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We used CLC Genomics Workbench 9 ( to assemble Illumina reads from outbreak isolate E (1,736 contigs; assembly length 8,816,302 bp) and from unrelated isolates.
In an effort to generate complete virus genome sequences, specific primers were designed to fill the gaps between siRNA contigs according to the consensus sequences of the specific contigs involved and their relative positions.
Table A1 List of all taxa analyzed and total number of contigs after assembly Taxon Total contig number Choanoflagelata Acanthoeca spectabilis W.Ellis, 1930 198,922 Salpingoeca pyxidium Kent 202,399 Metazoa Porifera Hyalonema papilliferum Schulze, 1899 58,839 Kirkpatrickia variolosa (Kirkpatrick, 1907) 100,231 Latrunculia apicalis Ridley & Dendy, 1886 76.210 Rossella fibulata Schulze & Kirkpatrick.
De novo Assembly and different metrics Attributes CLC Workbench N50 563,631 bp Longest Contig 1,740,531 bp Total Contigs 146 Assembly Length 5,396,710 bp Gap Length 918 bp Table 3.
The paired-end sequence reads were assembled into 254,446 contigs with an N50 length of 1,324 bp and average contig length of 831.68 bp (Table 2).
To determine the function and taxonomy of the mRNA reads, they were merged and de novo assembled into larger contigs, creating a single contig reference set for all samples.
Region Contig mRNA dbSNP rs # RefSNP position position cluster id allele exon_4 32462028 458 rs5787 G COX-1 A exon_3 32461411 258 rs3842788 A G GPIIb exon_26 1106870 2653 rs5911 A C Protein Codon Amino acid residue position position Arg [R] 2 108 COX-1 Gln [Q] 2 108 Gln [Q] 3 41 Gln [Q] 3 41 GPIIb Ile [I] 2 874 Ser [S] 2 874 Notes.
The draft genome consists of 90 scaffolds, which are composed of 101 contigs. The N50 length is 129 kb and the largest contig approximately 293 kb.
The variables used as input of ANN for simultaneous estimation of diversity indices were: a categorical index (H': 1 and J: 2) and the number related to the medium (M) and standard deviations (D) of vegetation indices (NDVIM, NDVID, SAVIM, SAVID, EVIM, EVID, MVI5N, MVI5D, MVI7M and MVI7D) and landscape metrics (AREA, GYRATE, SHAPE, CONTIG, CORE and ENN).
Five of these six strains were investigated because they had the same serotype and sequence type (ST) as outbreak strains in this study, and the sixth was investigated because a BLAS Tn search of the genomic island to the NCBI wgs database identified a match to a contig from this strain.
The databases of nonreluctant (NR) protein and UniProtKb/SwissProt were used to BLAST the assembly contigs. The cutoff E-value was le-5, and only the top gene ID and the name were assigned to each contig.
For visualization, quality assessment, contig (contiguous) assembly, and editing, DNA trace files were im ported to CodonCode Aligner, vers.4.2.5 (CodonCode Corp., Centerville, MA).