Table accession numbers and references for the 16 taxa used in this study




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Table S1. Accession numbers and references for the 16 taxa used in this study

Taxon

Accession number

Reference

Angiosperms







Nicotianatabacum

NC_001879

Shinozaki et al. (1986)

Morusindica

NC_008359

Ravi et al. (2006)

Amborellatrichopoda

NC_005086

Goremykin et al. (2003)

Gymnosperms







Cycasmicronesica

EU016802–EU016882

Jansen et al. (2007)

Cycastaitungensis

NC_009618

Wu et al. (2007)

Ginkgo biloba

DQ069337-DQ069702

Leebens-Mack et al. (2005)

Pinusthunbergii

NC_001631

Wakasugi et al. (1994)

Pinuskoraiensis

NC_004677

Noh et al. 2003

Keteleeriadavidiana

AP010820

Wu et al. (2009)

Gnetumparvifolium

AP009569

Wu et al. (2009)

Welwitschia mirabilis

EU342371

McCoy et al. (2008)

Ephedra equisetina

AP010819

Wu et al. (2009)

Cryptomeria japonica

AP009377

Hirao et al. (2008)

Halocarpus sp.

JN627246-JN627297

this study

Podocarpus totara

JN627350-JN627401

this study

Agathis australis

JN627298-JN627349

this study

Table References


Goremykin VV, KI Hirsch-Ernst, S Wolfl, FH Hellwig. 2003. Analysis of the Amborella trichopoda chloroplast genome sequence suggests that Amborella is not a basal angiosperm. Mol Biol Evol. 20:1499-1505.

Hirao T, A Watanabe, M Kurita, T Kondo, K Takata. 2008. Complete nucleotide sequence of the Cryptomeria japonica D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species. BMC Plant Biol. 8:70.

Jansen RK, Z Cai , LA Raubeson , H Daniell , CW dePamphilis , J Leebens-Mack , K F Müller et al. 2007. Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proc Natl Acad Sci USA. 104:19369-19374.

Leebens-Mack J, LA Raubeson, L Cui, JV Kuehl, MH Fourcade, TW Chumley , JL Boore , RK Jansen, CW dePamphilis. 2005. Identifying the basal angiosperm node in chloroplast genome phylogenies: sampling one's way out of the Felsenstein zone. Mol Biol Evol. 22:1948-1963.

McCoy SR, JV Kuehl, JL Boore, LA Raubeson. 2008. The complete plastid genome sequence of Welwitschia mirabilis: an unusually compact plastome with accelerated divergence rates. BMC Evol Biol. 8:130.

Noh EW, JS Lee, YI Choi, MS Han, YS Yi, SU Han. 2003. Complete nucleotide sequence of Pinus koraiensis. Direct Submission to GenBank. Accession No. NC_00467.

Ravi V, JP Khurana, AK Tyagi, P Khurana. 2006. The chloroplast genome of mulberry: complete nucleotide sequence, gene organization, and comparative analysis. Tree Genet. Genomes. 3:49-59.

Shinozaki K, M Ohme, M Tanaka et al. (23 co-authors). 1986. The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO J. 5:2043–2049.

Wakasugi T, J Tsudzuki, S Ito, K Nakashima, T Tsudzuki, and M Sugiura. 1994. Loss of all ndh genes as determined by sequencing the entire chloroplast genome of the black pine Pinus thunbergii. Proc Natl Acad Sci USA. 91:9794-9798.

Wu CS, YN Wang, SM Liu, SM Chaw. 2007. Chloroplast genome (cpDNA) of Cycas taitungensis and 56 cp protein-coding genes of Gnetum parvifolium: Insights into cpDNA evolution and phylogeny of extant seed plants. Mol Biol Evol. 24:1366-1379.



Wu CS, YT Lai, CP Lin, YN Wang, SM Chaw. 2009. Evolution of reduced and compact chloroplast genomes (cpDNAs) in gnetophytes: selection toward a lower-cost strategy. Mol Phylogenet Evol. 52:115-124.




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