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. 2021 Feb 10;10(2):342.
doi: 10.3390/plants10020342.

Generation of Chloroplast Molecular Markers to Differentiate Sophora toromiro and Its Hybrids as a First Approach to Its Reintroduction in Rapa Nui (Easter Island)

Ignacio Pezoa  1   2   3 , Javier Villacreses  2   3   4 , Miguel Rubilar  4 , Carolina Pizarro  2 , María Jesús Galleguillos  2 , Troy Ejsmentewicz  2 , Beatriz Fonseca  2 , Jaime Espejo  5 , Víctor Polanco  1 , Carolina Sánchez  2   6
Affiliations

Generation of Chloroplast Molecular Markers to Differentiate Sophora toromiro and Its Hybrids as a First Approach to Its Reintroduction in Rapa Nui (Easter Island)

Ignacio Pezoa et al. Plants (Basel). .

Abstract

Sophora toromiro is an endemic tree of Rapa Nui with religious and cultural relevance that despite being extinct in the wild, still persists in botanical gardens and private collections around the world. The authenticity of some toromiro trees has been questioned because the similarities among hybrid lines leads to misclassification of the species. The conservation program of toromiro has the objective of its reinsertion into Rapa Nui, but it requires the exact genotyping and certification of the selected plants in order to efficiently reintroduce the species. In this study, we present for the first time the complete chloroplast genome of S. toromiro and four other Sophora specimens, which were sequenced de-novo and assembled after mapping the raw reads to a chloroplast database. The length of the chloroplast genomes ranges from 154,239 to 154,473 bp. A total of 130-143 simple sequence repeats (SSR) loci and 577 single nucleotide polymorphisms (SNPs) were identified.

Keywords: Easter Island; NGS; Rapa Nui; SNP; SSR; Sophora toromiro; chloroplast; conservation; genome; molecular markers.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Sophora toromiro (ST2) chloroplastidial genome schematic map. Key in colors at bottom left. Genes with introns are indicated with “*”.
Figure 2
Figure 2
Chloroplast borders comparison between the 5 Sophora samples. The length of each segment in base pairs (bp) is shown in blue and the name of the region in white.
Figure 3
Figure 3
Phylogenomic reconstruction of the relationship of fourteen species from the Papilionoideae subfamily with A. thaliana as an outgroup.
Figure 4
Figure 4
CgView Comparison Tool v1.0 (CCT) map displaying ST2 chloroplast in the outer ring in the form of genes (CDS, rRNA and tRNA). All samples were aligned according to ST2 and were ordered by similarity as shown in bottom left. Blast identity color codes shown in top left. The inner ring shows CG percentage in the ST2 chloroplast genome. Genes with introns are indicated with “*”.
Figure 5
Figure 5
Phylogenetic reconstruction using molecular markers identified through CgView.
Figure 6
Figure 6
Heatmap of SNP distribution and impact caused in the genes. ST2 annotation data was used as reference for calculating gene variants. Each row represents a window of 1 kbps. Number of variants caused by SNPs are represented with a red coloration to the right.
See this image and copyright information in PMC

References

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