An Integrated Resource for Genetics and Breeding of Erva/Yerba Mate (Ilex paraguariensis)

The erva/yerba mate tree Ilex paraguariensis is a South American crop significant to the industry and local economies of producer countries. Here, we provide a leading omics integral framework of high-quality annotated markers in yerba mate, notable for its exhaustive employed resources and rigorous curation and validation steps. We assembled the yerba mate nuclear genome (872.9 Mb; BUSCO: 97.3%) using a reference-guided approach, plastome (157.6 Kb), and mitogenome (521.3 Kb) to chromosome level, in addition to nuclear rDNA units 5S (511 bp) and 18S-25S (10,760 bp). The nuclear assembly exhibited 64.9% repetitiveness, while 23.1% corresponded to 41,922 protein-coding genes (PCGs) (BUSCO: 97.1%), with 93.5% mapped to 20 chromosomes and 99.1% supported by joint evidence from RNA-seq (89.1%), orthology in Ilex (84.7%), and functional annotation (92.9%); additionally, 23,089 alternative splice variants for 10,446 genes, 78,992 UTRs for 18,100 genes, and 500 tRNA genes were annotated. Genes were further categorized through description labels, GO terms, KEGG identifiers, EC numbers, structural signatures, pathway identifiers, subcellular localization, and membership in transcription factor families and kinase gene groups. The plastome conformed to the typical Ilex structure, contained 811 repeats and 131 genes (86 PCGs, 37 tRNAs, 8 rRNAs), and featured a single transcript with 53 PCG editing sites. The mitogenome comprised two chromosomes, 2,439 repeats, 65 genes (40 PCGs, 22 tRNAs, 3 rRNAs), and multiple transcripts with 578 PCG editing sites; Ilex mitogenomes showed comparable sequences but lacked synteny. Nuclear rDNA units were further annotated for genes, spacers, transcription-associated sites, and repeats. This comprehensive approach is anticipated to be pivotal for genetics, breeding programs, and downstream genomics research in yerba mate.

Keywords:
chromosome-level genome; plastome; mitogenome; rDNA units; high-quality annotation.

We assembled the yerba mate nuclear genome, plastome, and mitogenome to chromosome level, and also the nuclear rDNAs, to achieve a comprehensively annotated original set of high-quality genetic markers.

These valued original sets of sequences and markers are now openly available to support genetic analyses, breeding programs, and genomics research in this significant crop species.