文献速递 (2017年7月)

Rapid Genetic Adaptation during the First Four Months of Survival under Resource Exhaustion >>>

Molecular Biology and Evolution, Volume 34, Issue 7, 1 July 2017, Pages 1758–1769
大肠杆菌微进化。研究培养基耗尽后,大肠杆菌的适应性。

PopNet: A Markov Clustering Approach to Study Population Genetic Structure >>>

Molecular Biology and Evolution, Volume 34, Issue 7, 1 July 2017, Pages 1799–1811
新的群体遗传聚类软件。不依赖单一的参考序列,因此可以避免参考序列的选择带来的偏好性,比较适用于细菌。

The population genomics of archaeological transition in west Iberia: Investigation of ancient substructure using imputation and haplotype-based methods >>>

PLoS Genet 13(7): e1006852
作者收集了葡萄牙从新石器时代中期到青铜器时代中期的14个人类古DNA样本,发现这两个时期的遗传差异很小,说明相较欧洲其他地区,葡萄牙在当时群体流动性较小。作者还预测了新石器时代当地人的身高,暗示后来的群体混合导致的身高降低。作者还检测了其他重要的受选择性状,以及这些性状的来源及时间。

Genetic compensation: A phenomenon in search of mechanisms >>>

PLoS Genet 13(7): e1006780.
基因敲除或敲低后遗传补偿现象机制的综述。

GARLIC: Genomic Autozygosity Regions Likelihood-based Inference and Classification >>>

Bioinformatics, Volume 33, Issue 13, 1 July 2017, Pages 2059–2062
检测ROH区域的软件。

LASER server: ancestry tracing with genotypes or sequence reads >>>

Bioinformatics, Volume 33, Issue 13, 1 July 2017, Pages 2056–2058
这篇文章的思路就是先定义一个参考的祖先空间(reference ancestry space),即拿目前已有的具有代表性的群体做PCA,形成一个参考的变量空间,再将新样本映射到这个变量空间,从而判断这个样本的遗传组成。这样就不用合并新测序的样本,不管测序还是芯片,可以直接映射。

Fast admixture analysis and population tree estimation for SNP and NGS data >>>

Bioinformatics, Volume 33, Issue 14, 15 July 2017, Pages 2148–2155
STRUCTURE-like群体聚类软件,与ADMIXTURE相比,他能在相同的时间内,得到更大的likelihood值。能基于基因型的likelihood值计算,因此更适用于低深度测序。另外,该软件可以基于估计的祖先型构树。不得不提的是该文有Rasmus Nielsen和Thomas Mailund两位大牛站台。

Tagging SNP-set selection with maximum information based on linkage disequilibrium structure in genome-wide association studies >>>

Bioinformatics, Volume 33, Issue 14, 15 July 2017, Pages 2078–2081
tag SNP筛选,在保留最多变异信息的同时,挑选最少的SNP。作者用于全基因组关联分析的场景。主要基于LD,因此也可能可以用于群体遗传分析的其他分析,如PCA, ADMIXTURE等。

GenomeScope: fast reference-free genome profiling from short reads >>>

Bioinformatics, Volume 33, Issue 14, 15 July 2017, Pages 2202–2204
基于短读长测序数据的基因组特征评估软件,包括基因组大小,杂合度,重复含量等。

Discovery and genotyping of novel sequence insertions in many sequenced individuals >>>

Bioinformatics, Volume 33, Issue 14, 15 July 2017, Pages i161–i169
插入序列检测,基于局部组装。评估效果好于MindTheGap。

Comparison of computational methods for Hi-C data analysis >>>

Nature Methods 14, 679–685 (2017)
Hi-C不同数据分析方法比较。

1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life >>>

Nature Biotechnology 35, 676–683 (2017)
1,003珠细菌或古菌基因组。

Wild emmer genome architecture and diversity elucidate wheat evolution and domestication >>>

Science 07 Jul 2017: Vol. 357, Issue 6346, pp. 93-97
利用Hi-C技术组装野生异源四倍体小麦(二粒小麦)的全基因组序列。找到了控制脱粒性状的基因。

Evolution of the wheat blast fungus through functional losses in a host specificity determinant >>>

Science 07 Jul 2017:
Vol. 357, Issue 6346, pp. 80-83
麦瘟病是一种真菌引起的小麦病害,起源于巴西,本研究阐明了麦瘟病的传播和爆发机制。

Sequencing and de novo assembly of 150 genomes from Denmark as a population reference >>>

Nature 548, 87–91 (03 August 2017)
组装了150个丹麦人基因组,只用了短读长reads和20 kb mate-pair reads。

Assessment of Genetic Diversity and Structure of Large Garlic (Allium sativum) Germplasm Bank, by Diversity Arrays Technology “Genotyping-by-Sequencing” Platform (DArTseq) >>>

Front. Genet., 20 July 2017
通过GBS测序评估大蒜种质资源的遗传多样性和群体结构。

Evaluation of Quality Assessment Protocols for High Throughput Genome Resequencing Data >>>

几种重测序策略的评估(WGS, WES, gene panel),及数据处理策略评估。

Ancient European dog genomes reveal continuity since the Early Neolithic >>>

作者测了新石器时代早期和晚期欧洲狗的化石,通过分析,推翻了去年Science狗的双地起源的推论,认为狗是一次起源。

Deeply divergent archaic mitochondrial genome provides lower time boundary for African gene flow into Neanderthals >>>

Nature Communications 8, Article number: 16046 (2017)
作者测了一个更新世人的线粒体基因组,分析发现他和其他尼安德特人在 ∼270,000 分歧,因此推断尼安德特人向现代人线粒体introgression的时间下限是∼270,000年。

A mitogenomic timetree for Darwin’s enigmatic South American mammal Macrauchenia patachonica >>>

Nature Communications 8, Article number: 15951 (2017)
作者测了一个长颈驼线粒体基因组,确定了其进化地位及分化时间。

The evolutionary significance of polyploidy >>>

Nature Reviews Genetics 18, 411–424 (2017)
综述,多倍体化和环境变化/压力的相关性,及多倍体化带来的短期适应性,以及对生物长期的影响。

Reevaluation of SNP heritability in complex human traits >>>

Nature Genetics 49, 986–992 (2017)
估计SNP的遗传力,发现不同MAF、LD水平等的SNP遗传力差异很大。

Genomic analyses in cotton identify signatures of selection and loci associated with fiber quality and yield traits >>>

Nature Genetics 49, 1089–1098 (2017)
棉花纤维的选择和关联分析。

Whole-genome resequencing of 292 pigeonpea accessions identifies genomic regions associated with domestication and agronomic traits >>>

Nature Genetics 49, 1082–1088 (2017)
对292珠木豆选育品种/地方品种及野生种的选择及关联分析,揭示驯化性状的遗传机制。

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