October 2013

Sequencing the “Tree of Life”
By sequencing the baobab tree, Monsanto is providing scientists with the genomic resources toprotect and sustain the baobab, while informing our understanding of tree evolution.

Recognizing that its technology could
play a critical role in alleviating global
hunger, malnutrition, and poverty, Illumina
created the Agricultural Greater Goodinitiative. Each year, Illumina awards
Greater Good grants to agriculturalresearch organizations that are focusedon identifying and breeding plants and animals that will increase
the sustainability, productivity, and nutritional density of crop andlivestock species. Under the grants, Illumina sequencing andgenotyping reagents are provided free of charge.

Monsanto
2012 Illumina Greater Good
Initiative Award WinnerIntroduction
For people familiar with Disney’s The Lion King, the African baobab
tree is the “Tree of Life.” The depiction in the animated movie isn’t
far from the truth. Capable of living thousands of years, it provides
shelter, food, and water for animals and humans living on theAfrican savannah.
In a departure from its usual focus on crop species, Monsanto is using
its expertise and resources to better understand the baobab tree andwhat makes it so resilient. “We don’t often have the opportunity towork on species outside of our portfolio,” said Todd Michael, Ph.D.,
former Head of the Genome Analysis Center at Monsanto andTodd Michael, Ph.D., was formerly the Head of the Genome Analysis Centerat Monsanto and is now a Senior Principal Research Scientist at Ibis
Biosciences, Abbott Laboratories.

now Senior Principal Research Scientist, Ibis Biosciences, Abbott
Laboratories. “In fact, we couldn’t have initiated this project withoutreceiving the Greater Good Initiative award. We decided to sequence
the African baobab species, Adanonia digitata, providing scientists inAfrica with the genomic resources to protect and sustain the baobab,
while informing our understanding of tree evolution.”
Baobab trees can reach over 80 feet (25 meters) in height, withtrunk diameters that range from 20–40 feet (6–12 meters). With large
branches and leaves creating huge shade canopies, the trees rely on
animals and humans for seed dispersal. “The baobab generates huge
pods containing 50–100 seeds,” said Dr. Michael. “While the pod isused for bowls and decorative items, the pulp is ground into a drink
that’s high in vitamin C, similar in taste to lemonade. The seeds areabout the size of a pea and are disbursed by people and animals.
People grow them and eat the seedlings, which are tasty and very
nutritious. The bark is used for medicinal purposes.”Dr. Michael’s team is using the Illumina HiSeq® 2000 system tosequence the A. digitata genome. “As far as I know, we’re the firstteam to sequence the Baobab tree,” said Dr. Michael. “Our first goal
was to make a reference genome of A. digitata in order to access thevariation of the organism itself, and then sequence the seven otherbaobab species at a lower level. One of the original scientific papers
about this species reported that it is heterozygous, polyploidy, andhas between 50 and 150 chromosomes1. Chromosome number andthe ploidy level will all play into how we develop markers for breeders.
There are several groups in West Africa that want to use molecularmarkers to optimize baobab cultivation.”
The team obtained seeds from four different A. digitata seed pods,
taken from a cluster of baobab trees that were presumably crossBaobab trees can liver for thousands of years, reaching over 80 feet
(25 meters) in height, with trunk diameters that range from 20–40 feet
(6–12 meters).

October 2013pollinated. They sequenced five seeds at 100× and one seed at
30×. “The amount of variation between the different seeds in that
small population was very large,” said Dr. Michael. “The interesting
thing about a long-lived species is that typically they hold a lot ofheterozygosity. That dovetails with being polyploidy and having lots ofdifferent chromosomes.”
Scientists had estimated that the baobab genome was over agigabyte. “We found it to be smaller than predicted, about 700 MB,”said Dr. Michael. “That could mean several things. Since we don’t
have physical resources, such as BAC sequencing or physical maps,
there’s a chance that we’re still missing part of the genome.”
Low coverage sequencing was performed on seeds fromthe seven other baobab species, five of which are native toMadagascar (A. grandidieri, A. suarezensis, A. rubrostipa, A. perrieri,
A. madagascariensis, and A. za) and one to Western Australia(A. gibbosa). “Our initial look at the data shows that the variation
between the species found on different continents is as great asthe variation within any given baobab species,” Dr. Michael said.
“Interestingly, we performed our initial sequencing on seeds, and manyof the reports about genome size and characteristics were done on
the leaf tissue of mature trees. We’re wondering if there’s a dramaticdifference between the two, implying that the genome is going throughlots of changes over time.”
The team will be performing deeper sequencing at higher coverageof some of the species samples to determine the degree of variation.
“With that information, we’ll work with the Donald Danforth Science
Center to develop markers,” said Dr. Michael. “Those will be used toperform a larger population study to determine the extent of variationin places where there’s been human selection versus places where
there hasn’t been any selective breeding.”
The final goal is to understand how these trees live so long. “Clearly,they’ve been saved by the fact that they have no value from a woodstandpoint,” Dr. Michael said. “It’s a succulent. You can remove thebark all the way around the tree and it won’t kill it. There have beenreports that when these trees die, they turn to mush.”
The tree’s longevity may also coincide with being high in nutrients orother beneficial characteristics. Understanding the genetic architectureof the baobab genome might help to explain the baobab’s longevity.
“A recent study showed there’s definitely a positive selection or aselective force resulting from cultivation in West Africa2. We want todetermine whether cultivation is driving the baobab away from being along-lived organism.”points in the lifetime of the tree, possibly separated by thousands ofyears. By sequencing the methylome, and maybe even parts of theepigenome, such as histones, we could see the impact time has hadon the genome.”
According to Dr. Michael, the opportunity to explore genomes isreally unprecedented. “A year or two ago, you wouldn’t have thought
about doing this type of project, because it would be too expensive
to even think of trying. But the amount of sequence the HiSeq 2000
produces for its price point changes the questions we’re able to ask
and explore.”
Scientists can’t learn a lot from just one genome, preferring to view
them in the context of larger populations. “We’ve spent the last 10
to 12 years in plant genomics learning a lot about a few genomes,Arabidopsis, rice, maize, etc.,” said Dr. Michael. “There’s a realopportunity to leverage the information we’re getting from non-model,
non-crop genomes like the baobab. We can start making observations
about a greater number of genes and what they control.”
Only several tree species have been sequenced to date. “Themore genomes we sequence that represent different parts of theevolutionary tree, the more data we have to make deductions about
the evolution of gene families,” Dr. Michael said. “It turns out thatthe baobab is in the same family (Malvaceae) as cotton. It would
be interesting to look at the differences between the diploid cotton
putative D-genome parent (Gossypium raimondii), which is a small tree
found in Mexico, and baobab genomes to identify the genes involvedin driving the baobab to be long lived and those that confer medicinal
characteristics. As we sequence more genomes, we can use themas positive and negative controls in studies. Marrying genomics,proteomics, and metabolomics will speed up the process of finding
these beneficial characteristics.”

References
1.

Baum, DA and Oginuma, K (1994) A review of chromosome numbers in
Bombacaceae with new counts for Adansonia. Taxon 43:11–20.

2.

Assogbadjo AE, Kyndt T, Sinsin B, Gheysen G, and van Damme P (2006)
Patterns of genetic and morphometric diversity in baobab (Adansoniadigitata) populations across different climatic zones of Benin (West Africa).
Ann Bot. 97: 819–30.

To study baobab longevity, the team would like to obtain leaf samples
from several of the very old trees living in Africa. “We’d like to take aleaf from one side of the tree and compare it to a leaf from the otherside of the tree, said Dr. Michael. “Those samples represent different

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