The draft genome of mandrill (Mandrillus sphinx): An Old World monkey.

Mandrill (Mandrillus sphinx) is a primate species, which belongs to the Old World monkey (Cercopithecidae) family. It is closely related to human, serving as a model for human health related research. However, the genetic studies on and genomic resources of mandrill are limited, especially in comparison to other primate species. Here we produced 284 Gb data, providing 96-fold coverage (considering the estimated genome size of 2.9 Gb), to construct a reference genome for the mandrill. The assembled draft genome was 2.79 Gb with contig N50 of 20.48 Kb and scaffold N50 of 3.56 Mb. We annotated the mandrill genome to find 43.83% repeat elements, as well as 21,906 protein-coding genes. The draft genome was of good quality with 98% gene annotation coverage by Benchmarking Universal Single-Copy Orthologs (BUSCO). Based on comparative genomic analyses of  the Major Histocompatibility Complex (MHC) of the immune system in mandrill and human, we found that 17 genes in the mandrill that have been associated with disease phenotypes in human such as Lung cancer, cranial volume and asthma, barbored amino acids changing mutations. Gene family analyses revealed expansion of several genes, and several genes associated with stress environmental adaptation and innate immunity responses exhibited signatures of positive selection. In summary, we established the first draft genome of  the mandrill of value for studies on evolution and human health.

Minke whale genome and aquatic adaptation in cetaceans.

The shift from terrestrial to aquatic life by whales was a substantial evolutionary event. Here we report the whole-genome sequencing and de novo assembly of the minke whale genome, as well as the whole-genome sequences of three minke whales, a fin whale, a bottlenose dolphin and a finless porpoise. Our comparative genomic analysis identified an expansion in the whale lineage of gene families associated with stress-responsive proteins and anaerobic metabolism, whereas gene families related to body hair and sensory receptors were contracted. Our analysis also identified whale-specific mutations in genes encoding antioxidants and enzymes controlling blood pressure and salt concentration. Overall the whale-genome sequences exhibited distinct features that are associated with the physiological and morphological changes needed for life in an aquatic environment, marked by resistance to physiological stresses caused by a lack of oxygen, increased amounts of reactive oxygen species and high salt levels.

Predicting the state of cysteines based on sequence information.

A three-stage support vector machine (SVM) was constructed to predict the state of cysteines by fusing sequence information, evolution information and annotation information of protein sequences. The first and second stages were for predicting whether the protein sequences contain disulfide bonds and whether all of the cysteines are involved in disulfide bonds. In the last stage, one SVM was constructed for predicting which cysteines are involved in disulfide bonds, among all these cysteines in proteins. The three SVMs give a good performance and the overall prediction accuracy are 90.05%, 96.36% and 80.00%, respectively, which indicates that the features selected in this work are effective for predicting the state of cysteines. In addition, current methods only paid too much attention to the prediction performance and never showed us how much important the roles of these features played in the prediction. As a result a feature importance measurement designated as F-score function was used to evaluate these features. The result shows that among these protein descriptors; evolution information is the most important feature for representing the disulfide-containing proteins. The prediction software and data sets used in this article are freely available at http://cic.scu.edu.cn/bioinformatics/Predict_Cys.zip.