康蒂格
生物
基因组
顺序装配
基因分型
遗传学
DNA测序
多倍体
人口
计算生物学
纳米孔测序
全基因组测序
参考基因组
基因型
基因
社会学
人口学
基因表达
转录组
作者
Chenxi Zhou,Bode A. Olukolu,Dorcus C. Gemenet,Shan Wu,Wolfgang J. Grüneberg,Minh Duc Cao,Zhangjun Fei,Zhao‐Bang Zeng,Andrew W. George,Awais Khan,G. Craig Yencho,Lachlan Coin
出处
期刊:Nature Genetics
[Springer Nature]
日期:2020-10-30
卷期号:52 (11): 1256-1264
被引量:17
标识
DOI:10.1038/s41588-020-00717-7
摘要
Despite advances in sequencing technologies, assembly of complex plant genomes remains elusive due to polyploidy and high repeat content. Here we report PolyGembler for grouping and ordering contigs into pseudomolecules by genetic linkage analysis. Our approach also provides an accurate method with which to detect and fix assembly errors. Using simulated data, we demonstrate that our approach is of high accuracy and outperforms three existing state-of-the-art genetic mapping tools. Particularly, our approach is more robust to the presence of missing genotype data and genotyping errors. We used our method to construct pseudomolecules for allotetraploid lawn grass utilizing PacBio long reads in combination with restriction site-associated DNA sequencing, and for diploid Ipomoea trifida and autotetraploid potato utilizing contigs assembled from Illumina reads in combination with genotype data generated by single-nucleotide polymorphism arrays and genotyping by sequencing, respectively. We resolved 13 assembly errors for a published I. trifida genome assembly and anchored eight unplaced scaffolds in the published potato genome.
科研通智能强力驱动
Strongly Powered by AbleSci AI