Alignment of the genomes

Task 1 and Task 3 / Part 1

I chose three genomes of bacteria belonging to the same species (Acinetobacter baumannii) which have one chromosome.

Acinetobacter baumannii strain SAA14 (CP020579.1), Complete Genome
Acinetobacter baumannii strain AB042 (CP019034.1), Complete Genome
Acinetobacter baumannii strain AB031 (CP009256.1), Complete Genome

As you can see, these sequences have large sections of homologous and contain large genomic rearrangements. Here are dot matrix view of pairvise alignment made by blast 2 sequences* (BLASTN 2.8.0) and them analysis - see fig. 1-3.
*I used Word size = 256.

Figure 1. SAA14 vs AB031. Alignment.

Sequences start from different places. Deletions or inserts are marked in red.

Figure 2. SAA14 vs AB042. Alignment.

Sequences start from different places. Deletions or inserts are marked in red and inversionsions are marked in green.

Figure 3. AB031 vs AB042. Alignment.

equences start from different places. Deletions or inserts are marked in red and inversionsions are marked in green.

Task 2

According the instruction I created file genomes.tsv for NPG-explorer with references to FASTA files contains sequenses of genomes of chosen bacterias. Then I run npge MakePangenome and PostProcessing (protocol of it's work) and visualised the result by qnpge.

The result of searching you can see in table 1. To complete this table I used data from pangenome.info. The summary length of blocks is 37056887, the summary cover of blocks is 74.98%.

Table 1.

All non-minor blocks
of at least 2 fragments S-blocks H-blocks R-blocks M-blocks

Number 941 338 305 298 434

Block identity min=0.7692
median=0.952
avg=0.9374
max=1 min=0.812
median=0.9678
avg=0.9515
max=1 min=0.8017
median=0.9633
avg=0.948
max=1 min=0.7692
median=0.8951
avg=0.9107
max=1 min=0
median=0.8492
avg=0.7162
max=1

Identity of joined blocks 0.971479 0.973221 0.965706 0.94722 0.877436

Length and cover of fragments 10557660 (89.61%) 9242570 (78.45%) 726889 (6.17%) 588201 (4.99%) 24492 (0.2%)

Total length and cover of blocks 3581022 (74.73%) 3082501 (64.32%) 363773 (7.59%) 134748 (2.81%) 12465 (0.26%)

Task 3 / Part 2

To find the large genomic rearrangements I used qnpge-visualisation, blocks.gbi, blocks.blocks. I found out that there are 33 of g-blocks and 64 of i-blocks. Below you can see some examples of rearrangements.

Figure 4. Inversion of the fragment g3x157172-i2x15531-g3x200780 in AB042 (see positions 10-12).

Figure 5. Translocation of g3x102 in SAA14 (see position 54 and 58).

Figure 6. Conserved blocks in positions 40 and 44. Insert of a fragment between them in AB042.

Phylogeny

The phylogenetic tree made by Blast Tree View (see fig. 7).

Figure 7.

Term 3

← Pr 9 Block 3 →