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# System prepended metadata

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

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# 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++
