Open Access Highly Accessed Research article

De novo transcriptome assembly of drought tolerant CAM plants, Agave deserti and Agave tequilana

Stephen M Gross12, Jeffrey A Martin12, June Simpson3, María Jazmín Abraham-Juarez3, Zhong Wang12 and Axel Visel12*

Author Affiliations

1 DOE Joint Genome Institute, Walnut Creek, CA, USA

2 Genomics Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA, 94720, USA

3 Department of Genetic Engineering, CINVESTAV, Irapuato, Guanajuato, Mexico

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BMC Genomics 2013, 14:563  doi:10.1186/1471-2164-14-563

Published: 19 August 2013



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.