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Diversity and evolution of plastomes in Saharan mimosoids: potential use for phylogenetic and population genetic studies

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Abstract

Acacias (Mimosoideae) represent a major woody group in arid and subarid habitats of all tropical and subtropical regions. The genetic diversity and population dynamic of African species are still poorly investigated, in particular due to ploidy variation among and within species. Here, we aim to investigate the diversity of the plastid genome (or plastome) of Central Saharan mimosoids, in order to assess its potential utility for phylogenetic and population genetic analyses. We first used a genome skimming strategy to assemble the complete plastome plus the nuclear ribosomal DNA cluster of six species belonging to three genera (Vachellia, Senegalia, and Faidherbia). Phylogenetic relationships based on these data confirm the existence of three main evolutionary lineages in the Hoggar range (southern Algeria). An analysis of the plastome structure reveals an extension of the inverted repeat (IR) in Faidherbia albida as recently reported in two other genera of the same lineage (Inga and Acacia s.s.). Higher substitution rates are detected in this lineage, and our species sampling allows revealing genes (particularly accD, clpP, rps2, rps3, ycf1, ycf2, and ycf4) under positive selection following the IR extension. The reasons for this evolutionary transition need to be unraveled. We then develop 21 plastid microsatellites to be used on a large panel of mimosoid species. At a local scale, 18 of these loci reveal intra-specific polymorphism in at least one species. These markers may be useful to assess the genetic diversity of the plastome for comparative phylogeographies or population genetic studies.

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Acknowledgments

This work has been conducted in the Laboratoire Evolution & Diversité Biologique (EDB) part of the LABEX entitled TULIP managed by Agence Nationale de la Recherche (ANR-10-LABX-0041). CVDP and GB were funded by the Regional Council Midi-Pyrenees (AAP 13053637, 2014-EDB-UT3-DOCT). This work was performed in collaboration with the GeT core facility, Toulouse, France (http://get.genotoul.fr), and was supported by France Génomique National infrastructure, funded as part of “Investissement d’avenir” program managed by Agence Nationale pour la Recherche (ANR-10-INBS-09). We are grateful to Pascal-Antoine Christin for helpful advices on the use of positive selection tests and Salah Abdelaoui who helped for the plant sampling.

Author’s contribution statement

MM, DBC, and GB conceived the initial project; MM and DBC conducted field expeditions and sampling; MM, SM, OB, and GB performed laboratory works; CVDP and GB analyzed the data; MM, CVDP, and GB wrote the paper; and all authors commented and approved the final version of the manuscript.

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Author notes

  1. Mohamed Mensous and Céline Van de Paer contributed equally to this work.

Authors and Affiliations

  1. Laboratoire de Recherche sur la Phoeniciculture, Faculté des Sciences de la Nature et de la Vie, Université Kasdi Merbah—Ouargla, 30000 Route de Ghardaia, Ouargla, Algeria

    Mohamed Mensous

  2. UMR 5174 EDB (Laboratoire Evolution et Diversité Biologique), CNRS-UPS-ENSFEA-IRD, Université Paul Sabatier, Bât. 4R1, 31062, Toulouse Cedex 9, France

    Céline Van de Paer, Sophie Manzi & Guillaume Besnard

  3. INRA, GeT-PlaGe, Genotoul, 31326, Castanet-Tolosan, France

    Olivier Bouchez

  4. GenPhySE, Université de Toulouse, INRA, INPT, ENVT, 31326, Castanet-Tolosan, France

    Olivier Bouchez

  5. Laboratoire de Recherche sur les Zones Arides, USTHB/ENSA, BP44, Alger, Algeria

    Djamel Baâli-Cherif

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  1. Mohamed Mensous
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Correspondence to Mohamed Mensous or Guillaume Besnard.

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Communicated by G. G. Vendramin

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Data archiving statement

Plastome and nuclear ribosomal DNA-annotated sequences are deposited in GenBank (KY100263 to KY100269 and KY316152 to KY316159), and cpSSR datasets are provided in Supplementary Material (Tables S7 and S8).

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Mensous, M., Van de Paer, C., Manzi, S. et al. Diversity and evolution of plastomes in Saharan mimosoids: potential use for phylogenetic and population genetic studies. Tree Genetics & Genomes 13, 48 (2017). https://doi.org/10.1007/s11295-017-1131-2

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