DOE Joint Genome Institute, Walnut Creek, CA, USA.
BMC Genomics. 2013 Aug 19;14:563. doi: 10.1186/1471-2164-14-563.
Agaves are succulent monocotyledonous plants native to xeric environments of North America. Because of their adaptations to their environment, including crassulacean acid metabolism (CAM, a water-efficient form of photosynthesis), and existing technologies for ethanol production, agaves have gained attention both as potential lignocellulosic bioenergy feedstocks and models for exploring plant responses to abiotic stress. However, the lack of comprehensive Agave sequence datasets limits the scope of investigations into the molecular-genetic basis of Agave traits.
Here, we present comprehensive, high quality de novo transcriptome assemblies of two Agave species, A. tequilana and A. deserti, built from short-read RNA-seq data. Our analyses support completeness and accuracy of the de novo transcriptome assemblies, with each species having a minimum of approximately 35,000 protein-coding genes. Comparison of agave proteomes to those of additional plant species identifies biological functions of gene families displaying sequence divergence in agave species. Additionally, a focus on the transcriptomics of the A. deserti juvenile leaf confirms evolutionary conservation of monocotyledonous leaf physiology and development along the proximal-distal axis.
Our work presents a comprehensive transcriptome resource for two Agave species and provides insight into their biology and physiology. These resources are a foundation for further investigation of agave biology and their improvement for bioenergy development.
龙舌兰是原产于北美的肉质单子叶植物，生长在干旱环境中。由于其对环境的适应，包括景天酸代谢（CAM，一种高效节水的光合作用形式），以及现有的乙醇生产技术，龙舌兰作为潜在的木质纤维素生物能源原料和探索植物对非生物胁迫响应的模型，受到了关注。然而，缺乏全面的龙舌兰序列数据集限制了对龙舌兰特性的分子遗传基础的研究范围。
本文从短读 RNA-seq 数据构建了两种龙舌兰（A. tequilana 和 A. deserti）的综合、高质量的从头转录组组装。我们的分析支持从头转录组组装的完整性和准确性，每个物种至少有大约 35000 个编码蛋白的基因。将龙舌兰蛋白组与其他植物物种的蛋白组进行比较，确定了在龙舌兰物种中显示序列分化的基因家族的生物学功能。此外，对 A. deserti 幼叶转录组的关注证实了单子叶植物叶片生理学和发育在近-远轴上的进化保守性。
本文为两种龙舌兰提供了一个全面的转录组资源，并深入了解了它们的生物学和生理学。这些资源为进一步研究龙舌兰生物学及其在生物能源开发中的改良提供了基础。
