Intrageneric chloroplast genome comparison in the genus Euglena (Phylum: Euglenophyta) with annotated chloroplast genomes of Euglena hiemalis and Euglena clara

[1]  W. Shin,et al.  Morphological and genetic diversity of Euglena deses group (Euglenophyceae) with emphasis on cryptic species , 2016 .

[2]  E. Linton,et al.  The chloroplast genome of Phacus orbicularis (Euglenophyceae): an initial datum point for the phacaceae , 2016, Journal of phycology.

[3]  R. Triemer,et al.  Chloroplast Genome Evolution in the Euglenaceae , 2015, The Journal of eukaryotic microbiology.

[4]  W. Shin,et al.  Taxon-rich multigene phylogeny of the photosynthetic euglenoids (Euglenophyceae) , 2015, Front. Ecol. Evol..

[5]  A. Karnkowska,et al.  Phylogenetic Relationships and Morphological Character Evolution of Photosynthetic Euglenids (Excavata) Inferred from Taxon‐rich Analyses of Five Genes , 2015, The Journal of eukaryotic microbiology.

[6]  Robert D. Finn,et al.  Rfam 12.0: updates to the RNA families database , 2014, Nucleic Acids Res..

[7]  W. Shin,et al.  Molecular Phylogeny and Cryptic Diversity of the Genus Phacus (Phacaceae, Euglenophyceae) and the Descriptions of Seven New Species , 2014, Journal of phycology.

[8]  R. Triemer,et al.  Characterization of Euglenaformis gen. nov. and the chloroplast genome of Euglenaformis [Euglena] proxima (Euglenophyta) , 2014 .

[9]  Koichiro Tamura,et al.  MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. , 2013, Molecular biology and evolution.

[10]  R. Triemer,et al.  Tracing Patterns of Chloroplast Evolution in Euglenoids: Contributions from Colacium vesiculosum and Strombomonas acuminata (Euglenophyta) , 2013, The Journal of eukaryotic microbiology.

[11]  P. Keeling,et al.  Evidence for Transitional Stages in the Evolution of Euglenid Group II Introns and Twintrons in the Monomorphina aenigmatica Plastid Genome , 2012, PloS one.

[12]  R. Triemer,et al.  Evolution of the chloroplast genome in photosynthetic euglenoids: a comparison of Eutreptia viridis and Euglena gracilis (Euglenophyta). , 2012, Protist.

[13]  R. Triemer,et al.  Comparative chloroplast genomics between Euglena viridis and Euglena gracilis (Euglenophyta) , 2012 .

[14]  Shane S. Sturrock,et al.  Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data , 2012, Bioinform..

[15]  V. Hampl,et al.  The Plastid Genome of Eutreptiella Provides a Window into the Process of Secondary Endosymbiosis of Plastid in Euglenids , 2012, PloS one.

[16]  W. Shin,et al.  MULTIGENE ANALYSES OF PHOTOSYNTHETIC EUGLENOIDS AND NEW FAMILY, PHACACEAE (EUGLENALES) 1 , 2010 .

[17]  W. Shin,et al.  Reconstructing euglenoid evolutionary relationships using three genes: nuclear SSU and LSU, and chloroplast SSU rDNA sequences and the description of Euglenaria gen. nov. (Euglenophyta). , 2010, Protist.

[18]  R. Triemer,et al.  A Color Atlas of Photosynthetic Euglenoids , 2010 .

[19]  Ning Ma,et al.  BLAST+: architecture and applications , 2009, BMC Bioinformatics.

[20]  Paul D. Shaw,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2022 .

[21]  L. Hug,et al.  Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic “supergroups” , 2009, Proceedings of the National Academy of Sciences.

[22]  C. O'kelly,et al.  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. , 2009, Molecular biology and evolution.

[23]  W. Shin,et al.  PHYLOGENY OF THE EUGLENALES INFERRED FROM PLASTID LSU rDNA SEQUENCES 1 , 2008, Journal of phycology.

[24]  Stacy Brosnan,et al.  PHYLOGENY OF THE EUGLENOID LORICATE GENERA TRACHELOMONAS AND STROMBOMONAS (EUGLENOPHYTA) INFERRED FROM NUCLEAR SSU AND LSU rDNA 1 , 2008, Journal of phycology.

[25]  Kenneth H. Wolfe,et al.  GenomeVx: simple web-based creation of editable circular chromosome maps , 2008, Bioinform..

[26]  Peter F. Hallin,et al.  RNAmmer: consistent and rapid annotation of ribosomal RNA genes , 2007, Nucleic acids research.

[27]  Eric Linton,et al.  PHYLOGENY OF THE EUGLENALES BASED UPON COMBINED SSU AND LSU RDNA SEQUENCE COMPARISONS AND DESCRIPTION OF DISCOPLASTIS GEN. NOV. (EUGLENOPHYTA) 1 , 2006 .

[28]  F. Blattner,et al.  Mauve: multiple alignment of conserved genomic sequence with rearrangements. , 2004, Genome research.

[29]  M. Melkonian,et al.  Phylogeny and taxonomic revision of plastid-containing euglenophytes based on SSU rDNA sequence comparisons and synapomorphic signatures in the SSU rRNA secondary structure. , 2003, Protist.

[30]  W. Hachtel,et al.  Complete gene map of the plastid genome of the nonphotosynthetic euglenoid flagellate Astasia longa. , 2000, Protist.

[31]  R. Triemer,et al.  A MOLECULAR ANALYSIS OF THE EUGLENOPHYTES USING SSU RDNA , 2000, Journal of phycology.

[32]  R. Triemer,et al.  A Molecular Study of Euglenoid Phylogeny using Small Subunit rDNA , 1999, The Journal of eukaryotic microbiology.

[33]  R. Triemer,et al.  PHYLOGENETIC RELATIONSHIPS OF SELECTED EUGLENOID GENERA BASED ON MORPHOLOGICAL AND MOLECULAR DATA 1 , 1997 .

[34]  S. Eddy,et al.  tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. , 1997, Nucleic acids research.

[35]  A. Monfort,et al.  Complete sequence of Euglena gracilis chloroplast DNA. , 1993, Nucleic acids research.

[36]  R. Hallick,et al.  Group II twintron: an intron within an intron in a chloroplast cytochrome b‐559 gene. , 1991, The EMBO journal.

[37]  D. Christopher,et al.  Euglena gracilis chloroplast ribosomal protein operon: a new chloroplast gene for ribosomal protein L5 and description of a novel organelle intron category designated group III. , 1989, Nucleic acids research.

[38]  S. P. Gibbs.  THE CHLOROPLASTS OF SOME ALGAL GROUPS MAY HAVE EVOLVED FROM ENDOSYMBIOTIC EUKARYOTIC ALGAE , 1981, Annals of the New York Academy of Sciences.

[39]  S. P. Gibbs,et al.  The chloroplasts of Euglena may have evolved from symbiotic green algae , 1978 .

[40]  A. Preisfeld,et al.  The Chloroplast Genome of Euglena mutabilis—Cluster Arrangement, Intron Analysis, and Intrageneric Trends , 2017, The Journal of eukaryotic microbiology.

[41]  H. Mewes,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2004 .

[42]  G. Benson,et al.  Tandem repeats finder: a program to analyze DNA sequences. , 1999, Nucleic acids research.

[43]  S. Schwartzbach,et al.  Characterization of the unique intron-exon junctions of Euglena gene(s) encoding the polyprotein precursor to the light-harvesting chlorophyll a/b binding protein of photosystem II. , 1994, Nucleic acids research.

[44]  H. Skuja.  Taxonomie des Phytoplanktons einiger Seen in Uppland, Schweden , 1948 .