Department of Genetics ETSIAM, University of Córdoba, Córdoba, Spain.
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD, 20894, USA.
BMC Genomics. 2019 Jul 18;20(1):591. doi: 10.1186/s12864-019-5952-2.
During the last decade, plant biotechnological laboratories have sparked a monumental revolution with the rapid development of next sequencing technologies at affordable prices. Soon, these sequencing technologies and assembling of whole genomes will extend beyond the plant computational biologists and become commonplace within the plant biology disciplines. The current availability of large-scale genomic resources for non-traditional plant model systems (the so-called 'orphan crops') is enabling the construction of high-density integrated physical and genetic linkage maps with potential applications in plant breeding. The newly available fully sequenced plant genomes represent an incredible opportunity for comparative analyses that may reveal new aspects of genome biology and evolution. The analysis of the expansion and evolution of gene families across species is a common approach to infer biological functions. To date, the extent and role of gene families in plants has only been partially addressed and many gene families remain to be investigated. Manual identification of gene families is highly time-consuming and laborious, requiring an iterative process of manual and computational analysis to identify members of a given family, typically combining numerous BLAST searches and manually cleaning data. Due to the increasing abundance of genome sequences and the agronomical interest in plant gene families, the field needs a clear, automated annotation tool.
Here, we present the geneHummus package, an R-based pipeline for the identification and characterization of plant gene families. The impact of this pipeline comes from a reduction in hands-on annotation time combined with high specificity and sensitivity in extracting only proteins from the RefSeq database and providing the conserved domain architectures based on SPARCLE. As a case study we focused on the auxin receptor factors gene (ARF) family in Cicer arietinum (chickpea) and other legumes.
We anticipate that our pipeline should be suitable for any taxonomic plant family, and likely other gene families, vastly improving the speed and ease of genomic data processing.
在过去的十年中，随着价格合理的下一代测序技术的快速发展，植物生物技术实验室引发了一场巨大的革命。很快，这些测序技术和整个基因组的组装将超越植物计算生物学家的范畴，在植物生物学领域变得司空见惯。目前，非传统植物模式系统（所谓的“孤儿作物”）的大规模基因组资源的可用性正在使构建具有高密度整合物理和遗传连锁图谱成为可能，这些图谱具有在植物育种中的潜在应用。新获得的全序列植物基因组为比较分析提供了一个极好的机会，这可能揭示基因组生物学和进化的新方面。跨物种基因家族的扩张和进化分析是推断生物学功能的常用方法。迄今为止，植物中基因家族的范围和作用仅部分得到解决，许多基因家族仍有待研究。基因家族的手动鉴定非常耗时且费力，需要手动和计算分析的迭代过程来识别给定家族的成员，通常需要结合多次 BLAST 搜索并手动清理数据。由于基因组序列的大量增加以及植物基因家族在农业方面的兴趣，该领域需要一个清晰、自动化的注释工具。
在这里，我们介绍了 geneHummus 包，这是一种基于 R 的植物基因家族鉴定和特征分析的管道。该管道的影响来自于手动注释时间的减少，同时在从 RefSeq 数据库中提取仅蛋白质方面具有高度的特异性和敏感性，并基于 SPARCLE 提供保守结构域架构。作为一个案例研究，我们专注于鹰嘴豆（鹰嘴豆）和其他豆科植物中的生长素受体因子（ARF）基因家族。
我们预计我们的管道应该适用于任何分类植物家族，并且可能适用于其他基因家族，极大地提高了基因组数据处理的速度和易用性。
