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. 2018 Mar 1;19(3):701.
doi: 10.3390/ijms19030701.

Complete Chloroplast Genome Sequences of Four Meliaceae Species and Comparative Analyses

Malte Mader  1 , Birte Pakull  2 , Céline Blanc-Jolivet  3 , Maike Paulini-Drewes  4 , Zoéwindé Henri-Noël Bouda  5 , Bernd Degen  6 , Ian Small  7 , Birgit Kersten  8
Affiliations

Complete Chloroplast Genome Sequences of Four Meliaceae Species and Comparative Analyses

Malte Mader et al. Int J Mol Sci. .

Abstract

The Meliaceae family mainly consists of trees and shrubs with a pantropical distribution. In this study, the complete chloroplast genomes of four Meliaceae species were sequenced and compared with each other and with the previously published Azadirachta indica plastome. The five plastomes are circular and exhibit a quadripartite structure with high conservation of gene content and order. They include 130 genes encoding 85 proteins, 37 tRNAs and 8 rRNAs. Inverted repeat expansion resulted in a duplication of rps19 in the five Meliaceae species, which is consistent with that in many other Sapindales, but different from many other rosids. Compared to Azadirachta indica, the four newly sequenced Meliaceae individuals share several large deletions, which mainly contribute to the decreased genome sizes. A whole-plastome phylogeny supports previous findings that the four species form a monophyletic sister clade to Azadirachta indica within the Meliaceae. SNPs and indels identified in all complete Meliaceae plastomes might be suitable targets for the future development of genetic markers at different taxonomic levels. The extended analysis of SNPs in the matK gene led to the identification of four potential Meliaceae-specific SNPs as a basis for future validation and marker development.

Keywords: DNA marker; Meliaceae; Next Generation Sequencing; SNP; chloroplast genome; genome skimming; indel; matK; rps19.

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Conflict of interest statement

The authors declare no conflict of interest. The funding sponsors had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, and in the decision to publish the results.

Figures

Figure 1
Figure 1
Gene map of the complete chloroplast genome of Cedrela odorata (GenBank MG724915). The grey arrows indicate the direction of transcription of the two DNA strands. A GC-content graph is depicted within the inner circle. The circle inside the GC content graph marks the 50% threshold. The maps were created using OrganellarGenomeDRAW [22].
Figure 2
Figure 2
Visualization of pairwise alignments of complete cpDNA sequences of four Meliaceae species each with the cpDNA sequence of Azadirachta indica (reference). VISTA-based similarity plots portraying the sequence identity of each of the four Meliacea species with the reference Azadirachta indica are shown. The annotation (protein-encoding genes) is provided for Azadirachta indica on top (based on the related GenBank file; KF986530.1). Plastome regions with the highest diversity between the 5 Meliaceae individuals are marked by blue arrows (top1–3). Further details are provided in the text below.
Figure 3
Figure 3
Phylogenetic tree (maximum likelihood) based on whole-plastome sequences of five Meliaceae species and Acer buergerianum (outgroup). Bootstrap values (%) are shown above branches. The bootstrap value on the branch separating Azadirachta indica from the other Meliaceae is below 70% and was not shown for this reason. GenBank accession numbers of the plastomes are given in Table 2.
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References

    1. The Plant List. [(accessed on 15 January 2018)]; Available online: http://www.theplantlist.org/
    1. The IUCN Red List of Threatened Species. [(accessed on 11 January 2018)]; Available online: http://www.iucnredlist.org/
    1. CITES—Convention on International Trade in Endangered Species of Wild Fauna and Flora/the Cites Species. [(accessed on 11 January 2018)]; Available online: https://cites.org/eng/disc/species.php.
    1. Birky C.W. Uniparental inheritance of mitochondrial and chloroplast genes—Mechanisms and evolution. Proc. Natl. Acad. Sci. USA. 1995;92:11331–11338. doi: 10.1073/pnas.92.25.11331. - DOI - PMC - PubMed
    1. Drouin G., Daoud H., Xia J. Relative rates of synonymous substitutions in the mitochondrial, chloroplast and nuclear genomes of seed plants. Mol. Phylogenet. Evol. 2008;49:827–831. doi: 10.1016/j.ympev.2008.09.009. - DOI - PubMed

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