To analyze regions present in the reference genome but not covered in the sequenced mutant strains (putative deletions), a consensus sequence for the sequenced strains was extracted with pileup (Li et al. 2009), and subsequently screened for regions not covered in the mutant strains using custom-made Perl scripts.
Similarity searches for the sequenced cloned inserts revealed no similar sequences in the GenBank database or its associated databases.
The sequence information for these indels was compiled into signature files such as those presented in Figures 2 and 3. Phylogenetic trees for the sequenced ε-proteobacteria species were constructed based on 16S rRNA sequences as well as a number of conserved proteins (viz.
For the sequenced Duroc sow 2 14, we downloaded its draft genome sequence (i.e. Sus scrofa 10.2 reference assembly) from ftp://ftp.ensembl.org/pub/release-67/fasta/sus_scrofa/dna/ and corresponding NGS data from DDBJ (ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/ERA009/ERA009086/) for the use of sequence alignment and SD map construction.
There are Species Overview and Sequence Summary pages as well as genome browsers for the sequenced genome species.
Multiple sequence alignments and the construction of parsimony trees for the sequenced regions of these genes support the idea of lineage specific expansions in cassava (Data not shown).
In order to anchor the obtained genomic sequences to the genetic linkage map, DNA markers were developed for the sequenced TAC and BAC clones, and genetic mapping was carried out.
To determine their evolutionary significance, phylogenetic trees were constructed for the sequenced ε-proteobacteria species based on 16S rRNA and a concatenated dataset of sequences for 9 highly conserved proteins (viz. RpoB, RpoC, Hsp70, Hsp60, elongation factor (EF -Tu, EF -TuGyrase A, Gyrase B and alanyl-tRNA synthetase).
The fact that different sequence sets from the same BAC - although both being representative for the sequenced clone - required different parameters for yielding a 'best' assembly, suggested that experimental and stochastic conditions like fragmentation profile, library representativeness and sequence length distribution influenced the outcome of the assemblies.
