WEEK42:植物基因组研究进展
文献解读
染色体规模的assembly正迅速成为高质量从头参考植物基因组的标准。结合纳米孔技术测序和optical map是实现这一目标的一种方法。
植物基因组研究目的：
- provides novel insights into important aspects of plant biology such as development, metabolism, evolution and adaptation
- serve a wide community of plant biologists and bioinformaticians
发展进程：
BAC： bacterial artificial chromosome (BAC) technique
- gold standard for sequencing — the investments in labour and costs were huge
NGS：
- massive numbers of short reads of DNA can be generated quickly and at low cost.
Limitation：
- difficult, in particular for larger and complex plant genomes
- contiguity of genome assembly affected by heterozygosity, repetitive sequences and duplicated regions.
TGS: third generation, sequencing that allows the generation of longer reads and thus higher quality
- span entire repeat-containing regions, reconstruct haplotypes, resolve structural rearrangements
- ead to chromosome-scale ‘reference’ genomes
- long-read sequencing alone will not (yet) do the job.
目前趋势：nanopore +optiocal map with organized into longer scaffolds
Nanopore: isolate high-molecular weight DNA is thus essential — and a couple million bases may be sequenced in a single continuous read
- Compared to short-read assemblies of close relatives sequenced earlier, the long-read assembled contig N50s were between 100 and 450 times larger
- greatly improved the completeness of the transposable element (TE)
- S-locus, a region strongly enriched in TEs,now be completely reconstructed.
- centromeric regions (which are rich in repeats) and disease resistance genes, clusters of tandem-duplicated genes
- correct evolutionary history of genomes, identification of duplicated regions is often tricky and relies on finding long stretches of similarity in gene order and conten.
- it has proven impossible to correctly assemble polyploid genomes with short read technologies, the sequencing of polyploids has been considered one of the last great challenges
Pacbio: long-read PacBio sequencing
**Hic:**chromosome conformation capture techniques
Optical map: ordered, genome-wide, high-resolution restriction maps from single, stained molecules of DNA
