Penicillium marneffei is the most important thermal dimorphic, pathogenic fungus endemic in China and Southeast Asia and is particularly important in HIV-positive patients. The 28,887,485-bp draft genome sequence of P. marneffei, which contains its complete mitochondrial genome, sexual cycle genes, a high diversity of Mp1p homologues, and polyketide synthase genes, is now reported [PMID: 22131218]. The picture from the wikipedia shows various fungi including Penicillium and Aspergillus spp. growing in axenic culture.

Frontiers in Evolutionary and Population Genetics, a Specialty Section of Frontiers in Genetics, is a forum for the publication of articles on contemporary data and novel laboratory and statistical methods in molecular evolution, population genetics, population genomics, comparative genomics, ancient DNA, experimental genetics, evolutionary and developmental genetics and gene mapping. Studies on human, model organism, and natural populations are all appropriate for this Specialty Section.

Ence Yang from the Key Laboratory of Systematic Mycology and Lichenology, Institute of Microbiology, Chinese Academy of Sciences, has joined our lab. He has broad interest in fungal adaptive evolution driven by biotic and environmental challenges. As a lead author, he published the study on the adaptive evolution of carnivorous fungi to nematode hosts in PNAS in 2007. He also developed mathematical model for mass extinctions of fungal species. In our lab, he is going to study the adaptive evolution of human pathogen fungi to chemical factors, temperature, and so on using comprehensive genomic approaches.

James' book chapter entitled "Evolutionary bioinformatics with a scientific computing environment" has been accepted for publication in Bioinformatics—Experimental Biology Systems, Ning-Sun Yang (Ed.), ISBN 978-953-307-280-7, by InTech. This chapter introduces the application of an emerging programming language—Matlab, in evolutionary bioinformatics. Many examples are given for preliminary and advanced analyses in molecular evolution and population genetics, with special emphasis on Matlab-based solutions. The examples relating to molecular evolution are focused on the mathematical modeling of sequence evolution; the examples relating to population genetics are focused on summary statistics and neutrality tests.

"How can chimps and humans be 96% genetically identical, and yet differ in so many ways? One answer is a stretch of DNA called Alu, that can move around the genome. Alu elements, which are found in primates but no other mammals, can alter existing genes and can affect the speed of protein production. Because they tend to jump into genes that regulate thousands of other genes, they could have an enormous impact on the characteristics of an organism." Read more... 

Cover illustration by Roberto Torres (www.torresdecomunicacion.com) has been selected for the January 2011 issue of Genome Research, in which our paper "Adaptive selection of an incretin gene in Eurasian population" will appear. The design included several key components of ideas reflected in the paper, including the change of allele frequency of mutation, the out-of-Africa hypothesis, emergency of agriculture, local adaptation, and population differentiation. We specially thank pepi and roberto for the effort on interpreting and rendering.

Rice, one of the world's most important crops, originates from eastern Asia. Here in a newly published Genome Research paper, we show that major dietory change due to rice domestication may lead to the rapid increase of allele frequency of a mutation in an incretin gene in humans. We report that the human GIP locus was differentially selected among human populations based on the analysis of a nonsynonymous SNP (rs2291725). Haplotype structure analysis suggests that, owing to positive selection, the derived allele at 2291725 arose to dominance in East Asians ~8.1 thousand years ago. In addition, cComparative and functional analyses showed that the human GIP gene encodes a cryptic glucose-dependent insulinotropic polypeptide (GIP) isoform (GIP55S or GIP55G) that encompasses the SNP and is resistant to serum degradation relative to the known mature GIP peptide. Importantly, we found that GIP55G, which is encoded by the derived allele, exhibits a higher bioactivity as compared to GIP55S, which is derived from the ancestral allele. Haplotype structure analysis suggested that the derived allele of the SNP arose to dominance in East Asians ~8kya (This is the exact time when rice was domesticated!). The combined results suggested that SNP rs2291725 represents a functional mutation and may contribute to the population genetics observation. Given that GIP signaling plays a critical role in homeostasis regulation at both enteroinsular and enteroadipocyte axes, our study highlights the importance of understanding adaptations in energy-balance regulation in the face of the emerging diabetes and obesity epidemics.