The complete organellar genomes of the entheogenic plant Psychotria viridis (Rubiaceae), a main component of the ayahuasca brew

Abstract

Psychotria viridis (Rubioideae: Rubiaceae), popularly known as chacrona, is commonly found as a shrub in the Amazon region and is well-known to produce psychoactive compounds, such as the N,N-dimethyltryptamine (DMT). Together with the liana Banisteropsis caapi, P. viridis is one of the main components of the Amerindian traditional, entheogenic beverage known as ayahuasca. In this work, we assembled and annotated the organellar genomes (ptDNA and mtDNA), presenting the first genomics resources for this species. The P. viridis ptDNA exhibits 154,106 bp, encoding all known ptDNA gene repertoire found in angiosperms. The Psychotria genus is a complex paraphyletic group, and according to phylogenomic analyses, P. viridis is nested in the Psychotrieae clade. Comparative ptDNA analyses indicate that most Rubiaceae plastomes present conserved ptDNA structures, often showing slight differences at the junction sites of the major four regions (LSC-IR-SSC). For the mitochondrion, assembly graph-based analysis supports a complex mtDNA organization, presenting at least two alternative and circular mitogenomes structures exhibiting two main repeats spanning 24 kb and 749 bp that may symmetrically isomerize the mitogenome into variable arrangements and isoforms. The circular mtDNA sequences (615,370 and 570,344 bp) encode almost all plant mitochondrial genes (except for the ccmC, rps7, rps10, rps14, rps19, rpl2 and rpl16 that appears as pseudogenes, and the absent genes sdh3, rps2, rsp4, rsp8, rps11, rpl6, and rpl10), showing slight variations related to exclusive regions, ptDNA integration, and relics of previous events of LTR-RT integration. The detection of two mitogenomes haplotypes is evidence of heteroplasmy as observed by the complex organization of the mitochondrial genome using graph-based analysis. Taken together, these results elicit the primary insights into the genome biology and evolutionary history of Psychotria viridis and may be used to aid strategies for conservation of this sacred, entheogenic species.

Characterization and phylogenetic analysis of the chloroplast genome of galium spurium

“… 2020 ), Oldenlandia brachypoda NC057984 (Varani et al. 2022 ), Oldenlandia corymbosa NC057983 (Varani et al. 2022 ), Pentas lanceolata KY378685 (Wikström et al.…”

“… 2022 ), Oldenlandia corymbosa NC057983 (Varani et al. 2022 ), Pentas lanceolata KY378685 (Wikström et al. 2020 ), Galium aparine KY562587 (Dann et al.…”

“… 2017 ), Pseudogalium paradoxum OK236360 (Varani et al. 2022 ), Rubia cordifolia NC047470 (Zhao et al. 2020 ), Rubia yunnanensis OL467345 (Wang et al.…”

The mitogenomic landscape of Banisteriopsis caapi (Malpighiaceae), the sacred liana used for ayahuasca preparation

“…The procedures involved in gathering, storing, DNA extraction, validating, sequencing and assembling the mtDNA were conducted following the same approach outlined in our previous study ( Varani et al, 2022 ). In summary, one PacBio Sequel II SMRT cell was generated.…”

Genetic diversity of Coffea arabica L. mitochondrial genomes caused by repeat- mediated recombination and RNA editing

“…Oldenlandia corymbosa’s smaller mitochondrial genome size compared to other family members indicates variations in size and content within the Rubiaceae species ( Julca et al., 2023 ). The intricacies of the Psychotria viridis mitochondrial genome, presented through multiple mitogenome structures and evidence of heteroplasmy, enrich our understanding of mitochondrial genome organization ( Varani et al., 2022 ). Meanwhile, the mitogenome of Scyphiphora hydrophyllacea stands out due to its intricate intron content and its phylogenetic positioning within the Gentianales ( Chen Y. et al., 2020 ).…”