Gene expression and protein length influence codon usage and rates of sequence evolution in Populus tremula

Codon bias is generally thought to be determined by a balance between mutation, genetic drift, and natural selection on translational efficiency. However, natural selection on codon usage is considered to be a weak evolutionary force and selection on codon usage is expected to be strongest in species with large effective population sizes. In this paper, I study associations between codon usage, gene expression, and molecular evolution at synonymous and nonsynonymous sites in the long-lived, woody perennial plant Populus tremula (Salicaceae). Using expression data for 558 genes derived from expressed sequence tags (EST) libraries from 19 different tissues and developmental stages, I study how gene expression levels within single tissues as well as across tissues affect codon usage and rates sequence evolution at synonymous and nonsynonymous sites. I show that gene expression have direct effects on both codon usage and the level of selective constraint of proteins in P. tremula, although in different ways. Codon usage genes is primarily determined by how highly expressed a genes is, whereas rates of sequence evolution are primarily determined by how widely expressed genes are. In addition to the effects of gene expression, protein length appear to be an important factor influencing virtually all aspects of molecular evolution in P. tremula.     

Reversed selection responses in small populations of the housefly (Musca domestica L.)

We compared the efficacy of artificial and natural selection processes in purging the genetic load of perpetually small populations. We subjected replicate lines of the housefly (Musca domestica L.), recently derived from the wild, to artificial selection for increased mating propensity (i.e., the proportion of male–female pairs initiating copulation within 30 min) in efforts to cull out the inbreeding depression effects of long-term small population size (as determined by a selection protocol for increased assortative mating). We also maintained parallel non-selection lines for assessing the spontaneous purge of genetic load due to inbreeding alone. We thus evaluated the fitness of artificially and ‘naturally’ purging populations held at census sizes of 40 individuals over the course of 18 generations. We found that the artificially selected lines had significant increases in mating propensity (up to 46% higher from the beginning of the protocol) followed by reversed selection responses back to the initial levels, resulting in non-significant heritabilities. Nevertheless, the ‘naturally’ selected lines had significantly lower fitness overall (a 28% reduction from the beginning of the protocol), although lower effective population sizes could have contributed to this effect. We conclude that artificial selection bolstered fitness, but only in the short-term, because the inadvertent fixation of extant genetic load later resulted in pleiotropic fitness declines. Still, the short-term advantage of the selection protocol likely contributed to the success of the speciation experiment since our recently-derived housefly populations are particularly vulnerable to inbreeding depression effects on mating behavior.     

黄瓜AGAMOUS同源基因的分离和表达(英文)

黄瓜花发育的早期均有雌蕊和雄蕊原基的分化,但在发育过程中,由于雌蕊或雄蕊的发育受到阻滞,导致雄花和雌花的形成。近年来在拟南芥和金鱼草等植物中遗传学的研究表明,花器官的特征是由同源异形基因决定的。在拟南芥中,由于ＡＧ在决定雄蕊和雌蕊特征方面起重要作用,本研究利用 ＲＴ－ＰＣＲ技术,从黄瓜的雌、雄蕊中分离出 ＡＧ的同源基因,并对其在花发育过程中的表达和可能作用进行了分析。首先,根据ＡＧ同源基因的保守区域设计５’简并引物５’－ＧＡ（Ａ／Ｇ）ＡＴ（Ｔ／Ｃ／Ａ）ＡＡ（Ｔ／Ｃ／Ａ）ＡＡ（Ｇ／Ａ）（Ａ／Ｃ）Ｇ（Ｇ／Ｔ／Ｃ）ＡＴＣＧＡ（Ｃ／Ａ）ＡＡＣ－３’,然后进行３’,ＲＡ ＣＥ ＰＣＲ,扩增出约１ｋｂ大小的片段,序列分析表明该片段含有非常保守的ＭＡＤＳ ｂｏｘ。进而,利用５’ ＲＡＣＥ ＰＣＲ得到全长度的ｃＤＮＡ。该ｃＤＮＡ的核苷酸序列与ＣＵＭ１（黄瓜 ＭＡＤＳ ｂｏｘ ｇｅｎｅ１）同源性高达９７％。 ＣＵＭ１在接牵牛中过量表达可引起花萼变为心皮状和花瓣变为雄蕊,说明ＣＵＭ１为ＡＧ的同源基因。基于该基因与ＣＵＭ１序列上的高度同源,我们认为其为黄瓜的ＡＧ同源基因。该基因命名为ＣＭＢ１,基因银行登记号为ＡＦ２８６６４９。Ｓｏｕｔｈｅｒ     

Molecular evolution and functional divergence of HAK potassium transporter gene family in rice （Oryza sativa L.）

The high-affinity K＋ （HAK） transporter gene family is the largest family in plant that functions as potassium transporter and is important for various aspects of plant life. In the present study, we identified 27 members of this family in rice genome. The phylogenetic tree divided the land plant HAK transporter proteins into 6 distinct groups. Although the main characteristic of this family was established before the origin of seed plants, they also showed some differences between the members of non-seed and seed plants. The HAK genes in rice were found to have expanded in lineage-specific manner after the split of monocots and dicots, and both segmental duplication events and tandem duplication events contributed to the expansion of this family. Functional divergence analysis for this family provided statistical evidence for shifted evolutionary rate after gene duplication. Further analysis indicated that both point mutant with positive selection and gene conversion events contributed to the evolution of this family in rice.     

Biomass allocation is an important determinant of the tannin concentration in growing plants

BACKGROUND AND AIMS: Condensed tannins (CTs) in the diet affect consumers in a concentration-dependent manner. Because of their importance in plant defence against herbivores and pathogens as well as their potential application against gastrointestinal parasites of ruminants in agronomy, an understanding of the seasonal dynamics of CT concentrations during plant growth is essential. METHODS: Over a vegetation period, CT concentrations in leaves, stems and roots and the biomass proportions between these organs were investigated in Onobrychis viciifolia, Lotus corniculatus and Cichorium intybus. Based on the experimental data, a model has been suggested to predict CT concentrations in harvestable biomass of these species. KEY RESULTS: During the experiment, leaf mass fractions of plants decreased from 85, 64, 85 to 30, 18, 39 % d. wt in Onobrychis, Lotus and Cichorium, respectively, and proportions of stems and roots increased accordingly. While CT concentrations almost doubled in leaves in Onobrychis (from 52 to 86 mg g(-1) d. wt, P<0.001) and Lotus (from 25 to 54 mg g(-1) d. wt, P<0.001), they were stable at low levels in expanding leaves of Cichorium (5 mg g(-1) d. wt) and in stems and roots of all investigated species. Due to an inverse effect of the increasing CT concentrations in leaves and simultaneous dilution from increasing proportions of 'CT-poor' stems, CT concentrations in harvestable biomass were stable over time in all investigated species: 62, 26 and 5 mg g(-1) d. wt for Onobrychis, Lotus and Cichorium, respectively. CONCLUSIONS: As a consequence of the unequal distribution of tannins in different plant parts and due to the changing biomass proportions between them, various herbivores (e.g. a leaf-eating insect and a grazing ruminant) may find not only different concentrations of CT in their diets but also different CT dynamics during the season. For the prediction of seasonal variations of CT concentrations, biomass allocation and accumulation of none-CT plant material are likely to be as important predictors as the knowledge of CT synthesis and its regulation.     

Adaptive population differentiation in phenology across a latitudinal gradient in European aspen (Populus tremula, L.): a comparison of neutral markers, candidate genes and phenotypic traits

A correct timing of growth cessation and dormancy induction represents a critical ecological and evolutionary trade-off between survival and growth in most forest trees (Rehfeldt et al. 1999; Horvath et al. 2003; Howe et al. 2003). We have studied the deciduous tree European Aspen (Populus tremula) across a latitudinal gradient and compared genetic differentiation in phenology traits with molecular markers. Trees from 12 different areas covering 10 latitudinal degrees were cloned and planted in two common gardens. Several phenology traits showed strong genetic differentiation and clinal variation across the latitudinal gradient, with Q(ST) values generally exceeding 0.5. This is in stark contrast to genetic differentiation at several classes of genetic markers (18 neutral SSRs, 7 SSRs located close to phenology candidate genes and 50 SNPs from five phenology candidate genes) that all showed F(ST) values around 0.015. We thus find strong evidence for adaptive divergence in phenology traits across the latitudinal gradient. However, the strong population structure seen at the quantitative traits is not reflected in underlying candidate genes. This result fit theoretical expectations that suggest that genetic differentiation at candidate loci is better described by F(ST) at neutral loci rather than by Q(ST) at the quantitative traits themselves.     

Carboxylesterase-2 in the development of the loach (Misgurnus fossilis L.)

Two esterases splitting -naphthylacetate have been found in the tissues of adult loaches and in embryos. These were identified as arylesterase (E-1) (arylester hydrolase, E.C. 3.1.1.2) and carboxylesterase (E-2) (carboxylic ester hydrolase, E.C. 3.1.1.1.). In unfertilized loach eggs E-1 and E-2 synthesized during oogenesis were found. Active E-2 synthesized under the control of E-2 genes of the embryo appeared in embryos from the stage of 40–50 h of development. Maternal E-2 molecules synthesized in oogenesis or on the stored templates in embryogenesis persisted in larvae up to days 5–6 of development. Two genes controlling the synthesis of two forms of E-2 differing in electric mobility were found in the loach population from the delta of the Danube. The genes for fast and slow E-2 were shown to segregate in meiosis and to be allelic.     

Differential expression of triplicate phosphoribosylanthranilate isomerase isogenes in the tryptophan biosynthetic pathway of Arabidopsis thaliana (L.) Heynh.

Phosphoribosylanthranilate isomerases (PAI) in the tryptophan biosynthetic pathway of Arabidopsis thaliana are encoded by a gene family. Expression patterns of each individual PAI isogene were investigated by analyzing expression of translation-fusions of promoter-β-glucuronidase (GUS) chimeras in transgenic plants. Quantification and histochemical staining of GUS activities expressed in PAI transgenic plants demonstrated that, first, expression of the three PAI isogenes was differentially regulated under normal growth conditions. Both PAI1 and PAI3 showed approximately 10-fold stronger expression than PAI2. Second, PAI isogenes differentially responded to environmental stresses such as ultraviolet irradiation and the abiotic elicitor silver nitrate. PAI2 displayed a stronger response to stresses than the other two PAI isogenes. Third, each individual PAI isogene was differentially expressed in a tissue- and cell-type-specific manner. Fourth, expression of PAI isogenes was coordinated to meet the requirement for normal growth and development of A. thaliana. Deletion of PAI1 is partially responsible for abnormal growth and development in the PAI deletion mutant trp6 as well as strong blue fluorescence in young leaves under ultraviolet irradiation. Received: 15 June 2000 / Accepted: 16 August 2000     

Rapid evolution of an adaptive cyanogenesis cline in introduced North American white clover (Trifolium repens L.)

White clover is polymorphic for cyanogenesis (HCN production after tissue damage), and this herbivore defence polymorphism has served as a classic model for studying adaptive variation. The cyanogenic phenotype requires two interacting biochemical components; the presence/absence of each component is controlled by a simple Mendelian gene (Ac/ac and Li/li). Climate-associated cyanogenesis clines occur in both native (Eurasian) and introduced populations worldwide, with cyanogenic plants predominating in warmer locations. Moreover, previous studies have suggested that epistatic selection may act within populations to maintain cyanogenic (AcLi) plants and acyanogenic plants that lack both components (acli plants) at the expense of plants possessing a single component (Acli and acLi plants). Here, we examine the roles of selection, gene flow and demography in the evolution of a latitudinal cyanogenesis cline in introduced North American populations. Using 1145 plants sampled across a 1650 km transect, we determine the distribution of cyanogenesis variation across the central United States and investigate whether clinal variation is adaptive or an artefact of population introduction history. We also test for the evidence of epistatic selection. We detect a clear latitudinal cline, with cyanogenesis frequencies increasing from 11% to 86% across the transect. Population structure analysis using nine microsatellite loci indicates that the cline is adaptive and not a by-product of demographic history. However, we find no evidence for epistatic selection within populations. Our results provide strong evidence for rapid adaptive evolution in these introduced populations, and they further suggest that the mechanisms maintaining adaptive variation may vary among populations of a species.     

Uridine and the Control of Phototropism in Oat (Avena sativa L.) Coleoptiles

The short-term growth response of oat (Avena sativa L.) coleoptiles to exogenously applied uridine was studied both in excised apical segments and in the intact seedlings. In both cases growth of coleoptile tissue was inhibited by uridine. The inhibition of coleoptile growth consistently occurred 20–30 min after uridine treatment, which is within the lag period of their phototropic response. Asymmetric application of uridine to coleoptiles in the intact seedlings resulted in their bending toward the direction to which uridine was applied in the absence of light stimulus. These findings suggest that uridine or its metabolites, plays an important role in the phototropism of oat coleoptiles and provide support to the Bruinsma–Hasegawa theory as an alternative to the Cholodny–Went theory for explaining phototropism.     

斜纹夜蛾幼虫诱导的油菜抗虫性及其与茉莉酸信号途径的关系

植物在受植食性昆虫为害时能产生防御反应,并且植物的茉莉酸信号转导途径在这一过程中发挥着重要作用。然而, 迄今为止对于油菜Brassica campestris的诱导防御反应很少有研究报道。为此, 本实验通过测定油菜内茉莉酸和胰蛋白酶抑制剂含量研究了油菜在斜纹夜蛾Spodoptera litura幼虫为害后的抗虫性和胰蛋白酶抑制剂含量的变化,并分析这些变化在油菜诱导抗虫性与茉莉酸信号转导途径中的关系。结果表明：斜纹夜蛾幼虫取食能导致油菜体内茉莉酸和胰蛋白酶抑制剂含量系统性上升,外用茉莉酸甲酯处理也能系统性增加油菜的胰蛋白酶抑制剂含量,并且取食茉莉酸甲酯处理或斜纹夜蛾幼虫取食过的叶片能显著降低斜纹夜蛾幼虫的体重,两者的体重分别为对照植株上的67.5%和60.2%。机械损伤加斜纹夜蛾幼虫口腔分泌物处理能引起处理叶中茉莉酸和胰蛋白酶抑制剂含量的增加,但其诱导效果与机械损伤加水没有显著差异,并且两者明显低于虫害的诱导效果,两种处理的茉莉酸和胰蛋白酶抑制剂含量分别为虫害诱导的68.4%和24.4%及62.9%和36.9%;多次连续机械损伤的诱导效果与一次损伤的没有明显差异。结果说明斜纹夜蛾幼虫诱导的油菜抗虫性与茉莉酸信号转导途径有关,而其激活油菜抗虫反应的机理则可能与其特定的取食行为相关。     

不同化感潜力水稻(Oryza sativa L.)苗期的氮素养分效率及相关基因的表达

为了阐明养分水平引起水稻(Oryza sativa L.)化感抑草潜力变化的生理生态机制,研究了不同N素营养处理下,不同化感潜力水稻苗期对N素营养逆境的响应特性及N素养分效率的差异,并运用实时荧光定量RT-PCR技术(FQ-PCR)检测与N素代谢和次生代谢关键酶的基因表达.结果表明:弱化感水稻品种Lemont对N素营养胁迫较敏感,强化感水稻品种PI312777对资源波动的适应性较强,N素养分效率较高.FQ-PCR分析结果显示,在低N条件下Lemont中的亚硝酸还原酶基因(nir),谷氨酰胺合成酶基因(gs)相对表达量均有不同幅度的下调, PI312777分别下调了1.2倍和1.4倍,而Lemont分别下调了3.0倍和1.8倍, Lemont下调的幅度分别是PI312777的2.5倍和1.3倍,但对于苯丙氨酸解氨酶基因(pal)与3-羟基-3甲基戊二酰辅酶A还原酶基因(hmgr)而言, PI312777叶组织中的pal和hmgr均上调表达,与对照相比上调了6.0倍和1.6倍,而Lemont中对应的基因均下调表达,分别下调了1.3倍和6.8倍,佐证了上述差异的分子生态学特性.     

Molecular signatures of lineage‐specific adaptive evolution in a unique sea basin: the example of an anadromous goby Leucopsarion petersii

Climate changes on various time scales often shape genetic novelty and adaptive variation in many biotas. We explored molecular signatures of directional selection in populations of the ice goby Leucopsarion petersii inhabiting a unique sea basin, the Sea of Japan, where a wide variety of environments existed in the Pleistocene in relation to shifts in sea level by repeated glaciations. This species consisted of two historically allopatric lineages, the Japan Sea (JS) and Pacific Ocean (PO) lineages, and these have lived under contrasting marine environments that are expected to have imposed different selection regimes caused by past climatic and current oceanographic factors. We applied a limited genome‐scan approach using seven candidate genes for phenotypic differences between two lineages in combination with 100 anonymous microsatellite loci. Neuropeptide Y (NPY) gene, which is an important regulator of food intake and potent orexigenic agent, and three anonymous microsatellites were identified as robust outliers, that is, candidate loci potentially under directional selection, by multiple divergence‐ and diversity‐based outlier tests in comparisons focused on multiple populations of the JS vs. PO lineages. For these outlier loci, populations of the JS lineage had putative signals of selective sweeps. Additionally, real‐time quantitative PCR analysis using fish reared in a common environment showed a higher expression level for NPY gene in the JS lineage. Thus, this study succeeded in identifying candidate genomic regions under selection across populations of the JS lineage and provided evidence for lineage‐specific adaptive evolution in this unique sea basin.     

Thiourea mediates alleviation of UV-B stress-induced damage in the Indian mustard (Brassica juncea L.)

Abstract

UV-B radiation (280–320 nm) as an environmental stress has damaging effect on plants and its overexposure can potentially interfere with growth and development. The effect of thiourea (TU) on UV-B stress tolerance of 10-day-old Brassica juncea seedlings subjected to supplementary UV-B for 5 days was investigated. An increase in the UV-B absorbing compounds anthocyanin, flavonoids and phenolic compounds was observed in UV-B + TU treated seedlings as compared to that of control. The enhanced synthesis of UV-B screening compounds resulted in lesser damage to chlorophyll and also gain in fresh weight and dry weight in UV-B + TU as compared to UV-B alone treatment. The enzymatic activities of guaiacol peroxidase (GPX) and superoxide dismutase (SOD) also increased in UV-B + TU. The expression profiling of phenylalanine ammonia lyase (pal) and chalcone synthase (chs) indicated an upregulation under UV-B + TU treatment, compared to that of control, suggesting that TU treatment ensured an early and efficient induction of flavonoid biosynthetic pathway. The results indicate that TU helps in ameliorating the damaging effects of UV-B stress by efficiently maintaining the antioxidant status and attenuating the penetration of the UV-B.