List of sequenced plastomes (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "List of sequenced plastomes" in English language version.

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Moore MJ, Soltis PS, Bell CD, Burleigh JG, Soltis DE (March 2010). "Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots". Proceedings of the National Academy of Sciences of the United States of America. 107 (10): 4623–8. Bibcode:2010PNAS..107.4623M. doi:10.1073/pnas.0907801107. PMC 2842043. PMID 20176954.
Wickett NJ, Zhang Y, Hansen SK, Roper JM, Kuehl JV, Plock SA, Wolf PG, DePamphilis CW, Boore JL, Goffinet B (February 2008). "Functional gene losses occur with minimal size reduction in the plastid genome of the parasitic liverwort Aneura mirabilis". Molecular Biology and Evolution. 25 (2): 393–401. doi:10.1093/molbev/msm267. PMID 18056074.
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Villarreal JC, Forrest LL, Wickett N, Goffinet B (March 2013). "The plastid genome of the hornwort Nothoceros aenigmaticus (Dendrocerotaceae): phylogenetic signal in inverted repeat expansion, pseudogenization, and intron gain". American Journal of Botany. 100 (3): 467–77. doi:10.3732/ajb.1200429. PMID 23416362.
Grosche C, Funk HT, Maier UG, Zauner S (2012). "The chloroplast genome of Pellia endiviifolia: gene content, RNA-editing pattern, and the origin of chloroplast editing". Genome Biology and Evolution. 4 (12): 1349–57. doi:10.1093/gbe/evs114. PMC 3542565. PMID 23221608.
Sugiura C, Kobayashi Y, Aoki S, Sugita C, Sugita M (September 2003). "Complete chloroplast DNA sequence of the moss Physcomitrella patens: evidence for the loss and relocation of rpoA from the chloroplast to the nucleus". Nucleic Acids Research. 31 (18): 5324–31. doi:10.1093/nar/gkg726. PMC 203311. PMID 12954768.
Laura L. Forrest; Norman J. Wickett, Cymon J. Cox & Bernard Goffinet (2011). "Deep sequencing of Ptilidium (Ptilidiaceae) suggests evolutionary stasis in liverwort plastid genome structure" (PDF). Plant Ecology and Evolution. 144 (1): 29–43. doi:10.5091/plecevo.2011.535. hdl:10400.1/5518.
Oliver MJ, Murdock AG, Mishler BD, Kuehl JV, Boore JL, Mandoli DF, Everett KD, Wolf PG, Duffy AM, Karol KG (February 2010). "Chloroplast genome sequence of the moss Tortula ruralis: gene content, polymorphism, and structural arrangement relative to other green plant chloroplast genomes". BMC Genomics. 11: 143. doi:10.1186/1471-2164-11-143. PMC 2841679. PMID 20187961.
Wolf PG, Rowe CA, Sinclair RB, Hasebe M (April 2003). "Complete nucleotide sequence of the chloroplast genome from a leptosporangiate fern, Adiantum capillus-veneris L". DNA Research. 10 (2): 59–65. doi:10.1093/dnares/10.2.59. PMID 12755170.
Gao L, Yi X, Yang YX, Su YJ, Wang T (June 2009). "Complete chloroplast genome sequence of a tree fern Alsophila spinulosa: insights into evolutionary changes in fern chloroplast genomes". BMC Evolutionary Biology. 9: 130. doi:10.1186/1471-2148-9-130. PMC 2706227. PMID 19519899.
Roper JM, Hansen SK, Wolf PG, Karol KG, Mandoli DF, Everett KD, Kuehl J, Boore JL (2007). "The Complete Plastid Genome Sequence of Angiopteris evecta (G. Forst.) Hoffm. (Marattiaceae)". American Fern Journal. 97 (2): 95–106. doi:10.1640/0002-8444(2007)97[95:TCPGSO]2.0.CO;2.
Wolf PG, Karol KG, Mandoli DF, Kuehl J, Arumuganathan K, Ellis MW, Mishler BD, Kelch DG, Olmstead RG, Boore JL (May 2005). "The first complete chloroplast genome sequence of a lycophyte, Huperzia lucidula (Lycopodiaceae)". Gene. 350 (2): 117–28. doi:10.1016/j.gene.2005.01.018. PMID 15788152.
Tsuji S, Ueda K, Nishiyama T, Hasebe M, Yoshikawa S, Konagaya A, Nishiuchi T, Yamaguchi K (March 2007). "The chloroplast genome from a lycophyte (microphyllophyte), Selaginella uncinata, has a unique inversion, transpositions and many gene losses". Journal of Plant Research. 120 (2): 281–90. doi:10.1007/s10265-006-0055-y. PMID 17297557. S2CID 7691300.
Hirao T, Watanabe A, Kurita M, Kondo T, Takata K (June 2008). "Complete nucleotide sequence of the Cryptomeria japonica D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species". BMC Plant Biology. 8: 70. doi:10.1186/1471-2229-8-70. PMC 2443145. PMID 18570682.
Jansen RK, Cai Z, Raubeson LA, Daniell H, Depamphilis CW, Leebens-Mack J, Müller KF, Guisinger-Bellian M, Haberle RC, Hansen AK, Chumley TW, Lee SB, Peery R, McNeal JR, Kuehl JV, Boore JL (December 2007). "Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns". Proceedings of the National Academy of Sciences of the United States of America. 104 (49): 19369–74. Bibcode:2007PNAS..10419369J. doi:10.1073/pnas.0709121104. PMC 2148296. PMID 18048330.
Wu CS, Wang YN, Liu SM, Chaw SM (June 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". Molecular Biology and Evolution. 24 (6): 1366–79. doi:10.1093/molbev/msm059. PMID 17383970.
Leebens-Mack J, Raubeson LA, Cui L, Kuehl JV, Fourcade MH, Chumley TW, Boore JL, Jansen RK, depamphilis CW (October 2005). "Identifying the basal angiosperm node in chloroplast genome phylogenies: sampling one's way out of the Felsenstein zone". Molecular Biology and Evolution. 22 (10): 1948–63. doi:10.1093/molbev/msi191. PMID 15944438.
Lin, Diana; Coombe, Lauren; Jackman, Shaun D.; Gagalova, Kristina K.; Warren, René L.; Hammond, S. Austin; McDonald, Helen; Kirk, Heather; Pandoh, Pawan; Zhao, Yongjun; Moore, Richard A. (2019-06-13). Stajich, Jason E. (ed.). "Complete Chloroplast Genome Sequence of an Engelmann Spruce ( Picea engelmannii , Genotype Se404-851) from Western Canada". Microbiology Resource Announcements. 8 (24): e00382–19, /mra/8/24/MRA.00382–19.atom. doi:10.1128/MRA.00382-19. ISSN 2576-098X. PMC 6588038. PMID 31196920.
Jackman, Shaun D.; Warren, René L.; Gibb, Ewan A.; Vandervalk, Benjamin P.; Mohamadi, Hamid; Chu, Justin; Raymond, Anthony; Pleasance, Stephen; Coope, Robin; Wildung, Mark R.; Ritland, Carol E. (January 2016). "Organellar Genomes of White Spruce ( Picea glauca ): Assembly and Annotation". Genome Biology and Evolution. 8 (1): 29–41. doi:10.1093/gbe/evv244. ISSN 1759-6653. PMC 4758241. PMID 26645680.
Lin, Diana; Coombe, Lauren; Jackman, Shaun D.; Gagalova, Kristina K.; Warren, René L.; Hammond, S. Austin; Kirk, Heather; Pandoh, Pawan; Zhao, Yongjun; Moore, Richard A.; Mungall, Andrew J. (2019-06-06). Rokas, Antonis (ed.). "Complete Chloroplast Genome Sequence of a White Spruce ( Picea glauca , Genotype WS77111) from Eastern Canada". Microbiology Resource Announcements. 8 (23): e00381–19, /mra/8/23/MRA.00381–19.atom. doi:10.1128/MRA.00381-19. ISSN 2576-098X. PMC 6554609. PMID 31171622.
Coombe, Lauren; Warren, René L.; Jackman, Shaun D.; Yang, Chen; Vandervalk, Benjamin P.; Moore, Richard A.; Pleasance, Stephen; Coope, Robin J.; Bohlmann, Joerg; Holt, Robert A.; Jones, Steven J. M. (2016-09-15). Budak, Hikmet (ed.). "Assembly of the Complete Sitka Spruce Chloroplast Genome Using 10X Genomics' GemCode Sequencing Data". PLOS ONE. 11 (9): e0163059. Bibcode:2016PLoSO..1163059C. doi:10.1371/journal.pone.0163059. ISSN 1932-6203. PMC 5025161. PMID 27632164.
Wakasugi T, Tsudzuki J, Ito S, Nakashima K, Tsudzuki T, Sugiura M (October 1994). "Loss of all ndh genes as determined by sequencing the entire chloroplast genome of the black pine Pinus thunbergii". Proceedings of the National Academy of Sciences of the United States of America. 91 (21): 9794–8. Bibcode:1994PNAS...91.9794W. doi:10.1073/pnas.91.21.9794. PMC 44903. PMID 7937893.
McCoy SR, Kuehl JV, Boore JL, Raubeson LA (May 2008). "The complete plastid genome sequence of Welwitschia mirabilis: an unusually compact plastome with accelerated divergence rates". BMC Evolutionary Biology. 8: 130. doi:10.1186/1471-2148-8-130. PMC 2386820. PMID 18452621.
Yan M, Moore MJ, Meng A, Yao X, Wang H (2016-09-21). "The first complete plastome sequence of the basal asterid family Styracaceae (Ericales) reveals a large inversion". Plant Systematics and Evolution. 303 (1): 61–70. doi:10.1007/s00606-016-1352-0. ISSN 0378-2697. S2CID 25942874.
Kim JS, Kim JH (2013-06-18). "Comparative genome analysis and phylogenetic relationship of order Liliales insight from the complete plastid genome sequences of two Lilies (Lilium longiflorum and Alstroemeria aurea)". PLOS ONE. 8 (6): e68180. Bibcode:2013PLoSO...868180K. doi:10.1371/journal.pone.0068180. PMC 3688979. PMID 23950788.
Goremykin VV, Hirsch-Ernst KI, Wolfl S, Hellwig FH (September 2003). "Analysis of the Amborella trichopoda chloroplast genome sequence suggests that amborella is not a basal angiosperm". Molecular Biology and Evolution. 20 (9): 1499–505. doi:10.1093/molbev/msg159. PMID 12832641.
Sato S, Nakamura Y, Kaneko T, Asamizu E, Tabata S (October 1999). "Complete structure of the chloroplast genome of Arabidopsis thaliana". DNA Research. 6 (5): 283–90. doi:10.1093/dnares/6.5.283. PMID 10574454.
Schmitz-Linneweber C, Regel R, Du TG, Hupfer H, Herrmann RG, Maier RM (September 2002). "The plastid chromosome of Atropa belladonna and its comparison with that of Nicotiana tabacum: the role of RNA editing in generating divergence in the process of plant speciation". Molecular Biology and Evolution. 19 (9): 1602–12. doi:10.1093/oxfordjournals.molbev.a004222. PMID 12200487. S2CID 1111063.
Hansen DR, Dastidar SG, Cai Z, Penaflor C, Kuehl JV, Boore JL, Jansen RK (November 2007). "Phylogenetic and evolutionary implications of complete chloroplast genome sequences of four early-diverging angiosperms: Buxus (Buxaceae), Chloranthus (Chloranthaceae), Dioscorea (Dioscoreaceae), and Illicium (Schisandraceae)". Molecular Phylogenetics and Evolution. 45 (2): 547–63. doi:10.1016/j.ympev.2007.06.004. PMID 17644003.
Goremykin V, Hirsch-Ernst KI, Wölfl S, Hellwig FH (2003). "The chloroplast genome of the basal angiosperm Calycanthus fertilis – structural and phylogenetic analyses". Plant Systematics and Evolution. 242 (1–4): 119–135. doi:10.1007/s00606-003-0056-4. S2CID 44377635.
Yang Y, Wang M, Lu Z, Xie X, Feng S (2017-01-04). "Characterization of the complete chloroplast genome of Carpinus tientaiensis". Conservation Genetics Resources. 9 (2): 339–341. doi:10.1007/s12686-016-0668-y. ISSN 1877-7252. S2CID 5184815.
Bausher MG, Singh ND, Lee SB, Jansen RK, Daniell H (September 2006). "The complete chloroplast genome sequence of Citrus sinensis (L.) Osbeck var 'Ridge Pineapple': organization and phylogenetic relationships to other angiosperms". BMC Plant Biology. 6: 21. doi:10.1186/1471-2229-6-21. PMC 1599732. PMID 17010212.
Huang YY, Matzke AJ, Matzke M (2013-08-30). "Complete sequence and comparative analysis of the chloroplast genome of coconut palm (Cocos nucifera)". PLOS ONE. 8 (8): e74736. Bibcode:2013PLoSO...874736H. doi:10.1371/journal.pone.0074736. PMC 3758300. PMID 24023703.
Samson N, Bausher MG, Lee SB, Jansen RK, Daniell H (March 2007). "The complete nucleotide sequence of the coffee (Coffea arabica L.) chloroplast genome: organization and implications for biotechnology and phylogenetic relationships amongst angiosperms". Plant Biotechnology Journal. 5 (2): 339–53. doi:10.1111/j.1467-7652.2007.00245.x. PMC 3473179. PMID 17309688.
Leseberg CH, Duvall MR (October 2009). "The complete chloroplast genome of Coix lacryma-jobi and a comparative molecular evolutionary analysis of plastomes in cereals". Journal of Molecular Evolution. 69 (4): 311–8. Bibcode:2009JMolE..69..311L. doi:10.1007/s00239-009-9275-9. PMID 19777151. S2CID 24418374.
Wicke S, Müller KF, de Pamphilis CW, Quandt D, Wickett NJ, Zhang Y, Renner SS, Schneeweiss GM (October 2013). "Mechanisms of functional and physical genome reduction in photosynthetic and nonphotosynthetic parasitic plants of the broomrape family". The Plant Cell. 25 (10): 3711–25. doi:10.1105/tpc.113.113373. PMC 3877813. PMID 24143802.
Plader W, Yukawa Y, Sugiura M, Malepszy S (2007). "The complete structure of the cucumber (Cucumis sativus L.) chloroplast genome: its composition and comparative analysis". Cellular & Molecular Biology Letters. 12 (4): 584–94. doi:10.2478/s11658-007-0029-7. PMC 6275786. PMID 17607527.
McNeal JR, Kuehl JV, Boore JL, de Pamphilis CW (October 2007). "Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus Cuscuta". BMC Plant Biology. 7: 57. doi:10.1186/1471-2229-7-57. PMC 2216012. PMID 17956636.
Funk HT, Berg S, Krupinska K, Maier UG, Krause K (August 2007). "Complete DNA sequences of the plastid genomes of two parasitic flowering plant species, Cuscuta reflexa and Cuscuta gronovii". BMC Plant Biology. 7: 45. doi:10.1186/1471-2229-7-45. PMC 2089061. PMID 17714582.
Lin CS, Chen JJ, Huang YT, Chan MT, Daniell H, Chang WJ, Hsu CT, Liao DC, Wu FH, Lin SY, Liao CF, Deyholos MK, Wong GK, Albert VA, Chou ML, Chen CY, Shih MC (March 2015). "The location and translocation of ndh genes of chloroplast origin in the Orchidaceae family". Scientific Reports. 5: 9040. Bibcode:2015NatSR...5E9040L. doi:10.1038/srep09040. PMC 4356964. PMID 25761566.
Roquet C, Coissac É, Cruaud C, Boleda M, Boyer F, Alberti A, Gielly L, Taberlet P, Thuiller W, Van Es J, Lavergne S (July 2016). "Understanding the evolution of holoparasitic plants: the complete plastid genome of the holoparasite Cytinus hypocistis (Cytinaceae)". Annals of Botany. 118 (5): 885–896. doi:10.1093/aob/mcw135. PMC 5055816. PMID 27443299.
Ruhlman T, Lee SB, Jansen RK, Hostetler JB, Tallon LJ, Town CD, Daniell H (August 2006). "Complete plastid genome sequence of Daucus carota: implications for biotechnology and phylogeny of angiosperms". BMC Genomics. 7: 222. doi:10.1186/1471-2164-7-222. PMC 1579219. PMID 16945140.
Cai Z, Penaflor C, Kuehl JV, Leebens-Mack J, Carlson JE, dePamphilis CW, Boore JL, Jansen RK (October 2006). "Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogenetic relationships of magnoliids". BMC Evolutionary Biology. 6: 77. doi:10.1186/1471-2148-6-77. PMC 1626487. PMID 17020608.
Wolfe KH, Morden CW, Palmer JD (November 1992). "Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant". Proceedings of the National Academy of Sciences of the United States of America. 89 (22): 10648–52. Bibcode:1992PNAS...8910648W. doi:10.1073/pnas.89.22.10648. PMC 50398. PMID 1332054.
Schelkunov MI, Shtratnikova VY, Nuraliev MS, Selosse MA, Penin AA, Logacheva MD (January 2015). "Exploring the limits for reduction of plastid genomes: a case study of the mycoheterotrophic orchids Epipogium aphyllum and Epipogium roseum". Genome Biology and Evolution. 7 (4): 1179–91. doi:10.1093/gbe/evv019. PMC 4419786. PMID 25635040.
Blazier JC, Jansen RK, Mower JP, Govindu M, Zhang J, Weng ML, Ruhlman TA (June 2016). "Variable presence of the inverted repeat and plastome stability in Erodium". Annals of Botany. 117 (7): 1209–20. doi:10.1093/aob/mcw065. PMC 4904181. PMID 27192713.
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Lee SB, Kaittanis C, Jansen RK, Hostetler JB, Tallon LJ, Town CD, Daniell H (March 2006). "The complete chloroplast genome sequence of Gossypium hirsutum: organization and phylogenetic relationships to other angiosperms". BMC Genomics. 7: 61. doi:10.1186/1471-2164-7-61. PMC 1513215. PMID 16553962.
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