Figures (2)  Tables (1)

    • Figure 1. 

      Overview of currently sequenced polyploid vegetables with the contig N50 (log10) of assemblies and publication year as Y and X axis, respectively. The type of sequencing technology (Next-generation sequencing, NGS and Third-generation sequencing, TGS) are indicated with different colors. The size of data points is scaled by the ploidy level. Neo- and paleo- polyploids are differentiated with closed and open data points.

    • Figure 2. 

      Schematic diagram illustrating the application of high-throughput sequencing for evolutionary genomics, promoting germplasm innovation and effective breeding in neo- and paleo- polyploid vegetables with cucumber as an example.

    • SpeciesRefAnalysis toolsYear of publication
      Solanum tuberosum[38]SOAPdenovo; EMBOSS; SOAPdenovoalign2011
      Solanum lycopersicum[39]Newbler; CABOG; BAC FISH; EuGene; ABySS2012
      Brassica napus[40]SOAPdenovo; Newbler; GapCloser;2014
      Fragaria × ananassa[25]SOAPdenovo; Newbler; GapCloser;2014
      Camelina sativa[41]SOAPdenovo; Bambus; GapCloser; NUCmer2014
      Brassica oleracea[42]SOAPdenovo; Bambus; GapCloser;2014
      Brassica juncea var. tumida[43]ALLPATHS-LG; PBjelly; IrysView2016
      Cucurbita maxima Duch.[44]ShortRead; QuorUM; SOAPdenovo; Newbler; GapCloser; Pilon2017
      Lactuca sativa[45]SOAPdenovo; HiRis2017
      Fragaria × ananassa[46]NRGene; HiRise; PBJelly; Pilon; CoGe2019
      Brassica oleracea[47]FALCON; Quiver; BWA-MEM2019
      Brassica napus[48]Falcon; CANU; pbalign; pilon; 3D-DNA; Juicebox; Juicer2020
      Medicago sativa[49]CANU; MECAT; HERA; BWA-MEM; Redundans; Purge Haplotigs; BWA-MEM; Pilon2020
      Medicago sativa[36]CANU; ALLHiC; Jcvi; Juicebox2020
      Brassica oleracea[50]PBcR wgs8.3rc1; FALCON; Quiver; Pilon; BWA-MEM; SALSA; Mummer2020
      Solanum melongena[51]wtdbg2; Racon; Pilon; fragScaff; LACHESIS2020
      Allium sativum[52]FALCON; Quiver; Pilon; Purge Haplotigs; FragScaff; Burrows-Wheeler Aligner; ALLHiC2020
      Brassica napus[53]CANU; Pilon; 3D-DNA; ALLMAPS; ALLHiC2021
      Brassica juncea[54]CANU; BWA mem; MaSuRcA; RefAligner; IrysSolve; Pilon2021
      Brassica juncea[55]Jellyfish; FALCON; Sspace-longread; Quiver; BioNano Solve; BioNano Access; Juicebox; HiCPlotter2021
      Cucumis × hytivus[26]CANU; Pilon; SOAPdenovo; SSPACE; RefAligner; cutadapt; LACHESIS; HiC-Pro2021
      Brassica oleracea[56]Falcon; Arrow; PBJelly2021
      Solanum tuberosum[22]pbccs; hifiasm; BWA-MEM; ALLHiC; jcvi2022
      Solanum tuberosum[57]hifiasm; pilon;2022
      Capsicum annuum[58]MECAT2; Pilon; CANU; Juicer; Juicerbox; 3D-DNA; Phred; CA592022
      Raphanobrassica[59]JELLYFISH; CANU; Arrow; Pilon; JUICER;2023
      Vicia faba[60]hifiasm; Sniffles; findGSE; purge_haplotigs; Merqury; RagTag; GSAlign; Liftoff2023
      Lactuca sativa[61]CANU; WTDBG2; Arrow; Pilon; 3D-DNA; Juicer; Falcon2023

      Table 1. 

      Analysis tools used for vegetable polyploid genome assembly.