# CompBio Research '22-'23 (#1)

## Notes on Preliminary Research (09/16/22)
++Comparative genomics support reduced-genome Paraburkholderia symbionts of Dictyostelium discoideum amobas are ancestrally adapted professional symbionts++
- *D. discoideum* --> predatory soil protists
- a subset of these protists have P. agricolaris, P. bonniea, and P. hayleyella as symbionts
- fitness outcomes for both host and symbiont are context-dependent
- comparative genomics analysis of the three strains of *Parburkholderia*
- large difference in genome size and GC content between *P. agricoloaris* and the other two --> evidence of genome reduction
- focus on shared orthologous genes
- specifically horizontally transfered genetic elements
- presence of insertion sequence (IS) elements/pseudogenes --> connects genome reduction and HGT since they are unstable and eventually lead to genome deterioration
- methods...
- used genome sequencing methods to sequence *Parburkholderia* genomes of interest
- annotated each genome using Prokka
- found putative pseudogenes using Pseudofinder
- completed whole genome alignment
- used ISFinder to identify putative IS elements to test their proliferation in each genome
- used COG and KO for functional annotation
- core genome molecular evolution
- essential amino acid biosynthetic repertoire
- used TXSScan to identify protein secrestion systems in *Parburkholderia* genomes
- built a web genome browser for each *Parburkholderia* genomes of interest
- results and discussion...
- *P.agricolaris* is non-reduced while *P. bonniea* and *P. hayleyella* are reduced
- the reduced *Parburkholderia* genomes had fewer genes for transcription and metabolistic processes suggesting that they have adapted to the host's enviornment
- the reduced *Parburkholderia* genomes of interest expereince stronger selective restriants compared to other genomes
- relationship between host and its symbionts is unlikely to be based on amino acid exchange
- the *Parburkholderia* genomes of interest share few HGT elements
- the *Parburkholderia* genomes of interest do share secretion systems
- bacterial secretion systems are frequently impicated in host-symbiont interactions
- type III and type VI secreation systems

++Comparative Genomic Analysis of *Acanthamoeba* Endosymbionts Highlights the Role of Amoebae as a "Melting Pot" Shaping the *Ricettsiales* Evolution++
- Introduction
- amoebae are known to harbor a wide range of intracellular bacteria
- some are endosymbionts
- amoebae may serves as a training groud for the emergence of specialized bacterial pathogens
- melting pot hypothesis --> amoebae act as a fertile ground for genetic exchange
- lateral gene transfers (LGTs)
- Methods
- BLASTp search aganist 2461 bacterial genomes exculding self hits to *Rickettsiales*
- choose query sequences that have non alpha-proteobacterial best hits as candidate genes for LGTs
- COG functional annotation using hidden markov model HMMer3
- ranked the non alpha-proteobacterial species by frequency as best hits
- using top ten species, phylogentic analysis
- compare to species tree
- look for conjugative T4SS or phage genes mechanistic evidence of how genes were shared
- Results and Discussion
- Conclusion

++Genome analysis of microorganisms living in amoebae reveals a melting pot of evolution++
(https://academic.oup.com/femsre/article/34/3/281/628845)
- Introduction
- studied the genomes of microorganisms living and multiplying naturally in free-living amoebae

++Genome Sequence of *Rickettsia bellii* Illuminates the Role of Amoebae in Gene Exchanges between Intracellular Pathogens++
(https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.0020076)
- Synopsis
- intracellular pathogens tend to have little opportunity to exchange DNA with other microbes because of their isolated way of life
- sequencing and computer analysis of its genome now provides evidence that many genes were transfered between ancestors of *Rickettsia*
- found a complete set of predicted genes for conjugative DNA transfer
- Sca family
- used sex pili-like surface appendages for mating with other bacteria
- can survive in amoeba for a long time
- Methods
- purification of bacteria
- extracted DNA from bacteria
- shotgun sequencing to get genome
- annotation of genome
- used SelfIF to predict protein-coding genes (ORFs)
- functional analysis using BLAST aganist SWISS, NCBI, and SMART
- evalue of 0.001
- numbers of transposases, ankyrin/tetratricopeptide repeat–containing genes, and integrases were computed using RPS-BLAST
- evalue of 10^-5
- tRNA genes were identified usig tRNAscan-SE
- palindromic element sequences found using hidden Markov models
- multiple sequence alignments using clustalW, T-coffee, and MUSCLE
- phylogentic reconstruction
- for proteins encoded by tra genes and proteins recognized as candidates for HGT...
- BLAST searches aganist SWISS for homologs exhibiting high scores to ORFs
- MUSCLE for aligning sequences
- ignored gap-containing columns of alignment
- MEGA to reconstruct neighbor-joining trees with JTT sub model

++Illuminating the Evolutionary History of Chlamydiae++
(https://www.science.org/doi/full/10.1126/science.1096330)

++Lateral gene exchanges shape the genomes of amoeba-resisting microorganisms++

++Insight into cross-talk between intra-amoebal pathogens++