A pattern recognition-based approach for phylogenetic network construction with constrained recombination

The tree representation of evolutionary relationship oversimplifies the view of the process of evolution as it cannot take into account the events such as horizontal gene transfer, hybridization, homoplasy and genetic recombination. Several algorithms exist for constructing phylogenetic networks which result from events such as horizontal gene transfer, hybridization and homoplasy. Very little work has been published on the algorithmic detail of phylogenetic networks with constrained recombination. The problem of minimizing the number of recombinations in a phylogenetic network, constructed using binary DNA sequences, is NP-hard. In this paper, we propose a pattern recognition-based O(n²) time approach for constructing the phylogenetic network, where n is the number of nodes or sequences in the input data. The network is constructed with the restriction that no two cycles in the network share a common node.     

An Improved (and Practical) Parameterized Algorithm for the Individual Haplotyping Problem MFR with Mate-Pairs

The Individual Haplotyping MFR problem is a computational problem that, given a set of DNA sequence fragment data of an individual, induces the corresponding haplotypes by dropping the minimum number of fragments. Bafna, Istrail, Lancia, and Rizzi proposed an algorithm of time O(2^2k m ² n+2^3k m ³) for the problem, where m is the number of fragments, n is the number of SNP sites, and k is the maximum number of holes in a fragment. When there are mate-pairs in the input data, the parameter k can be as large as 100, which would make the Bafna-Istrail-Lancia-Rizzi algorithm impracticable. The current paper introduces a new algorithm PM-MFR of running time , where k ₁ is the maximum number of SNP sites that a fragment covers (k ₁ is smaller than n), and k ₂ is the maximum number of fragments that cover a SNP site (k ₂ is usually about 10). Since the time complexity of the algorithm PM-MFR is not directly related to the parameter k, the algorithm solves the Individual Haplotyping MFR problem with mate-pairs more efficiently and is more practical in real biological applications. This research was supported in part by the National Natural Science Foundation of China under Grant Nos. 60433020 and 60773111, the Program for New Century Excellent Talents in University No. NCET-05-0683, the Program for Changjiang Scholars and Innovative Research Team in University No. IRT0661, and the Scientific Research Fund of Hunan Provincial Education Department under Grant No. 06C526.     

基于SNP基因型谱和表达谱的乳腺癌相关基因网络的构建

拟构建乳腺癌相关基因网络并从系统生物学角度解析乳腺癌发病的分子机制,采用基于SNP基因型谱和乳腺癌基因芯片表达谱数据分别进行全基因组关联分析和差异表达基因的筛选,并以此为基础构建乳腺癌相关基因网络,网络分析结果显示乳腺癌相关基因主要参与代谢、信号传导、蛋白质修饰等功能。该网络能够从系统层面上解释乳腺癌的遗传互作机制,并为研究其它复杂疾病提供一定的理论依据。     

生物质谱作为SNP分型检测方法的研究

利用改良的 Miller法从人血中提取人类基因组 DNA。采用聚合酶链式反应 ( Polymerase chain reac-tion,PCR) ,对含有单核苷酸多态性 ( SNP)点的 DNA片段进行扩增 ,然后用 CIP和 Eox I去除掉 PCR体系中剩余的脱氧核糖核苷三磷酸 ( d NTP)和引物 ,最后用单碱基延伸反应获得 SNP位点处碱基类型。用基质辅助激光解吸电离 -飞行时间质谱 ( MALDI-TOFMS)或电喷雾电离 -四极杆飞行时间质谱 ( ESI-Qq TOFMS)检测延伸产物与未延伸引物间的分子量差异 ,确定该点处碱基。对不同的生物质谱检方法以及生物质谱检测方法与其它检测方法的优缺点进行了分析比较     

Genetic Variants Associated with Long-Terminal Repeats Can Diagnostically Classify Cannabis Varieties

Cannabis sativa (Cannabis) has recently been legalized in multiple countries globally for either its recreational or medicinal use. This, in turn, has led to a marked increase in the number of Cannabis varieties available for use in either market. However, little information currently exists on the genetic distinction between adopted varieties. Such fundamental knowledge is of considerable value and underpins the accelerated development of both a nascent pharmaceutical industry and the commercial recreational market. Therefore, in this study, we sought to assess genetic diversity across 10 Cannabis varieties by undertaking a reduced representation shotgun sequencing approach on 83 individual plants to identify variations which could be used to resolve the genetic structure of the assessed population. Such an approach also allowed for the identification of the genetic features putatively associated with the production of secondary metabolites in Cannabis. Initial analysis identified 3608 variants across the assessed population with phylogenetic analysis of this data subsequently enabling the confident grouping of each variety into distinct subpopulations. Within our dataset, the most diagnostically informative single nucleotide polymorphisms (SNPs) were determined to be associated with the long-terminal repeat (LTRs) class of retroelements, with 172 such SNPs used to fully resolve the genetic structure of the assessed population. These 172 SNPs could be used to design a targeted resequencing panel, which we propose could be used to rapidly screen different Cannabis plants to determine genetic relationships, as well as to provide a more robust, scientific classification of Cannabis varieties as the field moves into the pharmaceutical sphere.     

Identification and Functional Analysis of the Caffeic Acid O-Methyltransferase (COMT) Gene Family in Rice (Oryza sativa L.)

Caffeic acid O-methyltransferase (COMT) is one of the core enzymes involved in lignin synthesis. However, there is no systematic study on the rice COMT gene family. We identified 33 COMT genes containing the methyltransferase-2 domain in the rice genome using bioinformatic methods and divided them into Group I (a and b) and Group II. Motifs, conserved domains, gene structure and SNPs density are related to the classification of OsCOMTs. The tandem phenomenon plays a key role in the expansion of OsCOMTs. The expression levels of fourteen and thirteen OsCOMTs increased or decreased under salt stress and drought stress, respectively. OsCOMTs showed higher expression levels in the stem. The lignin content of rice was measured in five stages; combined with the expression analysis of OsCOMTs and multiple sequence alignment, we found that OsCOMT8, OsCOMT9 and OsCOMT15 play a key role in the synthesis of lignin. Targeted miRNAs and gene ontology annotation revealed that OsCOMTs were involved in abiotic stress responses. Our study contributes to the analysis of the biological function of OsCOMTs, which may provide information for future rice breeding and editing of the rice genome.     

利用外转录间隔区对中国人参和西洋参进行分子鉴定

人参和西洋参是我国两种重要的中药材。两者虽然形态相似,但药性差异较大。为了建立一种简单高效的中国人参和西洋参的分子鉴别方法,作者利用从核DNA的外转录间隔(ETS)发掘的人参和西洋参单核苷酸多态性位点(SNP),分别设计了人参和西洋参的等位基因特异性引物,并利用多重PCR对人参和西洋参进行了鉴定。结果表明,作者建立的多重PCR体系可以有效地对人参、西洋参及两者的混合品进行鉴定。