Table 2
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Comparison of the assembly and statistics among the Prunus genomes so far published

Peach v2.0Peach v1.0P. mumePAV_r1.0 (P. avium)P. yedoensis
Sequencing strategySanger–NGS IlluminaSangerNGS IlluminaNGS IlluminaNGS Illumina–PacBio
Genome coverage8.47×–NGS 64×Sanger 8.47×180×130.34×1265.6× (1192× + 73×)
Scaffold number total191 (241)a202 (234)144910,1483185
Contig number total2525273010,894–4292
Scaffold sequence total227.4 Mb227.3237.1 Mb272.4 Mb323.8 Mb
Mapped scaffold sequence total225.7 Mb (99.2%)218.4 Mb (96%)198.9 (83.9%)191.7 Mb (70.4%)281.6 Mb (87.0%)
Oriented scaffold sequence223.3 Mb (98.2%)194.6 Mb (85.6%)–––
Contig sequence total224.6 Mb224.6 Mb219.9 Mb–318.7 Mb
Scaffold N50/L5010/7.3 Mb9/8.9 Mb120/577.8 kb–/219.6 kb519/198.9 kb
Scaffold N50/L50 (chromosome-scale assembly)4/27.4 Mb4/26.8 Mb–––
Contig N50/L50250/255.4 kb294/214.2 kb2009/31.8 kb–/276 bp706/132.6 kb
Number of scaffolds >50 kb1121–––
% main genome in scaffolds >50 kb99.4%99.4–––
Repetitive sequences79.38 Mb (35.34%)84.41 Mb (37.14%)106.8 Mb (44.9%)119.4 Mb (43.8%)150.8 Mb (47.2%)
Protein-coding genes26,87327,85231,39043,67341,294
Protein-coding transcripts47,08928,689––45,581
Alternative transcripts20,216837––4287
Peach v2.0Peach v1.0P. mumePAV_r1.0 (P. avium)P. yedoensis
Sequencing strategySanger–NGS IlluminaSangerNGS IlluminaNGS IlluminaNGS Illumina–PacBio
Genome coverage8.47×–NGS 64×Sanger 8.47×180×130.34×1265.6× (1192× + 73×)
Scaffold number total191 (241)a202 (234)144910,1483185
Contig number total2525273010,894–4292
Scaffold sequence total227.4 Mb227.3237.1 Mb272.4 Mb323.8 Mb
Mapped scaffold sequence total225.7 Mb (99.2%)218.4 Mb (96%)198.9 (83.9%)191.7 Mb (70.4%)281.6 Mb (87.0%)
Oriented scaffold sequence223.3 Mb (98.2%)194.6 Mb (85.6%)–––
Contig sequence total224.6 Mb224.6 Mb219.9 Mb–318.7 Mb
Scaffold N50/L5010/7.3 Mb9/8.9 Mb120/577.8 kb–/219.6 kb519/198.9 kb
Scaffold N50/L50 (chromosome-scale assembly)4/27.4 Mb4/26.8 Mb–––
Contig N50/L50250/255.4 kb294/214.2 kb2009/31.8 kb–/276 bp706/132.6 kb
Number of scaffolds >50 kb1121–––
% main genome in scaffolds >50 kb99.4%99.4–––
Repetitive sequences79.38 Mb (35.34%)84.41 Mb (37.14%)106.8 Mb (44.9%)119.4 Mb (43.8%)150.8 Mb (47.2%)
Protein-coding genes26,87327,85231,39043,67341,294
Protein-coding transcripts47,08928,689––45,581
Alternative transcripts20,216837––4287
a

In brackets, assembled scaffolds prior the build of pseudomolecules

Table 2
Open in new tab

Comparison of the assembly and statistics among the Prunus genomes so far published

Peach v2.0Peach v1.0P. mumePAV_r1.0 (P. avium)P. yedoensis
Sequencing strategySanger–NGS IlluminaSangerNGS IlluminaNGS IlluminaNGS Illumina–PacBio
Genome coverage8.47×–NGS 64×Sanger 8.47×180×130.34×1265.6× (1192× + 73×)
Scaffold number total191 (241)a202 (234)144910,1483185
Contig number total2525273010,894–4292
Scaffold sequence total227.4 Mb227.3237.1 Mb272.4 Mb323.8 Mb
Mapped scaffold sequence total225.7 Mb (99.2%)218.4 Mb (96%)198.9 (83.9%)191.7 Mb (70.4%)281.6 Mb (87.0%)
Oriented scaffold sequence223.3 Mb (98.2%)194.6 Mb (85.6%)–––
Contig sequence total224.6 Mb224.6 Mb219.9 Mb–318.7 Mb
Scaffold N50/L5010/7.3 Mb9/8.9 Mb120/577.8 kb–/219.6 kb519/198.9 kb
Scaffold N50/L50 (chromosome-scale assembly)4/27.4 Mb4/26.8 Mb–––
Contig N50/L50250/255.4 kb294/214.2 kb2009/31.8 kb–/276 bp706/132.6 kb
Number of scaffolds >50 kb1121–––
% main genome in scaffolds >50 kb99.4%99.4–––
Repetitive sequences79.38 Mb (35.34%)84.41 Mb (37.14%)106.8 Mb (44.9%)119.4 Mb (43.8%)150.8 Mb (47.2%)
Protein-coding genes26,87327,85231,39043,67341,294
Protein-coding transcripts47,08928,689––45,581
Alternative transcripts20,216837––4287
Peach v2.0Peach v1.0P. mumePAV_r1.0 (P. avium)P. yedoensis
Sequencing strategySanger–NGS IlluminaSangerNGS IlluminaNGS IlluminaNGS Illumina–PacBio
Genome coverage8.47×–NGS 64×Sanger 8.47×180×130.34×1265.6× (1192× + 73×)
Scaffold number total191 (241)a202 (234)144910,1483185
Contig number total2525273010,894–4292
Scaffold sequence total227.4 Mb227.3237.1 Mb272.4 Mb323.8 Mb
Mapped scaffold sequence total225.7 Mb (99.2%)218.4 Mb (96%)198.9 (83.9%)191.7 Mb (70.4%)281.6 Mb (87.0%)
Oriented scaffold sequence223.3 Mb (98.2%)194.6 Mb (85.6%)–––
Contig sequence total224.6 Mb224.6 Mb219.9 Mb–318.7 Mb
Scaffold N50/L5010/7.3 Mb9/8.9 Mb120/577.8 kb–/219.6 kb519/198.9 kb
Scaffold N50/L50 (chromosome-scale assembly)4/27.4 Mb4/26.8 Mb–––
Contig N50/L50250/255.4 kb294/214.2 kb2009/31.8 kb–/276 bp706/132.6 kb
Number of scaffolds >50 kb1121–––
% main genome in scaffolds >50 kb99.4%99.4–––
Repetitive sequences79.38 Mb (35.34%)84.41 Mb (37.14%)106.8 Mb (44.9%)119.4 Mb (43.8%)150.8 Mb (47.2%)
Protein-coding genes26,87327,85231,39043,67341,294
Protein-coding transcripts47,08928,689––45,581
Alternative transcripts20,216837––4287
a

In brackets, assembled scaffolds prior the build of pseudomolecules

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