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

Stephen M Gross,María Jazmín Abraham-Juarez,Zhong Wang,June Simpson,Jeffrey A Martin,Axel Visel

doi:10.1186/1471-2164-14-563

Abstract

BackgroundAgaves 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.ResultsHere, 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.ConclusionsOur 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.

Highlights

Agaves are succulent monocotyledonous plants native to xeric environments of North America
Deep sequencing of Agave tissues captures the majority of Agave transcripts Both A. tequilana and A. deserti spend the majority of their 5–10 year lifespan as vegetative rosettes (Figure 1A, 1B) before a single flowering event followed by rapid senescence [5]. mRNA was harvested from various Agave tissues (Additional file 1: Table S1, Figure S1), and strandspecific cDNA sequencing libraries of specific insert sizes were prepared for Illumina sequencing (Methods)
To assess coverage of the agave transcriptomes, we plotted the frequency of observing a new unique 25-mer sequence over an increasing number of randomly sampled reads

Summary

Introduction

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. The lack of genomic and transcriptomic sequence information for agaves, succulent plants native to the arid regions of North America, limits molecular investigation of their adaptations to the abiotic stresses of xeric environments. Subject of numerous ecological and physiological studies [reviewed in 19], is native to the Sonoran Desert regions of the Southwestern United States and Northwestern Mexico [5] and grows within elevation ranges that experience both hot, dry summers and occasional freezing temperatures in winter [20,21]. While A. deserti is comparatively smaller and slowergrowing than A. tequilana, it provides a valuable model to study molecular and physiological mechanisms of plant drought and heat resistance [19,24,25]

Methods

Results

Conclusion