Within the Horizon 2020 funded project "ROTATES" (rotates.eu), we are 
looking for a PhD student to work on cassava and taro genomics hosted by 
the DEFI team (AGAP institute, CIRAD), Montpellier, France.

Application Deadline: 15th of December 2025.

How to apply: send a CV, letter of motivation, and two referees contact 
to hana.chair[at]cirad.fr and bertrand.fouks[at]cirad.fr

Taro and cassava exemplify convergent evolution in response to human 
selection, despite wide phylogenetic and genomic divergence.

Both plants have undergone convergent evolution to become starch-rich, 
clonally propagated crops suited to tropical agriculture. Indeed, both 
developed enlarged underground storage organs (corms in taro, tuberous 
roots in cassava), driven by human selection for carbohydrate yield. 
These two crops are primarily propagated vegetatively (taro via corms, 
cassava via stem cuttings), leading to clonality and reduced effective 
recombination. Domestication of those two crops led to changes in the 
regulation of starch biosynthesis genes, storage organ development 
genes, as well as changes in hormonal signalling (e.g., auxin and 
cytokinin). In addition, both crops show signs of domestication 
syndrome, with reduced toxicity (cyanogenic compounds in cassava; 
acridity in taro) and enhanced yield.

Despite these phenotypic similarities, both crops have many different 
life-history traits. While taro (Araceae) is a monocot with a haploid 
genome size of ~2.5 Gb, displaying different levels of ploidy (2n$) 
(diploid or triploid), and with most likely two origins of domestication 
in South East Asia and in Oceania, cassava (Euphorbiaceae) is a eudicot 
with a haploid genome size of ~770 Mb diploid (2n = 36), domesticated in 
the Amazon basin- South America. Furthermore, taro is often sterile with 
limited sexual reproduction, while sexual reproduction is still more 
proliferative in cassava.

To unravel the molecular basis and consequences of selection in both 
taro and cassava, a pangenome approach will be applied, allowing a 
holistic comparison of the molecular processes underlying their 
convergent domestication. The advent of sequencing technologies, along 
with the development of powerful bioinformatic tools, has led to a sharp 
understanding of the molecular mechanisms underlying evolutionary 
processes, unveiling the significant impact of structural variants (copy 
number variations, chromosomal rearrangements, transposable elements, 
presence/absence variations …) (even) at the population level. The 
pangenome approach bears several advantages compared to the classic 
comparative genomics approach, allowing to unravel, among other things, 
gene family size variation within a single species, identify genomic 
regions and features that are shared by a whole species or those that 
are specific to some populations and account for both single nucleotide 
and structural variant polymorphisms.

Using whole genome re-sequencing data of cassava (~ 100 accessions) and 
taro (~ 50 accessions) produced within the ROTATES project, the 
methodology will be as follow:

- Pangenome Construction: to identify within each species core vs. 
accessory genes, gene presence/absence variations, and structural 
rearrangements, pangenome graphs will be constructed for each species 
using at least two already published high quality genome assemblies 
(from different accessions) for each species. Those graphs will then be 
augmented with the reads obtained from the sequencing of the different 
accessions collected during ROTATES, as well as accessions already 
sequenced (cassava > 300, taro > 5).

- Comparative Genomics: To unravel the molecular basis of convergent 
evolution in cassava and taro, a phylogenomic approach will be applied 
using the target species (cassava and taro), their wild relatives, and 
sister groups, as well as outlier species. Those analyses will yield a 
wide phylogenetic reconstruction, the characterization of ortholog genes 
for the different clades and families, and the dynamics of gene family 
size variation and protein domains rearrangements.

- Detection of Selection Analyses: To detect footprint selection, 
genome-wide inter- and intraspecific selection tests will be performed. 
Interspecific selection tests will be conducted with the detection of 
selection in phylogenies. At the intraspecific level, several population 
genetic metrics will be calculated to account for different types of 
selection.

For all the approaches described above, the PhD student will adapt its 
workflow according to the literature and the development of new tools 
and algorithms, enabling state-of-the-art analyses to unravel the 
molecular basis underlying the convergent evolution of cassava and taro.

The successful candidate will be hosted within our team (DEFI, part of 
the AGAP institute [https://umr-agap.cirad.fr/en] at CIRAD) in 
Montpellier, France. The successful candidate will have social benefits 
(french health care), a gross salary of  2300 euro , and company benefits 
from CIRAD (e.g. reduced prices for cultural events, ...).

Best,

Bertrand

-- 

FOUKS Bertrand <bertrand.fouks@cirad.fr>

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