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| 1 | Profiling of the transcriptome of Porphyra yezoensis with Solexa sequencing technology显示文摘With high-throughput Solexa sequencing technology,we profiled Porphyra yezoensis transcriptomes from 8 different samples. More than 1200 megabases from 13333334 quality paired-end reads were generated,which were assembled into 31538 unigenes. Blast analysis showed that 56.7%unigenes were novel,which represented the specific genes of Porphyra and/or rhodophytes. Several hundreds of unigenes related to stress tolerance were discovered,including genes related to desiccation-(211) and high light-tolerance(31) ,flavonoid biosynthesis(10) ,reactive oxygen scavenging(48) and other stress-tolerance processes(208) ,which indicated there existed complex and diversity modes of stress tolerance in this species.A complete set of essential genes involved in the C3-(57) and C4-(44) carbon fixation pathway(except pyruvate phosphate dikinase) were discovered,which not only proved that they were actively transcribed but also clearly outlined the panoptic view of carbon fixation in Porphyra.Moreover,by statistically analyzing the types,proportions and frequencies of the interspersed repeats(TEs) and simple sequence repeats(SSRs) ,we discovered that the top three types of TEs were all retrotransposons and the trinucleotide was the absolute predominant type among SSRs,promoting our understanding of structural characteristics of the transcriptome.This study substantially improved the global view of the Porphyra genome and provided a valuable resource for future research. | YANG Hui MAO YunXiang KONG FanNa YANG GuanPin MA Fei WANG Li | 2011 | Chinese Science Bulletin2011，56，20： | 13 |
| 2 | Genome editing mediated by SpCas9 variants with broad non-canonical PAM compatibility in plants显示文摘Streptococcus pyogenes Cas9(SpCas9)is the most widely used genome editing tool in plants.The editing induced by SpCas9 strictly requires a canonical NGG protospacer-adjacent motif(PAM),significantly limiting its scope of application.Recently,five SpCas9 variants,SpCas9-NRRH,SpCas9-NRCH,SpCas9-NRTH,SpG,and SPRY,were developed to recognize non-canonical PAMs in human cells.In this study,these variants were engineered for plant genome editing,and their targeted mutagenesis capabilities were comprehensively examined at various canonical and non-canonical PAM sites in rice(Oryza sativa)by stable transformation.Moreover,both cytosine base editors using a rat APOBEC1 or a human APO-BEC3a and adenine base editors using a directly evolved highly compatible TadA*-8e deaminase were developed from these SpCas9 variants.Our results demonstrated that the developed SpCas9 variantsbased base editors readily generated conversions between C.G and T.A in the target sites with noncanonical PAMs in transgenic rice lines.Collectively,the toolbox developed in this study substantially expands the scope of SpCas9-mediated genome editing and will greatly facilitate gene disruption and precise editing in plants. | Juan Li Rongfang Xu Ruiying Qin Xiaoshuang Liu Fanna Kong Pengcheng Wei | 2021 | Molecular Plant2021，14，2： | 6 |
| 3 | Generation and analysis of expressed sequence tags from the salt-tolerant eelgrass species, Zostera marina显示文摘Zostera marina, a monocotyledonous angiosperm, is one of the most important seagrass species. To investigate the salt-tolerance mechanism and discover salt-tolerant genes in Z. marina, a cDNA library was constructed. Single-pass sequencing of the 5'ends of 4 081 clones yielded 4 002 high quality expressed sequence tags (ESTs), which were assembled into 241 contigs and 1 673 singletons, representing 1 914 unigenes. The average length of the ESTs was 582 bp, with sizes ranging from 100-1 500 bp. Basic Local Alignment Search Tool (BLASTX) analysis revealed that 1 664 unigenes had significant homology to known genes in the National Center for Biotechnology Information (NCBI) non-redundant (nr) database (E-value 5-10). Among them, the two most abundant genes encoded metallothionein (157 ESTs) and chlorophyll a/b-binding protein (38 ESTs), accounting for 7.1% and 1.7% of the total ESTs, respectively. Using Kyoto Encyclopedia of Genes and Genomes (KEGG), 1 462 unigenes were assigned to 1 161 pathways (E-value 5-10). A total of 938 unigenes were assigned Gene Ontology (GO) terms based on the GO hierarchy analysis, and InterProScan searches recognized 1 003 InterPro families. Three genes for metallothionein in Z. marina that belonged to Class II was identified. Results of this study will improve understanding of the molecular mechanisms of saline tolerance in Z. marina. | KONG Fanna ZHOU Yang SUN Peipei LIU Limin MAO Yunxiang | 2013 | Acta Oceanologica Sinica2013，32，8： | 5 |
| 4 | Development of an efficient plant dual cytosine and adenine editor显示文摘An enhanced CDA-like(eCDAL)was established from Japanese lamprey CDA1-like 4 to achieve a high editing frequency in a broad region as a C-terminal cytosine base editors(CT-CBE).Then,a novel plant dual-base editor version1(pDuBE1)was developed by integrating TadA-8e into eCDAL.The editing efficiency of pDuBE1 could reach to 87.6%,with frequencies of concurrent A-to-G and C-to-T conversions as high as 49.7%in stably transformed plant cells.Our results showed that pDuBE1 could mediate robust dual editing in plant genome,providing a powerful manipulation tool for precise crop breeding and screening platforms for in planta direct evolution. | Rongfang Xu Fanna Kong Ruiying Qin Juan Li Xiaoshuang Liu Pengcheng Wei | 2021 | Journal of Integrative Plant Biology2021，63，9： | 4 |
| 5 | Cloning and Analysis of Calmodulin Gene from Porphyra yezoensis Ueda (Bangiales, Rhodophyta)显示文摘In order to understand the mechanisms of signal transduction and anti-desiccation mechanisms of Porphyra yezoensis, cDNA and its genomic sequence of Calmodulin gene (CaM) was cloned by the technique of polymerase chain reaction (PCR) based on the analysis of P. yezoensis ESTs from dbEST database. The result shows that the full-length cDNA of CaM consists of 603 bps including an ORF encoding for 151 amino acids and a terminate codon UGA, while the length of genomic sequence is 1231 bps including 2 exons and 1 intron. The average GC content of the coding region is 58.77%, while the GC content of the third position of this gene is as high as 82.23%. Four Ca2+ binding sites (EF-hand) are found in this gene. The predicted molecular mass of the deduced peptide is 16688.72 Da and the pI is 4.222. By aligning with known CaM genes, the similarity of CaM gene sequence with homologous genes in Chlamydomonas incerta and Chlamydomonas reinhardtii is 72.7% and 72.2% respectively, and the similarity of the deduced amino acid sequence of CaM gene with homologous genes in C. incerta and C. reinhardtii are both 71.5%. This is the first report on CaM from a species of Rhodophyta. | WANG Mengqiang MAO Yunxiang ZHUANG Yunyun KONG Fanna SUI Zhenghong | 2009 | Journal of Ocean University of China2009，8，3： | 3 |
| 6 | Identification of Light-Harvesting Chlorophyll a/b-Binding Protein Genes of Zostera marina L.and Their Expression Under Different Environmental Conditions显示文摘Photosynthesis includes the collection of light and the transfer of solar energy using light-harvesting chlorophyll a/b-binding(LHC) proteins.In high plants,the LHC gene family includes LHCA and LHCB sub-families,which encode proteins constituting the light-harvesting complex of photosystems I and II.Zostera marina L.is a monocotyledonous angiosperm and inhabits submerged marine environments rather than land environments.We characterized the Lhca and Lhcb gene families of Z.marina from the expressed sequence tags(EST) database.In total,13 unigenes were annotated as Zm Lhc,6 in Lhca family and 7 in Zm Lhcb family.Zm LHCA and Zm LHCB contained the conservative LHC motifs and amino acid residues binding chlorophyll.The average similarity among mature Zm LHCA and Zm LHCB was 48.91% and 48.66%,respectively,which indicated a high degree of divergence within Zm LHChc gene family.The reconstructed phylogenetic tree showed that the tree topology and phylogenetic relationship were similar to those reported in other high plants,suggesting that the Lhc genes were highly conservative and the classification of Zm Lhc genes was consistent with the evolutionary position of Z.marina.Real-time reverse transcription(RT) PCR analysis showed that different members of Zm Lhca and Zm Lhcb responded to a stress in different expression patterns.Salinity,temperature,light intensity and light quality may affect the expression of most Zm Lhca and Zm Lhcb genes.Inorganic carbon concentration and acidity had no obvious effect on Zm Lhca and Zm Lhcb gene expression,except for Zm Lhca6. | KONG Fanna ZHOU Yang SUN Peipei CAO Min LI Hong MAO Yunxiang | 2016 | Journal of Ocean University of China2016，15，1： | 3 |
| 7 | A bestrophin-like protein modulates the proton motive force across the thylakoid membrane in Arabidopsis显示文摘During photosynthesis, photosynthetic electron transport generates a proton motive force(pmf) across the thylakoid membrane, which is used for ATP biosynthesis via ATP synthase in the chloroplast. The pmf is composed of an electric potential(△Ψ) and an osmotic component(△pH).Partitioning between these components in chloroplasts is strictly regulated in response to fluctuating environments.However, our knowledge of the molecular mechanisms that regulate pmf partitioning is limited. Here, we report a bestrophin-like protein(At Best), which is critical for pmf partitioning. While the Dp H component was slightly reduced in atbest, the △Ψ component was much greater in this mutant than in the wild type, resulting in less efficient activation of nonphotochemical quenching(NPQ) upon both illumination and a shift from low light to high light. Although no visible phenotype was observed in the atbest mutant in the greenhouse, this mutant exhibited stronger photoinhibition than the wild type when grown in the field. At Best belongs to the bestrophin family proteins, which are believed to function as chloride(Cl^-) channels. Thus, our findings reveal an Researimportant Cl^- channel required for ion transport and homeostasis across the thylakoid membrane in higher plants. These processes are essential for fine-tuning photosynthesis under fluctuating environmental conditions. | Zhikun Duan Fanna Kong Lin Zhang Wenjing Li Jiao Zhang Lianwei Peng | 2016 | Journal of Integrative Plant Biology2016，58，10： | 2 |
| 8 | R-ISSR as a new tool for genomic fingerprinting, mapping, and gene tagging显示文摘 | Chunjiang Ye Zhanwang Yu Fanna Kong Suowei Wu Bin Wang | 2005 | Plant Molecular Biology Reporter2005，，2： | 1 |
| 9 | Cloning and characterization of the DHDPS gene encoding the lysine biosyn- thetic enzyme dihydrodipocolinate synthase from Zizania latifolia (Griseb) 显示文摘 | Kong Fanna Jiang Shaomei Meng Xiangbing | 2009 | Plant Mol Biol Rep2009，27，2： | 1 |
| 10 | Cloning, characterization and expression of the gene encoding polygalacturonase-inhibiting proteins (PGIPs) of peach [ prunus persica (L.) Batch]显示文摘 | Fengshan Liang Kaichun Zhang Chunjiang Zhou Fanna Kong Jun Li Bin Wang | 2004 | Plant Science2004，，2： | 1 |
| 11 | Genetic anal- ysis of Porphyra yezoensis using microsatellite markers 显示文摘 | KONG Fanna MAO Yunxiang YANG Hui | 2009 | Plant Mol Biol Rep2009，27，4： | 1 |
| 12 | Development of organelle single nucleotide polymorphism (SNP) markers and their application for the identification of cytoplasmic inheritance patterns in Pyropia yezoensis (Bangiales,Rhodophyta)显示文摘The genus Pyropia contains several important cultivated species.Genetic research in nori species has mainly focused on the cell nucleus,with few studies on organelles(chloroplast and mitochondria).Due to the high copy numbers of organelles in cells,which influence the development and traits of algae,it is necessary to study their genetic mechanism.In this study,the marine red alga Pyropia yezoensis,an important economic macroalga,was selected as the study object.To investigate organelle(chloroplast and mitochondria)inheritance in P.yezoensis,the wild type RZ(maternal strain)was crossed with the red mutant HT(paternal strain)and 30 color-sectors from 11 F1 gametophytic blades were examined.The complete chloroplast and mitochondrial genomes of the red mutant(HT)were assembled for the first time.One reliable and stable single nucleotide polymorphism(SNP)loci filtrated by bioinformatics analysis was used as a molecular marker for chloroplast and mitochondrial DNA,respectively,in subsequent experiments.PCR amplification and sequence analysis showed that the haplotypes of color-sectors detected were consistent with those of the maternal parent,confirming that both chloroplast and mitochondrial genomes were inherited maternally in P.yezoensis.The inheritance pattern of organelles in P.yezoensis can be used to guide the hybridization and breeding of nori.Additionally,the organelle SNP markers developed in this study can be applied in subsequent genetic research. | Lu WANG Junhao WANG Yunke ZHU Zhengcai CUI Fanna KONG Xianghai TANG Yunxiang MAO | 2021 | Journal of Oceanology and Limnology2021，39，4： | 0 |
| 13 | Morphology and Molecular Identification of Ulva Forming Green Tides in Qingdao,China显示文摘Green tides are caused by the proliferation of chlorophytes under suitable hydrographic conditions.These blooms lead to environmental degradation and negatively impact the waters and seagrass beds,as well as fishing and other recreational activities in the bay.A comprehensive ecological understanding of the bloom dynamics,including the origin and persistence,is needed to foster management decisions.The algae in the great majority of green tide blooms usually belong to two genera of Ulvophyceae,Ulva and Enteromorpha.Ulva has been observed more often in recent years.In China,green tides occurred for the first time in the middle area of the Yellow Sea in 2007,and a large-scale algae blooming broke out in the middle and southern areas of the Yellow Sea in late May 2008.We identified them as Ulva prolifera by comparative analysis of the rDNA internal transcribed spacer 1 (ITS1),5.8S and ITS2 sequences in combination with microscopic observation.Morphological differences were found between the free-floating algae and the attached thalli.Various reproduction patterns of the free-floating algae include sexual,asexual and vegetative propagations,which played important roles in the long-term green tide persistence in China.The ITS sequences of the blooming algae were identical to those of the samples from the Lianyungang sea area but were different from the attached samples from the Qingdao sea area.The results infer that the blooms are originated from other sea areas rather than from the local attached populations. | KONG Fanna MAO Yunxiang CUI Fujun ZHANG Xingkui GAO Zhen | 2011 | Journal of Ocean University of China2011，10，1： | 0 |
| 14 | Construction of high-density genetic linkage map of Pyropia yezoensis(Bangiales,Rhodophyta)and identifi cation of red color trait QTLs in the thalli显示文摘Pyropia yezoensis is an important macroalga because of its extensive global distribution and economic importance.Color is an important trait in the thalli of P.yezoensis,it is also an effective marker to identify the hybridization in genetic breeding.In this study,a high-density genetic linkage map was constructed based on high-throughput single nucleotide polymorphism(SNP)markers,and used for analyzing the quantitative trait loci(QTLs)of red color trait in the thalli of P.yezoensis.The conchospore undergoes meiosis to develop into an ordered tetrad,and each cell has a haploid phenotype and can grow into a single individual.Based on this theory,F1 haploid population was used as the mapping population.The map included 531 SNP markers,394.57 cM long on average distance of 0.74 cM.Collinear analysis of the genetic linkage map and the physical map indicated that the coverage between the two maps was 79.42%.Furthermore,QTL mapping identified six QTLs for the chromosomal regions associated with the red color trait of the thalli.The value of phenotypic variance explained(PVE)by an individual QTL ranged from 4.71%-63.11%.And QTL qRed-1-1,with a PVE of 63.11%,was considered the major QTL.Thus,these data may provide a platform for gene and QTL fine mapping,and marker-assisted breeding in P.yezoensis in the future. | Lu WANG Kuipeng XU Xianghai TANG Junhao WANG Fanna KONG Yunxiang MAO | 2021 | Journal of Oceanology and Limnology2021，39，3： | 0 |
| 15 | Characterization of the squalene-rich Botryococcus braunii Abt02 strain显示文摘Botryococcus braunii is widely studied due to its high hydrocarbon content. In this study, B . braunii Abt02 was subjected to several analyses, including cytological observation, hydrocarbon composition analysis by gas chromatography mass spectrometry (GC-MS), phylogenetic identification using known races (A, B and L) of B . braunii strains based on their 18S rDNA sequences, and qPCR-based investigation of transcript accumulation levels of hydrocarbon biosynthesis-related enzymes (DXS, MCS, DLS, SQS) during diff erent growth phases (lag phase, log phase, early stationary growth phase, late stationary growth phase) under nitrogen-replete and nitrogen-depleted growth conditions, respectively. Based on cytological observation and on the 18S rDNA phylogenetic analysis, strain Abt02 was assigned to race B. Analysis of the strain’s chemical composition showed that the B . braunii Abt02 contained high levels of hydrocarbons, which accounted for 43.75% of the cell’s dry weight. Of these hydrocarbons, squalene and its derivatives accounted for up to 87.54%. In addition, all four enzymes investigated were expressed at higher levels during the log growth phase under nitrogen depleted conditions than under nitrogen replete conditions. | CAO Min ZHANG Fangfang MAO Yunxiang KONG Fanna WANG Dongmei | 2019 | Journal of Oceanology and Limnology2019，37，2： | 0 |
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