Finding the missing honey bee genes: lessons learned from a genome upgrade
Finding the missing honey bee genes: lessons learned from a genome upgrade
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DOI：
10.1186/1471-2164-15-86
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发表时间：
2014-01-30
期刊：
影响因子：
4.4
通讯作者：
Gibbs, Richard A.
中科院分区：
文献类型：
--
作者：
Elsik, Christine G.;Worley, Kim C.;Gibbs, Richard A.
背景：第一代基因组序列组装和注释对我们理解被测序物种的生物学、物种之间的系统发育关系、物种内和物种间的种群研究以及人类生物学产生了重大影响。由于只有少数后生动物基因组接近完成质量（人类、小鼠、苍蝇和蠕虫），大多数基因组组装还有改进的空间。2006年发表的蜜蜂（Apis mellifera）基因组以其双峰GC含量分布而闻名，该分布影响了某些区域的组装质量，并且与基于其他测序昆虫基因组的预期相比，初始基因集（OGSv1.0）中的基因较少。结果：在此，我们报告了一个新的基因注释集（OGSv3.2）改进的蜜蜂基因组组装（Amel_4.5），并表明蜜蜂基因组包含许多与其他昆虫基因组相似的基因，这与OGSv1.0中提出的相反。新的基因组组装更加连续和完整，新的基因集包括大约5000个蛋白质编码基因，比以前报道的多50%。大约1/6的额外基因是由于组装的改进，其余的是根据新的RNAseq和蛋白质数据推断出来的。结论：从这次基因组升级中获得的经验教训对未来的基因组测序项目具有重要意义。此外，这些改进显著增加了蜜蜂的基因组资源，蜜蜂是社会行为的关键模型，通过授粉对全球生态至关重要。
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 similar to 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.