对玉米泛基因组和泛转录组的见解

物种水平的基因组是动态的，基因存在于每个个体（核心）中，也存在于个体子集（可有可无）中，共同构成泛基因组。使用来自 503 个玉米 （Zea mays） 自交系的幼苗 RNA 的转录组测序来表征玉米泛基因组，我们鉴定了 8681 个代表性转录组件 （RTA），其中 16.4% 在所有品系中表达，82.7% 在品系亚群中表达。有趣的是，通过连锁不平衡定位，76.7% 的具有至少一个单核苷酸多态性 （SNP） 的 RTA 可以定位到单个遗传位置，主要分布在基因组的非着丝粒周围部分。RTA 的逐步迭代聚类表明，在本研究中使用的基因型的背景下，玉米基因组受到限制，并且在该种质基础中对幼苗 RNA 进行进一步采样将导致最小的发现。基于泛基因组中 SNP 和转录本丰度的全基因组关联研究揭示了与幼年到成人营养人和营养人到生殖发育转变的时间相关的基因座，这两个特征对适应性和适应很重要。这项研究揭示了玉米泛基因组的动态性质，并表明很大一部分变异可能位于一个物种的单个参考基因组之外。

内容来自文献

Hirsch C, Foerster J, Johnson J et al. (2014) Insights into the Maize Pan-Genome and Pan-Transcriptome. The Plant Cell 26(1):121-135. https://doi.org/10.1105/tpc.113.119982

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TY  - JOUR
AU  - Hirsch, Candice N.
AU  - Foerster, Jillian M.
AU  - Johnson, James M.
AU  - Sekhon, Rajandeep S.
AU  - Muttoni, German
AU  - Vaillancourt, Brieanne
AU  - Peñagaricano, Francisco
AU  - Lindquist, Erika
AU  - Pedraza, Mary Ann
AU  - Barry, Kerrie
AU  - de Leon, Natalia
AU  - Kaeppler, Shawn M.
AU  - Buell, C. Robin
T1  - Insights into the Maize Pan-Genome and Pan-Transcriptome  
PY  - 2014
Y1  - 2014/01/01
DO  - 10.1105/tpc.113.119982
JO  - The Plant Cell
JA  - Plant Cell
VL  - 26
IS  - 1
SP  - 121
EP  - 135
SN  - 1040-4651
AB  - Genomes at the species level are dynamic, with genes present in every individual (core) and genes in a subset of individuals (dispensable) that collectively constitute the pan-genome. Using transcriptome sequencing of seedling RNA from 503 maize (Zea mays) inbred lines to characterize the maize pan-genome, we identified 8681 representative transcript assemblies (RTAs) with 16.4% expressed in all lines and 82.7% expressed in subsets of the lines. Interestingly, with linkage disequilibrium mapping, 76.7% of the RTAs with at least one single nucleotide polymorphism (SNP) could be mapped to a single genetic position, distributed primarily throughout the nonpericentromeric portion of the genome. Stepwise iterative clustering of RTAs suggests, within the context of the genotypes used in this study, that the maize genome is restricted and further sampling of seedling RNA within this germplasm base will result in minimal discovery. Genome-wide association studies based on SNPs and transcript abundance in the pan-genome revealed loci associated with the timing of the juvenile-to-adult vegetative and vegetative-to-reproductive developmental transitions, two traits important for fitness and adaptation. This study revealed the dynamic nature of the maize pan-genome and demonstrated that a substantial portion of variation may lie outside the single reference genome for a species.
Y2  - 9/6/2024
UR  - https://doi.org/10.1105/tpc.113.119982
ER  -