title: From museums to genomics: old herbarium specimens shed light on a C3 to C4 transition.
abstract: Collections of specimens held by natural history museums are invaluable material for biodiversity inventory and evolutionary studies, with specimens accumulated over 300 years readily available for sampling. Unfortunately, most museum specimens yield low-quality DNA. Recent advances in sequencing technologies, so called next-generation sequencing, are revolutionizing phylogenetic investigations at a deep level. Here, the Illumina technology (HiSeq) was used on herbarium specimens of Sartidia (subfamily Aristidoideae, Poaceae), a small African-Malagasy grass lineage (six species) characteristic of wooded savannas, which is the C3 sister group of Stipagrostis, an important C4 genus from Africa and SW Asia. Complete chloroplast and nuclear ribosomal sequences were assembled for two Sartidia species, one of which (S. perrieri) is only known from a single specimen collected in Madagascar 100 years ago. Partial sequences of a few single-copy genes encoding phosphoenolpyruvate carboxylases (ppc) and malic enzymes (nadpme) were also assembled. Based on these data, the phylogenetic position of Malagasy Sartidia in the subfamily Aristidoideae was investigated and the biogeographical history of this genus was analysed with full species sampling. The evolutionary history of two genes for C4 photosynthesis (ppc-aL1b and nadpme-IV) in the group was also investigated. The gene encoding the C4 phosphoenolpyruvate caroxylase of Stipagrostis is absent from S. dewinteri suggesting that it is not essential in C3 members of the group, which might have favoured its recruitment into a new metabolic pathway. Altogether, the inclusion of historical museum specimens in phylogenomic analyses of biodiversity opens new avenues for evolutionary studies.
authors.affiliation: CNRS-UPS-ENFA, UMR5174, EDB (Laboratoire Evolution et Diversité Biologique), 118 route de Narbonne, F-31062 Toulouse, France guillaume.besnard@univ-tlse3.fr.
authors.forename: Guillaume
authors.initials: G
authors.lastname: Besnard
authors.affiliation: Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK.
authors.forename: Pascal-Antoine
authors.initials: PA
authors.lastname: Christin
authors.affiliation: CNRS-UPS-ENFA, UMR5174, EDB (Laboratoire Evolution et Diversité Biologique), 118 route de Narbonne, F-31062 Toulouse, France Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada.
authors.forename: Pierre-Jean G
authors.initials: PJ
authors.lastname: Malé
authors.affiliation: GeT-PlaGe, Campus INRA-Auzeville, F-31326 Castanet-Tolosan, France; INRA, UAR 1209 Département de Génétique Animale, INRA Auzeville, F-31326 Castanet-Tolosan, France.
authors.forename: Emeline
authors.initials: E
authors.lastname: Lhuillier
authors.affiliation: CNRS-UPS-ENFA, UMR5174, EDB (Laboratoire Evolution et Diversité Biologique), 118 route de Narbonne, F-31062 Toulouse, France.
authors.forename: Christine
authors.initials: C
authors.lastname: Lauzeral
authors.affiliation: Laboratoire d'écologie Alpine (LECA), UMR5553, CNRS/Université Joseph Fourier-Grenoble I, Université de Savoie, F-38041 Grenoble, France.
authors.forename: Eric
authors.initials: E
authors.lastname: Coissac
authors.affiliation: Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK.
authors.forename: Maria S
authors.initials: MS
authors.lastname: Vorontsova
mesh_terms: D000349:Africa; D001482:Base Composition; D002244:Carbon / Q000378:metabolism*; D002467:Cell Nucleus / Q000235:genetics; D020451:Contig Mapping; D018628:Gene Dosage; D017343:Genes, Plant; D023281:Genomics; D005843:Geography; D005810:Multigene Family; D009144:Museums; D010802:Phylogeny; D018087:Plastids / Q000235:genetics; D006109:Poaceae / Q000235:genetics*; D012270:Ribosomes / Q000235:genetics; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D013048:Specimen Handling
chemical_list: D002244:Carbon
keywords: Aristidoideae; Madagascar; NGS; Poaceae; Sartidia; Stipagrostis.; herbarium; plastid genome; ribosomal DNA; single-copy genes