Evolution of genes and taxa: a primer

The rapidly growing fields of molecular evolution and systematics have much to offer to molecular biology, but like any field have their own repertoire of terms and concepts. Homology, for example, is a central theme in evolutionary biology whose definition is complex and often controversial. Homology extends to multigene families, where the distinction between orthology and paralogy is key. Nucleotide sequence alignment is also a homology issue, and is a key stage in any evolutionary analysis of sequence data. Models based on our understanding of the processes of nucleotide substitution are used both in the estimation of the number of evolutionary changes between aligned sequences and in phylogeny reconstruction from sequence data. The three common methods of phylogeny reconstruction – parsimony, distance and maximum likelihood – differ in their use of these models. All three face similar problems in finding optimal – and reliable – solutions among the vast number of possible trees. Moreover, even optimal trees for a given gene may not reflect the relationships of the organisms from which the gene was sampled. Knowledge of how genes evolve and at what rate is critical for understanding gene function across species or within gene families. The Neutral Theory of Molecular Evolution serves as the null model of molecular evolution and plays a central role in data analysis. Three areas in which the Neutral Theory plays a vital role are: interpreting ratios of nonsynonymous to synonymous nucleotide substitutions, assessing the reliability of molecular clocks, and providing a foundation for molecular population genetics.     

The phylogenetic placement of Chondrichthyes: inferences from analysis of multiple genes and implications for comparative studies

Elasmobranch fishes (sharks and rays) have proven valuable for inferring general and specific properties of molecular evolution through comparative studies with crown group vertebrates because they are the most ancient group of gnathostomes. Recent studies have questioned the conventional phylogenetic placement of sharks in the vertebrate tree, however. In this paper I review the importance of the basal position of Chondrichthyes for comparative biology and compile evidence from multiple, independent genes to evaluate the phylogenetic placement of sharks. The results suggests that alternative phylogenetic hypotheses of the relationships among the Chondrichthyes, Actinopterygii and Sarcopterygii can not be refuted with available data, implying that the assumption of the basal placement of sharks in the vertebrate tree is suspect. Resolving the phylogeny of basal vertebrates is important for testing hypotheses about the evolution of vertebrates, and the current lack of a robust phylogeny limits evolutionary inferences that can be gained from comparative studies that include sharks and rays.     

Genome sequence and genetic transformation of a widely distributed and cultivated poplar

Populus alba is widely distributed and cultivated in Europe and Asia. This species has been used for diverse studies. In this study, we assembled a de novo genome sequence of P. alba var. pyramidalis (= P. bolleana) and confirmed its high transformation efficiency and short transformation time by experiments. Through a process of hybrid genome assembly, a total of 464 M of the genome was assembled. Annotation analyses predicted 37 901 protein‐coding genes. This genome is highly collinear to that of P. trichocarpa, with most genes having orthologs in the two species. We found a marked expansion of gene families related to histone and the hormone auxin but loss of disease resistance genes in P. alba if compared with the closely related P. trichocarpa. The genome sequence presented here represents a valuable resource for further molecular functional analyses of this species as a new tree model, poplar breeding practices and comparative genomic analyses across different poplars.     

The size distribution of protein families within different types of folds

It is well known that the structure is currently available only for a small fraction of known protein sequences. It is urgent to discover the important features of known protein sequences based on present protein structures. Here, we report a study on the size distribution of protein families within different types of folds. The fold of a protein means the global arrangement of its main secondary structures, both in terms of their relative orientations and their topological connections, which specify a certain biochemical and biophysical aspect. We first search protein families in the structural database SCOP against the sequence-based database Pfam, and acquire a pool of corresponding Pfam families whose structures can be deemed as known. This pool of Pfam families is called the sample space for short. Then the size distributions of protein families involving the sample space, the Pfam database and the SCOP database are obtained. The results indicate that the size distributions of protein families under different kinds of folds abide by similar power-law. Specially, the largest families scatter evenly in different kinds of folds. This may help better understand the relationship of protein sequence, structure and function. We also show that the total of proteins with known structures can be considered a random sample from the whole space of protein sequences, which is an essential but unsettled assumption for related predictions, such as, estimating the number of protein folds in nature. Finally we conclude that about 2957 folds are needed to cover the total Pfam families by a simple method.     

枣ZjMADS1-box基因克隆与表达分析

以‘金丝4号’枣花蕾和叶片为材料,通过抑制消减杂交文库(SSH文库)的构建、RACE技术和半定量RT-PCR等方法,克隆了枣花发育基因并研究了其时空表达模式,为枣花发育机理研究奠定基础。结果表明:(1)从枣花SSH文库中鉴定出476bp的花发育B类PISTILLATA(PI)基因的EST序列,命名为ZjMADS1-box;通过RACE技术获得了枣ZjMADS1-box基因的全长cDNA序列。(2)枣ZjMADS1-box基因表现出PI基因的序列结构特征。其全长cDNA长度为957bp,编码220个氨基酸残基;在氨基酸序列水平上,该基因与巨桉EgM2(Eu-calyptus grandis M2)和白千层MqPI(Melaleuca quinquenervia PI)的相似性最高为72.6%,与辣椒CaPI(Capsi-cum annuum PI)的相似性最低为61.8%;系统进化树分析显示,枣ZjMADS1-box与MqPI和EgM2基因聚在一起;枣ZjMADS1-box基因编码蛋白的等电点为9.75,分子量为25 587.5Da,属亲水性的非分泌性蛋白。(3)Zj-MADS1-box基因在花器官中特异表达,在嫩茎、成熟叶、腋芽等营养器官中不表达;在4月30日和5月8日花蕾中的表达量略高于5月4日、5月12日、5月16日的表达量,但差异不显著。     

The role of molecular structure of sugar‐phosphate backbone and nucleic acid bases in the formation of single‐stranded and double‐stranded DNA structures

Our previous DFT computations of deoxydinucleoside monophosphate complexes with Na⁺‐ions (dDMPs) have demonstrated that the main characteristics of Watson‐Crick (WC) right‐handed duplex families are predefined in the local energy minima of dDMPs. In this work, we study the mechanisms of contribution of chemically monotonous sugar‐phosphate backbone and the bases into the double helix irregularity. Geometry optimization of sugar‐phosphate backbone produces energy minima matching the WC DNA conformations. Studying the conformational variability of dDMPs in response to sequence permutation, we found that simple replacement of bases in the previously fully optimized dDMPs, e.g. by constructing Pyr‐Pur from Pur‐Pyr, and Pur‐Pyr from Pyr‐Pur sequences, while retaining the backbone geometry, automatically produces the mutual base position characteristic of the target sequence. Based on that, we infer that the directionality and the preferable regions of the sugar‐phosphate torsions, combined with the difference of purines from pyrimidines in ring shape, determines the sequence dependence of the structure of WC DNA. No such sequence dependence exists in dDMPs corresponding to other DNA conformations (e.g., Z‐family and Hoogsteen duplexes). Unlike other duplexes, WC helix is unique by its ability to match the local energy minima of the free single strand to the preferable conformations of the duplex. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 640–650, 2014.     

谷子β-胡萝卜素异构酶家族基因的表达与变异分析

株型是影响谷类作物产量的重要性状, 株型改良对提高作物产量具有重要意义。独脚金内酯(strigolactones, SLs)作为一种最新被鉴定的植物激素, 其通过抑制腋芽的伸长调控分枝/分蘖的形成。β-胡萝卜素异构酶(D27s)是SLs合成途径的关键酶, 通过对谷子(Setaria italica) β-胡萝卜素异构酶典型结构域Pfam:DUF4033进行分析, 鉴定到3个谷子D27s基因家族成员(Seita.8G168400、Seita.6G088800和Seita.3G050900)。蛋白质特性分析显示, 谷子D27s蛋白由271-277个氨基酸残基组成, 分子量为30.1-30.4 kDa, 等电点为5.85-9.31, 不稳定系数介于38.48-74.47之间, 且均定位于叶绿体; 系统进化分析发现, 谷子D27s家族成员位于3个不同进化分支; 顺式作用元件预测显示, SiD27-1 (Seita.8G168400)可能参与调控生物节律、生长素介导的生长发育以及干旱和低温等胁迫应答过程。基因表达分析显示, SiD27-1在谷子多分蘖材料中表达下调, 在低磷胁迫处理下, D27s基因均能产生不同程度的响应, 并且SiD27-1的响应较其它成员更快速。单倍型分析结果表明, SiD27-1的H001单倍型为优异单倍型, 对谷子的株高、抽穗期和产量改良具有重要应用价值。综上, 推测SiD27-1极可能在SLs合成中发挥关键作用并对谷子株型产生影响。研究结果为深入揭示D27s对谷子分蘖形成的调控机制奠定了基础, 也为谷子株型分子设计育种提供了优异的等位变异位点。     

Fertility status,dominance, and scent marking behavior of family-housed female cotton-top tamarins (Saguinus oedipus) in absence of their mothers

The effect of the mother's absence on the fertility status and expression of scent marking behavior was examined in 12 sexually mature female cotton-top tamarins (Saguinus oedipus) living in four motherless families. Behavioral data and urine samples were collected on an average of five times per week and levels of estrone-glucuronide (E1G) were quantified directly by radioimmunoassay to establish whether the females showed ovarian cyclicity. Of the 12 females investigated only the dominant female in each motherless group exhibited regular E1G cycles. By contrast, low and acyclic hormonal profiles were found for subordinate sisters. In addition to differences in the patterns and levels of E1G, scent gland morphology and rates of scent marking differed between females: dominant, cycling females had elaborate glands and significantly higher rates of scent marking than subordinates. These results indicate that the presence of the mother (breeding female) is one important factor regulating ovarian function in cotton-top tamarin daughters. The findings also show that dominance status is a vital determinant of each female's subsequent physiological reproductive competence, with only the dominant female obtaining complete fertility and probably inhibiting ovulatory activity in her subordinate sisters. Scent marking behavior seems to be involved in the regulation of this phenomenon of intrasexual reproductive competition.