March 15, 2021, by Andrew Edwards (Ed)
The Baobab Genome Project: approaching the mysteries of diversification and death – by Levi Yant
With its unmistakeable shape synonymous with the continent, the baobab is an African icon. It is also important on a very practical level: its nutritious fruit, pulp and seeds have been eaten across Africa for ages. High in vitamin C and other nutrients, the use of baobab in the global diet is radically increasing, with the powder from their enormous fruits billed as a new superfood. Given that baobab is traditionally considered a ‘womens’ crop’ in many African cultures, this exploding interest is helping female smallholders rise out of poverty.
Understanding the biology of baobab, ensuring the sustainability of its utilisation, and maximising benefit for farmers and end users alike are challenges the Baobab Genome Project is addressing. This project is co-led by Professor Todd Michael (The Salk Institute for Biological Studies, San Diego, CA USA) and myself: we are combining genomics and plant physiology with African academic partners and African citizen science.
My fascination with the enigmatic baobab
It all began when I met Senior Lecturer Rose Kigathi and Professor Santie de Villiers, who have recently established excellent international research collaborations in the state-of-the-art Pwani University Biosciences Research Centre (PUBReC) in coastal Kenya. Rose suggested we work on this mighty tree, but I was initially sceptical that there could be traction as a food source. However, she easily won me over, showing me on several visits diverse uses of baobab, from consumption of young tubers (similar to potatoes) to the widespread sustainable harvesting of seeds and fruits, which are foraged ubiquitously in much of Africa.
Rose, who lived in the village where the university is located, Kilifi, also knew of exceptional baobabs growing right up against the shoreline, adapted to harsh saline conditions. We therefore hatched a plan to study natural variation in salinity tolerance and to apply genomic approaches to understand the basis of this trait.
The baobab harbours a host of scientific mysteries
Since this beginning a few years ago, the scientific plot lines surrounding baobab have thickened greatly: two important scientific mysteries have come to to the foreground. The first one concerns its genome: only one of the Madagascan baobab species has successfully invaded and spread across Africa, Adansonia digitata. It is totally unknown how A. digitata achieved such dominance across a diversity of harsh conditions. A hint may be found in the fact that only the Africa-wide species is a tetraploid, meaning it has doubled its genome and so has four sets of chromosomes, rather than the usual two. In contrast, all the species that did not invade Africa are normal diploids.
A hundred years of evolutionary theory has postulated ways genome doubling may promote adaptation. Certainly, the clear majority of key crops that have lifted humanity out of hunger are genome-doubled, as are many (overly successful) invasive weeds, along with some of the most aggressive human cancers. However, the functional basis for this occasionally spectacular adaptability in genome doubled lineages is not understood. I have therefore made this a key focus of my research, supported by a European Research Council Starting Grant that harmonises with the BGP.
The second great mystery, in contrast, is a recent horror: a 2018 report details many of the largest and most ancient baobabs—some over 2,000 years old, the eldest of all angiosperm trees—suddenly dying at a dramatically increased rate from an unknown cause, all in the 12 years preceding the report. Shockingly, the eldest of these gentle giants have disintegrated in a single growing season, after thriving for two millennia. We aim, with our ambitious genomics programme, to provide a foundation to understand this carnage and to provide a framework for conservation efforts.
Genesis of the Baobab Genome Project
Motivated by this combination of urgent, fascinating science, practical importance, and the fact that baobab is grossly understudied, I have been linking complementary groups to gain critical mass. With the support of the Future Food Beacon and a University of Nottingham GCRF award with Professors David Salt and Martin Broadley, I have recently set out with Todd Michael to form the BGP, with the key assistance of highly motivated and resourceful citizen scientists.
Key among them is our South African colleague, Pieter van Rooyen, who is organising overlanding expeditions across the African continent to assess baobab population distributions, as well as relevant environmental metrics. I have also enlisted a pioneering lifelong baobab scholar and enthusiast, Professor David Baum (yes, ‘Baum’ means ‘tree’ in German!), of the University of Wisconsin. David has organised continent- and genus-wide sampling, which is invaluable to the project, along with deep phylogenomic experience.
Our contribution to understanding these mysteries is to begin by producing high quality genomes of all baobab species and then hundreds of A. digitata genome-doubled plants across Africa. We are combining this genomic information with complementary phenotyping data generated by our African partners and citizen scientists.
While this project has only coalesced in the last few months, there are exciting new results: Todd’s group has generated a near-chromosome level genome for A. digitata, which carries a possible signature of being a ‘recovering tetraploid.’ That is, we believe that the genome duplication event in A. digitata is old enough that it is now re-diploidizing. This phenomenon of ‘re-diploidizing’ is thought to create a genetic advantage, enabling adaptability and organismal diversity following genome duplication: a genome first ‘hops’ up to doubled status, fully doubling its content and then over generations ‘drops’ randomly bit by bit, losing a chunk here and a chunk there, creating diversification between lineages within a species. Such an evolutionary dance has been observed most dramatically in cancers. There, genome duplication is associated with short term evolutionary gain for the cancer (but of course not the patient): usually these are the most aggressive cancers. Of course, the same universal rules of evolution apply across both of these examples, in the one case causing adaptability of a disease against host responses over the course of months, and on the other, diversification of this beautiful tree across the African continent over millennia.
We accordingly speculate that this genomic process may be occurring among A. digitata lineages, a speculation that we can explore by sequencing the genomes of many baobab individuals and comparing them. This initial dataset will consist of genome sequencing between 300 and 500 individual baobab genomes. In addition to this speculative idea, these studies will allow us to perform genome-wide association studies in the context of various environmental parameters – from salinity tolerance to drought to nutritional content – as well as determine the demographic history and current genetic conservation status of this iconic tree.
The BGP is also working with interested citizens in a citizen science effort. This aspect is led by South Africa-based entrepreneur Pieter van Rooyen, who is performing ‘overlanding’ expeditions across Africa. Pieter is organising a citizen science effort to enable surveillance of at-risk baobab populations, as well as basic population status monitoring across the continent. Given that very little is understood even about the basic demography of the African baobab, we expect that this work, paired with our population genomic data, will facilitate understanding of disease susceptibility as well as underpin an understanding of environmental adaptation and response in the diverse baobab lineages.
We hope the BGP will prove foundational for these practical and fundamental aspects of understanding baobab. Indeed, the urgent need to better understand baobab in order to help protect this giant of the African continent is about as powerful a motivational factor as any scientist could wish to experience. That this project can bring together such a diversity of interested citizens and scientists around these goals is an inspiration to me.
Funding to date has come from Illumina’s Greater Good Initiative, a University of Nottingham GCRF award and the Future Food Beacon
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