# Complete plastome sequences of 14 African yam species
( Dioscorea spp.)

Jacqueline Magwé-Tindo, Jan J. Wieringa, Bonaventure Sonké, Louis

Zapfack, Yves Vigouroux, Thomas Couvreur, Nora Scarcelli

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Jacqueline Magwé-Tindo, Jan J. Wieringa, Bonaventure Sonké, Louis Zapfack, Yves Vigouroux, et al. Complete plastome sequences of 14 African yam species (Dioscorea spp.). Mitochondrial DNA Part B Resources, 2019, 4 (1), pp.74-76. 10.1080/23802359.2018.1536466. hal-03364209

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# Complete plastome sequences of 14 African yam species (Dioscorea spp.)

Jacqueline Magwé-Tindo, Jan J. Wieringa, Bonaventure Sonké, Louis Zapfack, Yves Vigouroux, Thomas L. P. Couvreur & Nora Scarcelli

To cite this article: Jacqueline Magwé-Tindo, Jan J. Wieringa, Bonaventure Sonké, Louis Zapfack, Yves Vigouroux, Thomas L. P. Couvreur & Nora Scarcelli (2019) Complete plastome sequences of 14 African yam species (Dioscorea spp.), Mitochondrial DNA Part B, 4:1, 74-76, DOI: 10.1080/23802359.2018.1536466

To link to this article: https://doi.org/10.1080/23802359.2018.1536466

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# Complete plastome sequences of 14 African yam species (Dioscorea spp.)

Jacqueline Magwé-Tindoª, Jan J. Wieringaᵇ, Bonaventure Sonkéᶜ, Louis Zapfackª, Yves Vigourouxᵈ, Thomas L. P. Couvreurᵇ,ᵈ and Nora Scarcelliᵈ

ªDepartment of Plant Biology, Faculty of Science, The University of Yaoundé I, Yaoundé, Cameroon; ᵇNational Herbarium of The Netherlands, Naturalis Biodiversity Centre, Leiden, The Netherlands; ᶜDepartment of Biology, Higher Teachers' Training College, The University of Yaoundé I, Yaoundé, Cameroon; ᵈIRD, University Montpellier, Montpellier, France

## ABSTRACT

Complete plastomes of 14 African yam species were reconstructed from whole genome sequencing. These plastomes sizes varied from 151,908 to 155,155 bp. We predicted 130 genes, including 18 duplicated genes located in the two inverted regions. Phylogenetic analysis obtained using the maximum likelihood procedure revealed that each species was distinct with high support. This resource will be useful for phylogenetic and diversity analysis of *Dioscorea* species.

## ARTICLE HISTORY

Received 7 September 2018
Accepted 20 September 2018

## KEYWORDS

Africa; chloroplast;
*Dioscorea*; NGS; yam

The genus *Dioscorea* L. (Dioscoreaceae) plays a considerable role in tropical Africa because of its important staple crop *D. rotundata*, a vine cultivated for its starchy tuber. *Dioscorea* is a very species-rich and morphologically complex genus. Therefore, the taxonomy of this genus is difficult, as proven by the variation in the number of accepted species names (Caddick et al. 2002; Wilkin et al. 2005; Govaerts et al. 2017). Molecular phylogenetic analyses focusing on the genus are also poorly resolved (Terauchi et al. 1992; Ramser et al. 1997; Chaïr et al. 2005). Here we reconstructed complete plastomes of 14 West-African species.

Fourteen *Dioscorea* leaf samples, (*D. abyssinica*, *D. baya*, *D. bulbifera*, *D. burkilliana*, *D. cayenensis*, *D. dumetorum*, *D. hirtiflora*, *D. praehensilis*, *D. preussii*, *D. quartiniana*, *D. sagittifolia*, *D. sansibarensis*, *D. schimperiana*, and *D. togoensis*), were collected from WAG and G herbaria (Table 1). DNAs were extracted from dried leaves according to Scarcelli et al. (2006) and whole genome sequencing was performed as described in Mariac et al. (2014) on an Illumina MiSeq (Illumina, San Diego, CA). For each sample, the whole plastome was reconstructed using MITObim 1.7 (Hahn et al. 2013) as explained in Magwé-Tindo et al. (2018) with *D. rotundata* plastome as a reference (GenBank NC_024170.1). Annotations were recovered from the alignment of the target plastome to NC_024170.1 using Geneious Pro 4.8.5 with Mauve 2.2.0 plugin (Darling et al. 2010), then manually checked for start and stop codons (protein-coding genes) and by blasting the tRNA and rRNA sequences to GenBank nucleotide database (nr/nt, Altschul et al. 1990). Annotated

plastomes were deposited into the GenBank database (Table 1).

Plastome lengths varied from 151,908 bp (*D. burkilliana*) to 155,155 bp (*D. baya*) and exhibited a typical quadripartite structure with a LSC (Large Single Copy) and a SSC (Short Single Copy) separated by two IR (Inverted Region). The mean GC content was 37% and varied from 31% within the SSC to 43% within the IR. The 14 species presented the same genetic structure as the reference (NC_024170.1): 130 genes corresponding to 84 protein-coding genes, 38 tRNA and 8 rRNA. Among these genes, 18 were duplicated in the IR: 6 protein-coding genes, 8 tRNA and 4 rRNA. The only exception was *D. quartiniana* which missed the *matK* gene due to a mutation of the second codon into a stop codon. All species lost the *rps16* gene.

A phylogenetic study was conducted using these 14 complete plastomes, with *D. rotundata* (NC_024170.1) as reference and *D. elephantipes* (NC_009601.1) as outgroup species. The 16 plastomes were aligned using MAFFT 7 (Katoh et al. 2002) and the alignment was cleaned using Gblocks 0.91b (Talavera and Castresana 2007). The phylogenetic tree was constructed using RAxML 8.2.9 (Stamatakis 2014) with 500 bootstraps. The phylogenetic tree obtained was well-resolved and revealed that each species was clearly distinct with strong support (Figure 1), except within the cultivated species complex.

Resources reconstructed here will help to understand the relationships between cultivated yams and their wild relatives and provide useful information for further taxonomic study.
<figure><img src="image_10.png" /><figcaption>Table 1. Characterization of the samples used for sequencing.</figcaption></figure>

<table><thead><tr><th>Species</th><th>Herbarium voucher accession</th><th>Collection locality</th><th>Longitude</th><th>Latitude</th><th>Plastome GenBank ID</th></tr></thead><tbody><tr><td>D. abyssinica</td><td>WAG.1781186</td><td>Cameroon</td><td>13.9</td><td>10.9</td><td>MG805602</td></tr><tr><td>D. baya</td><td>WAG.1781135</td><td>Cameroon</td><td>10.6</td><td>2.9</td><td>MG805603</td></tr><tr><td>D. bulbifera</td><td>WAG.1783436</td><td>Liberia</td><td>-8.6</td><td>6.3</td><td>MG805604</td></tr><tr><td>D. burkilliana</td><td>WAG.1783323</td><td>Cameroon</td><td>11.2</td><td>2.8</td><td>MG805605</td></tr><tr><td>D. cayenensis</td><td>WAG.1783287</td><td>Cameroon</td><td>11.5</td><td>3.9</td><td>MG805606</td></tr><tr><td>D. dumetorum</td><td>WAG.1943398</td><td>Gabon</td><td>10.7</td><td>-3.5</td><td>MG805607</td></tr><tr><td>D. hirtiflora</td><td>WAG.1783636</td><td>Senegal</td><td>-16.7</td><td>12.9</td><td>MG805608</td></tr><tr><td>D. praehensilis</td><td>G00420196</td><td>Côte d'Ivoire</td><td>-5.1</td><td>6.3</td><td>MG805609</td></tr><tr><td>D. preussii</td><td>WAG.1786123</td><td>Gabon</td><td>11.8</td><td>-0.1</td><td>MG805610</td></tr><tr><td>D. quartiniana</td><td>WAG.1786396</td><td>Malawi</td><td>35.5</td><td>-15.9</td><td>MG805611</td></tr><tr><td>D. sagittifolia</td><td>WAG.1786430</td><td>Cameroon</td><td>13.8</td><td>7</td><td>MG805612</td></tr><tr><td>D. sansibarensis</td><td>WAG.1786456</td><td>Gabon</td><td>11.6</td><td>-0.2</td><td>MG805613</td></tr><tr><td>D. schimperiana</td><td>WAG.1786876</td><td>Cameroon</td><td>11.5</td><td>3.9</td><td>MG805614</td></tr><tr><td>D. togoensis</td><td>WAG0283548</td><td>Togo</td><td>1.6</td><td>6.7</td><td>MG805615</td></tr></tbody></table>

<figure><img src="image_11.png" /><figcaption>Figure 1. Phylogenetic tree of 16 African *Dioscorea* species constructed using maximum likelihood procedure and whole plastome sequences. *Dioscorea elephantipes* was included as outgroup species. Bootstrap values are indicated for each node. Each species is followed by its GenBank accession ID.</figcaption></figure>

## Acknowledgements

The authors thank the Conservatoire et Jardin botaniques de la ville de Genève (G) for the *D. praehensilis* sample.

## Disclosure statement

No potential conflict of interest was reported by the authors.

## Funding

This project is supported by Agropolis Fondation under the reference ID 1502-206 through the « Investissements d'avenir » program (Labex Agro:ANR-10-LABX-0001-01), under the frame of I-SITE MUSE (ANR-16-IDEX-0006); by ARCAD and FEDER; and by Agence Nationale de la Recherche under Grant ANR-13-BSV7-0017. This work was done in collaboration with the GeT core facility, Toulouse, France (ANR-10-INBS-09).
<figure><img src="image_12.png" /></figure>

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