Abstract
Yerba mate (Ilex paraguariensis A. St.-Hil.) is an important subtropical tree crop cultivated on 326,000 ha in Argentina, Brazil and Paraguay, with a total yield production of more than 1,000,000 t. Yerba mate presents a strong limitation regarding sequence information. The NCBI GenBank lacks an EST database of yerba mate and depicts only 80 DNA sequences, mostly uncharacterized. In this scenario, in order to elucidate the yerba mate gene landscape by means of NGS, we explored and discovered a vast collection of I. paraguariensis transcripts. Total RNA from I. paraguariensis was sequenced by Illumina HiSeq-2000 obtaining 72,031,388 pair-end 100 bp sequences. High quality reads were de novo assembled into 44,907 transcripts encompassing 40 million bases with an estimated coverage of 180X. Multiple sequence analysis allowed us to predict that yerba mate contains ∼32,355 genes and 12,551 gene variants or isoforms. We identified and categorized members of more than 100 metabolic pathways. Overall, we have identified ∼1,000 putative transcription factors, genes involved in heat and oxidative stress, pathogen response, as well as disease resistance and hormone response. We have also identified, based in sequence homology searches, novel transcripts related to osmotic, drought, salinity and cold stress, senescence and early flowering. We have also pinpointed several members of the gene silencing pathway, and characterized the silencing effector Argonaute1. We predicted a diverse supply of putative microRNA precursors involved in developmental processes. We present here the first draft of the transcribed genomes of the yerba mate chloroplast and mitochondrion. The putative sequence and predicted structure of the caffeine synthase of yerba mate is presented. Moreover, we provide a collection of over 10,800 SSR accessible to the scientific community interested in yerba mate genetic improvement. This contribution broadly expands the limited knowledge of yerba mate genes, and is presented as the first genomic resource of this important crop.
Highlights
Ilex paraguariensis (Aquifoliaceae) is a dioecious crop tree native to the subtropical rainforest of Northeastern Argentina, Southwestern Brazil and Eastern Paraguay, where it is widely cultivated [1]
In order to shed light on the transcriptional landscape of yerba mate, total RNA was extracted from pooled leaves of I. paraguariensis breeding line Pg538 from INTA EEA-Cerro Azul, Misiones, Argentina
We have identified over 1,000 putative transcription factors of yerba mate (Table S1), 50 transcripts involved in heatstress, more than 200 oxidative stress responsive putative genes, 30 transcripts associated with pathogen response, a significant number of transcripts associated with ribosome constituents, ribosome processing, trafficking, rRNA maturation, and ribosome assembly (Figure S8), as well as 60 assembled transcripts involved in disease resistance and 150 transcripts probably engaged in hormone response (Figure S9)
Summary
Ilex paraguariensis (Aquifoliaceae) is a dioecious crop tree native to the subtropical rainforest of Northeastern Argentina, Southwestern Brazil and Eastern Paraguay, where it is widely cultivated [1]. This evergreen holly is colloquially known as ‘‘yerba mate’’ or ‘‘erva mate’’ as it is mainly consumed as a nutritional and stimulant beverage named ‘‘mate’’, a type of hot infusion made from dried milled leaves and twigs of I. paraguariensis. Yerba mate is an economically important crop cultivated and produced on a total area of more than 326,000 ha [4,5]. To emphasize the relevance of yerba mate in South American tradition and its introduction and dissemination in Argentinean culture, in 2009 a 5,000 people survey projected that while 81% of the Argentinean population consumes coffee, a striking 98% of the population consumes yerba mate [12]
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