Acidovorax JS42 Parales Project: Difference between revisions

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== Objectives ==
Use whole genome sequencing to find mutations involve with the evolution of novel trains in Acidovorax JS42 (3- or 4-nitrotoluene metabolism)
== Genomes ==
== Genomes ==


== Objectives ==
454 400bp sequence unpaired
Coverage ~8x
 
Genomes assembled with newbler and no-split option
# Assembled the contigs against the reference genome (aka syntenic path assembly)
## Unordered: http://genomevolution.org/r/3ipl
## Ordered: http://genomevolution.org/r/3ipk
## Assembled: http://genomevolution.org/r/3ipn
# Annotated the genomes using
## Prodigal for protein coding genes
## tRNAScan-SE for tRNAs
## Don't have a solution for rRNAs
# Used the syntenic relationships from 1.c to lift over the annotations from the reference genome to the new genomes


=== Sept. 2nd 2011 ===
You can find the genomes (syntenic path assembly and contig level assembly for each organism) using this link:
Overall goals:
http://genomevolution.org/CoGe/OrganismView.pl?org_name=JS42
# ID functional polymorphisms with low false negative rate and low false positive rate
# Support upcoming KJS metabolism paper using strains 2 and 4


Becky:
==Polymorphisms==
# Budget for more sequencing
# Number of new strains to sequence
# Gene list organized by operon/pathway section for upcoming paper
'''From Becky'''
Ajs 204: a GntR-type regulator; snp changing R to W in KSJ4
Ajs 205: a sigma 54; snp changing A to T in KSJ2
Ajs 205: a sigma 54; deletion frameshift in KSJ4
And I assume the deletion in the string of Gs in Ajs 205 in KSJ4 may be a sequencing error.
Am I missing anything? If that's it, I guess that would be a pretty easy line in the paper...


# Validated polymorphisms from (3) in KSJ2 and KSJ4 (unless those are in a previous email)
*Collective table: http://genomevolution.org/elyons/polymorphisms/JS42/JS42_polymorphisms.html
*Description of the table: http://genomevolution.org/wiki/index.php/PolyMFind


Eric:
==Notes==
# Fold-coverage of prior strain sequencing
Google doc: https://docs.google.com/document/d/1LhKKh_i2EvkdHGq7q75h9D8rZKvhrCbdb22X2fmOAUo/edit?hl=en_US
##Is more coverage/different technology going to help reduce false positive rate?
## single strain unique polymorphism tables
## Focus on gene list provided in Becky(3)
## Check polymorphisms provided in Becky(4)
# New sequencing:
## Which technology will be appropriate for upping coverage
## Which technology will be most cost-effective for sequencing new strains
## For different sequencing center tech:
### Cost (consider that prior KJS strain libraries are prepped for 454)
### Amount of data
### Lengh of reads
### wait-time for sequences

Latest revision as of 19:37, 25 August 2011

Objectives

Use whole genome sequencing to find mutations involve with the evolution of novel trains in Acidovorax JS42 (3- or 4-nitrotoluene metabolism)

Genomes

454 400bp sequence unpaired Coverage ~8x

Genomes assembled with newbler and no-split option

  1. Assembled the contigs against the reference genome (aka syntenic path assembly)
    1. Unordered: http://genomevolution.org/r/3ipl
    2. Ordered: http://genomevolution.org/r/3ipk
    3. Assembled: http://genomevolution.org/r/3ipn
  2. Annotated the genomes using
    1. Prodigal for protein coding genes
    2. tRNAScan-SE for tRNAs
    3. Don't have a solution for rRNAs
  3. Used the syntenic relationships from 1.c to lift over the annotations from the reference genome to the new genomes

You can find the genomes (syntenic path assembly and contig level assembly for each organism) using this link: http://genomevolution.org/CoGe/OrganismView.pl?org_name=JS42

Polymorphisms

Notes

Google doc: https://docs.google.com/document/d/1LhKKh_i2EvkdHGq7q75h9D8rZKvhrCbdb22X2fmOAUo/edit?hl=en_US

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