文献速递 (2017年8月)

Human Y-chromosome variation in the genome-sequencing era >>>

Nature Reviews Genetics 18, 485–497 (2017)
人Y染色体的综述。

Reference standards for next-generation sequencing >>>

Nature Reviews Genetics 18, 473–484 (2017)
基因组的大小和复杂度,以及样本准备、测序和分析过程中带来的技术错误对NGS数据的解读是很大的挑战。通过参考标准物的使用,可以理解和减少这些错误。(参考标准物是研究很透彻的对照DNA)

The origin of Metazoa: a unicellular perspective >>>

Nature Reviews Genetics 18, 498–512 (2017)
多细胞动物起源综述。

SeqArray—a storage-efficient high-performance data format for WGS variant calls >>>

Bioinformatics, Volume 33, Issue 15, 1 August 2017
一种新的变异存储格式,与vcf格式相比,文件只有其1/5左右,且比vcftools计算速度更快。

ploidyNGS: visually exploring ploidy with Next Generation Sequencing data >>>

Bioinformatics, Volume 33, Issue 16, 15 August 2017
基因组倍性检测和可视化开源软件。

Northeast African genomic variation shaped by the continuity of indigenous groups and Eurasian migrations >>>

PLoS Genet 13(8): e1006976.
非洲东北部人群的遗传特征(群体结构,基因流等)。非洲东北部是现代人走出非洲以及欧洲人向非洲迁徙的大门。

Composite likelihood method for inferring local pedigrees >>>

PLoS Genet 13(8): e1006963.
基于SNP的系谱推断软件。大牛出品,必属精品?!

Deconstructing isolation-by-distance: The genomic consequences of limited dispersal >>>

PLoS Genet 13(8): e1006911.
以丛灌鸦为例解析isolation-by-distance。作者发现雄性isolation-by-distance现象比雌性更显著。(雄性领地观念更强,雌性择偶,所以迁徙更多?)

Genomic estimation of complex traits reveals ancient maize adaptation to temperate North America >>>

Science 04 Aug 2017:
Vol. 357, Issue 6350, pp. 512-515
通过对15个1900年前温带地区玉米进行测序,揭示了玉米适应温带环境的遗传机制。

Genetic origins of the Minoans and Mycenaeans >>>

Nature 548, 214–218 (10 August 2017)
通过对19个古人DNA全基因组测序,揭示了米诺斯人和迈锡尼人的遗传起源。

Genome-wide association studies dissect the genetic networks underlying agronomical traits in soybean >>>

Genome Biology201718:161
大豆GWAS。

A tandem simulation framework for predicting mapping quality >>>

Genome Biology201718:152
对比对质量进行校正。

Estimating the human mutation rate from autozygous segments reveals population differences in human mutational processes >>>

Nature Communications 8, Article number: 303 (2017)
对3222个人外显子测序,估计人的碱基突变率。发现不同人群的突变模式不同。

Genome re-sequencing reveals the history of apple and supports a two-stage model for fruit enlargement >>>

Nature Communications 8, Article number: 249 (2017)
通过对117个苹果重测序,揭示苹果果实经过两个阶段变大的遗传机制。

Adaptive and non-adaptive divergence in a common landscape>>>

Nature Communications 8, Article number: 267 (2017)
三刺鱼和九刺鱼在相同环境中,在基因组上面存在不同的适应信号。

Inferring Allele Frequency Trajectories from Ancient DNA Indicates That Selection on a Chicken Gene Coincided with Changes in Medieval Husbandry Practices >>>

Molecular Biology and Evolution, Volume 34, Issue 8, 1 August 2017
通过古DNA位点频率推断选择的强度和时间。

Mitochondrial Recombination and Introgression during Speciation by Hybridization >>>

Molecular Biology and Evolution, Volume 34, Issue 8, 1 August 2017
一般细胞器DNA都是单亲遗传的,不存在重组事件。作者发现两种不同芽殖酵母杂交后代的线粒体DNA存在重组。

Evidence for Very Recent Positive Selection in Mongolians >>>

Molecular Biology and Evolution, Volume 34, Issue 8, 1 August 2017
通过对96个蒙古人的SNP进行分析,发现了蒙古人基因组中环境适应性的信号。

Patterns of Genome-Wide Diversity and Population Structure in the Drosophila athabasca Species Complex >>>

Molecular Biology and Evolution, Volume 34, Issue 8, 1 August 2017
作者组装了1个阿萨巴斯卡果蝇基因组草图,并对28个个体进行了重测序。发现阿萨巴斯卡果蝇X染色体的分化模式和常染色体有较大区别。作者对3个亚群的分化时间和基因流进行了研究。

Soft Sweeps Are the Dominant Mode of Adaptation in the Human Genome >>>

Molecular Biology and Evolution, Volume 34, Issue 8, 1 August 2017
作者通过机器学习的方法对6个人群的选择消除位点进行了检测,发现soft sweep为人类近期适应性的主要方式。作者还发现选择作用影响了基因组的变异模式,且增加了有害突变的积累。

Bioinformatic processing of RAD-seq data dramatically impacts downstream population genetic inference >>>

Methods Ecol Evol, 8: 907–917. 2017
作者通过对RAD数据分析流程的评估:组装或比对到不同分化程度的参考基因组,以及不同的过滤策略,发现组装和比对的差异很大,过滤策略影响较小。最后建议RAD数据比对到近缘参考序列。

GenomeVIP: a cloud platform for genomic variant discovery and interpretation >>>

Genome Res. 2017. 27: 1450-1459
基于web的开源变异检测框架,包含GATK等主流软件和注释数据库。

如果我的博客能帮你节约时间,我会非常高兴你请我喝杯咖啡。