Comparative analysis of chloroplast genomes: Functional annotation, genome-based phylogeny, and deduced evolutionary patterns

Genome Research

Volumn 12, Issue 4, 2002, Pages 567-583

  De Las Rivas, Javier ^a   Lozano, Juan Jose ^a   Ortiz, Angel R ^b  

^a INSTITUTO DE RECURSOS NATURALES Y AGROBIOLOGÍA DE SALAMANCA   (Spain)

^b NEW YORK UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ABC TRANSPORTER; ACETYL COENZYME A CARBOXYLASE; ALLOPHYCOCYANIN; CARBAMOYL PHOSPHATE SYNTHASE; CARRIER PROTEIN; CHAPERONIN; CHLOROPLAST DNA; CYTOCHROME C; FARNESYL TRANS TRANSFERASE; FERREDOXIN; INITIATION FACTOR 3; M PROTEIN; MOLYBDOPTERIN; PENICILLIN BINDING PROTEIN; PERMEASE; PROTEIN DNAK; PROTEOME; PROTON TRANSPORTING ADENOSINE TRIPHOSPHATE SYNTHASE; QUINOLINIC ACID; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE DEHYDROGENASE; RIBONUCLEOTIDE REDUCTASE; RIBOSOME PROTEIN; RIBULOSEBISPHOSPHATE CARBOXYLASE; THIOREDOXIN; TRYPTOPHAN SYNTHASE;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENOME; CHLOROPLAST GENETICS; CLUSTER ANALYSIS; CONTROLLED STUDY; CORRELATION ANALYSIS; CYANOBACTERIUM; FACTUAL DATABASE; GENE ASSIGNMENT; GENE CLUSTER; GENOME ANALYSIS; MOLECULAR EVOLUTION; NONHUMAN; OPEN READING FRAME; ORTHOLOGY; PHYCOBILISOME; PHYLOGENY; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN FUNCTION; SPECIES DIFFERENTIATION;

ALGAE, GREEN; BACTERIAL PROTEINS; CHLOROPLASTS; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; CYANOBACTERIA; EVOLUTION, MOLECULAR; GENES, BACTERIAL; GENES, PLANT; GENOME, BACTERIAL; GENOME, PLANT; PHYLOGENY; PLANT PROTEINS; QUALITY CONTROL;

BACTERIA (MICROORGANISMS); CYANOBACTERIA; SYNECHOCYSTIS;

EID: 0036225307     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.209402     Document Type: Article

References (51)

1. Do aligned sequences share the same fold?
2. Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA
3. Balancing the two photosystems: Photosynthetic electron transfer governs transcription of reaction centre genes in chloroplasts
4. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
5. Bioinformatics: From genome data to biological knowledge
6. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
7. Photoinhibition of photosystem II. Inactivation, protein damage and turnover
8. Abnormal regulation of photosynthetic electron transport in a chloroplast ycf9 inactivation mutant
9. Molecular biology of chloroplast biogenesis: Gene expression, protein import and intraorganellar sorting
10. Predicting function: From genes to genomes and back
11. Identification of a functional respiratory complex in chloroplasts through analysis of tobacco mutants containing disrupted plastid ndh genes
12. Membrane heredity and early chloroplast evolution
13. Synthesis, assembly and degradation of thylakoid membrane proteins
14. Acceptor side mechanism of photoinduced proteolysis of the D1 protein in photosystem II reaction centers
15. The plastid genome of the cryptophyte alga, Guillardia theta: Complete sequence and conserved synteny groups confirm its common ancestry with red algae
16. The highly reduced genome of an enslaved algal nucleus
17. The two largest chloroplast genome-encoded open reading frames of higher plants are essential genes
18. Biological sequence analysis
19. Protein function in the post-genomic era
20. An aminoacyl tRNA synthetase whose sequence fits into neither of the two known classes
21. Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods
22. Exhaustive matching of the entire protein sequence database
23. Ebb and flow of the chloroplast inverted repeat
24. Evolution of organellar genomes
25. Complete sequence of Euglena gracilis chloroplast DNA
26. A plastid of probable green algal origin in Apicomplexan parasites
27. The chloroplast genome of a chlorophyll a+c-containing alga, Odontella sinensis
28. Ancestral chloroplast genome in Mesostigma viride reveals an early branch of green plant evolution
29. Gene transfer to the nucleus and the evolution of chloroplasts
30. An examination of the effect of six types of error perturbation on fifteen clustering algorithms
31. The origin of red algae and the evolution of chloroplasts
32. Benchmarking PSI-BLAST in genome annotation
33. Computational methods for protein function analysis
34. Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles
35. Chloroplast microsatellites: New tools for studies in plant ecology and evolution
36. Chloroplast
37. The neighbor-joining method: A new method for reconstructing phylogenetic trees
38. A regulatory role of the PetM subunit in a cyanobacterial cytochrome b6f complex
39. An independent role of cytochrome c550 in cyanobacterial photosystem II as revealed by double-deletion mutagenesis of the psbO and psbV genes in Synechocystis sp PCC 6803
40. Gene-cluster analysis in chloroplast genomics
41. The chloroplast genome
42. Evolution and mechanism of translation in chloroplasts
43. The chloroplast gene ycf9 encodes a photosystem II (PSII) core subunit, PsbZ, that participates in PSII supramolecular architecture
44. Chlorophyll b and phycobilins in the common ancestor of cyanobacteria and chloroplasts
45. The complete chloroplast DNA sequence of the green alga Nephroselmis olivacea: Insights into the architecture of ancestral chloroplast genomes
46. Hierarchical grouping to optimize an objective function
47. The gene for the ribulose-1,5-bisphosphate carboxylase/oxygenase rubisco. Small subunit relocated to the plastid genome of tobacco directs the synthesis of small subunits that assemble into rubisco
48. Ins and outs of plastid genome evolution
49. Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant