Table II. Basic statistics of the Illumina assemblies from P. uvella and C. leiostraca.
Numbers in parentheses indicate the number of genes/sequences considered for each estimation.
| Parameter | P. uvella | C. leiostraca |
|---|---|---|
| No. of Illumina paired-end reads (100 bp) | 3.4 × 107 × 2 | 4.0 × 107 × 2 |
| No. of contigs of 500 nucleotides or greatera | 15,240 | 10,222 |
| Average contig sizea | 4,531 nucleotides | 9,122 nucleotides |
| Largest contiga | 102,330 nucleotides | 167,968 nucleotides |
| Plastid genome cumulative size | ∼230 kb | 167.4 kb |
| Illumina average coverage (reads per nucleotide ± sd) | ||
| Plastid protein-coding genes | 5,776 ± 601 (25) | 6,239 ± 620 (65)b |
| Plastid rRNA genes | 5,917 ± 716 (2)c | 11,851 ± 1,311 (9)d |
| Plastid tRNA genese | 6,274 ± 1,230 (27) | 6,282 ± 828 (23) |
| Plastid scaffolds/complete genome | 6,662 ± 441 (4)f | 6,753 ± 766 |
| Mitochondrial protein-coding genes | 5,813 ± 970 (7) | 8,326 ± 228 (7) |
| Mitochondrial rRNA genes | 6,997 ± 911 (2)g | 8,320 ± 617 (2) |
| Mitochondrial complete genome | 6,047 ± 1,268 | 8,163 ± 955 |
| Nuclear sequences | 38 ± 8 (20) | 67 ± 23 (10) |
a
Using Ray assembler with a k-mer size of 31. bCoverage calculated in protein-coding genes present in the long and short single-copy regions. cOnly considering plastid rRNA-coding regions (see Supplemental Fig. S3). dGenes localized in the C. leiostraca ptDNA inverted-repeat regions: three rRNAs, two tRNAs, and four open reading frames (ORFs). etRNA genes located in the long and short single-copy regions. fThe average coverage estimations by read mapping in the P. uvella ptDNA intragenic regions are ambiguous given the presence of numerous short repeats. gOnly considering mitochondrial rRNA-coding regions.