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Exploring the History of Chloroplast Capture in Arabis Using Whole Chloroplast Genome Sequencing
Open AccessArticle

Complete Chloroplast Genome Sequences of Four Meliaceae Species and Comparative Analyses

1
Thünen Institute of Forest Genetics, Sieker Landstrasse 2, D-22927 Grosshansdorf, Germany
2
Australian Research Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2018, 19(3), 701; https://doi.org/10.3390/ijms19030701
Received: 31 January 2018 / Revised: 26 February 2018 / Accepted: 26 February 2018 / Published: 1 March 2018
(This article belongs to the Special Issue Chloroplast)
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. View Full-Text
Keywords: chloroplast genome; Next Generation Sequencing; genome skimming; Meliaceae; DNA marker; SNP; indel; matK; rps19 chloroplast genome; Next Generation Sequencing; genome skimming; Meliaceae; DNA marker; SNP; indel; matK; rps19
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Mader, M.; Pakull, B.; Blanc-Jolivet, C.; Paulini-Drewes, M.; Bouda, Z.H.-N.; Degen, B.; Small, I.; Kersten, B. Complete Chloroplast Genome Sequences of Four Meliaceae Species and Comparative Analyses. Int. J. Mol. Sci. 2018, 19, 701.

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