Exploring the Genes of Yerba Mate (Ilex paraguariensis A. St.-Hil.) by NGS and De Novo Transcriptome Assembly

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.

Gene expression changes in response to drought stress in Ilex paraguariensis leaves

“…This up-regulation is correlated with a significant increase in SDH activity in the absence of mitochondrial damage (Acevedo et al, 2013). Recently, Debat et al (2014), using NGS and homology sequence searches, have generated a draft transcriptome from an uncharacterized pool of I. paraguariensis leaves.…”

Dataset of the first transcriptome assembly of the tree crop “yerba mate” (Ilex paraguariensis) and systematic characterization of protein coding genes

“…The complete raw sequencing data at SRA under the accession SRP043293 [1], [2] was used to generate a full transcriptome assembly employing the Trinity 2.0.6 platform [4]. All raw sequenced reads were quality filtered and then de novo assembled -using optimal parameters of 25 kmer word and group pairs distance of 500- into 44,840 transcripts (~ 180X coverage) which encompass ca.…”

“…St.-Hil.) by NGS and de novo transcriptome assembly” (Debat et al, 2014) [1]. By means of a bioinformatic approach involving extensive NGS data analyses, we provide a resource encompassing the full transcriptome assembly of yerba mate, the first available reference for the Ilex L. genus.…”

The 18S–25S ribosomal RNA unit of yerba mate (Ilex paraguariensis A. St.-Hil.)

“…Illumina reads from the NCBI Short Read Archive (SRA) database under Accession no. SRP043293 (Debat et al 2014) were relaxedly mapped to a Helianthus annuus L. ribosomal sequence (NCBI Accession no. KF767534), employing the map to reference utility of the Geneious 7.0 software (Geneious assembler, medium sensitivity, iterations up to 5 times).…”

“…The "mate" has a profound socio-cultural influence in Latin America, and particularly in Argentina where its regular intake is superior to that of coffee (OPSM 2009). Recently, through next-generation sequencing (NGS) Debat et al (2014) developed the first genomic resource of yerba mate, characterizing the gene repertoire and generating a vast amount of information for further studies that attempt to reveal the molecular profile of this significant crop.…”