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Chloroplast genomes for crop evolution: Chlorodiv

Les génomes chloroplastiques comme un outil pour la génétique des populations, la phylogéographie et la phylogénie en agrobiodiversité

Developing the plant of the future Microscopic (Gene/cell) Genomics Operation/adaptation Agrobiodiversity Evolution/domestication Method/tool/technic Phylogeography Corn Palm tree Mil Ignam Fonio
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Abstract

Biodiversity, phylogeography and population genetic studies will be revolutionized by access to large data sets
thanks to next-generation sequencing methods. In this study, we develop an easy and cost-effective protocol for in solution enrichment hybridization capture of complete chloroplast genomes applicable at deep-multiplexed levels.
The protocol uses cheap in-house species-specific probes developed via long-range PCR of the entire chloroplast.
Barcoded libraries are constructed, and in-solution enrichment of the chloroplasts is carried out using the probes.
This protocol was tested and validated on six economically important West African crop species, namely African rice,
pearl millet, three African yam species and fonio. For pearl millet, we also demonstrate the effectiveness of this pro tocol to retrieve 95% of the sequence of the whole chloroplast on 95 multiplexed individuals in a single MiSeq run at
a success rate of 95%. This new protocol allows whole chloroplast genomes to be retrieved at a modest cost and will
allow unprecedented resolution for closely related species in phylogeography studies using plastomes.

Project Number : 1202-040

Year : 2012

Type of funding : AAP

Project type : AAP OS

Research units in the network : AGAP

Start date :
01 Feb 2013

End date :
28 Feb 2015

Flagship project :
Non

Project leader :
Thomas Couvreur

Project leader's institution :
IRD

Project leader's RU :
DIADE

Budget allocated :
45552 €

Total budget allocated ( including co-financing) :
45552 €

Funding :
Labex