油棕基因组结构和功能注释的循证基因模型
Evidence-based gene models for structural and functional annotations of the oil palm genome
摘要：
快速而廉价的DNA测序的出现导致了等待转化为有关基因组组织和功能的知识的数据爆炸。基因预测通常是基因组分析的起点。本文介绍了油棕基因组的生物信息学研究，包括比较基因组学分析，数据库和工具的开发，和挖掘的生物学数据感兴趣的基因。我们已经注释了从两个独立的基因预测管道Fgenesh++和Seqping整合的26，059个油棕基因。与2013年发布的初步注释相比，这一综合注释是一项重大改进。我们对无内含子、抗性和脂肪酸生物合成基因进行了综合分析，并证明了目前基因组注释的高质量。在油棕基因组中发现了3，658个无内含子基因，这是进化研究的重要资源。对油棕基因的进一步分析揭示了210个参与病原体防御的候选抗性基因。脂肪酸具有从食品到工业原料的多种应用，我们确定了42个参与油棕脂肪酸生物合成的关键基因。这些结果为植物基因组研究提供了重要的资源，也为油棕及相关作物的分子标记辅助育种提供了理论基础。
英文摘要：
The advent of rapid and inexpensive DNA sequencing has led to an explosion of data waiting to be transformed into knowledge about genome organization and function. Gene prediction is customarily the starting point for genome analysis. This paper presents a bioinformatics study of the oil palm genome, including comparative genomics analysis, database and tools development, and mining of biological data for genes of interest. We have annotated 26,059 oil palm genes integrated from two independent gene-prediction pipelines, Fgenesh++ and Seqping. This integrated annotation constitutes a significant improvement in comparison to the preliminary annotation published in 2013. We conducted a comprehensive analysis of intronless, resistance and fatty acid biosynthesis genes, and demonstrated that the high quality of the current genome annotation. 3,658 intronless genes were identified in the oil palm genome, an important resource for evolutionary study. Further analysis of the oil palm genes revealed 210 candidate resistance genes involved in pathogen defense. Fatty acids have diverse applications ranging from food to industrial feedstocks, and we identified 42 key genes involved in fatty acid biosynthesis in oil palm. These results provide an important resource for studies of plant genomes and a theoretical foundation for marker-assisted breeding of oil palm and related crops.
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