Bioinformatics and Comparative Genomics of Chlorobi
Genome sequencing, assembly and annotation
Sanger sequencing: (with JGI-DOE except as noted; abbreviations used are noted in parentheses)
- Chlorobium chlorochromatii CaD3 (cagg)
- Chlorobium ferrooxidans DSM 13031 (cfer)
- Chlorobium limicola DSM 245 (clim)
- Chlorobium phaeobacteroides BS1 (cphb)
- Chlorobium phaeobacteroides DSM 266 (cpha)
- Chlorobaculum (formerly Chlorobium) tepidum TLS (ctep) (sequenced in collaboration with TIGR)
- Pelodictyon luteolum DSM 273 (plut)
- Pelodictyon phaeoclathratiforme BU-1 (ppha)
- Prosthecochloris aestuarii DSM 271 (paes)
- Prosthecochloris vibrioformis DSM 265 (cvib)
- Chlorobaculum parvum (cpar)
- Chloroherpeton thalassium (cher)
Assembly methods
- Phred/Phrap/Consed
- Multiplex PCR
- Pheromone-based genetic algorithm for comparative genome assembly
Annotation methods
- Glimmer
- COG, NCBI-NR database
- TIGR Manatee
Whole-genome phylogeny of Chlorobi
Phylogenetic relationships among 12 sequenced GSBs based on their 813 core gene sets. Bootstrap values in green are estimated by concatenated protein sequences of 813 core sets using NJ method. Red numbers are consensus values estimated by randomly choosing 100 proteins from 813 core sets to construct the phylogeny with their concatenated sequences (ML method), then repeating this process 100 times. Blue values are estimated by the consensus tree with 50% cutoff from 813 phylogenies constructed by ML method. |
General genome features of Chlorobi
| |
Cvib |
Ctep |
Cpar |
Plut |
Cfer* |
Cagg |
Paes |
Cphb |
Clim |
Ppha |
Cpha |
Cher* |
| Size (bp) |
1,966,858 |
2,154,939 |
2,289,237 |
2,364,842 |
~2,538,957 |
2,572,079 |
2,579,695 |
2,736,403 |
2,763,182 |
3,018,240 |
3,133,902 |
~3,270,419 |
| GC content(%) |
52.99 |
56.53 |
55.81 |
57.33 |
50.11 |
44.28 |
50.05 |
48.92 |
51.33 |
48.05 |
48.35 |
45.06 |
| # ORFs |
1,809 |
2,026 |
2,141 |
2,188 |
2,349 |
2,099 |
2,380 |
2,596 |
2,623 |
2,971 |
3,070 |
2,955 |
| ORF aver. Length(bp) |
997 |
926 |
932 |
967 |
941 |
1087 |
933 |
900 |
930 |
889 |
883 |
975 |
| # rRNA operon |
1 |
2 |
2 |
2 |
2 |
1 |
1 |
2 |
2 |
3 |
2 |
1 |
| # tRNA |
45 |
50 |
49 |
48 |
44 |
45 |
46 |
46 |
48 |
49 |
47 |
44 |
| # ORFs in COG |
1,390 |
1,543 |
1,581 |
1,613 |
1,645 |
1,460 |
1,674 |
1,760 |
1,794 |
1,916 |
1,890 |
1,976 |
| # unique ORFs |
119 |
140 |
216 |
214 |
328 |
307 |
303 |
371 |
349 |
528 |
643 |
1,139 |
| # ISs |
22 |
19 |
2 |
8 |
5 |
25 |
43 |
45 |
56 |
48 |
88 |
10 |
Note: * indicates data retrieved from the incomplete but nearly finished genome.
Genomic structures of Chlorobi
Comparisons of genome structures among Chlorobi. The central blue lines represent the chromosomes of four Chlorobi species. |
Linear genomic comparison of C. aggregatum (Top), C. tepdium (Center), and C. limicola (Bottom). Red lines show the orthologous genes on the forward strands; blue lines show the orthologous genes on the reverse strands. |
 |
 Orthologous and Non-orthologous genes in C. vibrioforme and P. luteolum. Circles on the map show the genomic islands along the chromosome.
|
Unequal evolutionary rates in Chlorobi
The accelerated evolution of C. aggregatum. (A) Comparisons of nonsynonymous substitution rates (dN) between C. aggregatum (in yellow) and C. limicola (in blue). The rate of dN is significantly elevated in C. aggregatum, indicating the accelerated evolution of the symbiotic green sulfur bacterium. (B) The relative branch depth of C. aggregatum derived from 813 core gene sets shows the protein sequences of C. aggregatum evolve faster than other speices. (C) The relationships between evolutionary rates and topologies. (D) The frequency spectra of relative branch depth of C. aggregatum under three different topologies as shown in figure C. Thus, the incongruence of gene phylogeny in C. aggregatum with the species phylogeny may be due to the long branch attraction effect caused by the accelerated evolution of C. aggregatum. |
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