文献速递 (2017年9月)

Genomic Reconstruction of the History of Native Sheep Reveals the Peopling Patterns of Nomads and the Expansion of Early Pastoralism in East Asia >>>

Molecular Biology and Evolution, Volume 34, Issue 9, 1 September 2017
作者利用SNP芯片(54K或685K)对1016只羊进行了全基因组SNP检测,揭示了东亚绵羊的群体历史及其和游牧民族迁徙的关系。作者还研究了盘羊对驯化绵羊的基因渗透,及驯化绵羊内部的基因交流,以及驯化过程中对尾型等性状的人工选择。

Disentangling Timing of Admixture, Patterns of Introgression, and Phenotypic Indicators in a Hybridizing Wolf Population >>>

Molecular Biology and Evolution, Volume 34, Issue 9, 1 September 2017
作者研究意大利狼和狗近期杂交群体的历史,推断了杂交的时间,研究了杂交后保留的狗的性状。(这篇文章研究的近几十年的历史,在进化文章中少见)

Population Genomics Reveals Speciation and Introgression between Brown Norway Rats and Their Sibling Species >>>

Molecular Biology and Evolution, Volume 34, Issue 9, 1 September 2017
作者对51只挪威褐鼠及其近缘种进行了全基因组测序,揭示了两者分化与更新世中期气候剧烈变化相关,它们分化后存在基因流。渗透区域和化学通讯相关,说明基因流和挪威褐鼠适应性相关。

Variant Interpretation: Functional Assays to the Rescue >>>30292-6)

AJHG, Volume 101, Issue 3, p315–325, 7 September 2017
人类基因组突变大规模功能注释的方法。

The Genetic Legacy of Zoroastrianism in Iran and India: Insights into Population Structure, Gene Flow, and Selection >>>30291-4)

AJHG, Volume 101, Issue 3, p353–368, 7 September 2017
拜火教的起源,传播,遗传交流和正选择。

Genome-wide reconstruction of complex structural variants using read clouds >>>

Nature Methods 14, 915–920 (2017)
为10X Genomics或类似技术开发的结构变异检测工具。相较基于短读长数据检测结构变异,该技术检测能力有较大改善。

Shotgun metagenomics, from sampling to analysis >>>

Nature Biotechnology 35, 833–844 (2017) doi:10.1038/nbt.3935
宏基因组从取样到分析的综述。

Haplotype phasing of whole human genomes using bead-based barcode partitioning in a single tube >>>

Nature Biotechnology 35, 852–857 (2017)
类似10X Genomics的一种建库策略,但不需要微流体控制,利用了Tn5转座酶。

Detecting ancient positive selection in humans using extended lineage sorting >>>

Genome Res. 2017. 27: 1563-1572
通过与已经灭绝的近缘种和现存的近缘种比较,寻找基因组中快于中性进化的固定区域。这些区域很可能是近期受选择的区域。

Network propagation: a universal amplifier of genetic associations >>>

Nature Reviews Genetics 18, 551–562 (2017)
一般认为影响同一个性状的基因是相互作用的,这是网络分析的基础。本文对网络传播算法在遗传关联中的应用进行了综述。

Exploiting induced and natural epigenetic variation for crop improvement >>>

Nature Reviews Genetics 18, 563–575 (2017)
利用表观数据进行作物育种综述。

Concepts, estimation and interpretation of SNP- based heritability >>>

Nature Genetics 49, 1304–1310 (2017)
GWAS基于SNP的狭义遗传力计算。

OMSim: a simulator for optical map data >>>

Bioinformatics, Volume 33, Issue 17, 1 September 2017
模拟Bionano产生的光学图谱数据。

Estimation of kinship coefficient in structured and admixed populations using sparse sequencing data >>>

PLoS Genet13(9): e1007021.
适合稀疏测序数据(捕获或简化基因组测序)及高缺失数据(低深度测序)计算亲缘关系的算法(软件)。

A Neolithic expansion, but strong genetic structure, in the independent history of New Guinea >>>

Science, 15 Sep 2017: Vol. 357, Issue 6356, pp. 1160-1163
研究巴布亚新几内亚各人群关系及与亚洲和澳洲人群关系。

Strains, functions and dynamics in the expanded Human Microbiome Project >>>

Nature 550, 61–66 (05 October 2017)
对来自265个人的不同时间,不同部位的2,355个宏基因组进行了研究。

Parental influence on human germline de novo mutations in 1,548 trios from Iceland >>>

Nature 549, 519–522 (28 September 2017)
通过对1,548 个trios进行测序,发现了新突变产生的特征。如男女突变率不同,女人突变积累更快等。

The Apostasia genome and the evolution of orchids >>>

Nature 549, 379–383 (21 September 2017)
深圳拟兰基因组草图,研究了基因组复制时间,开花相关基因如MADS-box等。

DESMAN: a new tool for de novo extraction of strains from metagenomes >>>

Genome Biology, 2017 18:181
从宏基因组中抽出菌株的基因组。(?)

Acidophilic green algal genome provides insights into adaptation to an acidic environment >>>

PNAS, 2017 vol. 114 no. 39
嗜酸绿藻基因组发表,揭示其对酸性环境的适应性机制。

A Hypothesis and Review of the Relationship between Selection for Improved Production Efficiency, Coping Behavior, and Domestication >>>

Front. Genet., 28 September 2017
动物应激行为和驯化关系的一篇综述。驯化会选择与产量性状无关的能量消耗行为,因此,驯化的动物大多是温驯的。

Ultrafast Comparison of Personal Genomes via Precomputed Genome Fingerprints >>>

Front. Genet., 26 September 2017
基因组指纹技术。通过相邻SNP突变类型和距离及对应的频率构成三维特征指纹,实现超快比对。还支持不同参考基因组混合比对。

Y-STR Haplogroup Diversity in the Jat Population Reveals Several Different Ancient Origins >>>

Front. Genet., 20 September 2017
通过分析印度和巴基斯坦的302个贾特人的Y染色体STR,揭示贾特人起源。

A biologist’s guide to Bayesian phylogenetic analysis >>>

Nature Ecology & Evolution 1, 1446–1454 (2017)
贝叶斯树构建的综述。(大牛杨子恒出品)

Worldwide patterns of human epigenetic variation >>>

Nature Ecology & Evolution 1, 1577–1583 (2017)
不同人群的表观遗传差异。

Genome-Wide Variation Patterns Uncover the Origin and Selection in Cultivated Ginseng (Panax ginseng Meyer) >>>

Genome Biology and Evolution, Volume 9, Issue 9, 1 September 2017
栽培高丽参的起源和驯化选择研究,揭示了南方高丽参和北方高丽参是分别起源和驯化的。

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。