTEM, PROTEIN FAMILIES, DOMAIN DATABASE, TANDEM REPEATS, DNA-SEQUENCES, SOCIAL INSECT, DRAFT GENOME, Abelles, Genètica molecular, Seqüència d'aminoàcids, ddc:576.5, Research Article, Apis mellifera, GC content, Gene annotation, Gene prediction, Genome assembly, Genome improvement, Genome sequencing, Repetitive DNA, Transcriptome, Apis mellifera; GC content; Gene annotation; Gene prediction; Genome assembly; Genome improvement; Genome sequencing; Repetitive DNA; Transcriptome, Biotechnology, Genetics
Funded by
NIH| Genomes and Genetics at the BCM-HGSC
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 3U54HG003273-04S1
  • Funding stream: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
,
SNSF| Insect (meta)genomics
Project
  • Funder: Swiss National Science Foundation (SNSF)
  • Project Code: 31003A_143936
  • Funding stream: Project funding | Project funding (Div. I-III)
121 references, page 1 of 9

1. Honey Bee Genome Sequencing Consortium: Insights into social insects from the genome of the honeybee Apis mellifera. Nature 2006, 443:931-949. [OpenAIRE]

2. Zayed A, Robinson GE: Understanding the relationship between brain gene expression and social behavior: lessons from the honey bee. Annu Rev Genet 2012, 46:591-615.

3. Begna D, Han B, Feng M, Fang Y, Li J: Differential expressions of nuclear proteomes between honeybee (Apis mellifera L.) queen and worker larvae: a deep insight into caste pathway decisions. J Proteome Res 2012, 11:1317-1329.

4. Cornman RS, Tarpy DR, Chen Y, Jeffreys L, Lopez D, Pettis JS, vanEngelsdorp D, Evans JD: Pathogen webs in collapsing honey bee colonies. PLoS ONE 2012, 7:e43562.

5. Foret S, Kucharski R, Pellegrini M, Feng S, Jacobsen SE, Robinson GE, Maleszka R: DNA methylation dynamics, metabolic fluxes, gene splicing, and alternative phenotypes in honey bees. Proc Natl Acad Sci USA 2012, 109:4968-4973. [OpenAIRE]

6. Li-Byarlay H, Li Y, Stroud H, Feng S, Newman TC, Kaneda M, Hou KK, Worley KC, Elsik CG, Wickline SA, et al: RNA interference knockdown of DNA methyltransferase 3 affects gene alternative splicing in the honey bee. Proc Nat Aca Sci USA 2013, 110:12750-12755.

7. Calderone NW: Insect pollinated crops, insect pollinators and US agriculture: trend analysis of aggregate data for the period 1992-2009. PLos One 2012, 7:e37235.

8. Gallai N, Salles JM, Settele J, Vaissière BE: Economic valuation of the vulnerability of world agriculture confronted with pollinator decline. Ecol Econ 2009, 68:810-821. [OpenAIRE]

9. Alaux C, Dantec C, Parrinello H, Le Conte Y: Nutrigenomics in honey bees: digital gene expression analysis of pollen's nutritive effects on healthy and varroa-parasitized bees. BMC Genomics 2011, 12:496. [OpenAIRE]

10. Johnson RM, Mao W, Pollock HS, Niu G, Schuler MA, Berenbaum MR: Ecologically appropriate xenobiotics induce cytochrome P450s in Apis Mellifera. PLoS ONE 2012, 7:e31051.

11. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, et al: Initial sequencing and analysis of the human genome. Nature 2001, 409:860-921. [OpenAIRE]

12. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, et al: The sequence of the human genome. Science 2001, 291:1304-1351.

13. Church DM, Goodstadt L, Hillier LW, Zody MC, Goldstein S, She X, Bult CJ, Agarwala R, Cherry JL, DiCuccio M, et al: Lineage-specific biology revealed by a finished genome assembly of the mouse. PLoS Biol 2009, 7:e1000112. [OpenAIRE]

14. International Human Genome Sequencing Consortium: Finishing the euchromatic sequence of the human genome. Nature 2004, 431:931-945.

15. Celniker SE, Wheeler DA, Kronmiller B, Carlson JW, Halpern A, Patel S, Adams M, Champe M, Dugan SP, Frise E, et al: Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence. Genome Biol 2002, 3:RESEARCH0079.

121 references, page 1 of 9
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publication . Article . Other literature type . 2014

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

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.; ...