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Pipeline publication

[…] were included in the 167 longest scaffolds. According to the flow cytometry analysis, the genome size of Z. japonica ‘Nagirizaki’ is ∼390 Mb (0.80 pg/2C). This is 15% larger than the estimation by k-mer analysis (340 Mb) (Supplementary Table S3), presumably due to the effect of conserved regions on homeologous chromosome pairs in the tetraploid genome. Thus the genome assembly of Z. japonica ‘Nagirizaki’, designated as ‘Zjn_r1.1’, covered 86% of the whole genome as estimated by flow cytometry. Table 1.Contigs or scaffolds shorter than 499 bp were excluded., Contigs or scaffolds shorter than 499 bp were excluded., For Z. matrella ‘Wakaba’ and Z. pacifica ‘Zanpa’, the scaffolds were built by Opera using contigs generated by DISCOVAR de novo because DISCOVAR de novo constructed contigs with higher N50 values than the other assemblers. This may be because only a single MP library was generated for these species. The final assemblies for ‘Wakaba’ and ‘Zanpa’ were generated by gap-closing with GMcloser and resulted in 563 Mb (N50 length, 109 kb) and 397 Mb (N50 length, 111 kb), respectively (Table ). As with ‘Nagirizaki’, the genome size of ‘Zanpa’ estimated by flow cytometry (370 Mb; 0.76 pg/2C) was larger (by 23%) than the size estimated by k-mer analysis (302 Mb) (Supplementary Table S3). On the other hand, the flow cytometry estimate for ‘Wakaba’ was ∼380 Mb (0.79 pg/2C), which is 11% smaller than that estimated by k-mer analysis (423 Mb) (Supplementary Table S3). This difference was presumably due to the effect of heterozygosity exceeding the effect of tetraploidy. The genome assemblies of ‘Wakaba’ and ‘Zanpa’ were longer than those estimated by flow cytometry, suggesting tha […]

Pipeline specifications

Software tools Opera, DISCOVAR, GMcloser
Organisms Pseudaesopia japonica
Chemicals Nucleotides