Evolution of Histone H4 and H3 Genes in Different Ciliate Lineages

The histones H4 are known as highly conserved proteins. However, in ciliates a high degree of variation was found compared both to other eukaryotes and between the ciliate species. To date, only H4 histones of species belonging to two distantly related classes have been investigated. In order to obtain more detailed information on histone H4 variation in ciliates we undertook a comprehensive sequence analysis of PCR-amplified internal H4 fragments from 12 species belonging to seven out of the nine currently recognized ciliate classes. In addition, we used PCR primers to amplify longer fragments of H3 and H4 genes including the intergenic region. The encoded amino acid sequences reveal a high number of differences when compared with those of other eukaryotes and the ciliate species investigated. Furthermore, in some species H4 gene variants were detected, which result in amino acid differences. The greatest number of substitutions and insertions found was in the amino terminal region of the H4 histones. However, all sequences possess a conserved region corresponding to those of all other eukaryotic H4 histones. The histone gene variations were used to reconstruct phylogenetic relationships. The tree from our data matches perfectly with the ribosomal RNA data: The heterotrichs, which were considered as a late branching lineage, diverge at the base of the ciliate tree and groups formerly thought to represent ancestral lineages now appear as highly derived ciliates. Received: 4 April 1997 / Accepted: 1 August 1997     

Comparative Anatomy and Morphology of Leaves between C3 and C4 Species in Panicum

Anatomical and morphological structures of leaf blades werecompared between C₃ and C₄ species in Panicum. Inter-specificvariation of stomatal density, longitudinal vein density andmesophyll thickness was highly correlative either plus or minuswithin respective groups. The two groups could not be distinguishedby a single character, since the variation ranges overlappedeach other. However, the quantitative relations between veindensity and the other two characters differentiated the twogroups well. In C₃, stomatal density seemed to be a primaryfactor for regulating water balance, while in C₄ vein systemwas considered to be important for the regulation. The specieswith intermediate photosynthesis behaved similar to the C₃ species.In the C₃ group, correlative variation was observed betweenleaf width, leaf angle and the three characters mentioned above.Variation of light-receiving area due to the changes of widthand angle of leaf blades was considered to be one of the adaptivestrategies of this group. Increase of light-receiving area wasin connection with the thinning of leaves. On the other hand,in the C₄ correlations between length, width and angle of leaveswere low. Such loose character correlation may be achieved byits efficiency of CO₂ utilization and its well developed veinsystems. Besides, NAD-me type species tended to have relativelylower stomatal and vein densities as compared with the otherdecarboxylation types in this group. Panicum, photosynthesis, C₃, C₄, decarboxylation types, leaf, stomata, vein     

Identification of Multiple Gypsy LTR-Retrotransposon Lineages in Vertebrate Genomes

Gypsy LTR-retrotransposons have been identified in the genomes of many organisms, but only a small number of vertebrate examples have been reported to date. Here we show that members of this family are likely to be widespread in many vertebrate classes with the possible exceptions of mammals and birds. Phylogenetic analyses demonstrate that although there are several distinct lineages of vertebrate gypsy LTR-retrotransposons, the majority clusters into one monophyletic clade. Groups of fungal, plant, and insect elements were also observed, suggesting horizontal transfer between phyla may be infrequent. However, in contrast to this, there was little evidence to support sister relationships between elements derived from vertebrate and insect hosts. In fact, the majority of the vertebrate elements appeared to be most closely related to a group of gypsy LTR-retrotransposons present within fungi. This implies either that at least one horizontal transmission between these two phyla has occurred previously or that a gypsy LTR-retrotransposon lineage has been lost from insect taxa. Received: 22 December 1998 / Accepted: 6 April 1999     

Methionine Sulfoximine Effects on C4 Plant Leaf Discs: Comparison with C3 Species

Methionine sulfoximine caused ammonia accumulation and photosyntheticrate inhibition in leaf discs from two C₄ species, Zea maysL. cv. F. M. Cross (Hybrid) and Sorghum bicolor L. Moench cv.NC-70X, as well as one C₃ plant species, Datura stramonium L.cv. stramonium. Similar results were obtained earlier with theC₃ species Spinacia oleracea L. The effect occurred in the absenceof inorganic nitrogen reduction and was light dependent. Ammoniaaccumulation rates were similar in all four species examined.The results support a role for glutamine synthetase in leafammonia recycling in both C₄ and C₃ leaves. ¹ Current address: Cetus Madison Corporation, 2208 Parview Road,Middleton, WI 53562, U.S.A. (Received November 2, 1981; Accepted April 28, 1982)     

Identification of Candidate Growth Promoting Genes in Ovarian Cancer through Integrated Copy Number and Expression Analysis

Ovarian cancer is a disease characterised by complex genomic rearrangements but the majority of the genes that are the target of these alterations remain unidentified. Cataloguing these target genes will provide useful insights into the disease etiology and may provide an opportunity to develop novel diagnostic and therapeutic interventions. High resolution genome wide copy number and matching expression data from 68 primary epithelial ovarian carcinomas of various histotypes was integrated to identify genes in regions of most frequent amplification with the strongest correlation with expression and copy number. Regions on chromosomes 3, 7, 8, and 20 were most frequently increased in copy number (>40% of samples). Within these regions, 703/1370 (51%) unique gene expression probesets were differentially expressed when samples with gain were compared to samples without gain. 30% of these differentially expressed probesets also showed a strong positive correlation (r≥0.6) between expression and copy number. We also identified 21 regions of high amplitude copy number gain, in which 32 known protein coding genes showed a strong positive correlation between expression and copy number. Overall, our data validates previously known ovarian cancer genes, such as ERBB2, and also identified novel potential drivers such as MYNN, PUF60 and TPX2.     

Variations in the Leaf Anatomy among some C4 Panicum Species

The Dichotomiflora group of Panicum contains NAD-malic enzyme(ME) species with centrifugal chloroplasts in Kranz cells, NAD-ME(F)species as well as NAD-ME species with centripetal chloroplastsin Kranz cells, NAD-ME (P) species. Many attributes of leafanatomy of 22 C₄ Panicum species were investigated to identifydifferences among four different C₄ subtypes, i.e. NADP-ME,NAD-ME(F), NAD-ME(P) and PEP-CK species grouped by the C₄-aciddecarboxylating enzymes and chloroplast location in Kranz cellsin combination. Differences were found in the number of Kranzcells surrounding a large vein, and the number surrounding asmall vein, the interveinal distances, the proportion of leafcross sectional area occupied by epidermis plus sclerenchyma,by mesophyll cells, by Kranz cells, and by vascular bundles.There were also differences in the ratios of the area of thedifferent cell types. The number of the characters significantlydifferent between a respective pair of C₄ subtypes was the largestbetween NAD-ME(F) and NAD-ME(P) species. In principal componentanalysis applied to 11 leaf anatomical characters, the differentC₄ subtypes clustered into small groups, although the rangeof variations of PEP-CK species and those of NAD-ME(F) speciesoverlapped. The results were discussed in relation to taxonomyand ecological adaptation of Panicum species in the differentC₄ subtypes. C₄ photosynthesis, NADP-malic enzyme, NAD-malic enzyme, Phosphoenolpyruvate carboxykinase, C₄ leaf anatomy, Panicum, Kranz, Dichotomiflora group     

Transcriptome Analysis Reveals Candidate Lignin-Related Genes and Transcription Factors in Rosa roxburghii During Fruit Ripening

Plant Molecular Biology Reporter - The high lignin content of Rosa roxburghii fruits imparts a strong rough taste, which has restricted its use in industry. Little is known about the molecular...     

Identification of Salt Stress Response Genes in Rosa chinensis Leaves by Comparative RNA-seq Analysis of Transcriptome Dynamics

Russian Journal of Plant Physiology - Rosa chinensis Jacq., originating from China, occupied a pivotal position in the floral industry all over the world. Drought and soil salinization is a major...     

Effects of Prolonged Darkness on the Sensitivity of Leaf Respiration to Carbon Dioxide Concentration in C3and C4Species

Predicting responses of plant and global carbon balance to theincreasing concentration of carbon dioxide in the atmosphererequires an understanding of the response of plant respirationto carbon dioxide concentration ([CO₂]). Direct effects of thecarbon dioxide concentration at which rates of respiration ofplant tissue are measured are quite variable and their effectsremain controversial. One possible source of variation in responsivenessis the energy status of the tissue, which could influence thecontrol coefficients of enzymes, such as cytochrome-c oxidase,whose activity is sensitive to [CO₂]. In this study we comparedresponses of respiration rate to [CO₂] over the range of 60to 1000 µmol mol^-1in fully expanded leaves of four C₃andfour C₄herbaceous species. Responses were measured near themiddle of the normal 10 h dark period, and also after another24 h of darkness. On average, rates of respiration were reducedabout 70% by the prolonged dark period, and leaf dry mass perunit area decreased about 30%. In all species studied, the relativedecrease in respiration rate with increasing [CO₂] was largerafter prolonged darkness. In the C₃species, rates measured at1000 µmol mol^-1CO₂averaged 0.89 of those measured at 60µmol mol^-1in the middle of the normal dark period, and0.70-times when measured after prolonged darkness. In the C₄species,rates measured at 1000 µmol mol^-1CO₂averaged 0.79 of thoseat 60 µmol mol^-1CO₂in the middle of the normal dark period,and 0.51-times when measured after prolonged darkness. In threeof the C₃species and one of the C₄species, the decrease in theabsolute respiration rate between 60 and 1000 µmol mol^-1CO₂wasessentially the same in the middle of the normal night periodand after prolonged darkness. In the other species, the decreasein the absolute rate of respiration with increase in [CO₂] wassubstantially less after prolonged darkness than in the middleof the normal night period. These results indicated that increasingthe [CO₂] at the time of measurement decreased respiration inall species examined, and that this effect was relatively largerin tissues in which the respiration rate was substrate-limited.The larger relative effect of [CO₂] on respiration in tissuesafter prolonged darkness is evidence against a controlling roleof cytochrome-c oxidase in the direct effects of [CO₂] on respiration.Copyright 2001 Annals of Botany Company Carbon dioxide, respiration, Abutilon theophrasti(L.), Amaranthus retroflexus(L.),Amaranthus hypochondriacus (L.), Datura stramonium(L.), Helianthus annuus(L.), Solanum melongena(L.), Sorghum bicolor(L. Moench), Zea mays     

玉米叶形相关性状的Meta-QTL及候选基因分析

叶长、叶宽、叶面积及叶夹角不仅影响玉米(Zea mays)光合效率, 也是株型的重要构成因素。通过对620个叶形QTL进行整合, 构建不同遗传背景下的叶形QTL整合图谱, 利用元分析发掘出22个叶长、22个叶宽、12个叶面积以及17个叶夹角mQTL; 进一步运用生物信息学手段, 确定44个与叶片发育密切相关的候选基因。分析发现, 仅有NAL7-like、YABBY6- like和GRF2等13个基因位于mQTL区间内, 而玉米中已克隆的KNOTTED1、AN3/GIF1、rgd1/lbl1、mwp1及SRL2-like、HYL1-like和CYCB2;4-like等水稻(Oryza sativa)和拟南芥(Arabidopsis thaliana)叶形同源基因位于未被整合的QTL内; 对44个候选基因在叶片长、宽、厚发育过程中基部-末端、中央-边缘、远轴-近轴的调控机理进行归纳分析, 发现玉米中仅有少数几个候选基因被报道, 揭示了叶形发育的部分分子机理。因此, 对玉米叶形相关mQTL/QTL及基因进行全面深入的分析, 不仅有助于增加对其遗传结构的了解, 发掘更多候选基因, 阐明叶形发育和形成的分子机制, 还可为耐密理想株型的分子标记辅助选择提供依据。