Nexus file of 114 chloroplast genes and gene positions

Nexus file containing the 114 genes data set followed by the position of each gene with the matrix

M1 Langrange combined input and output

Combined Lagrange M1 model input python script followed by the results output. This includes the dispersal constraints, geographic coding for taxa, concatenated 85 genes ML tree, and inferred ancestral areas within two log-likelihoods of the most likely area with relative probabilities

<i>SCE</i>RNA Flowchart.

<p><i>SCE</i>RNA stands for <u>Sc</u>affolding and <u>E</u>rror correction for <i>de novo</i> assemblies of <u>RNA-Seq</u> data. This collection of post-processing tools allows flexible implementation at various steps post assembly and with multiple assemblers and data types.</p

Illumina Sequence coverage of <i>Arabidopsis</i> cDNAs.

<p>Coverage of all detected genes by sequencing reads. The darkest bar represents the number of detected genes not tagged, and each progressively lighter bar represents genes in a bin with a 5% increase in coverage, with the two lightest bars showing the number of genes covered at >90% and >99%, respectively. Normalized BR12 = Normalized Illumina library from pooled biological replicates 1 and 2, BR12 = combined coverage of Illumina biological replicates 1 and 2, BR1 = Illumina biological replicate 1, BR2 = Illumina biological replicate 2.</p

Post-processed assembly delta plot, showing the effect of post-processing in several assembly quality categories.

<p>The histogram shows the magnitude (% change) and direction of change in each category for the Mosaik-S, CLC-S and Trinity-ICB assemblies of Illumina biological replicate 1. The post processed values in each category are printed above the x axis for each assembly. A vertical line separates categories where an assembly improvement would result in a decrease in the respective measure (“Expect Δ<0” categories, left of line) or an increase in the respective measure (“Expect Δ>0” categories, right of line).</p

Read titration analysis.

<p>Reads were mapped to post-processed assemblies of biological replicate 1. The number of reads (X axis) that map to an assembly are an indicator of assembly completeness and quality, while the incidence of new tags (Y axis) indicates how completely the assembly reflects the diversity present in the read data.</p

Ultra-conserved orthologs (UCO) coverage in post-processed assemblies of BR1.

<p>The use of UCOs as a proxy for the transcriptome assembly helps to identify leading assemblies when considered with the read titration curve analysis. When considered together, Trinity-ICB, which was the clear leader in our reference-based analyses, is also selected as the leader by the reference-<i>independent</i> metrics.</p

4 Gbp is a practical target volume for <i>de novo</i> transcriptome assembly.

<p>Illumina biological replicate 1 was subsampled to produce datasets of 1, 2, 3, and 4 Gbp. Replicate subsamples at 1 Gbp (top row) show reproducible results. Increasing the data by 1 Gbp to 2, 3, and 4 show diminishing increases in well assembled (>1.5BS) genes. The 4 Gbp subsampled assembly showed highly similar results to the biological replicate datasets. Doubling the data volume (BR12) produced a small increase in well assembled genes (>1.5BS) accompanied by a small increase in Type I mis-assembly. This analysis indicates 4 Gbp is a practical target data volume for <i>de novo</i> plant transcriptomes.</p

Integration of our reference-independent metrics shows the top 3 are closest to Mosaik-<i>S</i>.

<p>Considering the N₅₀ length, proportion of mappable reads, and UCO recovery we recapitulate the reference-dependent ranking of <i>de novo</i> assemblers.</p