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Scaffolds match archea, bacteria and virus sequences. (XLSX 140 kb

Summary of BLASTx comparisons to the Solgenomics <i>N. benthamiana</i> v0.4.4 predicted proteins database.

<p>The orange tracks show the percentage of database hits from each assembly that were also found in other assemblies, represented by 18 data points in each track, including self-on-self comparison (see legend). The green tracks show the percentage of the database that were found in each assembly. The grey histograms are comparisons to the top 1000 longest proteins in the database, and the blue histograms are comparisons to all sequences in the database. Each set of histograms are sub-divided into 4 bars, representing from darkest to lightest colour, the total database (always 100%), the percentage of the database that is actually expressed in our assembly, the percentage of these expressed database sequences that were found in the assembly, and of these the percentage that were aligned to more than 80% of the database sequence length. The coloured links show the proportion of TaMraw, Trraw, Sotgi and OaMraw <i>de novo</i> assembled transcripts that were present in the SasmMraw and SasmMevi assemblies.</p

Number of protein sequences after clustering of top 1000 longest proteins in each assembly, using CD-HIT with an identity of 95%.

<p>Number of protein sequences after clustering of top 1000 longest proteins in each assembly, using CD-HIT with an identity of 95%.</p

Homeologous or paralogous RNA silencing gene transcript sequences, their nucleotide and protein identities, and whether they could be assembled separately in TaMraw, Trraw, Soraw and OaMraw assemblies.

<p>Homeologous or paralogous RNA silencing gene transcript sequences, their nucleotide and protein identities, and whether they could be assembled separately in TaMraw, Trraw, Soraw and OaMraw assemblies.</p

Alignment coverage of 35 RNA silencing gene transcript sequences.

<p>Sequences were queried against the 18 transcriptome assemblies in this study. The CDS of these <i>de novo</i> assembled transcripts were screened against the assemblies using BLASTn, and the query alignment coverages were calculated from the best match to the database.</p

Statistics of raw unprocessed k-mer assemblies (Tr and So) or merged k-mer assemblies (TaM and OaM), and their Tgi processed and Evi processed assemblies.

<p>Statistics of raw unprocessed k-mer assemblies (Tr and So) or merged k-mer assemblies (TaM and OaM), and their Tgi processed and Evi processed assemblies.</p

Feature response curves of assemblies using the ‘High_spanning_PE’ feature.

<p>This feature measures the number of PE reads where the pairs are mapped onto different contigs (<i>de novo</i> assembled transcripts). The feature threshold is used to filter out contigs that fall above a threshold. That is, only contigs that contain less than a threshold number of features are used to calculate the coverage at that threshold. Except for the TaMevi, the Evi processed assemblies appear to perform best or at least on par on all assemblies (raw vs Tgi vs Evi) as higher coverage is achieved at a lower feature threshold.</p

Overview of assemblies generated from two datasets, showing k-mer size ranges and respective assemblies used to generate the two combined assembly types (SasmM and SasmK).

<p>* k-mer assemblies merged by: Ta – Ta merge utility; So – TGI clustering software; Oa – Oa merge utility.</p

Dcl1 transcript assembly status by the Trinity assembler.

<p>Red bars indicate the known Dcl1 CDS used as query. Black bars indicate the transcripts assembled by the assembler. A: Alignment of <i>de novo</i> assembled transcripts generated with ds1 and ds2 reads to the query Dcl1 sequence. A full length Dcl1 sequence could be assembled with ds1 reads, but only two partial sequences were assembled with ds2 reads. B: Read depth profile from all RNA-seq reads mapped to the query Dcl1 CDS. Changes in read depth could indicate the presence of various isoforms. C: Alignment of the full length and partial Dcl1 <i>de novo</i> assembled transcripts at the region where there is a sharp change in read depth, to respective genome scaffolds in our v0.3 draft assembly. This shows that the partially assembled Dcl1 sequence contains unspliced intron, and that there may be two loci for Dcl1 as implied by the different intron sequences in the scaffolds (see text).</p

Predicted transmembrane topology of OR7.

<p>Variable sites between <i>P</i>. <i>octo</i> and <i>P</i>. <i>excessana</i> are highlighted. Red dots indicate the position of amino acid substitutions in <i>P</i>. <i>octo</i>, and black dots amino acid substitutions in <i>P</i>. <i>excessana</i> compared to a predicted common ancestor. The double line indicates the transmembrane region, with extracellular and cytoplasmic sides labelled.</p