The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.

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Initial sequencing and analysis of the human genome.

抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.

/pdf/initial-sequencing-and-comparative-analysis-of-the-mouse-5a9n62pifj.pdf

Initial sequencing and comparative analysis of the mouse genome.

GENOMIC imprinting, the inactivation of one allele dependent upon the sex of the parent from which it was derived, has understandably generated considerable interest from theoretical evolutionary biologists. Selection should favor diploid (biallelic) expression to protect against spontaneous

https://www.genetics.org/content/genetics/153/1/509.full.pdf

Is multiple paternity necessary for the evolution of genomic imprinting

Theory predicts that, owing to reduced Hill-Robertson interference, genomic regions with high crossing-over rates should experience more efficient selection In Saccharomyces cerevisiae a negative correlation between the local recombination rate, assayed as meiotic double-strand breaks (DSBs), and the local rate of protein evolution has been considered consistent with such a model Although DSBs are a prerequisite for crossing-over, they need not result in crossing-over With recent high-resolution crossover data, we now return to this issue comparing two species of yeast Strikingly, even allowing for crossover rates, both the rate of premeiotic DSBs and of noncrossover recombination events predict a gene's rate of evolution This both questions the validity of prior analyses and strongly suggests that any correlation between crossover rates and rates of protein evolution could be owing to slow-evolving genes being prone to DSBs or a direct effect of DSBs on sequence evolution To ask if classical theory of recombination has any relevance, we determine whether crossover rates predict rates of protein evolution, controlling for noncrossover DSB events, gene ontology (GO) class, gene expression, protein abundance, nucleotide content, and dispensability We find that genes with high crossing-over rates have low rates of protein evolution after such control, although any correlation is weaker than that previously reported considering meiotic DSBs as a proxy The data are consistent both with recombination enhancing the efficiency of purifying selection and, independently, with DSBs being associated with low rates of evolution

/pdf/protein-rates-of-evolution-are-predicted-by-double-strand-mqd6nuc1c0.pdf

Laurence D. Hurst

Papers

Is multiple paternity necessary for the evolution of genomic imprinting

Protein rates of evolution are predicted by double-strand break events, independent of crossing-over rates.

Sex, slime and selfish genes

Drunken walk of the diploid

Antibiotics cure asexuality