获得染色体水平的基因组

2019. NG. 玉米. Genome assembly of a tropical maize inbred line provides insights into structural variation and crop improvement
      组装流程：

      
      
      image.png
      
      

      利用重组自交系的高密度连锁图，将scaffolds安装到染色体:

This result, together with a high-density linkage map from a recombinant inbred population between SK and a widely adopted inbred of China, ZHENG58 (ref. 22 ), allowed the construction of ten pseudo-chromosomes.

2017. NG. 苹果. High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development
      组装流程：

      
      
      image.png
      
      

      利用高密度遗传连锁图谱中获得的SNP，将scaffolds安装到染色体：

together with single-nucleotide p morphism (SNP) markers derived from a high-density genetic linkage map 23 , allowed the construction of the 17 pseudochromosomes

2019. NG. 花生. The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication
      组装：

PB + Illumina

利用Hi-C数据和遗传图谱安装到染色体，其中利用Hi-C数据就能很好的分成20个群

Softwares: HiC-pro, LACHESIS, ALLMAPS
3,664 high-confident contigs were anchored to a total of 20 chromosomes accounting for 2,424,161,010 bp (95.5% of all assembly length) and leaving 3,902 contigs unanchored totaling 114,247,896 bp
Then, using the Hi-C assembled map and the integrated linkage maps, the whole chromosomes were assembled by ALLMAPS software 21 with a priority of Hi-C assembled map vs. integrated genetic map being 1:1.

2019. NG. 棉花. Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense
      组装：

PB + Illumina + Bionano + Hi-C

组装基因组

Hi-C + genetic map
The Hi-C data were mapped to these segments using BWA (version 0.7.10-r789) software 21 . The uniquely mapped data were retained to perform assembly by using LACHESIS software.
In addition, a published genetic map with 4,049 bins between G. hirsutum and G. barbadense was aligned to both genomes after Hi-C directed assembly