Permanent staff

Photo (c) IRD

Research interest

My research subject is the evolution and adaptation of plants.

During my master and Ph.D (2001-2005), I worked on understanding the impact of traditional farmers’ practices on the genetic diversity of yam, a tuber crop cultivated in tropical countries trough clonal multiplication. Then I did a post-doctoral position at the University of Manchester were I worked on the genetic basis of adaptation in Arabidopsis thaliana (2006-2008). British food and weather convinced me to go back in France.

Back in Montpellier, I am currently working on the genetic diversity and the adaptation of root and tuber crops. My current model is yam, an important staple food in West Africa. I am interesting in understanding the domestication process, i.e. where, when and how yam was domesticated.

Formation and research experience

2008-Present

Researcher, IRD Montpellier, France UMR DiADE, DYNADIV

Research subject: Genetics of diversity and adaptation of root and tuber crops.

2006-2008

Post doctoral position, University of Manchester, UK

Dr P. Kover lab, Evolutionary Biology group

Research subject: Molecular basis of adaptation in Arabidopsis thaliana.

2002-2005

Ph.D in Genetic Diversity and Population Genetics, University of Montpellier II, France

Supervisors: Dr J.-L. Pham and Dr S. Hamon (UMR DGPC, IRD, Montpellier)

Research subject: Dynamic of the genetic diversity of a vegetatively-propagated crop, yam (Dioscorea sp.).

2001-2002

DEA (Master degree) in Genetic Diversity and Population Genetics, University of Montpellier II, France

Supervisors: Dr J.-L. Pham and Dr S. Tostain (UMR DGPC, IRD, Montpellier)

Research subject: Study of gene flow between wild and cultivated yams in Benin: impact of domestication on the genetic diversity of cultivated plants.

Publications

Scarcelli N (2020) Population genomics of organelle genomes in crop plants. In Population genomics: Crop plants, Rajora OP (Ed.), Springer, Cham

Abrouk M, Ahmed HI, Cubry P, Simonikova D, Cauet S, Pailles Y, Bettgenhaeuser J, Gapa L, Scarcelli N, Couderc M, Zekraoui L, Kathiresan N, Cizkova J, Hribova E, Dolezel J, Arribat S, Bergès H, Wieringa JJ, Gueye M, Kane NA, Leclerc C, Causse S, Vancoppenolle S, Billot C, Wicker T, Vigouroux Y, Barnaud A, Krattinger SG (2020) Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate. Nature Communication 11:4488

Kusuma J, Scarcelli N, Couderc M, Mariac C, Zekraoui L, Duminil J (2020) Microsatellite markers development for Indonesian nutmeg (Myristica fragrans Houtt.) and transferability to other Myristicaceae spp. Molecular Biology Reports In press

Scarcelli N, Cubry P, Akakpo R, Thuillet AC, Obidiegwu J, Baco MN, Otoo E, Sonké B, Dansi A, Djedatin G, Mariac C, Couderc M, Causse S, Alix K, Chaïr H, François O, Vigouroux Y (2019) Yam genomics supports West Africa as a major cradle of crop domestication. Science Advances 5(5):eaaw1947

Bethune K, Mariac C, Couderc M, Scarcelli N, Santoni S, Ardisson M, Martin JF, Montúfar R, Klein V, Sabot F, Vigouroux Y, Couvreur TLP (2019) Long-fragment targeted capture for long-read sequencing of plastomes. Applications in Plant Sciences 7: e1243

Burgarella C, Barnaud A, Kane NA, Jankowski F, Scarcelli N, Billot C, Vigouroux Y, Berthouly-Salazar C (2019) Adaptive Introgression: An Untapped Evolutionary Mechanism for Crop Adaptation. Frontiers in Plant Science 10:1-17

Magwé-Tindo J, Wieringa JJ, Sonké B, Zapfack L, Vigouroux Y, Couvreur TLP, Scarcelli N (2018) Complete plastome sequences of 14 African yam species (Dioscorea spp.). Mitochondrial DNA part B 4(1):74-76

Magwé-Tindo J, Wieringa JJ, Sonké B, Zapfack L, Vigouroux Y, Couvreur TLP, Scarcelli N (2018) Guinea yam (Dioscorea spp.) wild relatives identified using whole plastome phylogenetic analyses. Taxon 67(5):905-915

Cubry P, Tranchant-Dubreuil C, Thuillet AC, Monat C, Ndjiondjop MN, Labadie MN, Cruaudd C, Engelen S, Scarcelli N, Rhoné B, Burgarella C, Dupuy C, Larmande P, Wincker P, François O, Sabot F, Vigouroux Y (2018) The rise and fall of African rice cultivation revealed by analysis of 246 new genomes. Current Biology 28:2274-2282.e6

Burgarella C, Cubry P, Kane NA, Varshney RK, Mariac C, Liu X, Shi C, Thudi M, Couderc M, Xu X , Chitikineni A, Scarcelli N, Barnaud A, Rhoné B, Dupuy C, François O, Berthouly-Salazar C, Vigouroux Y (2018) A western Sahara origin of African agriculture inferred from pearl millet genomes. Nature Ecology and Evolution 2:1377-1380

Scarcelli N, Chaïr H, Causse S, Vesta R, Couvreur T, Vigouroux Y (2017) Crop wild relative conservation: wild yams are not that wild. Biological Conservation 210:325-333

Akakpo R, Scarcelli N, Chair H, Dansi A, Djedatin G, Thuillet AC, Rhone B, Francois O, Alix K, Vigouroux Y (2017) Molecular basis of African yam domestication: analyses of selection point to root development, starch biosynthesis, and photosynthesis related genes. BMC Genomics 18:782

Clément Y, Sarah G, Holtz Y, Homa F, Pointet S, Contreras S, Nabholz B, Sabot F, Sauné L, Ardisson M, Bacilieri R, Besnard G, Berger A, Cardi C, De Bellis F, Fouet O, Jourda C, Khadari B, Lanaud C, Leroy T, Pot D, Sauvage C, Scarcelli N, Tregear J, Vigouroux Y, Yahiaoui N, Ruiz M, Santoni S, Labouisse JP, Pham JL, David J, Glémin S (2017) Evolutionary forces affecting synonymous variations in plant genomes. Plos One 13(5):e1006799

Glato K, Aidam A, Kane NA, Bassirou D, Couderc M, Zekraoui L, Scarcelli N, Barnaud A, Vigouroux Y (2017) Structure of sweet potato (Ipomoea batatas) diversity in West Africa covaries with a climatic gradient. PLoS One 12(5):e0177697

Ambrósio Moreira P, Mariac C, Scarcelli N, Couderc M, Picanço Rodrigues D, Clement CR, Vigouroux Y (2016) Chloroplast sequence of treegourd (Crescentia cujete, Bignoniaceae) to study phylogeography and domestication. Application in Plant Science. 4(10):1600048

Sarah G, Homa F, Pointet S, Contreras S, Sabot F, Nabholz B, Santoni S, Sauné L, Ardisson M, Chantret N, Sauvage C, Tregear J, Jourda C, Pot D, Vigouroux Y, Chair H, Scarcelli N, Billot C, Yahiaoui N, Bacilieri R, Khadari B, Boccara M, Barnaud A, Péros JP, Labouisse JP, Pham JL, David J, Glémin S, Ruiz M (2016) A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives. Molecular Ecology Ressources 17:565-580

Scarcelli N, Mariac C, Couvreur TLP, Faye A, Richard D, Sabot F, Berthouly-Salazar C, Vigouroux Y (2015) Intra-individual polymorphism in chloroplasts from NGS data: where does it come from and how to handle it?. Mol Ecol Res doi: 10.1111/1755-0998.12462

Mariac C, Scarcelli N, Pouzadou J, Barnaud A, Billot C, Faye A, Kougbeadjo A, Maillol V, Martin G, Sabot F, Santoni S, Vigouroux Y, Couvreur T (2014) Cost-effective enrichment hybridization capture of chloroplast genomes at deep multiplexing levels for population genetics and phylogeography studies. Mol Ecol Res doi:10.1111/1755-0998.12258

Scarcelli N,Couderc M, Baco MN, Egah J, Vigouroux Y (2013) Clonal diversity and estimation of relative clone age: application to agrobiodiversity of yam (Dioscorea rotundata). BMC Plant Biology 13:178-188

Scarcelli N, Tostain S, Vigouroux Y, Luong V, Baco MN, Agbangla C, Daïnou O, Pham JL (2011) Genetic structure of farmer-managed varieties in clonally-propagated crops. Genetica 139:1055-1064

Scarcelli N, Barnaud A, Eiserhardt W, Treier U, Seveno M, d’Anfray A, Vigouroux Y, Pintaud JC (2011) A set of 100 chloroplast DNA primer pairs to study population genetics and phylogeny in monocotyledons. PLoS One 6(5):e19954

Springate DA, Scarcelli N, Rowntree J, Kover PX (2011) Correlated response in plasticity to selection for early flowering in Arabidopsis thaliana. J Evol Biol 24:2280-2288

Vigouroux Y, Barnaud A, Scarcelli N, Thuillet AC (2011) Biodiversity, evolution and adaptation of cultivated crops. CR Biologies 334:450-457

Kover PX, Valdar W, Trakalo J, Scarcelli N, Ehrenreich IM, Purugganan MD, Durrant C, Mott R (2009) A multiparent advanced generation inter-cross to fine-map quantitative traits in Arabidopsis thaliana. PLoS Genetics 5(7):e1000551

Kover PX, Rowntree JK, Scarcelli N, Savriama Y, Eldridge T, Schaal BA (2009) Pleiotropic effects of environment-specific adaptation in Arabidopsis thaliana. New phytologist 183:816-825

Scarcelli N, Kover PX (2009) Standing genetic variation in FRIGIDA mediates experimental evolution of flowering time in Arabidopsis. Mol Ecol 18(9):2039-2049

Bousalem M, Durand O, Scarcelli N, Lebas BSM, Kenyon L, Marchand JL, Lefort F, Seal SE (2009) Dilemmas caused byendogenous pararetroviruses regarding the taxonomy and diagnosis of yam (Dioscorea spp.) badnaviruses: analyses to support safe germplasm movement. Arch Virol 154:297-314

Scarcelli N (2009) Entre sauvage et cultivé, les ignames. Plasticité ou sexualité ? Sciences au Sud 51:10

Scarcelli N, Tostain S, Baco MN, Agbangla C, Daïnou O, Vigouroux Y, Pham J-L (2008) Does agriculture conflict with in-situ conservation? A case study on the use of wild relatives by yam farmers in Benin. In Crop wild relative conservation and use, Maxted N, Ford-Lloyd BV, Kell SP, Iriondo JM, Dulloo ME and Turok J (Eds), CABI, UK. pp331-339

Scarcelli N, Cheverud JM, Schaal BA, Kover PA (2007) Antagonist pleiotropic effects reduce the potential adaptive value of the FRIGIDA locus. Proc Natl Acad Sci USA 104(43):16986-16991

Tostain S, Agbangla C, Scarcelli N, Mariac C, Daïnou O, Berthaud J, Pham J-L (2007) Genetic diversity analysis of yam cultivars (Dioscorea rotundata Poir.) in Benin using SSR markers. Plant Genetic Resources: Characterization and Utilization 5(2):71-81

Scarcelli N, Tostain S, Vigouroux Y, Agbangla C, Daïnou O, Pham J-L (2006) Farmers' use of wild relative and sexual reproduction in a vegetatively propagated crop. The case of yam in Benin. Mol Ecol 15:2421-2431

Scarcelli N, Tostain S, Mariac C, Agbangla C, Daïnou O, Berthaud J, Pham J-L (2006) Genetic nature of yams (Dioscorea sp.) domesticated by farmers in Benin (West Africa). Gen Res Crop Evol 53:121-130

Tostain S, Scarcelli N, Brottier P, Marchand J-L, Pham J-L, Noyer J-L (2006) Development of DNA microsatellite markers in tropical yam (Dioscorea sp.). Mol Ecol Notes 6:173-175

Scarcelli N, Daïnou O, Agbangla C, Tostain S, Pham J-L (2005) Segregation patterns of isozyme loci and microsatellite markers show the diploidy of African yam Dioscorea rotundata (2n=40). Theor Appl Genet 111:226-232

Scarcelli N (2005) Structure et dynamique de la diversité d’une plante cultivée à multiplication végétative : le cas des ignames au Bénin (Dioscorea sp.). Thèse de doctorat, Université de Montpellier II, 180p

Tostain S, Chaïr H, Scarcelli N, Noyer J-L, Agbangla C, Marchand J-L, Pham J-L (2005) Diversité, origine et dynamique évolutive des ignames cultivées Dioscorea rotundata Poir. au Bénin. Les Actes du BRG 5:465-482

Reboud X, Le Corre V, Scarcelli N, Roux F, David JL, Bataillon, Camilleri C, Brunel D, McKhann H (2004) Natural variation among accession of Arabidopsis thaliana: beyond the flowering date, what morphological traits are relevant to study adaptation? In Plant adaptation: Molecular genetic and ecology. Proceedings of an international workshop held December 11-13, 2002, in Vancouver, British Columbia, Canada. Edited by QCB Cronk, J Whitton, RH Ree, IEP Taylor. NRC Research Press, Ottawa, Ontario, PP 135-142