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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.
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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
- 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.
- 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
