Research Projects:

Genome scale study of symbiosis between plants and nitrogen-fixing bacteria – The Panama case (Funded by STRI, 2015-2019) and SENACYT (2018-2020)

Hornworts are arguably the oldest land plant lineage involved in the obligatory symbiosis with cyanobacteria, Nostoc. Most hornworts have globose colonies while their sister species, Leiosporoceros dussii, has bifurcating cyanobacterial strands locked inside the thallus. In cycads, the cyanobionts form a dark band between the inner and outer cortex of the roots, with elongated cortical cells, presumably related to metabolite transport, interconnecting the two partners.

The Panamanian project focuses on said species as well as the 2 endemic Zamia species, Zamia nana (terrestrial) and Zamia pseudoparasitica, the only epiphytic gymnosperm. We have transcriptomic data and genomic data of axenic (sterile) plants and plants re-infected in-vitro with cultured cyanobacteria. Additionally, we have gathered sequences from the genomic regions rbcL-rbcX, 16S, ITS and trnL intron to investigate the genetic diversity of Panamanian cyanobacteria, bacteria and endophytic fungi. The research addresses three contemporary topics in evolutionary biology:

  1. mRNA sharing is a likely mechanism for horizontal gene transfer
  2. horizontal gene transfer has been highlighted as a fundamental drive in the evolution of prokaryotes and eukaryotes (Cooper, Current Biol., 2013)
  3. our study will start to uncover the genetic diversity of symbionts in the tropics, providing a new dimension to tropical studies on plant-cyanobacterial symbiosis. This is research is done in conjunction with Noris Salazar Allen and José Gudiño (STRI), two undergraduates (Maycol Madrid and Yessenia Guadalupe, Univ. Panamá and STRI) and Fay-Wei Li (Cornell University)

The nuclear genome of a hornwort with putative sex chromosomes- Leio genome

Hornworts have garnered much interest over the past decade because of the unanticipated emergence of this group as being closely related to tracheophytes. Although recent phylogenomic studies have challenged this hypothesis and resurrected the phylogenetic hypothesis that hornworts are sister to all land plants, it is clear that this small group occupies a pivotal position in land plant evolution. We are developing genomic resources (RNA seq of the gametophyte and sporophyte) and nuclear data (Illumina and MinIon) of a hornwort with separate sexes (dioicous) and putative sex chromosomes: Leiosporoceros dussii (Leio for short). Besides the intriguing morphology, Leio is genetically divergent from all hornworts (sister taxon). This could be due to the low levels of RNA editing in organellar genomes (unlike all other hornworts). The plastid and mitochondrial genomes have been recently published in a collaborative effort with Maurane Bourgouin-Couture and the expertise of Monique Turmel and Claude Lemieux (IBIS, U. Laval).

We are interested in developing a dioicous hornwort model with an international team of experts including: Noris Salazar and José Gudiño (STRI), Karen Renzaglia (SIUC), Norman Wickett (Chicago Botanic Garden), Peter Szövény (U. of Zurich), Jérôme Laroche (IBIS, U. Laval) and Fay-Wei Li (Cornell U.) The genome of Leio will shed light on the evolution of plant-cyanobacterial symbiosis, sex chromosomes, sporogenesis and plastid and CCM evolution.


Genome scale study of symbiosis between hornworts and nitrogen-fixing bacteria- A global scale (led by with Fay-Wei Li, Boyce Thompson Institute, Cornell University).

In plants, symbiotic associations with cyanobacteria evolved ~500 Ma. Obligate cyanobacterial partnerships are found in all major plant lineages, particularly in all hornworts, the liverworts Blasia and Cavicularia, all hornworts, the fern Azolla, all cycads and the angiosperm Gunnera. A global effort to understand the symbiosis between hornworts and cyanobacteria is spearheaded by Fay-Wei Li (Cornell University) and funded by the National Science Foundation. The Panama project (see below) is carried out in close collaboration with this global effort. Understanding the genomic underpinnings of the plant-cyanobacterial association is essential to consider the future introduction of genes involved in nitrogen fixation into higher plants and to alleviate the need for fertilizers to satisfy our ever-increasing demand for food.


Spatial and temporal diversity of Arctic flora and associated cyanobacterial and fungal biota (Funded by NSERC, CRSNG, 2016-2021)

Inhabitable to most of the higher plants, the arctic environment is dominated by cryptogams, including those of mosses, liverworts (collectively, bryophytes) and lichenized fungi. Initial studies on the Arctic suggests the origin of the present bryophyte flora as a result of frequent long-distance dispersal events and local, pre-glaciation diversification.

As a means to uncover the origin of the Canadian arctic flora, I propose to use genomic resources to study the diversity, timing of origin and dispersal patterns of subarctic and arctic bryophytes. The high dispersal capacity of most bryophytes brings on the question of whether their associated epiphyte flora (bacteria and fungi) is equally dispersed with bryophyte fragments or spores or is it native to the Arctic. Some arctic cyanobacteria and fungi display broad ranges (even bipolar distributions) whereas others have more localized distributions in subarctic and arctic regions. Despite the dramatic contribution of cyanobacteria, and probably fungi, to boreal and arctic ecosystems, we know little about the genetic diversity of the epiphytic and endophytic flora of subarctic and arctic Canadian bryophytes. As such, we propose to take a concerted approach to study the bryophyte hosts and the associated epiphytes. This will provide a more complete picture of current Canadian Arctic diversity as well as uncover past diversity, revealing the ecosystem assemblage through time. Our project focuses on several moss species such as Racomitrium lanuginosum and related species. We also target lichens such as Stereocaulon (cyanolichen), Cladonia stellaris, Cladonia mitis and the charismatic reindeer lichen, Cladonia rangiferina. Our studies go from phylogenetic studies of each symbiont to the novel field of Arctic Cryptogamic virology (in collaboration with Alexander Culley ).

Related research:

Population genomics, microbial diversity and nutrient productivity of subarctic and arctic mosses with focus on the wholly moss Racomitrium lanuginosum. Project by Dennis Escolástico in collaboration with Jean-Philippe Bellenger

Functional diversity of nitrogen-fixing bacteria associated to hornworts, in particular Leiosporoceros dussii. Undergraduate project by Raphaël Bouchard, in collaboration with Fay-Wei Li.

Functional genomics of the symbiotic association between the hornwort Leiosporoceros dussii and cyanobacteria, a project by J.C.V.A.

Hornwort phylogenomics and character evolution, in collaboration with Emily Sessa (goflag,, Karen Renzaglia, Fay-Wei Li, Peter Szövény, Christine Cargill and Sahut Chantanoarrapint.

Barcoding of Canadian bryophytes, in collaboration with Maria Kuzmina, Nicole Fenton (UQAR) and Catherine Lafarge (University of Alberta)

Phylogenetic diversity and population genomics of epiphyllous liverworts, a project by Adriel Sierra