拟南芥耐盐基因ENH1在陆生植物中的进化

[目的]ENH1是最近鉴定的拟南芥耐盐基因,编码一个叶绿体定位的蛋白,N末端具有一个PZD结构域,C末端具有一个RUBR结构域;功能上与活性氧自由基的脱毒有关,本文研究ENH1基因的进化历史和功能分化。[方法]从陆地植物基因组中获得同源蛋白,重建这个基因家族的系统发生,通过生物信息学手段研究其蛋白质结构域组织,蛋白质相互作用和表达谱。[结果]总共获得35个ENH1同源蛋白序列,大多数物种保持一个基因拷贝,系统发育上单子叶与双子叶被明确划分,并获得高度的支持,在进化过程EHN1蛋白获得了PDZ结构域。[结论]功能上,这个基因家族通过获得PZD结构域适应被子植物细胞的复杂功能要求,ENH1样基因可能涉及叶绿体的多种功能,此外,ENH1基因家族适合作为系统发育重建的分子标记。     

基于基因家族大小的比较研究脊椎动物的适应性进化

同源基因家族的拷贝数在不同物种间普遍存在差异,这种差异是由不同的基因得失速率引起。众所周知,基因拷贝数变异是特定物种表型创新的可能原因。本研究选取具有代表性的脊椎动物主要类群并跨约6亿年进化时间的64个物种,鉴定了它们的同源基因家族,揭示了脊椎动物基因家族大小的进化模式。结果表明:在推断的存在于脊椎动物最近共同祖先的6857个基因家族中,有6712个都在至少一个种系中发生了大小的变化,而且基因家族在大多数种系中都是收缩的;其中,霍氏树懒(Choloepus hoffmanni)中有最高的基因家族收缩水平,而在斑马鱼(Danio rerio)中则相反。基于脊椎动物基因家族大小进化的高度动态性,本研究从基因家族大小变化的角度鉴定了一些可能与特定脊椎动物类群进化有关的基因组信号。结果观察到在现存真骨鱼类最近共同祖先基因组中出现了可能因全基因组复制所导致的高比例的基因家族扩增现象,随后在后裔物种中发生基因收缩事件。此外,本研究还发现了硬骨鱼特异性的orphan基因可能对这些鱼类在水生环境中的适应性进化有所贡献的证据,如在有些硬骨鱼中orphan基因与鳍、尾巴、肾脏等发育有关。本研究结果有助于深入了解脊椎动物基因家族大小的进化,同时为理解脊椎动物基因组进化与表型多样性的联系提供了理论证据。     

植物查尔酮合成酶超基因家族的分子进化

查尔酮合成酶(CHS)超基因家族又称为植物类型III聚酮合酶超基因家族, 其编码酶通过催化和合成一系列结构多样及生理活性各异的次生代谢物, 在植物生长发育和适应环境的过程中扮演着重要角色。为全面了解CHS超基因家族在植物中的进化规律, 重建其进化历史, 该研究利用14种具有全基因组数据的代表植物, 通过生物信息学手段, 深入挖掘和分析了不同植物类群基因组中查尔酮合成酶超基因家族的成员构成, 推测了其可能的扩增机制和功能分歧, 并探讨了该超基因家族在植物中的总体进化趋势。结果共识别144条具有表达信息的同源序列, 它们全部来自9种陆生植物的基因组, 藻类植物基因组中没有发现相关序列。系统发育和进化分析表明, CHS超基因家族的起源古老, 它们可能为适应复杂的生态环境而出现在早期的陆生植物中, 之后在长期的进化过程中不断发生谱系的特异扩张和拷贝丢失, 最后通过功能分歧的形式在不同植物类群中被分别固定。此外, 进化检验也显示, 尽管CHS超基因家族内部发生了多样的遗传改变, 但整个超基因家族仍处于强烈的纯化选择之下, 并且个体基因中也无任何单氨基酸位点受到正向选择的影响。     

文昌鱼肌动蛋白基因家族的扩增(英文)

肌动蛋白是一种分布广泛而且在进化上十分保守的蛋白,是构成细胞骨架的关键组分.肌动蛋白通常被分成肌肉型和胞质型两种类型,各自行使着不同的功能.在此,作者对弗罗里达文昌鱼基因组中的肌动蛋白基因家族进行了系统分析,发现文昌鱼中该基因家族成员多达30多个,其中很多都是连锁分布的.基因结构趋于多样,分别包含2～7个外显子.进化分析的结果显示,文昌鱼的肌动蛋白基因家族可能通过串联重复而发生了扩增.作者还克隆了厦门文昌鱼两个不同的肌肉犁肌动蛋白基因,并比较了它们在文昌鱼早期胚胎中的表达图式.结果显示,这两个基因在表达上有着细微的差别,提示文昌鱼肌动蛋白基因家族成员在功能上的分化.上述结果将有助于阐明肌动蛋白基因家族及其功能在脊索动物中的演化.     

裸子植物中光敏色素PHY-PAS1 结构域的适应性进化

光敏色素是一类红光/远红光受体, 在植物种子萌发到成熟的整个生长发育过程中均起重要的调节作用。光敏色素PHYPAS1 结构域存在于光敏色素基因家族的所有成员中, 对调节发色团的光谱特性和光信号转导非常关键。光敏色素基因家族通过基因重复产生, 而基因重复可能与物种形成有关。PHYP基因是裸子植物光敏色素基因家族发生第1次重复后产生的, 并且以单拷贝形式存在。为了研究不同裸子植物PHYP基因编码蛋白的PHY-PAS1结构域在进化过程中是否受到相同的选择压力以及是否发生了适应性进化, 该研究利用分支模型、位点模型以及分支-位点模型对裸子植物31条PHYP基因序列编码蛋白的PHY-PAS1结构域所受到的选择压力进行了分析。结果表明, 在由PHY-PAS1结构域序列构建的系统树中, 多数分支处于强烈的负选择压力下 (w<1); 有14个分支处于正选择压力下 (w>1), 其中13个分支发生在属内种间; 与之相比, 在较为古老的谱系中相对缺少这种正选择压力。     

裸子植物中光敏色素PHY-PAS1结构域的适应性进化

光敏色素是一类红光／远红光受体,在植物种子萌发到成熟的整个生长发育过程中均起重要的调节作用。光敏色素PHY-PAS1结构域存在于光敏色素基因家族的所有成员中,对调节发色团的光谱特性和光信号转导非常关键。光敏色素基因家族通过基因重复产生,而基因重复可能与物种形成有关。PHYP基因是裸子植物光敏色素基因家族发生第1次重复后产生的,并且以单拷贝形式存在。为了研究不同裸子植物PHYP基因编码蛋白的PHY-PAS1结构域在进化过程中是否受到相同的选择压力以及是否发生了适应性进化,该研究利用分支模型、位点模型以及分支．位点模型对裸子植物31条PHYP基因序列编码蛋白的PHY-PAS1结构域所受到的选择压力进行了分析。结果表明,在由PHY-PAS1结构域序列构建的系统树中,多数分支处于强烈的负选择压力下（ω〈1）：有14个分支处于正选择压力下（ω〉1）,其中13个分支发生在属内种间;与之相比,在较为古老的谱系中相对缺少这种正选择压力。     

大豆GeBP转录因子基因家族的生物信息学分析

GeBP转录因子调控植物表皮毛的生长发育,并且参与控制植物叶片的发育。该文利用生物信息学方法,在大豆全基因组范围内搜索GeBP基因家族,并从氨基酸理化性质、基因结构、染色体的物理分布、系统进化、序列比对、功能结构域、组织表达情况等基本特征方面对GmGeBP基因家族进行分析。结果表明:(1)共获得9个GmGeBP转录因子基因家族成员,其中仅2个基因含有内含子,且都只有1个内含子,表明该家族成员基因构造比较简单但稳定。(2)GmGeBP编码的蛋白分子量为39.65~49.24 kD,理论等电点为4.65~9.08;这些成员基本上都是酸性氨基酸,属于亲水性、不稳定蛋白。(3)这9个基因不均匀的分布于7条染色体上,10和20号染色体上分别分布2个GeBP基因,3、5、13、15、19号染色体上各分布1个基因。(4)系统进化分析表明,大豆与拟南芥对应的GeBP成员亲缘关系较近,分别聚类到4个分支,而与水稻的距离较远。(5)结构域分析表明,9个GmGeBP成员都包含DUF573结构域,推测该部分在GeBP转录因子中很可能是与靶标基因顺式作用元件互作的结构域。(6)通过分析大豆GmGeBP转录因子基因家族的组织表达,发现不同基因在大豆不同组织的表达量不同,具有一定的特异性。该文对大豆GeBP转录因子基因家族的分析和鉴定为进一步研究大豆表皮毛发育的分子作用提供了理论基础。     

文昌鱼肌动蛋白基因家族扩增的研究(英文）

肌动蛋白是一种分布广泛而且在进化上十分保守的蛋白,它是构成细胞骨架的关键组分。肌动蛋白通常被分成肌肉型和胞质型两种类型,它们各自行使着不同的功能。在此,我们对H弗罗里达H文昌鱼基因组中的肌动蛋白基因家族进行了系统分析,发现文昌鱼中该基因家族成员多达30多个,其中很多都是连锁分布的。基因结构趋于多样, 分别包含2~7个外显子。进化分析的结果显示,文昌鱼的肌动蛋白基因家族可能通过串联重复而发生了扩增。我们还克隆了厦门文昌鱼两个不同的肌肉型肌动蛋白基因,并比较了它们在文昌鱼早期胚胎中的表达图式。结果显示,这两个基因在表达上有着细微的差别,提示文昌鱼肌动蛋白基因家族成员在功能上的分化。上述结果将有助于阐明肌动蛋白基因家族及其功能在脊索动物中的演化。     

石笔木CHS基因家族成员的分析

用PCR方法从石笔木（Tutcheria spectabilis Dunn）的总DNA中扩增CHS基因外显子2的部分序列以代表该基因进行研究,经克隆后测序,得到长约740－780bp的序列共12个。以EMBL数据库中得到的紫花苜蓿和欧洲赤松各一个序列作为参照,进行排序和系统树的构建分析。结果显示,所有被测定的序列同源性均高于70％,为CHS基因家庭的成员,且这些序列由3大类共5种不同的基因拷贝组成：第一类家族成员因碱基的插入和缺失改变了读码框,推测已失去了CHS基因的功能,成为假基因,其中个别拷贝存在较大缺失,这在以前的研究中未见报道;第二类家族成员因活性位点的氨基酸发生突变,可能具有新的基因功能;第三类家族成员则具有原CHS基因的功能。综上结果,可预测,山茶科CHS基因家族较大,且有着复杂的进化式样。     

啮齿目泌乳刺激素基因家族的分子进化研究

在大鼠基因组数据库中搜索得到两个泌乳刺激素基因家族的新成员。进一步分析显示该基因家族起源于啮齿目和其他哺乳动物分歧之后,而且大部分基因座位的重排在大、小鼠分歧之前已经完成。但PL-Ⅰ和PL-Ⅱ基因簇却是例外,它们在基因树上以物种特异的方式聚类。结合基因转换的检验、染色体上相对位置比较和基因重复时间估计的结果,认为啮齿目PL-Ⅰ和PL-Ⅱ基因是物种特异的,它们由一系列在大、小鼠分歧之后发生的基因重复事件形成。结果还揭示了在啮齿目泌乳刺激素基因家族进化过程中持续不断的发生了基因重复和基因分化事件。     

Identification of a second egfr gene in Xiphophorus uncovers an expansion of the epidermal growth factor receptor family in fish

The epidermal growth factor receptor (EGFR) gives name to a family of receptors formed by four members in mammals (EGFR, ErbB2, ErbB3, and ErbB4). Members of this family can be activated to become potent oncogenes, and many human and animal tumors express qualitatively or quantitatively altered receptors from this group. We have isolated and characterized a second egfr gene in the melanoma model fish Xiphophorus. Both Xiphophorus egfra and egfrb duplicates are co-orthologs of the mammalian egfr gene. Database analysis showed that not only egfr but also erbB3 and erbB4 are present as duplicates in some fish species. They originated from ancient duplication events that might be consistent with the hypothesis of a fish-specific genome duplication. In Xiphophorus, the egfrb gene underwent a second duplication that generated the melanoma-inducing oncogene Xmrk. The study and comparison of some of the functional characteristics of both Xiphophorus EGF receptors, including expression profile, ligand-binding abilities, and intracellular signal transduction revealed that Xiphophorus Egfra not only shares common features with Egfrb and the human EGFR but also shows significant differences in its functional characteristics. The mechanism of maintenance of these duplicates remains to be clarified.     

Recent duplication and positive selection of the <Emphasis Type="Italic">GAGE</Emphasis> gene family

We report that the GAGE gene family of human Cancer/testis antigen (CTA) genes is likely to be in an early stage of its evolution. Members of this gene family are tandemly arranged on the X chromosome only in human, chimpanzee and macaque genomes and share a very high similarity. Phylogenetic trees show that the GAGE gene family began to duplicate after the split of human and chimpanzee. The estimated ages of the duplication events range from 4 million years ago to the present. The Ka/Ks values between the duplicates are significantly greater than 1, indicating that the mutation rate is higher in coding regions than non-coding regions of the genes, which suggests that the GAGE gene family is under positive selection. These findings indicate that the GAGE gene family may be a newly formed gene family undergoing rapid functional evolution. Yang Liu and Qiyun Zhu contributed equally to this work.     

Comparative evolution of photosynthetic genes in response to polyploid and nonpolyploid duplication

The likelihood of duplicate gene retention following polyploidy varies by functional properties (e.g. gene ontologies or protein family domains), but little is known about the effects of whole-genome duplication on gene networks related by a common physiological process. Here, we examined the effects of both polyploid and nonpolyploid duplications on genes encoding the major functional groups of photosynthesis (photosystem I, photosystem II, the light-harvesting complex, and the Calvin cycle) in the cultivated soybean (Glycine max), which has experienced two rounds of whole-genome duplication. Photosystem gene families exhibit retention patterns consistent with dosage sensitivity (preferential retention of polyploid duplicates and elimination of nonpolyploid duplicates), whereas Calvin cycle and light-harvesting complex gene families do not. We observed similar patterns in barrel medic (Medicago truncatula), which shared the older genome duplication with soybean but has evolved independently for approximately 50 million years, and in Arabidopsis (Arabidopsis thaliana), which experienced two nested polyploidy events independent from the legume duplications. In both soybean and Arabidopsis, Calvin cycle gene duplicates exhibit a greater capacity for functional differentiation than do duplicates within the photosystems, which likely explains the greater retention of ancient, nonpolyploid duplicates and larger average gene family size for the Calvin cycle relative to the photosystems.     

DNA hybridization as a guide to phylogeny: Chemical and physical limits

Summary The technique of forming interspecific DNA heteroduplexes and estimating phylogenetic distances from the depression in their duplex melting temperature has several physical and chemical constraints. These constraints determine the maximum phylogenetic distance that may be estimated by this technique and the most appropriate method of analyzing that distance.Melting curves of self-renatured single copy primate DNAs reveal the presence of components absent from the renaturation products of exactly paired sequences. This observation, which confirms existing literature, challenges a fundamental assumption: that orthologous (i.e., corresponding) DNA sequences in the divergent species are being compared in DNA heteroduplex melting experiments.As a model system, the thermal stabilities of heteroduplexes formed between a human alpha-globin cDNA and four alpha-like globin genes isolated from chimpanzee are qualitatively compared. The results of this comparison show that the cross-hybrids of imperfectly matched gene duplicates from divergent species can contribute to the additional components that are present in renatured single copy DNAs. Single copy DNA, as usually defined, includes sequence duplicates that will obscure phylogenetic comparisons in a mass hybridization of genomes.     

Duplication and divergence of 2 distinct pancreatic ribonuclease genes in leaf-eating African and Asian colobine monkeys

Unique among primates, the colobine monkeys have adapted to a predominantly leaf-eating diet by evolving a foregut that utilizes bacterial fermentation to breakdown and absorb nutrients from such a food source. It has been hypothesized that pancreatic ribonuclease (pRNase) has been recruited to perform a role as a digestive enzyme in foregut fermenters, such as artiodactyl ruminants and the colobines. We present molecular analyses of 23 pRNase gene sequences generated from 8 primate taxa, including 2 African and 2 Asian colobine species. The pRNase gene is single copy in all noncolobine primate species assayed but has duplicated more than once in both the African and Asian colobine monkeys. Phylogenetic reconstructions show that the pRNase-coding and noncoding regions are under different evolutionary constraints, with high levels of concerted evolution among gene duplicates occurring predominantly in the noncoding regions. Our data suggest that 2 functionally distinct pRNases have been selected for in the colobine monkeys, with one group adapting to the role of a digestive enzyme by evolving at an increased rate with loss of positive charge, namely arginine residues. Conclusions relating our data to general hypotheses of evolution following gene duplication are discussed.     

Retained duplicate genes in green alga Chlamydomonas reinhardtii tend to be stress responsive and experience frequent response gains

Background

Green algae belong to a group of photosynthetic organisms that occupy diverse habitats, are closely related to land plants, and have been studied as sources of food and biofuel. Although multiple green algal genomes are available, a global comparative study of algal gene families has not been carried out. To investigate how gene families and gene expression have evolved, particularly in the context of stress response that have been shown to correlate with gene family expansion in multiple eukaryotes, we characterized the expansion patterns of gene families in nine green algal species, and examined evolution of stress response among gene duplicates in Chlamydomonas reinhardtii.

Results

Substantial variation in domain family sizes exists among green algal species. Lineage-specific expansion of families occurred throughout the green algal lineage but inferred gene losses occurred more often than gene gains, suggesting a continuous reduction of algal gene repertoire. Retained duplicates tend to be involved in stress response, similar to land plant species. However, stress responsive genes tend to be pseudogenized as well. When comparing ancestral and extant gene stress response state, we found that response gains occur in 13% of duplicate gene branches, much higher than 6% in Arabidopsis thaliana.

Conclusion

The frequent gains of stress response among green algal duplicates potentially reflect a high rate of innovation, resulting in a species-specific gene repertoire that contributed to adaptive response to stress. This could be further explored towards deciphering the mechanism of stress response, and identifying suitable green algal species for oil production.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1335-5) contains supplementary material, which is available to authorized users.     

A human-specific subfamily of Alu sequences.

Of a total of 500,000 Alu family members, approximately 500 are present as a human-specific (HS) subfamily. Each of the HS subfamily members shares a high degree of nucleotide identity and is not present at orthologous positions in other primate genomes, suggesting that HS subfamily members have recently inserted within the human genome. This confirms the hypothesis that the majority of Alu family members are amplified copies of a "master" gene(s). This master gene appears to be amplifying at a rate much slower than that seen earlier in primate evolution. Some of the HS Alu subfamily members have amplified so recently that they are dimorphic in the human population, making them a potentially powerful tool for studies of human populations.