PCR assembly validation.

<p>Contigs assembled from 93 bp single-end reads were validated using standard PCR. A: genomic DNA, B: First-strand cDNA synthesis with reverse transcriptase, C: First-strand cDNA synthesis without reverse transcriptase. M: 100 bp O’GeneRuler. For primer and contig sequences, see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0123887#pone.0123887.s001" target="_blank">S1 Table</a>.</p

Summary of qPCR-based estimates of haploid genome sizes.

<p>Summary of qPCR-based estimates of haploid genome sizes.</p

Contig size distribution.

<p>Transcriptome assembly contig size distribution of all contigs (left) and predicted full-length contigs (right).</p

Genomic DNA purification and genome size estimate of <i>D</i>. <i>muscipula</i>.

<p><b>(A)</b> Agarose gel showing a purified fraction of <i>D</i>. <i>muscipula</i> genomic DNA (1) using a modified CTAB procedure. M1: DNA ladder D2000 (Tiangen), M2: DNA ladder λ-Hind3 digest (Takara). <b>(B)</b> Genome size estimate of <i>D</i>. <i>muscipula</i> using a single-copy qPCR method with <i>DmACT7</i> as amplicon. <i>A</i>. <i>thaliana</i> serves as a control, using <i>ACTIN1</i> as amplicon.</p

Gene Ontology (GO) categories of the unigenes.

<p>Distribution of the GO categories assigned to the <i>D</i>. <i>muscipula</i> transcriptome. Unique transcripts (unigenes) were annotated in three categories: cellular components, molecular functions, and biological processes.</p

Statistics of transcriptome sequencing and assembly of <i>D</i>. <i>muscipula</i>.

<p>Statistics of transcriptome sequencing and assembly of <i>D</i>. <i>muscipula</i>.</p

Nucleotide misincorporation bias for ancient DNA templates: AT <i>versus</i> BE libraries.

<p>Aliquots of a quagga museum specimen and an <i>Hippidion</i> bone fossil were built into AT and BE libraries. We report CT mismatch rates at the first 5 (positions 1 to 5) and last 5 (positions –1 to –5) nucleotide positions within sequence reads mapping with high quality a unique position of the EquCab2.0 genome. These rates are calculated using mapDamage output <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0078575#pone.0078575-Ginolhac1" target="_blank">[24]</a> by summing over positions where a C (G) is found in the reference genome but a T (A) is found in sequencing reads.</p

Summary of BLASTx search results of <i>D</i>. <i>muscipula</i> transcriptome.

<p>Summary of BLASTx search results of <i>D</i>. <i>muscipula</i> transcriptome.</p

Base composition bias for ancient DNA templates: AT <i>versus</i> BE libraries.

<p>Aliquots of a quagga museum specimen and an <i>Hippidion</i> bone fossil were built into AT and BE libraries. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0078575#pone-0078575-g002" target="_blank">Figure 2</a> captions for further information regarding base compositions.</p

Sequence data.

<p>The number of raw sequence read pairs generated as well as the number of collapsed trimmed reads and the number of unique hits to reference genomes and passing quality filters are indicated. Endogenous DNA content was calculated by dividing the total number of unique hits passing quality filters and the total number of collapsed reads. BE: Blunt-End adapter ligation. AT: AT-overhang adapter ligation. The final concentration of adapter used for ligation is reported as standard (S) or low (L; see Material and Methods). C: Covaris sonication. B: Bioruptor sonication. N: Nebulization. While most DNA libraries were sequenced as Paired-End (2×100 cycles), one, indicated with an asterisk, was sequenced as Single-End. For this DNA library, #Collapsed refers to the numbers of reads considered post-trimming and not post-collapsing, as for other DNA libraries.</p