Comparative Genomic Analysis of Agarolytic Flavobacterium faecale WV33T
Abstract
:1. Introduction
2. Results
2.1. Genome Assembly of Flavobacterium Faecale WV33T
2.2. Mining for Gene Encoding Agarases
2.3. CAZymes of Flavobacterium Faecale WV33T
2.4. ANI Analysis of the 27 Representative Genomes of Flavobacterium Strains
2.5. Pangenome Analysis of the 27 Representative Genomes of Flavobacterium Strains
2.6. Phylogenomic Analysis of the 27 Representative Genomes of Flavobacterium Strains
3. Discussion
4. Materials and Methods
4.1. Strains and Culture Conditions
4.2. Genome Sequencing and Assembly
4.3. Quantitative Reverse Transcription PCR
4.4. CAZyme Annotation
4.5. Analysis of ANI
4.6. Pangenome Analysis of Flavobacterium Strains Using Roary
4.7. Phylogenomics Analysis of Flavobacterium Strains Using GToTree
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Item 1 | Description |
---|---|
General features | |
Classification | Domain Bacteria Phylum Bacteroidetes Class Flavobacteriia Order Flavobacteriales Family Flavobacteriaceae Genus Flavobacterium Species faecale |
Strain | WV33T |
Gram stain | Negative |
Cell shape | Rods |
Motility | Non-motile |
Pigmentation | Orange (zeaxanthin) |
Temperature optimum | 16 °C |
Investigation | |
Investigation type | Bacteria |
Project name | Complete genome sequence of Flavobacterium faecale WV33T |
Environment | |
Geographic location | Antarctica |
Latitude and longitude | 62° 14′ 45.4″ S 58° 46′ 36.2″ W |
Collection date | 2011 |
Environment (biome) | Polar biome |
Environment (material) | Antarctic penguin stools |
Depth | NA |
Oxygen requirement | Strictly aerobic |
Pathogenicity | NA |
Isolation and growth condition | PMID: 24893942 |
Sequencing | |
Sequencing platform | PacBio RS II with P6-C4 chemistry |
Assembly method | Canu v1.3 |
Number of replicons | 1 |
Genome coverage | 180× |
Finishing strategy | Complete |
BioProject | PRJNA383909 |
BioSample | SAMN06819498 |
Genomic features | |
NCBI accession number | CP020918 |
Size (bp) | 4,621,116 |
DNA G + C content (%) | 35.2 |
CDSs | 3984 |
tRNAs | 67 |
16S-23S-5S rRNAs | 18 |
COG 1 Code | Function Category | Number of CDS 2 |
---|---|---|
A | RNA processing and modification | 1 |
B | Chromatin structure and dynamics | 0 |
C | Energy production and conversion | 134 |
D | Cell cycle control, cell division, chromosome partitioning | 22 |
E | Amino acid transport and metabolism | 170 |
F | Nucleotide transport and metabolism | 55 |
G | Carbohydrate transport and metabolism | 183 |
H | Coenzyme transport and metabolism | 114 |
I | Lipid transport and metabolism | 102 |
J | Translation, ribosomal structure, and biogenesis | 151 |
K | Transcription | 139 |
L | Replication, recombination, and repair | 183 |
M | Cell wall/membrane/envelope biogenesis | 260 |
N | Cell motility | 6 |
O | Post-translational modification, protein turnover, chaperones | 101 |
P | Inorganic ion transport and metabolism | 205 |
Q | Secondary metabolites biosynthesis, transport, and catabolism | 25 |
R | General function prediction only | 289 |
S | Function unknown | 232 |
T | Signal transduction mechanisms | 126 |
U | Intracellular trafficking, secretion, and vesicular transport | 27 |
V | Defense mechanisms | 48 |
Z | Cytoskeleton | 0 |
CAZyme Class * | |||||||
---|---|---|---|---|---|---|---|
GH | GT | PL | CE | CBM | AA | Total | |
Found in all 3 annotation programs ** | 88 | 48 | 10 | 3 | 5 | 0 | 154 |
Found in 2 annotation programs | 13 | 26 | 1 | 1 | 3 | 0 | 44 |
Found in 1 annotation program | 53 | 28 | 1 | 13 | 16 | 2 | 113 |
Assembly_id | Species Name | Size (bp) | Scaffold (n) * | N50 | L50 | N90 | L90 | GC (%) |
---|---|---|---|---|---|---|---|---|
GCF_003076455.1 | F. faecale | 4,621,116 | 1 | 1 | 4,621,116 | 1 | 4,621,116 | 0.351 |
GCF_023008245.1 | F. diminilitoris | 3,913,692 | 1 | 1 | 3,913,692 | 1 | 3,913,692 | 0.293 |
GCF_021650975.1 | F. jumunjinense | 4,694,567 | 3 | 1 | 4,671,850 | 1 | 4,671,850 | 0.304 |
GCF_017352115.1 | F. endoglycinae | 5,513,159 | 1 | 1 | 5,513,159 | 1 | 5,513,159 | 0.343 |
GCF_014844295.1 | F. columnare | 3,221,278 | 1 | 1 | 3,221,278 | 1 | 3,221,278 | 0.316 |
GCF_013389455.1 | F. inviolabile | 3,913,347 | 1 | 1 | 3,913,347 | 1 | 3,913,347 | 0.396 |
GCF_013343195.2 | F. psychrophilum | 2,830,557 | 2 | 1 | 2,827,614 | 1 | 2,827,614 | 0.325 |
GCF_008369745.1 | F. nitrogenifigens | 5,497,186 | 1 | 1 | 5,497,186 | 1 | 5,497,186 | 0.342 |
GCF_008000935.1 | F. alkalisoli | 3,985,855 | 1 | 1 | 3,985,855 | 1 | 3,985,855 | 0.379 |
GCF_004797125.1 | F. sangjuense | 3,130,338 | 1 | 1 | 3,130,338 | 1 | 3,130,338 | 0.360 |
GCF_004355225.1 | F. nackdongense | 4,217,227 | 1 | 1 | 4,217,227 | 1 | 4,217,227 | 0.362 |
GCF_003344925.1 | F. arcticum | 2,970,356 | 1 | 1 | 2,970,356 | 1 | 2,970,356 | 0.349 |
GCF_003312915.1 | F. fluviale | 4,839,571 | 1 | 1 | 4,839,571 | 1 | 4,839,571 | 0.338 |
GCF_003148385.1 | F. sediminis | 3,441,304 | 1 | 1 | 3,441,304 | 1 | 3,441,304 | 0.352 |
GCF_003122385.1 | F. crocinum | 5,877,431 | 1 | 1 | 5,877,431 | 1 | 5,877,431 | 0.339 |
GCF_003097535.1 | F. pallidum | 3,552,756 | 1 | 1 | 3,552,756 | 1 | 3,552,756 | 0.436 |
GCF_003096035.1 | F. album | 3,983,546 | 1 | 1 | 3,983,546 | 1 | 3,983,546 | 0.445 |
GCF_003076475.1 | F. kingsejongi | 4,224,053 | 1 | 1 | 4,224,053 | 1 | 4,224,053 | 0.397 |
GCF_003076455.1 | F. faecale | 4,621,116 | 1 | 1 | 4,621,116 | 1 | 4,621,116 | 0.351 |
GCF_003055625.1 | F. magnum | 3,464,207 | 1 | 1 | 3,464,207 | 1 | 3,464,207 | 0.469 |
GCF_001857965.1 | F. commune | 3,851,214 | 1 | 1 | 3,851,214 | 1 | 3,851,214 | 0.343 |
GCF_001831475.1 | F. crassostreae | 3,027,315 | 1 | 1 | 3,027,315 | 1 | 3,027,315 | 0.359 |
GCF_001761465.1 | F. gilvum | 4,402,594 | 1 | 1 | 4,402,594 | 1 | 4,402,594 | 0.351 |
GCF_001705175.1 | F. anhuiense | 5,109,718 | 1 | 1 | 5,109,718 | 1 | 5,109,718 | 0.343 |
GCF_001534645.1 | F. covae | 3,321,600 | 1 | 1 | 3,321,600 | 1 | 3,321,600 | 0.308 |
GCF_000455605.1 | F. indicum | 2,993,089 | 1 | 1 | 2,993,089 | 1 | 2,993,089 | 0.313 |
GCF_000253275.1 | F. branchiophilum | 3,563,292 | 2 | 1 | 3,559,884 | 1 | 3,559,884 | 0.328 |
GCF_000016645.1 | F. johnsoniae | 6,096,872 | 1 | 1 | 6,096,872 | 1 | 6,096,872 | 0.341 |
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Lee, J.H.; Lee, S.-R.; Han, S.; Lee, P.C. Comparative Genomic Analysis of Agarolytic Flavobacterium faecale WV33T. Int. J. Mol. Sci. 2022, 23, 10884. https://doi.org/10.3390/ijms231810884
Lee JH, Lee S-R, Han S, Lee PC. Comparative Genomic Analysis of Agarolytic Flavobacterium faecale WV33T. International Journal of Molecular Sciences. 2022; 23(18):10884. https://doi.org/10.3390/ijms231810884
Chicago/Turabian StyleLee, Jun Ho, Seong-Rae Lee, Sejong Han, and Pyung Cheon Lee. 2022. "Comparative Genomic Analysis of Agarolytic Flavobacterium faecale WV33T" International Journal of Molecular Sciences 23, no. 18: 10884. https://doi.org/10.3390/ijms231810884