-
1
-
-
84863230177
-
Phylogeny and molecular evolution of the green algae
-
Leliaert F, Smith DR, Moreau H, Herron MD, Verbruggen H, Delwiche CF, De Clerck O. Phylogeny and molecular evolution of the green algae. CRC Crit Rev Plant Sci 2012, 31:1-46.
-
(2012)
CRC Crit Rev Plant Sci
, vol.31
, pp. 1-46
-
-
Leliaert, F.1
Smith, D.R.2
Moreau, H.3
Herron, M.D.4
Verbruggen, H.5
Delwiche, C.F.6
De Clerck, O.7
-
2
-
-
80051663864
-
Into the deep: new discoveries at the base of the green plant phylogeny
-
21744372
-
Leliaert F, Verbruggen H, Zechman FW. Into the deep: new discoveries at the base of the green plant phylogeny. Bioessays 2011, 33(9):683-692. 10.1002/bies.201100035, 21744372.
-
(2011)
Bioessays
, vol.33
, Issue.9
, pp. 683-692
-
-
Leliaert, F.1
Verbruggen, H.2
Zechman, F.W.3
-
3
-
-
17644368841
-
Green algae and the origin of land plants
-
21652308
-
Lewis LA, McCourt RM. Green algae and the origin of land plants. Am J Bot 2004, 91(10):1535-1556. 10.3732/ajb.91.10.1535, 21652308.
-
(2004)
Am J Bot
, vol.91
, Issue.10
, pp. 1535-1556
-
-
Lewis, L.A.1
McCourt, R.M.2
-
4
-
-
0002980248
-
Classification of the green algae: a concept based on comparative cytology
-
London: Academic Press, Irvine DEG, John DM
-
Mattox KR, Stewart KD. Classification of the green algae: a concept based on comparative cytology. The Systematics of the Green Algae 1984, 29-72. London: Academic Press, Irvine DEG, John DM.
-
(1984)
The Systematics of the Green Algae
, pp. 29-72
-
-
Mattox, K.R.1
Stewart, K.D.2
-
5
-
-
11144274477
-
Pigment suites and taxonomic groups in Prasinophyceae
-
Latasa M, Scharek R, Le Gall F, Guillou L. Pigment suites and taxonomic groups in Prasinophyceae. J Phycol 2004, 40(6):1149-1155.
-
(2004)
J Phycol
, vol.40
, Issue.6
, pp. 1149-1155
-
-
Latasa, M.1
Scharek, R.2
Le Gall, F.3
Guillou, L.4
-
6
-
-
0001856962
-
Phylum Chlorophyta. Class Prasinophyceae
-
Boston: Jones and Bartlett Publishers, Margulis L, Corliss JO, Melkonian M, Chapman DJ
-
Melkonian M. Phylum Chlorophyta. Class Prasinophyceae. Handbook of Protoctista the Structure, Cultivation, Habitats and Life Histories of the Eukaryotic Microorganisms and their Descendants Exclusive of Animals, Plants and Fungi 1990, 600-607. Boston: Jones and Bartlett Publishers, Margulis L, Corliss JO, Melkonian M, Chapman DJ.
-
(1990)
Handbook of Protoctista the Structure, Cultivation, Habitats and Life Histories of the Eukaryotic Microorganisms and their Descendants Exclusive of Animals, Plants and Fungi
, pp. 600-607
-
-
Melkonian, M.1
-
7
-
-
0005591212
-
Flagellar apparatus architecture and the phylogeny of " green algae" : chlorophytes, euglenoids, glaucophytes
-
Boca Raton: CRC Press, Menzel D
-
O'Kelly CJ. Flagellar apparatus architecture and the phylogeny of " green algae" : chlorophytes, euglenoids, glaucophytes. The Cytoskeleton of the Algae 1992, 315-345. Boca Raton: CRC Press, Menzel D.
-
(1992)
The Cytoskeleton of the Algae
, pp. 315-345
-
-
O'Kelly, C.J.1
-
8
-
-
0000624211
-
The class Prasinophyceae
-
Bristol: Biopress Ltd, Round FE, Chapman DJ
-
Sym SD, Pienaar RN. The class Prasinophyceae. Progress Phycol Res, Volume 9 1993, 281-376. Bristol: Biopress Ltd, Round FE, Chapman DJ.
-
(1993)
Progress Phycol Res, Volume 9
, pp. 281-376
-
-
Sym, S.D.1
Pienaar, R.N.2
-
9
-
-
0028878420
-
A new marine picoeucaryote: Ostreococcus tauri gen. et sp. nov. (Chlorophyta, Prasinophyceae)
-
Chrétiennot-Dinet MJ, Courties C, Vaquer A, Neveux J, Claustre H, Lautier J, Machado MC. A new marine picoeucaryote: Ostreococcus tauri gen. et sp. nov. (Chlorophyta, Prasinophyceae). Phycologia 1995, 34(4):285-292.
-
(1995)
Phycologia
, vol.34
, Issue.4
, pp. 285-292
-
-
Chrétiennot-Dinet, M.J.1
Courties, C.2
Vaquer, A.3
Neveux, J.4
Claustre, H.5
Lautier, J.6
Machado, M.C.7
-
10
-
-
0027938679
-
Smallest eukaryotic organism
-
Courties C, Vaquer A, Troussellier M, Lautier J, Chretiennot-Dinet MJ, Neveux J, Machado C, Claustre H. Smallest eukaryotic organism. Nature 1994, 370(6487):255-255.
-
(1994)
Nature
, vol.370
, Issue.6487
, pp. 255-255
-
-
Courties, C.1
Vaquer, A.2
Troussellier, M.3
Lautier, J.4
Chretiennot-Dinet, M.J.5
Neveux, J.6
Machado, C.7
Claustre, H.8
-
11
-
-
0033857703
-
Phylogenetic analyses of 18S rDNA sequences reveal a new coccoid lineage of the Prasinophyceae (Chlorophyta)
-
Fawley MW, Yun Y, Qin M. Phylogenetic analyses of 18S rDNA sequences reveal a new coccoid lineage of the Prasinophyceae (Chlorophyta). J Phycol 2000, 36(2):387-393.
-
(2000)
J Phycol
, vol.36
, Issue.2
, pp. 387-393
-
-
Fawley, M.W.1
Yun, Y.2
Qin, M.3
-
12
-
-
3042806881
-
Diversity of picoplanktonic prasinophytes assessed by direct nuclear SSU rDNA sequencing of environmental samples and novel isolates retrieved from oceanic and coastal marine ecosystems
-
15305796
-
Guillou L, Eikrem W, Chrétiennot-Dinet M-J, Le Gall F, Massana R, Romari K, Pedrós-Alió C, Vaulot D. Diversity of picoplanktonic prasinophytes assessed by direct nuclear SSU rDNA sequencing of environmental samples and novel isolates retrieved from oceanic and coastal marine ecosystems. Protist 2004, 155:193-214. 10.1078/143446104774199592, 15305796.
-
(2004)
Protist
, vol.155
, pp. 193-214
-
-
Guillou, L.1
Eikrem, W.2
Chrétiennot-Dinet, M.-J.3
Le Gall, F.4
Massana, R.5
Romari, K.6
Pedrós-Alió, C.7
Vaulot, D.8
-
13
-
-
0032423364
-
The basal position of scaly green flagellates among the green algae (Chlorophyta) is revealed by analyses of nuclear-encoded SSU rRNA sequences
-
23194719
-
Nakayama T, Marin B, Kranz HD, Surek B, Huss VAR, Inouye I, Melkonian M. The basal position of scaly green flagellates among the green algae (Chlorophyta) is revealed by analyses of nuclear-encoded SSU rRNA sequences. Protist 1998, 149:367-380. 10.1016/S1434-4610(98)70043-4, 23194719.
-
(1998)
Protist
, vol.149
, pp. 367-380
-
-
Nakayama, T.1
Marin, B.2
Kranz, H.D.3
Surek, B.4
Huss, V.A.R.5
Inouye, I.6
Melkonian, M.7
-
14
-
-
44849104595
-
Wide genetic diversity of picoplanktonic green algae (Chloroplastida) in the Mediterranean Sea uncovered by a phylum-biased PCR approach
-
18430015
-
Viprey M, Guillou L, Ferreol M, Vaulot D. Wide genetic diversity of picoplanktonic green algae (Chloroplastida) in the Mediterranean Sea uncovered by a phylum-biased PCR approach. Environ Microbiol 2008, 10(7):1804-1822. 10.1111/j.1462-2920.2008.01602.x, 18430015.
-
(2008)
Environ Microbiol
, vol.10
, Issue.7
, pp. 1804-1822
-
-
Viprey, M.1
Guillou, L.2
Ferreol, M.3
Vaulot, D.4
-
15
-
-
77249178136
-
Molecular phylogeny and classification of the Mamiellophyceae class. nov. (Chlorophyta) based on sequence comparisons of the nuclear- and plastid-encoded rRNA operons
-
20005168
-
Marin B, Melkonian M. Molecular phylogeny and classification of the Mamiellophyceae class. nov. (Chlorophyta) based on sequence comparisons of the nuclear- and plastid-encoded rRNA operons. Protist 2010, 161(2):304-336. 10.1016/j.protis.2009.10.002, 20005168.
-
(2010)
Protist
, vol.161
, Issue.2
, pp. 304-336
-
-
Marin, B.1
Melkonian, M.2
-
16
-
-
0000111410
-
The origin, losses and gains of Chloroplasts
-
US: Springer, Lewin RA
-
Cavalier-Smith T. The origin, losses and gains of Chloroplasts. Origins of Plastids 1993, 291-348. US: Springer, Lewin RA.
-
(1993)
Origins of Plastids
, pp. 291-348
-
-
Cavalier-Smith, T.1
-
17
-
-
72849119546
-
Chlorodendrophyceae class. nov. (Chlorophyta, Viridiplantae) in the Ukrainian flora: I. The volume, phylogenetic relations and taxonomical status
-
Massjuk N. Chlorodendrophyceae class. nov. (Chlorophyta, Viridiplantae) in the Ukrainian flora: I. The volume, phylogenetic relations and taxonomical status. Ukr Bot J 2006, 63:601-614.
-
(2006)
Ukr Bot J
, vol.63
, pp. 601-614
-
-
Massjuk, N.1
-
18
-
-
0002514258
-
Picophytoplankton
-
Raven J. Picophytoplankton. Progress Phycol Res 1999, 13:33-106.
-
(1999)
Progress Phycol Res
, vol.13
, pp. 33-106
-
-
Raven, J.1
-
19
-
-
77958495156
-
The exceptionally large chloroplast genome of the green alga Floydiella terrestris illuminates the evolutionary history of the Chlorophyceae
-
2997540, 20624729
-
Brouard JS, Otis C, Lemieux C, Turmel M. The exceptionally large chloroplast genome of the green alga Floydiella terrestris illuminates the evolutionary history of the Chlorophyceae. Genome Biol Evol 2010, 2:240-256. 10.1093/gbe/evq014, 2997540, 20624729.
-
(2010)
Genome Biol Evol
, vol.2
, pp. 240-256
-
-
Brouard, J.S.1
Otis, C.2
Lemieux, C.3
Turmel, M.4
-
20
-
-
84872124943
-
Complete plastid genomes from Ophioglossum californicum, Psilotum nudum, and Equisetum hyemale reveal an ancestral land plant genome structure and resolve the position of Equisetales among monilophytes
-
3553075, 23311954
-
Grewe F, Guo W, Gubbels EA, Hansen AK, Mower JP. Complete plastid genomes from Ophioglossum californicum, Psilotum nudum, and Equisetum hyemale reveal an ancestral land plant genome structure and resolve the position of Equisetales among monilophytes. BMC Evol Biol 2013, 13:8. 10.1186/1471-2148-13-8, 3553075, 23311954.
-
(2013)
BMC Evol Biol
, vol.13
, pp. 8
-
-
Grewe, F.1
Guo, W.2
Gubbels, E.A.3
Hansen, A.K.4
Mower, J.P.5
-
21
-
-
37649007931
-
Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns
-
2148296, 18048330
-
Jansen RK, Cai Z, Raubeson LA, Daniell H, Depamphilis CW, Leebens-Mack J, Muller KF, Guisinger-Bellian M, Haberle RC, Hansen AK, Chumley TW, Lee SB, Peery R, McNeal JR, Kuehl JV, Boore JL. 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 2007, 104(49):19369-19374. 10.1073/pnas.0709121104, 2148296, 18048330.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, Issue.49
, pp. 19369-19374
-
-
Jansen, R.K.1
Cai, Z.2
Raubeson, L.A.3
Daniell, H.4
Depamphilis, C.W.5
Leebens-Mack, J.6
Muller, K.F.7
Guisinger-Bellian, M.8
Haberle, R.C.9
Hansen, A.K.10
Chumley, T.W.11
Lee, S.B.12
Peery, R.13
McNeal, J.R.14
Kuehl, J.V.15
Boore, J.L.16
-
22
-
-
33846849230
-
A clade uniting the green algae Mesostigma viride and Chlorokybus atmophyticus represents the deepest branch of the Streptophyta in chloroplast genome-based phylogenies
-
1781420, 17222354
-
Lemieux C, Otis C, Turmel M. A clade uniting the green algae Mesostigma viride and Chlorokybus atmophyticus represents the deepest branch of the Streptophyta in chloroplast genome-based phylogenies. BMC Biol 2007, 5:2. 10.1186/1741-7007-5-2, 1781420, 17222354.
-
(2007)
BMC Biol
, vol.5
, pp. 2
-
-
Lemieux, C.1
Otis, C.2
Turmel, M.3
-
23
-
-
33750303564
-
The deepest divergences in land plants inferred from phylogenomic evidence
-
1622854, 17030812
-
Qiu YL, Li LB, Wang B, Chen ZD, Knoop V, Groth-Malonek M, Dombrovska O, Lee J, Kent L, Rest J, Estabrook GF, Hendry TA, Taylor DW, Testa CM, Ambros M, Crandall-Stotler B, Duff RJ, Stech M, Frey W, Quandt D, Davis CC. The deepest divergences in land plants inferred from phylogenomic evidence. Proc Natl Acad Sci U S A 2006, 103(42):15511-15516. 10.1073/pnas.0603335103, 1622854, 17030812.
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, Issue.42
, pp. 15511-15516
-
-
Qiu, Y.L.1
Li, L.B.2
Wang, B.3
Chen, Z.D.4
Knoop, V.5
Groth-Malonek, M.6
Dombrovska, O.7
Lee, J.8
Kent, L.9
Rest, J.10
Estabrook, G.F.11
Hendry, T.A.12
Taylor, D.W.13
Testa, C.M.14
Ambros, M.15
Crandall-Stotler, B.16
Duff, R.J.17
Stech, M.18
Frey, W.19
Quandt, D.20
Davis, C.C.21
more..
-
24
-
-
44349111714
-
Deep division in the Chlorophyceae (Chlorophyta) revealed by chloroplast phylogenomic analyses
-
Turmel M, Brouard JS, Gagnon C, Otis C, Lemieux C. Deep division in the Chlorophyceae (Chlorophyta) revealed by chloroplast phylogenomic analyses. J Phycol 2008, 44(3):739-750.
-
(2008)
J Phycol
, vol.44
, Issue.3
, pp. 739-750
-
-
Turmel, M.1
Brouard, J.S.2
Gagnon, C.3
Otis, C.4
Lemieux, C.5
-
25
-
-
60149094050
-
The chloroplast genomes of the green algae Pyramimonas, Monomastix, and Pycnococcus shed new light on the evolutionary history of prasinophytes and the origin of the secondary chloroplasts of euglenids
-
Turmel M, Gagnon MC, O'Kelly CJ, Otis C, Lemieux C. The chloroplast genomes of the green algae Pyramimonas, Monomastix, and Pycnococcus shed new light on the evolutionary history of prasinophytes and the origin of the secondary chloroplasts of euglenids. Mol Biol Evol 2009, 26(3):631-648.
-
(2009)
Mol Biol Evol
, vol.26
, Issue.3
, pp. 631-648
-
-
Turmel, M.1
Gagnon, M.C.2
O'Kelly, C.J.3
Otis, C.4
Lemieux, C.5
-
26
-
-
64849088316
-
Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas
-
19359590
-
Worden AZ, J-h L, Mock T, Rouzé P, Simmons MP, Aerts AL, Allen AE, Cuvelier ML, Derelle E, Everett MV, Foulon E, Grimwood J, Gundlach H, Henrissat B, Napoli C, Badger JH, Coutinho PM, Demir E, Dubchak I, Gentemann C, Eikrem W, Gready JE, John U, Lanier W, Lindquist EA, Panaud O, Pangilinan J, Paulsen I, Piegu B, Poliakov A. Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas. Science 2009, 324:268-272. 10.1126/science.1167222, 19359590.
-
(2009)
Science
, vol.324
, pp. 268-272
-
-
Worden, A.Z.1
J-h, L.2
Mock, T.3
Rouzé, P.4
Simmons, M.P.5
Aerts, A.L.6
Allen, A.E.7
Cuvelier, M.L.8
Derelle, E.9
Everett, M.V.10
Foulon, E.11
Grimwood, J.12
Gundlach, H.13
Henrissat, B.14
Napoli, C.15
Badger, J.H.16
Coutinho, P.M.17
Demir, E.18
Dubchak, I.19
Gentemann, C.20
Eikrem, W.21
Gready, J.E.22
John, U.23
Lanier, W.24
Lindquist, E.A.25
Panaud, O.26
Pangilinan, J.27
Paulsen, I.28
Piegu, B.29
Poliakov, A.30
more..
-
27
-
-
34047227131
-
The complete chloroplast and mitochondrial DNA sequence of Ostreococcus tauri: organelle genomes of the smallest eukaryote are examples of compaction
-
17251180
-
Robbens S, Derelle E, Ferraz C, Wuyts J, Moreau H, Van de Peer Y. The complete chloroplast and mitochondrial DNA sequence of Ostreococcus tauri: organelle genomes of the smallest eukaryote are examples of compaction. Mol Biol Evol 2007, 24:956-968. 10.1093/molbev/msm012, 17251180.
-
(2007)
Mol Biol Evol
, vol.24
, pp. 956-968
-
-
Robbens, S.1
Derelle, E.2
Ferraz, C.3
Wuyts, J.4
Moreau, H.5
Van de Peer, Y.6
-
28
-
-
0033621040
-
The complete chloroplast DNA sequence of the green alga Nephroselmis olivacea: insights into the architecture of ancestral chloroplast genomes
-
17874, 10468594
-
Turmel M, Otis C, Lemieux C. The complete chloroplast DNA sequence of the green alga Nephroselmis olivacea: insights into the architecture of ancestral chloroplast genomes. Proc Natl Acad Sci U S A 1999, 96:10248-10253. 10.1073/pnas.96.18.10248, 17874, 10468594.
-
(1999)
Proc Natl Acad Sci U S A
, vol.96
, pp. 10248-10253
-
-
Turmel, M.1
Otis, C.2
Lemieux, C.3
-
29
-
-
36148986480
-
Phylogeny and ultrastructure of Nephroselmis and Pseudoscourfieldia (Chlorophyta), including the description of Nephroselmis anterostigmatica sp. nov. and a proposal for the Nephroselmidales ord. nov
-
Nakayama T, Suda S, Kawachi M, Inouye I. Phylogeny and ultrastructure of Nephroselmis and Pseudoscourfieldia (Chlorophyta), including the description of Nephroselmis anterostigmatica sp. nov. and a proposal for the Nephroselmidales ord. nov. Phycologia 2007, 46(6):680-697.
-
(2007)
Phycologia
, vol.46
, Issue.6
, pp. 680-697
-
-
Nakayama, T.1
Suda, S.2
Kawachi, M.3
Inouye, I.4
-
30
-
-
84894600564
-
Conflicting phylogenies for early land plants are caused by composition biases among synonymous substitutions
-
3926305, 24399481
-
Cox CJ, Li B, Foster PG, Embley TM, Civan P. Conflicting phylogenies for early land plants are caused by composition biases among synonymous substitutions. Syst Biol 2014, 63(2):272-279. 10.1093/sysbio/syt109, 3926305, 24399481.
-
(2014)
Syst Biol
, vol.63
, Issue.2
, pp. 272-279
-
-
Cox, C.J.1
Li, B.2
Foster, P.G.3
Embley, T.M.4
Civan, P.5
-
31
-
-
84903714806
-
Compositional biases among synonymous substitutions cause conflict between gene and protein trees for plastid origins
-
4069611, 24795089
-
Li B, Lopes JS, Foster PG, Embley TM, Cox CJ. Compositional biases among synonymous substitutions cause conflict between gene and protein trees for plastid origins. Mol Biol Evol 2014, 31(7):1697-1709. 10.1093/molbev/msu105, 4069611, 24795089.
-
(2014)
Mol Biol Evol
, vol.31
, Issue.7
, pp. 1697-1709
-
-
Li, B.1
Lopes, J.S.2
Foster, P.G.3
Embley, T.M.4
Cox, C.J.5
-
32
-
-
84871849373
-
Serine codon-usage bias in deep phylogenomics: pancrustacean relationships as a case study
-
22962005
-
Rota-Stabelli O, Lartillot N, Philippe H, Pisani D. Serine codon-usage bias in deep phylogenomics: pancrustacean relationships as a case study. Syst Biol 2013, 62(1):121-133. 10.1093/sysbio/sys077, 22962005.
-
(2013)
Syst Biol
, vol.62
, Issue.1
, pp. 121-133
-
-
Rota-Stabelli, O.1
Lartillot, N.2
Philippe, H.3
Pisani, D.4
-
33
-
-
34248159030
-
Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model
-
Lartillot N, Brinkmann H, Philippe H. Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model. BMC Evol Biol 2007, 7(Suppl 1):S4.
-
(2007)
BMC Evol Biol
, vol.7
, pp. S4
-
-
Lartillot, N.1
Brinkmann, H.2
Philippe, H.3
-
34
-
-
2442691520
-
A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process
-
15014145
-
Lartillot N, Philippe H. A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol Biol Evol 2004, 21(6):1095-1109. 10.1093/molbev/msh112, 15014145.
-
(2004)
Mol Biol Evol
, vol.21
, Issue.6
, pp. 1095-1109
-
-
Lartillot, N.1
Philippe, H.2
-
35
-
-
79951478430
-
Acoelomorph flatworms are deuterostomes related to Xenoturbella
-
4025995, 21307940
-
Philippe H, Brinkmann H, Copley RR, Moroz LL, Nakano H, Poustka AJ, Wallberg A, Peterson KJ, Telford MJ. Acoelomorph flatworms are deuterostomes related to Xenoturbella. Nature 2011, 470(7333):255-260. 10.1038/nature09676, 4025995, 21307940.
-
(2011)
Nature
, vol.470
, Issue.7333
, pp. 255-260
-
-
Philippe, H.1
Brinkmann, H.2
Copley, R.R.3
Moroz, L.L.4
Nakano, H.5
Poustka, A.J.6
Wallberg, A.7
Peterson, K.J.8
Telford, M.J.9
-
36
-
-
79953716259
-
Resolving difficult phylogenetic questions: why more sequences are not enough
-
3057953, 21423652
-
Philippe H, Brinkmann H, Lavrov DV, Littlewood DTJ, Manuel M, Worheide G, Baurain D. Resolving difficult phylogenetic questions: why more sequences are not enough. PLos Biol 2011, 9(3):e1000602. 10.1371/journal.pbio.1000602, 3057953, 21423652.
-
(2011)
PLos Biol
, vol.9
, Issue.3
, pp. e1000602
-
-
Philippe, H.1
Brinkmann, H.2
Lavrov, D.V.3
Littlewood, D.T.J.4
Manuel, M.5
Worheide, G.6
Baurain, D.7
-
37
-
-
80052067631
-
The GC-rich mitochondrial and plastid genomes of the green alga Coccomyxa give insight into the evolution of organelle DNA nucleotide landscape
-
3162594, 21887287
-
Smith DR, Burki F, Yamada T, Grimwood J, Grigoriev IV, Van Etten JL, Keeling PJ. The GC-rich mitochondrial and plastid genomes of the green alga Coccomyxa give insight into the evolution of organelle DNA nucleotide landscape. PLoS One 2011, 6(8):e23624. 10.1371/journal.pone.0023624, 3162594, 21887287.
-
(2011)
PLoS One
, vol.6
, Issue.8
, pp. e23624
-
-
Smith, D.R.1
Burki, F.2
Yamada, T.3
Grimwood, J.4
Grigoriev, I.V.5
Van Etten, J.L.6
Keeling, P.J.7
-
38
-
-
84864002352
-
Nested in the Chlorellales or independent class? Phylogeny and classification of the Pedinophyceae (Viridiplantae) revealed by molecular phylogenetic analyses of complete nuclear and plastid-encoded rRNA operons
-
22192529
-
Marin B. Nested in the Chlorellales or independent class? Phylogeny and classification of the Pedinophyceae (Viridiplantae) revealed by molecular phylogenetic analyses of complete nuclear and plastid-encoded rRNA operons. Protist 2012, 163(5):778-805. 10.1016/j.protis.2011.11.004, 22192529.
-
(2012)
Protist
, vol.163
, Issue.5
, pp. 778-805
-
-
Marin, B.1
-
39
-
-
84866924443
-
Modeling protein evolution with several amino acid replacement matrices depending on site rates
-
22491036
-
Le SQ, Dang CC, Gascuel O. Modeling protein evolution with several amino acid replacement matrices depending on site rates. Mol Biol Evol 2012, 29(10):2921-2936. 10.1093/molbev/mss112, 22491036.
-
(2012)
Mol Biol Evol
, vol.29
, Issue.10
, pp. 2921-2936
-
-
Le, S.Q.1
Dang, C.C.2
Gascuel, O.3
-
40
-
-
84878115695
-
A 20-state empirical amino-acid substitution model for green plant chloroplasts
-
23567023
-
Cox CJ, Foster PG. A 20-state empirical amino-acid substitution model for green plant chloroplasts. Mol Phylogenet Evol 2013, 68(2):218-220. 10.1016/j.ympev.2013.03.030, 23567023.
-
(2013)
Mol Phylogenet Evol
, vol.68
, Issue.2
, pp. 218-220
-
-
Cox, C.J.1
Foster, P.G.2
-
41
-
-
84959798530
-
Cases in which parsimony or compatibility methods will be positively misleading
-
Felsenstein J. Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool 1978, 27(4):401-410.
-
(1978)
Syst Zool
, vol.27
, Issue.4
, pp. 401-410
-
-
Felsenstein, J.1
-
42
-
-
0030292241
-
Glutamyl-transfer RNA: at the crossroad between chlorophyll and protein biosynthesis
-
Kumar AM, Schaub U, Söll D, Ujwal ML. Glutamyl-transfer RNA: at the crossroad between chlorophyll and protein biosynthesis. Trends Plant Sci 1996, 1(11):371-376.
-
(1996)
Trends Plant Sci
, vol.1
, Issue.11
, pp. 371-376
-
-
Kumar, A.M.1
Schaub, U.2
Söll, D.3
Ujwal, M.L.4
-
43
-
-
33746275499
-
The complete chloroplast genome sequence of the chlorophycean green alga Scenedesmus obliquus reveals a compact gene organization and a biased distribution of genes on the two DNA strands
-
1513399, 16638149
-
de Cambiaire JC, Otis C, Lemieux C, Turmel M. The complete chloroplast genome sequence of the chlorophycean green alga Scenedesmus obliquus reveals a compact gene organization and a biased distribution of genes on the two DNA strands. BMC Evol Biol 2006, 6:37. 10.1186/1471-2148-6-37, 1513399, 16638149.
-
(2006)
BMC Evol Biol
, vol.6
, pp. 37
-
-
de Cambiaire, J.C.1
Otis, C.2
Lemieux, C.3
Turmel, M.4
-
44
-
-
0034628462
-
Ancestral chloroplast genome in Mesostigma viride reveals an early branch of green plant evolution
-
10688199
-
Lemieux C, Otis C, Turmel M. Ancestral chloroplast genome in Mesostigma viride reveals an early branch of green plant evolution. Nature 2000, 403(6770):649-652. 10.1038/35001059, 10688199.
-
(2000)
Nature
, vol.403
, Issue.6770
, pp. 649-652
-
-
Lemieux, C.1
Otis, C.2
Turmel, M.3
-
45
-
-
0029905884
-
Ebb and flow of the chloroplast inverted repeat
-
Goulding SE, Olmstead RG, Morden CW, Wolfe KH. Ebb and flow of the chloroplast inverted repeat. Mol Gen Genet 1996, 252(1-2):195-206.
-
(1996)
Mol Gen Genet
, vol.252
, Issue.1-2
, pp. 195-206
-
-
Goulding, S.E.1
Olmstead, R.G.2
Morden, C.W.3
Wolfe, K.H.4
-
46
-
-
70349921146
-
The chloroplast genomes of the green algae Pedinomonas minor, Parachlorella kessleri, and Oocystis solitaria reveal a shared ancestry between the Pedinomonadales and Chlorellales
-
19578159
-
Turmel M, Otis C, Lemieux C. The chloroplast genomes of the green algae Pedinomonas minor, Parachlorella kessleri, and Oocystis solitaria reveal a shared ancestry between the Pedinomonadales and Chlorellales. Mol Biol Evol 2009, 26(10):2317-2331. 10.1093/molbev/msp138, 19578159.
-
(2009)
Mol Biol Evol
, vol.26
, Issue.10
, pp. 2317-2331
-
-
Turmel, M.1
Otis, C.2
Lemieux, C.3
-
47
-
-
27744492579
-
The complete chloroplast DNA sequences of the charophycean green algae Staurastrum and Zygnema reveal that the chloroplast genome underwent extensive changes during the evolution of the Zygnematales
-
1277820, 16236178
-
Turmel M, Otis C, Lemieux C. The complete chloroplast DNA sequences of the charophycean green algae Staurastrum and Zygnema reveal that the chloroplast genome underwent extensive changes during the evolution of the Zygnematales. BMC Biol 2005, 3:22. 10.1186/1741-7007-3-22, 1277820, 16236178.
-
(2005)
BMC Biol
, vol.3
, pp. 22
-
-
Turmel, M.1
Otis, C.2
Lemieux, C.3
-
48
-
-
33646890404
-
The chloroplast genome sequence of Chara vulgaris sheds new light into the closest green algal relatives of land plants
-
16611644
-
Turmel M, Otis C, Lemieux C. The chloroplast genome sequence of Chara vulgaris sheds new light into the closest green algal relatives of land plants. Mol Biol Evol 2006, 23(6):1324-1338. 10.1093/molbev/msk018, 16611644.
-
(2006)
Mol Biol Evol
, vol.23
, Issue.6
, pp. 1324-1338
-
-
Turmel, M.1
Otis, C.2
Lemieux, C.3
-
49
-
-
0029066770
-
Structure and activities of group II introns
-
7574489
-
Michel F, Ferat J. Structure and activities of group II introns. Annu Rev Biochem 1995, 64(1):435-461. 10.1146/annurev.bi.64.070195.002251, 7574489.
-
(1995)
Annu Rev Biochem
, vol.64
, Issue.1
, pp. 435-461
-
-
Michel, F.1
Ferat, J.2
-
50
-
-
0037143760
-
The chloroplast and mitochondrial genome sequences of the charophyte Chaetosphaeridium globosum: insights into the timing of the events that restructured organelle DNAs within the green algal lineage that led to land plants
-
123247, 12161560
-
Turmel M, Otis C, Lemieux C. The chloroplast and mitochondrial genome sequences of the charophyte Chaetosphaeridium globosum: insights into the timing of the events that restructured organelle DNAs within the green algal lineage that led to land plants. Proc Natl Acad Sci U S A 2002, 99(17):11275-11280. 10.1073/pnas.162203299, 123247, 12161560.
-
(2002)
Proc Natl Acad Sci U S A
, vol.99
, Issue.17
, pp. 11275-11280
-
-
Turmel, M.1
Otis, C.2
Lemieux, C.3
-
51
-
-
33748952472
-
Distinctive architecture of the chloroplast genome in the chlorophycean green alga Stigeoclonium helveticum
-
16944205
-
Bélanger AS, Brouard JS, Charlebois P, Otis C, Lemieux C, Turmel M. Distinctive architecture of the chloroplast genome in the chlorophycean green alga Stigeoclonium helveticum. Mol Genet Genomics 2006, 276(5):464-477. 10.1007/s00438-006-0156-2, 16944205.
-
(2006)
Mol Genet Genomics
, vol.276
, Issue.5
, pp. 464-477
-
-
Bélanger, A.S.1
Brouard, J.S.2
Charlebois, P.3
Otis, C.4
Lemieux, C.5
Turmel, M.6
-
52
-
-
46649089921
-
Chloroplast DNA sequence of the green alga Oedogonium cardiacum (Chlorophyceae): unique genome architecture, derived characters shared with the Chaetophorales and novel genes acquired through horizontal transfer
-
2442088, 18558012
-
Brouard JS, Otis C, Lemieux C, Turmel M. Chloroplast DNA sequence of the green alga Oedogonium cardiacum (Chlorophyceae): unique genome architecture, derived characters shared with the Chaetophorales and novel genes acquired through horizontal transfer. BMC Genomics 2008, 9:290. 10.1186/1471-2164-9-290, 2442088, 18558012.
-
(2008)
BMC Genomics
, vol.9
, pp. 290
-
-
Brouard, J.S.1
Otis, C.2
Lemieux, C.3
Turmel, M.4
-
53
-
-
0000221783
-
Structural and transcription analysis of two homologous genes for the P700 chlorophyll a-apoproteins in Chlamydomonas reinhardii: evidence for in vivo trans-splicing
-
553617, 16453785
-
Kück U, Choquet Y, Schneider M, Dron M, Bennoun P. Structural and transcription analysis of two homologous genes for the P700 chlorophyll a-apoproteins in Chlamydomonas reinhardii: evidence for in vivo trans-splicing. EMBO J 1987, 6:2185-2195. 553617, 16453785.
-
(1987)
EMBO J
, vol.6
, pp. 2185-2195
-
-
Kück, U.1
Choquet, Y.2
Schneider, M.3
Dron, M.4
Bennoun, P.5
-
54
-
-
70349969877
-
Trans-splicing of organelle introns - a detour to continuous RNAs
-
19644921
-
Glanz S, Kück U. Trans-splicing of organelle introns - a detour to continuous RNAs. Bioessays 2009, 31(9):921-934. 10.1002/bies.200900036, 19644921.
-
(2009)
Bioessays
, vol.31
, Issue.9
, pp. 921-934
-
-
Glanz, S.1
Kück, U.2
-
55
-
-
84891292267
-
The mitochondrial genome of the prasinophyte Prasinoderma coloniale reveals two trans-spliced group I introns in the large subunit rRNA gene
-
3873408, 24386369
-
Pombert JF, Otis C, Turmel M, Lemieux C. The mitochondrial genome of the prasinophyte Prasinoderma coloniale reveals two trans-spliced group I introns in the large subunit rRNA gene. PLoS One 2013, 8(12):e84325. 10.1371/journal.pone.0084325, 3873408, 24386369.
-
(2013)
PLoS One
, vol.8
, Issue.12
, pp. e84325
-
-
Pombert, J.F.1
Otis, C.2
Turmel, M.3
Lemieux, C.4
-
56
-
-
84864576853
-
Evolution of mitochondrial introns in plants and photosynthetic microbes
-
Bonen L. Evolution of mitochondrial introns in plants and photosynthetic microbes. Adv Bot Res 2012, 63:155-186.
-
(2012)
Adv Bot Res
, vol.63
, pp. 155-186
-
-
Bonen, L.1
-
57
-
-
84907658650
-
Biological Resource Center of the National Institute of Technology and Evaluation
-
Biological Resource Center of the National Institute of Technology and Evaluation. http://www.nbrc.nite.go.jp/e/.
-
-
-
-
58
-
-
84986764196
-
Media for the culture of oceanic ultraphytoplankton
-
Keller MD, Seluin RC, Claus W, Guillard RRL. Media for the culture of oceanic ultraphytoplankton. J Phycol 1987, 23:633-638.
-
(1987)
J Phycol
, vol.23
, pp. 633-638
-
-
Keller, M.D.1
Seluin, R.C.2
Claus, W.3
Guillard, R.R.L.4
-
59
-
-
0033197514
-
The complete mitochondrial DNA sequences of Nephroselmis olivacea and Pedinomonas minor. Two radically different evolutionary patterns within green algae
-
144307, 10488238
-
Turmel M, Lemieux C, Burger G, Lang BF, Otis C, Plante I, Gray MW. The complete mitochondrial DNA sequences of Nephroselmis olivacea and Pedinomonas minor. Two radically different evolutionary patterns within green algae. Plant Cell 1999, 11:1717-1730. 144307, 10488238.
-
(1999)
Plant Cell
, vol.11
, pp. 1717-1730
-
-
Turmel, M.1
Lemieux, C.2
Burger, G.3
Lang, B.F.4
Otis, C.5
Plante, I.6
Gray, M.W.7
-
60
-
-
79952453090
-
Green-colored plastids in the dinoflagellate genus Lepidodinium are of core chlorophyte origin
-
20829107
-
Matsumoto T, Shinozaki F, Chikuni T, Yabuki A, Takishita K, Kawachi M, Nakayama T, Inouye I, Hashimoto T, Inagaki Y. Green-colored plastids in the dinoflagellate genus Lepidodinium are of core chlorophyte origin. Protist 2011, 162(2):268-276. 10.1016/j.protis.2010.07.001, 20829107.
-
(2011)
Protist
, vol.162
, Issue.2
, pp. 268-276
-
-
Matsumoto, T.1
Shinozaki, F.2
Chikuni, T.3
Yabuki, A.4
Takishita, K.5
Kawachi, M.6
Nakayama, T.7
Inouye, I.8
Hashimoto, T.9
Inagaki, Y.10
-
61
-
-
0031955116
-
Consed: a graphical tool for sequence finishing
-
9521923
-
Gordon D, Abajian C, Green P. Consed: a graphical tool for sequence finishing. Genome Res 1998, 8:195-202. 10.1101/gr.8.3.195, 9521923.
-
(1998)
Genome Res
, vol.8
, pp. 195-202
-
-
Gordon, D.1
Abajian, C.2
Green, P.3
-
62
-
-
78349238864
-
Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies
-
3119603, 20958248
-
Boisvert S, Laviolette F, Corbeil J. Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. J Comput Biol 2010, 17(11):1519-1533. 10.1089/cmb.2009.0238, 3119603, 20958248.
-
(2010)
J Comput Biol
, vol.17
, Issue.11
, pp. 1519-1533
-
-
Boisvert, S.1
Laviolette, F.2
Corbeil, J.3
-
63
-
-
23944523620
-
The chloroplast genome sequence of the green alga Pseudendoclonium akinetum (Ulvophyceae) reveals unusual structural features and new insights into the branching order of chlorophyte lineages
-
15930151
-
Pombert JF, Otis C, Lemieux C, Turmel M. The chloroplast genome sequence of the green alga Pseudendoclonium akinetum (Ulvophyceae) reveals unusual structural features and new insights into the branching order of chlorophyte lineages. Mol Biol Evol 2005, 22(9):1903-1918. 10.1093/molbev/msi182, 15930151.
-
(2005)
Mol Biol Evol
, vol.22
, Issue.9
, pp. 1903-1918
-
-
Pombert, J.F.1
Otis, C.2
Lemieux, C.3
Turmel, M.4
-
64
-
-
34250665888
-
RNAmmer: consistent and rapid annotation of ribosomal RNA genes
-
1888812, 17452365
-
Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007, 35(9):3100-3108. 10.1093/nar/gkm160, 1888812, 17452365.
-
(2007)
Nucleic Acids Res
, vol.35
, Issue.9
, pp. 3100-3108
-
-
Lagesen, K.1
Hallin, P.2
Rodland, E.A.3
Staerfeldt, H.H.4
Rognes, T.5
Ussery, D.W.6
-
65
-
-
0030854739
-
TRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence
-
146525, 9023104
-
Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997, 25(5):955-964. 10.1093/nar/25.5.0955, 146525, 9023104.
-
(1997)
Nucleic Acids Res
, vol.25
, Issue.5
, pp. 955-964
-
-
Lowe, T.M.1
Eddy, S.R.2
-
66
-
-
0024428420
-
Comparative and functional anatomy of group II catalytic introns - a review
-
2684776
-
Michel F, Umesono K, Ozeki H. Comparative and functional anatomy of group II catalytic introns - a review. Gene 1989, 82(1):5-30. 10.1016/0378-1119(89)90026-7, 2684776.
-
(1989)
Gene
, vol.82
, Issue.1
, pp. 5-30
-
-
Michel, F.1
Umesono, K.2
Ozeki, H.3
-
67
-
-
0025678737
-
Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis
-
2258934
-
Michel F, Westhof E. Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J Mol Biol 1990, 216:585-610. 10.1016/0022-2836(90)90386-Z, 2258934.
-
(1990)
J Mol Biol
, vol.216
, pp. 585-610
-
-
Michel, F.1
Westhof, E.2
-
68
-
-
36048989002
-
OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes
-
17957369
-
Lohse M, Drechsel O, Bock R. OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Curr Genet 2007, 52:267-274. 10.1007/s00294-007-0161-y, 17957369.
-
(2007)
Curr Genet
, vol.52
, pp. 267-274
-
-
Lohse, M.1
Drechsel, O.2
Bock, R.3
-
69
-
-
0035890910
-
REPuter: the manifold applications of repeat analysis on a genomic scale
-
92531, 11713313
-
Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R. REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res 2001, 29:4633-4642. 10.1093/nar/29.22.4633, 92531, 11713313.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 4633-4642
-
-
Kurtz, S.1
Choudhuri, J.V.2
Ohlebusch, E.3
Schleiermacher, C.4
Stoye, J.5
Giegerich, R.6
-
70
-
-
84871197257
-
Repeat Masker
-
Repeat Masker. http://www.repeatmasker.org/.
-
-
-
-
71
-
-
84871926999
-
Cross match
-
Cross match. http://www.phrap.org/phredphrapconsed.html.
-
-
-
-
72
-
-
3042666256
-
MUSCLE: multiple sequence alignment with high accuracy and high throughput
-
390337, 15034147
-
Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004, 32(5):1792-1797. 10.1093/nar/gkh340, 390337, 15034147.
-
(2004)
Nucleic Acids Res
, vol.32
, Issue.5
, pp. 1792-1797
-
-
Edgar, R.C.1
-
73
-
-
67650757433
-
TrimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
-
2712344, 19505945
-
Capella-Gutierrez S, Silla-Martinez JM, Gabaldon T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 2009, 25(15):1972-1973. 10.1093/bioinformatics/btp348, 2712344, 19505945.
-
(2009)
Bioinformatics
, vol.25
, Issue.15
, pp. 1972-1973
-
-
Capella-Gutierrez, S.1
Silla-Martinez, J.M.2
Gabaldon, T.3
-
74
-
-
69949126557
-
PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating
-
19535536
-
Lartillot N, Lepage T, Blanquart S. PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics 2009, 25(17):2286-2288. 10.1093/bioinformatics/btp368, 19535536.
-
(2009)
Bioinformatics
, vol.25
, Issue.17
, pp. 2286-2288
-
-
Lartillot, N.1
Lepage, T.2
Blanquart, S.3
-
75
-
-
0000122573
-
PHYLIP - phylogeny inference package (version 3.2)
-
Felsenstein J. PHYLIP - phylogeny inference package (version 3.2). Cladistics 1989, 5(2):164-166.
-
(1989)
Cladistics
, vol.5
, Issue.2
, pp. 164-166
-
-
Felsenstein, J.1
-
76
-
-
33750403801
-
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
-
16928733
-
Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22(21):2688-2690. 10.1093/bioinformatics/btl446, 16928733.
-
(2006)
Bioinformatics
, vol.22
, Issue.21
, pp. 2688-2690
-
-
Stamatakis, A.1
-
77
-
-
84907662801
-
Data from: Six newly sequenced chloroplast genomes from prasinophyte green algae provide insights into the relationships among prasinophyte lineages and the diversity of streamlined genome architecture in picoplanktonic species
-
Lemieux C, Otis C, Turmel M. Data from: Six newly sequenced chloroplast genomes from prasinophyte green algae provide insights into the relationships among prasinophyte lineages and the diversity of streamlined genome architecture in picoplanktonic species. TreeBase repository http://purl.org/phylo/treebase/phylows/study/TB2:S16332.
-
TreeBase repository
-
-
Lemieux, C.1
Otis, C.2
Turmel, M.3
|