Cloning and expression profiles of 15 genes encoding WRKY transcription factor in wheat （Triticum aestivem L.）

WRKY proteins are involved in various physiological processes, including biotic and abiotic stress responses, hormone responses and development. However, no systematic identification, expression and function analysis of WRKY genes in wheat were reported. In this study, we isolated 15 wheat cDNAs with complete open reading frame （ORF） encoding putative WRKY proteins using in silico cloning. Phylogenetic analysis indicated that the 15 wheat WRKY genes belonged to three major WRKY groups. Expression analysis revealed that most genes expressed drastically in leaf, except Ta WRKYIO which expressed in crown intensively. Four genes were strongly up-regulated with the senescence of leaves. Eight genes were responsive to low temperature, high temperature, NaCl or PEG treatment. Moreover, differential expression patterns were also observed between wheat hybrid and its parents, and some genes were more responsive to PEG treatment in the hybrid. These results demonstrated that wheat WRKY genes are involved in leaf senescing and abiotic stresses. And the changed expression of these WRKY genes in hybrid might contribute to the heterosis by improving the stress tolerance in hybrids.     

Combinational electroporation and transplantation approach to studying gene functions in avian embryos

Gene transfection is an indispensable approach for studying gene function since it provides important information on gain- and/or loss-of-function. Chick embryos are also extensively employed for studying bio- logical function since they are easily accessible and can be maintained alive after manipulation. The combination of both techniques presents a powerful approach to under- standing how genes regulate embryo development. Fur- thermore, combining these approaches with tissue transplant techniques make even more attractive for elu- cidate gene function. Electroporation, employing parallelly fashioned electrodes, has been widely used in chick embryos. However, experimenters have been frustrated by unsuccessfully transfection in some embryonic tissue of interest because the electrodes were improperly positioned.We presently demonstrated the different patterns of orga- nizing and positioning the electrodes, in combination with tissue transplantation, to efficiently and specifically trans- fect the chick embryonic head, trunk neural tube, heart tube, somites and neural crest cells with the GFP reporter gene.     

A wound-induced small polypeptide gene family is upregulated in soybean nodules

Small peptides function as key signals in processes, such as plant cell differentiation, organ development and defenses to biotic stresses. A large number of small peptide precursor genes have been predicted from the analysis of the soybean (Glycine max) whole genome DNA sequence. However, most of these genes have unknown characteristics and functions. In this report, we systemically searched for the gene families of small peptide precursors that are up-regulated in soybean nitrogen-fixing root nodules. We found 212 genes (encoding peptides shorter than 150 amino acids) that were up-regulated, and among them, 79 genes belong to 38 multiple-gene families, but the other 133 genes are unique. Twenty-eight of 38 families are conserved in Arabidopsis, but the other 10 only exist in legumes. We also identified 16 out of the 38 members of the wound-induced polypeptide (WIP) gene family to be upregulated in nitrogen-fixing nodules. We further analyzed homologs of WIP genes in Medicago, Lotus, Arabidopsis and Oryza species and found that a few homologous genes from Medicago truncatula and Lotus japonicus were also upregulated in their nodules and some WIP genes were induced by specific fungal pathogens on soybean and rice. Structure prediction indicated that all WIP prepropeptides contain a conserved DUF3774 domain (including two hydrophobic regions) and most of them have an N-terminal signal sequence. Fluorescence microscopy analysis of two WIP prepropeptides fused to GFP revealed that these proteins are located on the plasma membrane of tobacco leaf cells. Interestingly, 34 soybean WIP genes are clustered onto three soybean chromosomes, different from known peptide gene families (such as CLE). Among them, 11 highly identical genes are aligned on the 6th chromosome, 12 on the 12th, and 11 on the 13th chromosomes. Most of WIP genes from the 12th chromosome share the highest identities with their homologs on the 13th chromosome, suggesting that ancestral WIP genes could have originated from the 13th chromosome, then spread onto the 12th chromosome by chromosome homologous recombination; the new WIP genes could have existed in multiple copies by gene duplication which then spread onto the 6th chromosome. In Arabidopsis and Oryza species, half of the WIP genes are also aligned on one chromosome and showed higher identity with those from the soybean 12th and 13th chromosomes, suggesting that WIP genes originated from one common ancestor.     

SRO1 regulates heavy metal mercury stress response in Arabidopsis thaliana

Heavy metals in the environment are harmful limiting factors for the normal growth and development of plants. Here, we isolated and identified an Arabidopsis thaliana T-DNA insertion mutant, named srol-1, which showed a hyper-sensitive response to HgCl2. The SRO1 protein contains a WWE domain that mediates proteinprotein interactions. Under HgCl2 treatment, when compared with the wild-type plants, the growth of srol-1 was repressed dramatically and the number of true leaves was reduced and etiolated. The electrolyte leakage rates showed that cell membrane integrity in srol-1 was damaged more severely than in the wild type. DAB （3,5-diaminobenzidine） staining and confocal microscopy showed that Hg2＋ stress induced more hydrogen peroxide accumulation in srol-1 than in the wild type. The qRT-PCR results indicated that the expression of some abiotic stress-induced genes, such as L-ascorbate peroxidase （APX1）, was reduced under oxidative or Hg2＋ stress. Transgenic plants containing a GFP：：SRO1 fusion protein showed that SRO1 was localized in the nucleus of the cells. SRO1 was shown to be expressed in various tissues, and was most highly expressed in the vigorous tissues. Our results suggest thatSRO1 may play an important role in the stress response of A. thaliana to heavy metals.     

Analysis of diversity of CO I gene and system generation of nine species of chitons

Cytochrome c oxidase subunit Ⅰ(COⅠ) genes from 9 chiton species in China’s coast area were sequenced. A phylogeny tree about these gene sequences were reconstructed together with other 4 COⅠgene sequences of chitons from Genbank. The affinity genetic relationship and the taxonomic status of molecular evolution for these 13 chiton species were analyzed. The results show that Liolophura japonica and Onithochiton hirasei belong to Chitonidae, Acanthochiton rubrolineatus and Acanthochiton dissimilis belong to Acanthochitonidae, and Placiphorella japonica and Mopalia retifera belong to the same family Mopliidae. However, Lepidozona coreanica, Ischnochiton comptus, and Ischnochiton hakodadensis are not supposed to be referred to Ischnochi-tonidae according to the genetic distance analysis (L. coreanica, I. comptus, and I. hakodadensis are usually classed as Ischnochitonidae according to their morphological character). Furthermore, I. hakodadensis could not been classed as Ischnochiton, and it is more likely to be treated as a close relative of Lepidozona.     

Morphological and physiological analysis of narrow and striped leaf 1 （nsl1） mutant of rice （Oryza sativa L.） and the gene mapping

The shape and color of rice leaves are impor- tant agronomic traits that directly influence the proportion of sunlight energy utilization and ultimately affect the yield and quality. A new mutant exhibiting stable inheritance was identified as derived from ethyl methane sulfonate （EMS）-treated restorer Jinhui 10, tentatively named as narrow and striped leaf 1 （nsll）. The nsll displayed pale white leaves at the seeding stage and then white striped leaves in parallel to the main vein at the jointing stage. Meanwhile, its leaf blades are significantly narrower than the control group of Jinhui 10. The chloroplast structures of cells in the white striped area of the nsll mutant break down, and the photosynthetic pigments are significantly lower than that of the wild type. Moreover, fluorescence parameters, such as Fo, Fv/Fm, ФpsⅡ, qP, and ETR, in the nsll mutant are significantly lower than those of the wild type, and the photosynthetic efficiency is also significantly decreased. These changes in leaf color and shape, together with physiological changes in the nsll, result in smaller plant height and a decrease in the most important agro- nomic traits, such as the number of grains per panicle, grain weight, etc. Genetic analysis shows that the narrow and striped traits of the nsll mutant are controlled by a single recessive nuclear gene, which is located between InDel 16 and InDel 12 in chromosome 3. The physical distance is 204 kb. So far, no similar genes of such leaf color and shape in this area have been reported, This study has laid asolid foundation for the gene cloning and function analysis of NSL 1.     

Functional analysis of the ABA-responsive protein family in ABA and stress signal transduction in Arabidopsis

The phytohormone abscisic acid (ABA) plays an important role in plant growth and development, for example in seed dormancy and germination, as well as in plant responses to environmental stresses, such as drought and high salinity. Previous studies have shown that ABA regulates the expression of genes with an ABA-responsive element (ABRE) and their corresponding physiological responses. Bioinformatics analysis identified a GRAM domain-containing gene family that has a multiple ABRE cis-element, which was termed the ABA-responsive protein (ABR) family. To analyze the function of the ABR family, we identified homozygous T-DNA insertion mutants and constructed abr1, 2, 3 double mutants and triple mutant. The abr1, abr2 and abr3 single mutants showed a normal phenotype; however, the germination of seeds of the double mutants and triple mutant were insensitive to ABA, NaCl, mannitol and glucose. ABR1-GFP was distributed as a punctate structure in the cytosol and may be localized in the endomembrane system. The ABR2-GFP and ABR3-GFP proteins localized in the cytoplasm. In addition, ABR1, ABR2 and ABR3 were expressed in various tissues, and could be induced by several abiotic stresses, especially by ABA. The expressions of these genes were significantly suppressed in aba2, abi1 and abi2 null mutants. These results suggested that the ABR family may act downstream of ABI1 and ABI2 in the ABA signal transduction process in plants.     

Derivation of P–T paths for Middle–Late Triassic very low-grade metapelite from Hongcan Well 1 in the Zoigê Depression and their tectonic implications

Using XRD measurements of illite crystallinity,b0values of K-rich white micas and chemical compositions of chlorites combined with homogenization temperatures of fluid inclusions in calcite,the metamorphic P–T conditions of very low-grade metapelites from different depths in the 7 km Hongcan Well 1 in the Zoige?Depression,Sichuan,China,have been obtained in this paper.Knowledge of the tectonic evolution of the studied basin allows us to derive geothermal curves for Middle and Late Triassic time(the geothermal peak)and the present day(from thermal logging of the borehole).The retrograde P–T tracks from clockwise P–T–t loops have been revealed by the plotting of individual samples on each geotherm,which can be interpreted by the lithospheric thickening due to sedimentation and folding followed by continuous uplift and erosion.A stratigraphic log indicates that the Well penetrates the steep limb of a fold which perturbed the peak geotherm and caused some P–T paths to cross.     

苦荞CCT基因家族生物信息学及表达分析

CCT转录因子在调控植物花期、生长发育及抗非生物胁迫等方面发挥着重要的功能。本研究以拟南芥AtCCT基因家族为参考序列,利用本地BLAST并结合保守结构域等生物信息学工具,筛选出苦荞FtCCT基因家族成员,并对其理化性质、染色体分布、基因结构、系统进化及表达水平进行分析。结果显示:从苦荞中共鉴定出35个FtCCT基因,含1-8个内含子;编码蛋白有117-753个氨基酸残基,等电点为4.96-9.51,均为亲水性蛋白。染色体定位分析表明,这些基因在8条染色体上均有分布。苦荞FtCCT基因家族含有10个保守基序和5个保守结构域,且都含有CCT保守结构域。系统进化分析表明,苦荞的FtCCT基因家族与拟南芥一样可分为3个亚家族,其中CMF亚家族的成员最多。35个FtCCT基因在苦荞根、茎、叶和花中的表达水平具有差异性,在叶和花中具有高表达量的成员较多,只有少数的成员在根和茎中高表达。本研究为进一步解析CCT基因调控苦荞花期及生长发育奠定基础。     

Mutual mate choice in the Asiatic toad, Bufo gargarizans, exerts stabilizing selection on body size

Sexual selection is critical to both reproduction and evolution.The effects of male–male competition and female choice regarding body size have been examined in a large number of taxa,including toad species.Males and females have different optimal reproductive strategies,achieving breeding advantages in discrepant ways.Further,the relative contributions of intra-and inter-sexual size selection vary among species.Thus,to understand the mechanisms affecting mating success,it is important to consider both male–male and male–female interactions simultaneously and elucidate their interrelationship.In this study,we measured body sizes of all mated and unmated individuals in a population of Asiatic toad(Bufo gargarizans)and counted fertilized eggs of several clutches.Based on correlation and regression techniques,we tested for female choice and intra-sexual competition among males relative to body size gradients,and we compared the relative importance of these two processes for mating success.Our results reveal that male–male competition and female choice simultaneously contribute to sexual selection in toads.Furthermore,both interactions are most intense among smaller toads.The synergistic trends of male–male competition and female choice support the mutual mate choice hypothesis and works to stabilize body size in B.gargarizans.Normal distributions of breeding success relative to body size were detected for both sexes,suggesting that medium-sized individuals enjoy a reproductive advantage in the population studied.     

Insights on evolution of virulence and resistance from the whole-genome analysis of a predominant methicillin-resistantStaphylococcus aureus clone sequence type 239 in China

Earlier, we reported that ST239 was the 15-year predominant methicillin-resistant Staphylococcus aureus （MRSA） clone in China. In this study, MRSA strain CN79 belonging to ST239 and isolated from blood was used to determine the whole tive genomics analysis was genome sequence. Compara- done between MRSA CN79 and 25 sequenced S. aureus in the NCBI GenBank data- base. A total of 2,734 protein-encoding genes were iden- tified in the MRSA CN79 genome, which carries 11 antibiotic resistance genes and 65 virulence genes. Two prophages phiCN79A and phiNM3-1ike were found on the MRSA CN79 genome. MRSA CN79 carries 30 specific genes that are absent from the 25 sequenced S. aureus genomes. Most of them were prophage-related genes. Several antibiotic resistance genes, such as [3-1actamase and ABC-type multidrug transport system gene, were located on the genomic island vSal3. The antibiotic resis- tance genes, such as tet （M）, ermA1, and blaZ, were also located on different transposons. The virulence genes sea,map, hlb, and sak are located on phiNM3-1ike prophage and the exotoxin genes are carried on the genomic island vSaa. These results suggest that ST239 MRSA strains are widespread owing to horizontal acquisition of the mobile genetic elements harbored antibiotic resistance genes and virulence genes in response to environmental selective pressures, such as antibiotics and the human immune sys- tem during evolution.     

Complex evolutionary history of the vertebrate sweet/umami taste receptor genes

Adaptive evolution plays a role in the functional divergence and specialization of taste receptors and the sense of taste is thought to be closely related to feeding ecology.To examine whether feeding ecology has shaped the evolution of taste receptor genes in vertebrates,we here focus on Tas1r gene family that encodes umami(Tas1r1 and Tas1r3 heterodimer) and sweet(Tas1r2 and Tas1r3 heterodimer) taste receptors.By searching currently available genome sequences in 48 vertebrates that contain 38 mammals,1 reptile,3 birds,1 frog,and 5 fishes,we found all three members of Tas1rs are intact in most species,suggesting umami and sweet tastes are maintained in most vertebrates.Interestingly,the absence and pseudogenization of Tas1rs were also discovered in a number of species with diverse feeding preferences and distinct phylogenetic positions,indicating widespread losses of umami and/or sweet tastes in these animals,irrespective of their diet.Together with previous findings showing losses of tastes in other vertebrates,we failed to identify common dietary factors that could result in the taste losses.Our results report here suggest the evolution of Tas1rs is more complex than we previously appreciated and highlight the caveat of analyzing sequences predicted from draft genome sequences.Future work for a better understanding of taste receptor function would help uncover what ecological factors have driven the evolution history of Tas1rs in vertebrates.     

簸箕柳R2R3-MYB转录因子家族全基因组分析

为研究簸箕柳中R2R3-MYB转录因子家族成员的分类和进化,以及在抗重力刺激中可能具有的功能,本研究使用全基因组鉴定策略和其它生物信息学手段对簸箕柳相关家族成员进行详细的分析.结果表明,在簸箕柳中共鉴定出158个R2R3-MYB蛋白,这些成员进一步被分为23个亚组.基因结构和基序组成分析表明,在同一亚组中的基因通常具有相似的内含子-外显子结构和相似的基序组成,进一步支持了系统发育分析的结果.通过共线性分析了SsMYB家族的进化,85对SsMYB基因被预测来自串联或者片段复制事件,这在SsMYB家族的扩展中起着重要作用.此外,本研究利用RNA-seq数据分析重力刺激下SsMYB基因的表达情况,筛选出20个潜在的MYB抗重力刺激蛋白.     

菠菜SoNAC转录因子家族的全基因组鉴定与分析

采用生物信息学分析方法,从菠菜基因组中筛选鉴定了57个菠菜NAC转录因子,并对其基因结构、编码蛋白和系统进化进行了分析;通过荧光定量聚合酶链式反应qRT-PCR分析,研究了高温和盐处理后菠菜叶片中NAC基因的表达模式.研究结果显示:菠菜NAC转录因子可以被归入2组17个亚组,GroupⅠ包含10个亚组,GroupⅡ包含...     

Phylogenetic positions of some genera and species of the family Buccinidae (Gastropoda: Mollusca) from China based on ribosomal RNA and COI sequences

A phylogenetic analysis of members of the family Buccinidae was conducted using 18S rRNA gene, 28S rRNA gene and the mitochondrial cytochrome oxidase Ⅰ gene. We studied 18 species of Buccinidae that belong to eight different genera and inhabit the China coastal seas. We analyzed the patterns of divergence between an outgroup and basal ingroup taxa, the monophyly of the genus Neptunea, and the position of one unnamed species within the Buccinidae. A phylogenetic tree (neighbor-joining (NJ) method) was reconstructed based on the sequences of 18S rRNA, 28S rRNA and COI, with Rapana venosa as outgroup. The NJ tree indicated that the 18 species could be divided into five groups. The genus Buccinum was monophyletic, whereas Neptunea was shown to be paraphyletic since it included Siphonalia subdilatata and Neptunea sp., a new species. This novel species otherwise clustered consistently with Neptunea cumingi in three other phylogenetic trees, showing a low genetic distance and divergence percentage of sequences belonging to the genus Neptunea. A smaller genetic distance and a smaller difference of 18S rRNA, 28S rRNA and COI sequences between Neptunea cumingii and Neptunea arthritica cumingii confirmed them to be the same species.     

Distribution,ecology, and oxygen and carbon isotope characteristics of modern planktonic foraminifers in the Makarov Basin of the Arctic Ocean

The Arctic region, with magnificent ice cover on the surface of the Arctic Ocean and adjacent seas, is not only extremely sensitive to but also has strong amplification effects on climate change. Observations during the past decades have documented substantial retreat and thinning of the Arctic sea-ice cover, a process that is accelerating. Its feedback and impact on the global climate has become an important subject of current climate change research. Calcite tests of planktonic foraminifers are major constituents in pelagic sediments, and they provide valuable materials for the reconstruction of past oceanographic conditions. However, research is still sparse in the Arctic sea area because of limited availability of the materials for investigation. Here, we present a study of modern foraminifers from the plankton tow samples taken in the Makarov Basin of the Arctic Ocean during the fourth Arctic expedition of China. We have analyzed ecological information stored in the modern planktonic foraminifers and in their stable isotope signals, and established a relationship between the distribution of the main taxa and the environment. Our main observations are as follows:(1) in the Makarov Basin, the polar species Neogloboquadrina pachyderma(sinistral coiling) dominates the [150 lm planktonic foraminiferal assemblages.(2) The planktonic foraminifers live mainly in the upper halocline at a water depth of 50–100 m and less in the depth interval of 100–200 m.(3) Temperature change in the halocline can affect the absolute abundance of planktonic foraminifers and their distribution in the water column. The warmer halocline is more favorable to the development of planktonic foraminifers.(4) A lighter d18O value(2.11 %) of N. pachyderma(sin.) is recorded in the depth interval of 100–200 m, which is likely related to the isotopically light brines separated out during sea ice freezing. The relatively heavy d18O value(1.68 %–2.68 %, average 2.27 %) in the depth interval of 50–100 m may be influenced by the low salinity water with the relatively heavy d18O value formed during the sea-ice melting in the surface layer.     

Gene duplication plays a major role in gene co-option: Studies into the evolution of the motilin/ghrelin family and their receptors

Extant genes can be modified, or ‘tinkered with’, to provide new roles or new characteristics of these genes. At the genetic level, this often involves gene duplication and specialization of the resulting genes into particular functions. We investigate how ligand-receptor partnerships evolve after gene duplication. While significant work has been conducted in this area, the examination of additional models should help us better understand the proposed models and potentially reveal novel evolutionary pattern...     

菠菜转录因子MYB基因家族的鉴定及表达分析

利用生物信息学手段鉴定了76个具有典型R结构的菠菜转录因子（Spinacia oleracea） MYB,其中包括72条R2R3-MYB基因（2R-MYB）和4条R1R2R3-MYB基因（3R-MYB）。通过生物信息学对菠菜MYB转录因子家族成员的理化性质、染色体定位、结构域序列保守性和系统进化关系进行了分析,结果表明：菠菜MYB家族有32个基因位于染色体正链,另外44个基因位于染色体反链;MYB的DNA结合域中的保守域主要位于两个R重复序列的第二和第三螺旋之间,结合域中每个R重复的第一和第二色氨酸之间的氨基酸序列相对不保守;根据菠菜、拟南芥及甜菜的MYB家族系统进化关系可以推测,菠菜MYB家族中56个成员可以按功能划分为4类,在菠菜的生长发育过程中可能起着重要的调节作用,其余成员中有7个MYB基因可能参与菠菜响应氮素浓度的氮素利用及生长发育进程。     

Molecular phylogenetic evidence that the Chinese viviparid genus Margarya (Gastropoda: Viviparidae) is polyphyletic

We investigated the phylogeny of the viviparid genus Margarya,endemic to Yunnan,China,using two mitochondrial gene fragments(COI and 16S rRNA).The molecular phylogeny based on the combined dataset indicates that Margarya is polyphyletic,as two of the three well-supported clades containing species of Margarya also comprise species from other viviparid genera.In one clade,sequences of four species of Margarya even cluster indiscriminately with those of two species of Cipangopaludina,indicating that the current state of Asian viviparid taxonomy needs to be revised.Additionally,these data suggest that shell evolution in viviparids is complex,as even the large and strongly sculptured shells of Margarya,which are outstanding among Asian viviparids,can apparently be easily converted to simple smooth shells.The molecular data also indicate that the species status of the six extant species of Margarya should be re-assessed.     

拟南芥、水稻和杨树ACTIN家族全基因组分析

鉴定了覆盖拟南芥、水稻和杨树3种模式植物全基因组的20个拟南芥、18个水稻、22个杨树ACTIN蛋白基因,对其染色体定位、基因结构、基因复制等进行了综合分析.并在系统进化分析基础上,将ACTIN基因家族分为12个亚家族,有助于揭示植物ACTIN基因家族的进化历史,为后续ACTIN基因家族的功能提供线索,对研究植物ACTIN基因家族功能和进化上的多样性提供理论基础.