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Localized hypermutation and associated gene losses in legume chloroplast genomes.

Magee AM, Aspinall S, Rice DW, Cusack BP, Sémon M, Perry AS, Stefanović S, Milbourne D, Barth S, Palmer JD, Gray JC, Kavanagh TA, Wolfe KH.

Genome Res. 2010 Dec;20(12):1700-10. doi: 10.1101/gr.111955.110. Epub 2010 Oct 26. Erratum in: Genome Res. 2014 Jun;24(6):1052.


The plastid genome-encoded Ycf4 protein functions as a nonessential assembly factor for photosystem I in higher plants.

Krech K, Ruf S, Masduki FF, Thiele W, Bednarczyk D, Albus CA, Tiller N, Hasse C, Schöttler MA, Bock R.

Plant Physiol. 2012 Jun;159(2):579-91. doi: 10.1104/pp.112.196642. Epub 2012 Apr 19.


Comparative genomics of four Liliales families inferred from the complete chloroplast genome sequence of Veratrum patulum O. Loes. (Melanthiaceae).

Do HD, Kim JS, Kim JH.

Gene. 2013 Nov 10;530(2):229-35. doi: 10.1016/j.gene.2013.07.100. Epub 2013 Aug 23.


Substitution of the gene for chloroplast RPS16 was assisted by generation of a dual targeting signal.

Ueda M, Nishikawa T, Fujimoto M, Takanashi H, Arimura S, Tsutsumi N, Kadowaki K.

Mol Biol Evol. 2008 Aug;25(8):1566-75. doi: 10.1093/molbev/msn102. Epub 2008 May 2.


The first complete chloroplast genome of the Genistoid legume Lupinus luteus: evidence for a novel major lineage-specific rearrangement and new insights regarding plastome evolution in the legume family.

Martin GE, Rousseau-Gueutin M, Cordonnier S, Lima O, Michon-Coudouel S, Naquin D, de Carvalho JF, Aïnouche M, Salmon A, Aïnouche A.

Ann Bot. 2014 Jun;113(7):1197-210. doi: 10.1093/aob/mcu050. Epub 2014 Apr 25.


Gene relocations within chloroplast genomes of Jasminum and Menodora (Oleaceae) are due to multiple, overlapping inversions.

Lee HL, Jansen RK, Chumley TW, Kim KJ.

Mol Biol Evol. 2007 May;24(5):1161-80. Epub 2007 Feb 28.


Complete chloroplast genome sequence of Gycine max and comparative analyses with other legume genomes.

Saski C, Lee SB, Daniell H, Wood TC, Tomkins J, Kim HG, Jansen RK.

Plant Mol Biol. 2005 Sep;59(2):309-22.


Conservation of plastid sequences in the plant nuclear genome for millions of years facilitates endosymbiotic evolution.

Rousseau-Gueutin M, Ayliffe MA, Timmis JN.

Plant Physiol. 2011 Dec;157(4):2181-93. doi: 10.1104/pp.111.185074. Epub 2011 Oct 27.


Complete chloroplast genome of Sedum sarmentosum and chloroplast genome evolution in Saxifragales.

Dong W, Xu C, Cheng T, Zhou S.

PLoS One. 2013 Oct 18;8(10):e77965. doi: 10.1371/journal.pone.0077965. eCollection 2013.


Insights from the complete chloroplast genome into the evolution of Sesamum indicum L.

Zhang H, Li C, Miao H, Xiong S.

PLoS One. 2013 Nov 26;8(11):e80508. doi: 10.1371/journal.pone.0080508. eCollection 2013.


The complete chloroplast genome sequence of Taxus chinensis var. mairei (Taxaceae): loss of an inverted repeat region and comparative analysis with related species.

Zhang Y, Ma J, Yang B, Li R, Zhu W, Sun L, Tian J, Zhang L.

Gene. 2014 May 1;540(2):201-9. doi: 10.1016/j.gene.2014.02.037. Epub 2014 Feb 26.


Contradiction between plastid gene transcription and function due to complex posttranscriptional splicing: an exemplary study of ycf15 function and evolution in angiosperms.

Shi C, Liu Y, Huang H, Xia EH, Zhang HB, Gao LZ.

PLoS One. 2013;8(3):e59620. doi: 10.1371/journal.pone.0059620. Epub 2013 Mar 18.


Complete chloroplast genome sequences of Mongolia medicine Artemisia frigida and phylogenetic relationships with other plants.

Liu Y, Huo N, Dong L, Wang Y, Zhang S, Young HA, Feng X, Gu YQ.

PLoS One. 2013;8(2):e57533. doi: 10.1371/journal.pone.0057533. Epub 2013 Feb 27.


The complete chloroplast genome sequence of Mahonia bealei (Berberidaceae) reveals a significant expansion of the inverted repeat and phylogenetic relationship with other angiosperms.

Ma J, Yang B, Zhu W, Sun L, Tian J, Wang X.

Gene. 2013 Oct 10;528(2):120-31. doi: 10.1016/j.gene.2013.07.037. Epub 2013 Jul 27. Erratum in: Gene. 2014 Jan 1;533(1):458.


Complete chloroplast genome sequence of a tree fern Alsophila spinulosa: insights into evolutionary changes in fern chloroplast genomes.

Gao L, Yi X, Yang YX, Su YJ, Wang T.

BMC Evol Biol. 2009 Jun 11;9:130. doi: 10.1186/1471-2148-9-130.


Relative rates of synonymous substitutions in the mitochondrial, chloroplast and nuclear genomes of seed plants.

Drouin G, Daoud H, Xia J.

Mol Phylogenet Evol. 2008 Dec;49(3):827-31. doi: 10.1016/j.ympev.2008.09.009. Epub 2008 Sep 21.

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