家蚕(Bombyx mori)全基因组框架图

我们在此报告了家蚕(Bombyx mori)的基因组序列框架图,它覆盖了所有已知家蚕基因的90.9%。我们估计的基因数是18510,超过黑腹果蝇报道的13379个基因。我们将家蚕基因组与果蝇、蚊子、蜘蛛和蝴蝶等进行了比较分析,揭示了它们在基因组成上同时具有相似性和差异性。

KaKs_Calculator:Calculating Ka and Ks Through Model Selection and Model Averaging

KaKs_Calculator is a software package that calculates nonsynonymous （Ka） and synonymous （Ks） substitution rates through model selection and model averaging. Since existing methods for this estimation adopt their specific mutation （substitution） models that consider different evolutionary features, leading to diverse estimates, KaKs_Calculator implements a set of candidate models in a maximum likelihood framework and adopts the Akaike information criterion to measure fitness between models and data, aiming to include as many features as needed for accurately capturing evolutionary information in protein-coding sequences. In addition, several existing methods for calculating Ka and Ks are also incorporated into this software. KaKs_Calculator, including source codes, compiled executables, and documentation, is freely available for academic use at http：//evolution.genomics.org.cn/software.htm.

Positive correlation between recombination rate and nucleotide diversity is shown under domestication selection in the chicken genome

Positive correlation between recombination rate and nucleotide diversity has been observed in a wide variety of eukaryotes on megabase scale. On the basis of genome-wide chicken genetic variation map generated by comparing three domestic breeds with wild ancestor and the positions of markers on the genetic linkage map, we found that SNPs rates were similar for all chromosomes while the recombina-tion rates increased in micro chromosomes. In other words no correlation exists in chromosome size. Nevertheless, when we scanned the genome by calculating the values of each characteristic within non-overlapping windows, instead of single value for each chromosomes, the nucleotide diversity was found to be significantly correlated with the recombination rate (r=0.27, P<0.0005). Furthermore, the significant association not only existed between these two features, but also existed between all 6 pairwise combinations of nucleotide diversity, recombination rate, GC content and average gene length. This co-variation is very meaningful for the studies of sequence evolution.

Genome Biology: The Second Modern Synthesis

A scientific dream proposed some 20 years ago has been realized-the completion of the DNA sequence for the Human Genome Project （HGP） in 2004. As a result, an entirely new field of biological research has arisen： genome biology or genomics is celebrated for its unprecedented scale, intrinsically digital output, and systematic approach to getting all the data. Its sequel, the HapMap Project, will reach fruition later this year. These projects established new precedents for international collaborations and open data access. Chinese scientists contributed to 1% of the

Evolutionary Transients in the Rice Transcriptome

In the canonical version of evolution by gene duplication, one copy is kept unaltered while the other is free to evolve. This process of evolutionary experimentation can persist for millions of years. Since it is so short lived in comparison to the lifetime of the core genes that make up the majority of most genomes, a substantial fraction of the genome and the transcriptome may—in principle—be attributable to what we will refer to as ＂evolutionary transients＂, referring here to both the process and the genes that have gone or are undergoing this process. Using the rice gene set as a test case, we argue that this phenomenon goes a long way towards explaining why there are so many more rice genes than Arabidopsis genes, and why most excess rice genes show low similarity to eudicots.