Noninvasive genome sampling in chimpanzees

The inevitable has happened: genomic technologies have been added to our noninvasive genetic sampling repertoire. In this issue of Molecular Ecology, Perry et al. (2010) demonstrate how DNA extraction from chimpanzee faeces, followed by a series of steps to enrich for target loci, can be coupled with next-generation sequencing. These authors collected sequence and single-nucleotide polymorphism (SNP) data at more than 600 genomic loci (chromosome 21 and the X) and the complete mitochondrial DNA. By design, each locus was 'deep sequenced' to enable SNP identification. To demonstrate the reliability of their data, the work included samples from six captive chimps, which allowed for a comparison between presumably genuine SNPs obtained from blood and potentially flawed SNPs deduced from faeces. Thus, with this method, anyone with the resources, skills and ambition to do genome sequencing of wild, elusive, or protected mammals can enjoy all of the benefits of noninvasive sampling.     

Transpositional landscape of the rice genome revealed by paired-end mapping of high-throughput re-sequencing data

Transposable elements (TEs) are mobile entities that densely populate most eukaryotic genomes and contribute to both their structural and functional dynamics. However, most TE-related sequences in both plant and animal genomes correspond to inactive, degenerated elements, due to the combined effect of silencing pathways and elimination through deletions. One of the major difficulties in fully characterizing the molecular basis of genetic diversity of a given species lies in establishing its genome-wide transpositional activity. Here, we provide an extensive survey of the transpositional landscape of a plant genome using a deep sequencing strategy. This was achieved through paired-end mapping of a fourfold coverage of the genome of rice mutant line derived from an in vitro callus culture using Illumina technology. Our study shows that at least 13 TE families are active in this genotype, causing 34 new insertions. This next-generation sequencing-based strategy provides new opportunities to quantify the impact of TEs on the genome dynamics of the species.     

转座子相关技术在微生物功能基因组研究中的应用

转座子是DNA插入因子的一种,是指能在基因组间或组内跳跃的DNA片段。转座子作为插入突变剂或分子标签已被广泛地应用于基因的分离和克隆,且因其独特的性质已成为发现新基因和基因功能分析的有效工具。这使得转座子无论是在单基因水平还是全基因组水平,都成为细菌、酵母和其他微生物研究的有力工具。简单而有效的体外转座反应可以对一些以往难以进行分析的顽固微生物进行转座诱变分析。而建立在转座子基础上的信号标签诱变技术和遗传足迹法的应用则发现了一些新的病原微生物毒力因子,从而可以更好地对这些病原微生物的致病机理进行阐述。这些再次说明转座子是微生物功能基因组研究中的有力工具。本文综述了转座子及其衍生载体介导的一些技术,并讨论其在微生物功能基因组研究中的应用。     

Ancient genomics

The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field''s focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequence throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when testing specific hypotheses related to the past.     

Evolutionary insight from whole-genome sequencing of experimentally evolved microbes

Experimental evolution (EE) combined with whole‐genome sequencing (WGS) has become a compelling approach to study the fundamental mechanisms and processes that drive evolution. Most EE‐WGS studies published to date have used microbes, owing to their ease of propagation and manipulation in the laboratory and relatively small genome sizes. These experiments are particularly suited to answer long‐standing questions such as: How many mutations underlie adaptive evolution, and how are they distributed across the genome and through time? Are there general rules or principles governing which genes contribute to adaptation, and are certain kinds of genes more likely to be targets than others? How common is epistasis among adaptive mutations, and what does this reveal about the variety of genetic routes to adaptation? How common is parallel evolution, where the same mutations evolve repeatedly and independently in response to similar selective pressures? Here, we summarize the significant findings of this body of work, identify important emerging trends and propose promising directions for future research. We also outline an example of a computational pipeline for use in EE‐WGS studies, based on freely available bioinformatics tools.     

Next-generation sequencing technology:A technology review and future perspective

As one of the most powerful tools in biomedical research,DNA sequencing not only has been improving its productivity at an exponential growth rate but has also been evolving into a new layout of technological territories toward engineering and physical disciplines over the past three decades.In this technical review,we look into technical characteristics of the next-generation sequencers and provide insights into their future development and applications.We envisage that some of the emerging platforms are c...     

Genome-wide association genetics of an adaptive trait in lodgepole pine

Pine cones that remain closed and retain seeds until fire causes the cones to open (cone serotiny) represent a key adaptive trait in a variety of pine species. In lodgepole pine, there is substantial geographical variation in serotiny across the Rocky Mountain region. This variation in serotiny has evolved as a result of geographically divergent selection, with consequences that extend to forest communities and ecosystems. An understanding of the genetic architecture of this trait is of interest owing to the wide-reaching ecological consequences of serotiny and also because of the repeated evolution of the trait across the genus. Here, we present and utilize an inexpensive and time-effective method for generating population genomic data. The method uses restriction enzymes and PCR amplification to generate a library of fragments that can be sequenced with a high level of multiplexing. We obtained data for more than 95,000 single nucleotide polymorphisms across 98 serotinous and nonserotinous lodgepole pines from three populations. We used a Bayesian generalized linear model (GLM) to test for an association between genotypic variation at these loci and serotiny. The probability of serotiny varied by genotype at 11 loci, and the association between genotype and serotiny at these loci was consistent in each of the three populations of pines. Genetic variation across these 11 loci explained 50% of the phenotypic variation in serotiny. Our results provide a first genome-wide association map of serotiny in pines and demonstrate an inexpensive and efficient method for generating population genomic data.     

The Application of Reverse Genetics to Polyploid Plant Species

Polyploidy events (polyploidization) followed by progressive loss of redundant genome components are a major feature of plant evolution, with new evidence suggesting that all flowering plants possess ancestral genome duplications. Furthermore, many of our most important crop plants have undergone additional, relatively recent, genome duplication events. Recent advances in DNA sequencing have made vast amounts of new genomic data available for many plants, including a range of important crop species with highly duplicated genomes. Along with assisting traditional forward genetics approaches to study gene function, this wealth of new sequence data facilitates extensive reverse genetics-based functional analyses. However, plants featuring high levels of genome duplication as a result of recent polyploidization pose additional challenges for reverse genetic analysis. Here we review reverse genetic analysis in such polyploid plants and highlight key challenges.