Supplementary table S1: List of chloroplast genomes sequences used for phylogenetic analysis




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Supplementary table S1: List of chloroplast genomes sequences used for phylogenetic analysis

























 

Specie

Family

Order

GenBank Accession No

References

1

Amborella trichopoda

Amborellaceae

Amborellales

NC_005086

Goremykin VV, Hirsch-Ernst KI, Wolfl S, Hellwig FH. 2003. Analysis of the Amborella trichopoda Chloroplast Genome Sequence Suggests That Amborella Is Not a Basal Angiosperm. Mol. Biol. Evol. 20 (9): 1499-1505

2

Acorus calamus

Acoraceae

Acorales

AJ879453

Goremykin VV, Holland B, Hirsch-Ernst KI, Hellwig FH. 2005. Analysis of Acorus calamus chloroplast genome and its phylogenetic implications Mol. Biol. Evol. 22 (9): 1813-1822

3

Chloranthus spicatus

Chloranthaceae

Chloranthales

EF380352

Hansen DR, et al. 2007. Phylogenetic and evolutionary implications of complete chloroplast genome sequences of four early-diverging angiosperms: Buxus (Buxaceae), Chloranthus (Chloranthaceae), Dioscorea (Dioscoreaceae), and Illicium (Schisandraceae). Mol. Phylogenet. Evol. 45 (2): 547-563

4

Nymphaea alba

Nymphaeaceae

Nymphaeales

NC_006050

Goremykin VV, Hirsch-Ernst KI, Wolfl S, Hellwig FH. 2004. The chloroplast genome of Nymphaea alba: whole-genome analyses and the problem of identifying the most basal angiosperm. Mol. Biol. Evol. 21 (7): 1445-1454

5

Nuphar advena

Nymphaeaceae

Nymphaeales

NC_008788

Raubeson LA, et al. 2007. Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus. BMC Genomics 8, 174

6

Colocasia esculenta

Araceae

Alismatales

NC_016753

Ahmed I, et al. 2012. Mutational dynamics of aroid chloroplast genomes. Genome Biol Evol 4 (12): 1316-1323

7

Lemna minor

Araceae

Alismatales

NC_010109

Mardanov AV, et al. 2008. Complete sequence of the duckweed (Lemna minor) chloroplast genome: structural organization and phylogenetic relationships to other angiosperms. J. Mol. Evol. 66 (6): 555-564

8

Wolffia australiana

Araceae

Alismatales

NC_015899

Wang W, Messing J. 2011. High-throughput sequencing of three lemnoideae (duckweeds) chloroplast genomes from total DNA. PLoS ONE 6 (9), E24670

9

Elodea canadensis

Hydrocharitaceae

Alismatales

NC_018541

Huotari T, Korpelainen H. 2012. Complete chloroplast genome sequence of Elodea canadensis and comparative analyses with other monocot plastid genomes. Gene 508 (1): 96-105

10

Dioscorea elephantipes

Dioscoreaceae

Dioscoreales

NC_009601

Hansen DR, et al. 2007. Phylogenetic and evolutionary implications of complete chloroplast genome sequences of four early-diverging angiosperms: Buxus (Buxaceae), Chloranthus (Chloranthaceae), Dioscorea (Dioscoreaceae), and Illicium (Schisandraceae). Mol. Phylogenet. Evol. 45 (2): 547-563

11

Lolium perenne

Poaceae

Poales

NC_009950

Diekmann K, Hodkinson TR, FrickeE, Barth S. 2008. An optimized chloroplast DNA extraction protocol for grasses (Poaceae) proves suitable for whole plastid genome sequencing and SNP detection PLoS ONE 3 (7), E2813

12

Bambusa emeiensis

Poaceae

Poales

NC_015830

Zhang YJ, Ma PF, Li DZ. 2011. High-throughput sequencing of six bamboo chloroplast genomes: phylogenetic implications for temperate woody bamboos (poaceae: bambusoideae). PLoS ONE 6 (5), E20596

13

Magnolia kwangsiensis

Magnoliaceae

Magnoliales

NC_015892

Kuang DY, et al. 2011. Complete chloroplast genome sequence of Magnolia kwangsiensis (Magnoliaceae): implication for DNA barcoding and population genetics Genome 54 (8):663-673

14

Musa acuminta subsp. Malaccensis

Musaceae

Zingiberales

HF677508

Martin G, Baurens FC, Cardi C, Aury JM, D'Hont A. The Complete Chloroplast Genome of Banana (Musa acuminata, Zingiberales): Insight into Plastid Monocotyledon Evolution PLoS ONE 8 (6), E67350

15

Petrosavia stellaris

Petrosaviaceae

Petrosaviales

KF482381

Logacheva MD, Schelkunov MI, Nuraliev MS, Samigullin TH, Penin AA. 2014. The plastid genome of mycoheterotrophic monocot Petrosavia stellaris exhibits both gene losses and multiple rearrangements Genome Biol Evol 6 (1): 238-246

16

Phalaenopsis aphrodite subsp formosana

Orchidaceae

Asparagales

NC_007499

Chang CC, et al. 2006. The chloroplast genome of Phalaenopsis aphrodite (Orchidaceae): comparative analysis of evolutionary rate with that of grasses and its phylogenetic implications Mol. Biol. Evol. 23 (2): 279-291

17

Oncidium Gower Ramsey

Orchidaceae

Asparagales

NC_014056

Wu FH, et al. 2010. Complete chloroplast genome of Oncidium Gower Ramsey and evaluation of molecular markers for identification and breeding in Oncidiinae. BMC Plant Biol. 10 (1), 68

18

Cymbidium aloifolium

Orchidaceae

Asparagales

NC_021429

Yang JB, Tang M, Li HT, Zhang ZR, Li DZ. 2013. Complete chloroplast genome of the genus Cymbidium: lights into the species identification, phylogenetic implications and population genetic analyses. BMC Evol. Biol. 13 (1), 84

19

Erycina pusilla

Orchidaceae

Asparagales

NC_018114

Pan IC, et al. 2012. Complete chloroplast genome sequence of an orchid model plant candidate: Erycina pusilla apply in tropical Oncidium breeding. PLoS ONE 7 (4), E34738

20

Yucca schidigera

Asparagaceae

Asparagales

EU016685

Jansen RK, 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. U.S.A. 104 (49): 19369-19374

21

Dendrocalamus latiflorus

Poaceae

Poales

FJ970916

Wu FH, et al. 2009. Complete nucleotide sequence of Dendrocalamus latiflorus and Bambusa oldhamii chloroplast genomes. Tree Physiol. 29 (6): 847-856

22

Anomochloa marantoidea

Poaceae

Poales

NC_014062

Morris LM, Duvall MR. 2010. The chloroplast genome of Anomochloa marantoidea (Anomochlooideae; Poaceae) comprises a mixture of grass-like and unique features. Am. J. Bot. 97 (4): 620-627

23

Phoenix dactylifera

Arecaceae

Arecales

NC_013991

Yang M, et al. 2010. The complete chloroplast genome sequence of date palm (Phoenix dactylifera L.). PLoS ONE 5 (9), E12762

24

Cocos nucifera

Arecaceae

Arecales

KF285453

Huang YY, Matzke AJ, Matzke M. 2013. Complete Sequence and Comparative Analysis of the Chloroplast Genome of Coconut Palm (Cocos nucifera). PLoS ONE 8 (8), E74736

25

Piper cenocladum

Piperaceae

Piperales

DQ887677

Cai Z, et al. 2006. Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogenetic relationships of magnoliids BMC Evol. Biol. 6, 77

26

Lilium longiflorum

Liliaceae

Liliales

KC968977

Kim JS, KimJ-H. 2013. Comparative Genome Analysis and Phylogenetic Relationship of Order Liliales Insight from the Complete Plastid Genome Sequences of TwoLilies (Lilium longiflorum and Alstroemeria aurea)
PLoS ONE 8 (6), E68180

27

Alstroemeria aurea

Alstroemeriaceae

KC968976

Kim JS, KimJ-H. 2013. Comparative Genome Analysis and Phylogenetic Relationship of Order Liliales Insight from the Complete Plastid Genome Sequences of TwoLilies (Lilium longiflorum and Alstroemeria aurea)
PLoS ONE 8 (6), E68180

28

Veratrum patulum

Melanthiaceae

KF437497

Do HDK, Kim JS, Kim J-H. 2013. Comparative genomics of four Liliales families inferred from the complete chloroplast genome sequence of Veratrum patulum O. Loes. (Melanthiaceae). Gene 530 (2): 229-235

29

Chionographis japonica

Melanthiaceae

KF951065

Bodin SS, Kim JS, Kim J-H. 2013. Complete Chloroplast Genome of Chionographis japonica (Willd.) Maxim. (Melanthiaceae): Comparative Genomics and Evaluation of Universal Primers for Liliales Plant Mol. Biol. Rep. 31 (6): 1407-1421

30

Smilax china

Smilacaceae

HM536959

Liu J, Qi ZC, Zhao YP, Fu CX, Xiang QY. 2012. Complete cpDNA genome sequence of Smilax china and phylogenetic placement of Liliales--influences of gene partitions and taxon sampling. Mol Phylogenet Evol. 64(3):545-62.

31

Paris verticillata

Melanthiaceae

KJ433485

Do HDK, Kim JS, Kim J-H. 2014.

32

Colchicum autumnale

Colchicaceae

Unpublished

Nguyen PAT, et al.

33

Gloriosa superba

Colchicaceae

Unpublished

Nguyen PAT, et al.

34

Lotus japonica

Fabaceae

Fabales

AP002983

Kato T, Kaneko T, Sato S, Nakamura Y, Tabata S. 2000. Complete structure of the chloroplast genome of a legume, Lotus japonicus. DNA Res. 7 (6): 323-330

35

Nicotiana tabacum

Solanaceae

Solanales

Z00044

Shinozaki K, et al. 1986. The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO J. 5 (9): 2043-2049

36

Cucumis sativus

Cucurbitaceae

Cucurbitales

DQ865976

Chung SM, Gordon VS, Staub JE. 2007. Sequencing cucumber (Cucumis sativus L.) chloroplast genomes identifies differences between chilling-tolerant and -susceptible cucumber lines. Genome 50 (2): 215-225

37

Ranunculus macranthus

Ranunculaceae

Ranunculales

DQ359689

Raubeson LA, et al. 2007. Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus. BMC Genomics 8, 174

38

Panax ginseng

Araliaceae

Apiales

NC_006290

Kim KJ, Lee HL. 2004. Complete chloroplast genome sequences from Korean ginseng (Panax schinseng Nees) and comparative analysis of sequence evolution among 17 vascular plants. DNA Res. 11 (4): 247-261

39

Arabidopsis thaliana

Brassicaceae

Brassicales

NC_000932

Sato S, Nakamura Y, Kaneko T, Asamizu E, Tabata S. 1999. Complete structure of the chloroplast genome of Arabidopsis thaliana. DNA Res. 6 (5): 283-290

40

Helianthus annuus

Asteraceae

Asterales

NC_007977

Timme RE, Kuehl JV, Boore JL, Jansen RK. (unpublished)



















*Angiosperm chloroplast genome data were downloaded from NCBI Organelle Genome Resources (http://www.ncbi.nlm.nih.gov/genomes/GenomesGroup.cgi?opt=plastid&taxid=3398).


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