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Microbial Genome Assembly and Finishing Alla Lapidus, Ph.D. Microbial genomics DOE Joint Genome Institute, Walnut Creek, CA. A typical Microbial project. Sequencing. Auto- assembly . Gap closure FINISHING . Annotation. Public release. Sanger only

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Microbial Genome Assembly

and Finishing

Alla Lapidus, Ph.D.

Microbial genomics

DOE Joint Genome Institute,

Walnut Creek, CA


A typical Microbial project




Gap closure



Public release

evolution of microbial drafts
Sanger only

4x of 3kb plasmids + 4x of 8kb plasmids + 1x of fosmids

~ $50k for 5MB genome draft

Evolution of Microbial Drafts

Hybrid Sanger/pyrosequence/Illumina

  • 4x 8kb Sanger + 15 x coverage 454 shotgun + 20x Illumina (quality improvement)
  • ~ $35k for 5MB genome draft

454 + Solexa (current)

-20x coverage 454 standard + 4x coverage 454 paired end (PE) + 50x coverage Illumina shotgun (quality improvement; gaps)

- ~ $10k per 5MB genome

assembly assembler
Sanger reads only (phrap, PGA, Arch, etc)


  • Hybrid Sanger/pyrosequence/Solexa (no special assemblers; use PGA and Arachne)

454 contig

454 shreds












  • 454/Solexa (Newbler, PCAP?) – 454 reads only

Shotgun reads

PE reads

Assembly (assembler)
use of illumina data
Align solexa reads

Identify errors

Automatically suggest corrections for manual curation

Automatically suggest and implement corrections

List Disc

x1 – G

x2 – T

x3 – A





Use of Illumina data





errors corrected with solexa polisher

Finished consensus

454 contig

Sanger reads

Errors corrected with Solexa (Polisher)

Frame shift detected in this area (454 contig)

























draft assembly what we get

Ordered sets of contigs (scaffolds)

PCR product






Clone walk

(Sanger lib)

PCR - sequence

Draft assembly - what we get

Assembly: set of contigs




New technologies: no clones to walk off even if you can scaffold contigs

why do we have gaps
Why do we have gaps

What are gaps (Sanger)?

- Genome areas not covered by random shotgun

  • Sequencing coverage may not span all regions of the genome, thus producing gaps in the assembly.
  • Assembly results of the shotgun reads may produce misassembled regions due to repetitive sequences.
  • A biased base content (this can result in failure to be cloned, poor stability in the chosen host-vector system, or inability of the polymerase to reliably copy the sequence):

~ AT-rich DNA clones poorly in bacteria (cloning bias;

promoters like structures )=> uncaptured gaps

~GC rich DNA is difficult to PCR and to sequence and often

requires the use of special chemistry => captured gaps


454 (pyrosequence) and low GC genome

Thermotoga lettingae TMO (JGI ID 4002278)

Draft assembly +454

- 2 total contigs; 1 contigs >2kb

- 454 – no cloning

Draft assembly:

- 55 total contigs; 41 contigs >2kb

- 38GC% - biased Sanger libraries

<166bp> - average length of gaps

high gc stops sanger and hybrid
The presence of small hairpins (inverted repeat sequences) in the DNA that re anneal ether during sequencing or electrophoresis resulting in failed sequencing reactions or unreadable electrophoresis results. (This can be aided by adding modifiers to the reaction, sequencing smaller clones and running gels at higher temperatures in the presence of stronger denaturants).High GC stops (Sanger and Hybrid)
454 and high gc project
454 and High GC project

Xylanimonas cellulosilytica DSM 15894 (3.8 MB; 72.1% GC)

PGA assembly - 9x of 8kb +454

PGA assembly - 9x of 8kb

genome closure issues
Genome closure issues
  • Resolve repeats and mis-assemblies
    • Repeats within or in vicinity of other repeats
    • Large repetitive regions
    • Complex repetitive regions (tandems)
  • Fill in gaps
    • DNA region lethal to E.coli (Sanger libraries)
    • Hairpins, GC rich, hard stops or other 2° structure/physical premature termination
    • Hard to PCR (new technologies)
  • Other issues
    • Homopolymeric tracts and other polymorphisms (SNPs, VNTRs, indels)
what is finishing
The process of taking a rough draft assembly composed of

shotgun sequencing reads, identifying and resolving miss

assemblies, sequence gaps and regions of low quality to

produce a highly accurate finished DNA sequence.

What is Finishing?

Final quality:

Final error rate should be less than 1 per 50 Kb.

No gaps, no misassembled areas, no characters other than ACGT

jgi microbial finishing
JGI Microbial Finishing

Currently: >250 individual microbes

metagenomic assembly
Typically size of metagenomic sequencing project is very large

Different organisms have different coverage. Non-uniform sequence coverage results in significant under- and over-representation of certain community members

Low coverage for the majority of organisms in highly complex communities leads to poor (if any) assemblies

Chimerical contigs produced by co-assembly of sequencing reads originating from different species.

Genome rearrangements and the presence of mobile genetic elements (phages, transposons) in closely related organisms further complicate assembly.

No assemblers developed for metagenomic data sets

Metagenomic assembly

The whole-genome shotgun sequencing approach was used for a number of microbial community projects, however useful quality control and assembly of these data require reassessing methods developed to handle relatively uniform sequences derived from isolate microbes.

qc annotation of poor quality sequence
QC: Annotation of poor quality sequence

To avoid this:

make sure you use high quality sequence

choose proper assembler

recommendations for metagenomic assembly sanger
Use Trimmer (Lucy etc) to treat reads PRIOR to assembly

None of the existing assemblers designed for metagenomic data but assemblers like PGA work better with paired reads information and produce better assemblies. We are not using pharp for metagenomic projects.

Recommendations for metagenomic assembly (Sanger)
finishing approach for metagenomes

Binning:Which DNA fragment

derived from which phylotype?

(BLAST; GC%; read depth)


Complete genome of Candidatus Accumulibacter phosphatis

CAP reads

~ 45%


Non-CAP reads

Finishing approach for metagenomes

Example: Candidatus Accumulibacter phosphatis(CAP)

metagenomic finishing projects
Metagenomic finishing: projects

Completed Projects:

Candidatus Korarchaeum cryptofilum OPF8 - is the first of this apparently ancient

hyperthermophilic phyletic group to be sequenced

Desulforudis audaxviator - isolated from old water in fissures of a South African gold mine at

a depth of 3000 meters. Finished with Sanger and 454

Candidatus Accumulibacter phosphatis Type IIA (CAP) - from EBPR sludge

community, US

In progress:

Candidatus Endomicrobium trichonymphae - an intracellular symbiont of a flagellate

protist, itself part of the hindgut community of a termite host. It is of interest in the pursuit of the

efficient breakdown of cellulose and lignin necessary in the hoped-for conversion of bulk plant

materials to CO2-neutral fuel