The impact of third generation genomic technologies on plant genome assembly 第三代基因组技术对植物基因组组装的影响

题目：The impact of third generation genomic technologies on plant genome assembly

第三代基因组技术  对植物  基因组组装 的影响

原文链接

文章重点信息

• 植物基因组比脊椎动物重复性更强，组装更复杂
• Long-read 组装优于 short-read 组装
• Long-range scaffolding可组装至染色体水平
• 重构建单体型允许拼接杂合体和多倍体基因组

背景
植物基因组的组装是一个具有挑战性的问题，并且可能比装配脊椎动物基因组更具挑战性。这个挑战是
由于转座元件的高重复性，极端基因组大小，如22 Gb火炬松和20 Gb挪威云杉基因组。又如，一些植物的多倍体性质，如作物的多倍体性质。最近，long read 还有long-range scaffolding的方法（optical mapping , chromosome conformation capture）变得越来越popular。

Long-read sequencing technologies

PacBio：

• with an average size of nearly 20 kb and a maximum length of over 60 kb
• sequencing error rates of up to 15%, correction with short sequencing read （错误率蛮高，需要通过short read进行校正）
• improve short-read assemblies by gap closure or scaffolding
• first plant genomes assembled from PacBio：Arabidopsis thaliana and Oropetium thomaeum （never reached by short-read assemblies，less gaps represented as Ns in the sequence ）

Oxford Nanopore：

• the longest reads are up to 200 kb

Synthetic Long-Reads (SLR)

• de novo assembly requires high amounts of short read coverage
• assemblies hardly reached N50 statistics of more than 100 kb

Long-range scaffolding technologies

optical mapping

• Bionano: generates fingerprints of DNA fragments of up to multiple hundred kb by imaging the patterns of restriction sites, then assembled into genome-wide (consensus) maps
• combination of sequencing data and optical maps
• optical maps can be used to control for errors in the sequence assembly, the sequence contigs can be used to control for errors in the optical maps.

Hi-C

• Hi-C data are complementary and can help bridging different regions in the genome
• improved assembly contiguity similar well as compared to optical mapping data

10X Genomics

• no published records of plant genomes assembled with the 10X Genomics

Assembly of heterozygous and polyploid genomes

 

• FALCON-Unzip, which uses PacBio sequencing data to phase the variation between individual chromosomes already during the assembly of the reads
• short and long-read sequencing data combined with optical maps, working well for the assembly of polyploid genomes
• longer reads or molecules will help improving the reconstruction of individual homeologs