小柯机器人

澳大利亚昆士兰大学Lachlan J. M. Coin课题组利用新方法实现多倍体植物基因组的全染色体组装。相关论文于2020年10月30日发表在《自然—遗传学》杂志上。

Title: Assembly of whole-chromosome pseudomolecules for polyploid plant genomes using outbred mapping populations

Author: Chenxi Zhou, Bode Olukolu, Dorcus C. Gemenet, Shan Wu, Wolfgang Gruneberg, Minh Duc Cao, Zhangjun Fei, Zhao-Bang Zeng, Andrew W. George, Awais Khan, G. Craig Yencho, Lachlan J. M. Coin

Issue&Volume: 2020-10-30

Abstract: 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. PolyGembler, a method for grouping and ordering contigs into complete pseudomolecules by combining long-read sequencing and genotype information from an outbred mapping population, improves the accuracy for assembly of polyploidy plant genomes.

DOI: 10.1038/s41588-020-00717-7

Source: https://www.nature.com/articles/s41588-020-00717-7

Nature Genetics：《自然—遗传学》，创刊于1992年。隶属于施普林格·自然出版集团，最新IF：41.307
官方网址：https://www.nature.com/ng/
投稿链接：https://mts-ng.nature.com/cgi-bin/main.plex