“Pan-genome”是指一个clade或品种中的所有个体都包含的一组基因集,其提供一个新的维度来进行研究,即通过基因在基因组上的存在或缺失来评价。在该研究前不久,the 3000 Rice Genome Project (3K RGP)以平均深度14.3x测序了超过3000个水稻基因组。本研究作者筛选出了水稻的pan-genome,并开发了基因组浏览器Rice P...
Zhao Q, Feng Q, Lu H, et al (2018) Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice. Nat Genet 50:278–284.https://doi.org/10.1038/s41588-018-0041-z 本篇与9#pan-genome#rice#同年发表,可对照学习。 水稻和普通稻丰富的遗传多样性是水稻育种的主要...
为了发现水稻中的等位基因变体，已经进行了大规模的重新测序，但通过 将短序列读数直接映射到参考基因组上往往会丢失许多遗传变异的信息 【pan基因组的根本意义】。通过对66份不同的材料进行深度测序和从头组装，构建了 O. sativa - O. rufipogon 物种复合体的泛基因组数据集。基因间比较发现水稻 基因组...
The advent of the pangenome era has unraveled previously unknown genetic variation existing within diverse crop plants, including rice. This untapped genetic variation is believed to account for a major portion of phenotypic variation existing in crop plants. However, the use of conventional single ...
genome assemblies - as a pan-genome proxy - that spanned the K = 1532population structure of cultivated Asian rice, plus two additional high-quality de novo assembled genomes from a representative species of the progenitor of Asian rice (O. rufipogon) and the BB genome species -O. ...
Cell:Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations 学校毕设任务之一,翻译文献。翻译了一小部分以后觉得这篇文章的细节对毕设方向帮助不大,外加太长了(30页+),决定换一篇。把半成品放在这,或许能为同行提供一些帮助。
Pan-genomes from large natural populations can capture genetic diversity and reveal genomic complexity. Using de novo long-read assembly, we generated a graph-based super pan-genome of rice consisting of a 251-accession panel comprising both cultivated and wild species of Asian and African rice. ...
Presence/absence variation analysis was performed by the same pipeline that was used to construct the pan-genome. 2.4. De novo assembly and analysis of transcriptomic data Total RNA with 3 biological replicates was extracted from tissues of different grain development stages of NER3, NER4, NER6 ...
(S.L.)In briefA high-quality rice pan-genome ofgenetically diverse rice accessions isconstructed through de novo genomeassemblies, demonstrating the impact ofstructural variation and gene copynumber variations on environmentaladaptations and agronomic traits.Qin et al., 2021, Cell 184, 1–17June 24...
A pangenome aims to capture the complete genetic diversity within a species and reduce bias in genetic analysis inherent in using a single reference genome. However, the current linear format of most plant pangenomes limits the presentation of position information for novel sequences. Graph pangenom...