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The Bioinformatic Analysis on the Plant Isopentenyl Pyrophosphate Isomerase
Xinyi YU, Huiyue JI, Pingping LU, Jiayu ZHOU, Hai LIAO
Bulletin of Botanical Research    2024, 44 (5): 774-782.   DOI: 10.7525/j.issn.1673-5102.2024.05.014
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Isopentenyl pyrophosphate isomerase(IPP) is responsible for the reversible isomerization of isopentenyl pyrophosphate and dimethylallylpyrophosphate(DMAPP), playing an important role in the biosynthesis of downstream terpenoid products. In this paper, 31 IPP genes were identified from genomes of various mono- and dicotyledonous plants such as Oryza sativa and Arabidopsis thaliana by bioinformatics method. Phylogenetic analysis indicated that these IPPs were divided into three clades, in which those from monocotyledon plants formed a monophyletic clade. IPPs within the same clade shared similar domains and might have similar biological functions. The analysis on cis-regulatory elements of O. sativa and A. thaliana IPP genes exhibited multiple response elements such as drought response elements. Finally, quantitative PCR results showed that the expression patterns of IPP transcription levels in O. sativa and A. thaliana were diversified. These above results provided theoretical basis for systematic understanding and further application of IPPs.

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Genetic Diversity Analysis of Tulip Based on SRAP Markers
Douwen QIN, Weiqiang LIU, Jiting TIAN, Nan TANG, Xiuting JU
Bulletin of Botanical Research    2024, 44 (5): 783-792.   DOI: 10.7525/j.issn.1673-5102.2024.05.015
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In order to explore the genetic background of tulip germplasm resources, accurately evaluate and screen excellent germplasm for genetic improvement of tulips, the genetic background of 40 tulip varieties was analyzed by SRAP molecular markers, and their genetic diversity and relationships were clarified, respectively. The results showed that out of 43 pairs of SRAP primers, 21 pairs of polymorphic primers were available for genetic diversity analysis of tulips, and 249 clear and stable bands were amplified in the 40 tulip varieties, of which 245 were polymorphic bands with a polymorphism rate of 98.39%. The genetic similarity index of the 40 tested varieties ranged from 0.502 0 to 0.867 5, and the genetic diversity parameters including the number of alleles(Na*), number of effective alleles(Ne*), Nei’s gene diversity index(H*), Shannon’s information index(I*), and polymorphic information content were 1.981 0, 1.514 9, 0.304 2, 0.460 3, and 0.321 2, resp-ectively, indicating rich genetic diversity in the tested materials. Cluster analysis and principal coordinate analysis showed that the 40 tulip varieties were classified into two major groups, among which ‘Christmas Magical’, ‘Banja Luka’, and ‘Madame Lefeber’ were relatively distant genetic relationships from other varieties and had certain differences in their genetic backgrounds.

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Metabolomics Analysis of Lilium davidii var. unicolor in Response to Autotoxicity Stress
Zhiyuan CHENG, Yanjiang ZHANG, Yue SHEN, Guang LI, Qin CHEN, Jie LI, Yanhong XING
Bulletin of Botanical Research    2024, 44 (5): 793-804.   DOI: 10.7525/j.issn.1673-5102.2024.05.016
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In order to explore the metabolic mechanism of Lanzhou lily(Lilium davidii var. unicolor) in response to autotoxicity stress, one-year-old(Lily1), two-year-old(Lily2) and three-year-old(Lily3) Lanzhou lilies were used as materials, and gas chromatography-mass spectrometry(GC-MS) was used to analyze the metabolomic changes of Lanzhou lily under continuous cropping years, and a total of 124 metabolites were detected and identified. R software was used to normalize the samples, and orthogonal partial least squares discriminant analysis(OPLS-DA) was used to find differential metabolites, and related metabolite pathways were screened for joint analysis. The results showed that there were 16 differential metabolites(lipids, flavonoids, saccharides and phenols) between Lily1 and Lily2, and all of them were up-regulated; and it was significantly enriched in tyrosine metabolism, propionic acid metabolism and flavonoid biosynthetic metabolic pathways. The contents of lipids, flavonoids and saccharides increased, indicating that in the second year of continuous cropping, Lanzhou lily responded to autotoxicity stress by actively synthesizing lipids, flavonoids and saccharides. There were 21 differential metabolites between the metabolomes of Lily1 and Lily3, including one up-regulated metabolite(3-α-mannobiose) and 20 down-regulated metabolite packages (amines, acids, and lipids); and five metabolic pathways were significantly enriched, including biosynthesis of tropane, piperidine and pyridine alkaloids, phosphate and hypophosphite metabolism, lysine degradation, glutathione metabolism and D-amino acid metabolism. There were 21 differential metabolites between Lily2 and Lily3 groups, and the only up-regulated metabolite was 3-α-mannobiose. The results showed that in the third year of continuous cropping of Lanzhou lily, saccharides, as carbohydrates, were directly involved in cell membrane stability, actively responded to autotoxicity stress. The 20 down-regulated metabolites were amines, acids and lipids; only the propionic acid metabolism and flavonoid biosynthetic metabolism pathways were significantly enriched.

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Cloning and Expression Activity Analysis of Rubisco Small Subunit Gene Promoter in Populus × xiaohei
Jiayu CAO, Lina CAO, Qiaoyi ZHANG, Shuang ZHANG, Zhibao HU, Tangrui ZHAO, Zhiru XU, Chunming LI, Xiankui QUAN, Guanjun LIU
Bulletin of Botanical Research    2024, 44 (4): 625-633.   DOI: 10.7525/j.issn.1673-5102.2024.04.014
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Ribulose-1,5-diphosphate carboxylase/oxygenase(Rubisco) is a key enzyme in photosynthesis, in which small subunits(rbcS) are encoded by nuclear genes and mainly expressed in leaves. In this study, the Rubisco small subunit genes PxrbcS1 and PxrbcS2, which are highly expressed in Populus × xiaohei’s leaves, were determined by RT-qPCR technology, and their upstream promoters of 2 240 and 2 174 bp were cloned respectively. The results of promoter element analysis showed that the promoters of PxrbcS1 and PxrbcS2 had multiple elements related to light induced expression, including G-box, MRE and Box4 elements. Plant expression vectors of pBI-121-pPxrbcS1::GUS and pBI-121-pPxrbcS2::GUS were constructed and genetically transformed into 84K poplar(P. alba×P. glandulosa). GUS histochemical staining and qPCR expression analysis showed that the promoters of PxrbcS1 and PxrbcS2 could drive the GUS gene to express in 84K poplar leaves with high specificity. In conclusion, the above results showed that PxrbcS1 and PxrbcS2 promoters with high leaf expression activity were successfully cloned from P.×xiaohei, and the promoters might be applied to the study of gene functions related to plant photosynthesis and genetic operations to improve photosynthesis in plants, including poplars.

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Composition of the Genome Repeat Sequences of Psathyrostachys juncea and Its Distribution on the Chromosomes in Leymus Species
Ying YANG, Yuan LI, Jie CHEN, Bo LIU, Quanwen DOU
Bulletin of Botanical Research    2024, 44 (4): 634-640.   DOI: 10.7525/j.issn.1673-5102.2024.04.015
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Psathyrostachys juncea was considered an important ancestral species of Leymus. The genomic Cot-1 DNA library with highly repeat sequences of Psa. juncea was constructed, and sequenced and characterized, and the results showed that the library could be classified into six types: retrotransposons, transposons, satellite DNA, LZ-NBS-LRR, uncharacterized sequences, and retrotransposon LTR mixed LTR/Copia, and the proportions were 49.5%, 1.0%, 28.7%, 5.9%, 13.9% and 1.0% of the Cot-1 DNA, respectively. Furthermore, two satellite DNAs and five retrotransposon sequences were used as probes, and chromosomes in Psa. junceaLeymus secalinus and L. racemosus were detected by florescence in situ hybridization (FISH). The results showed that the hybridization signals of satellite DNA sequences TaiI-family and pSc250-family were mainly distributed at the ends of chromosomes, and the number of TaiI-family hybridization signals were 20, 16, 7, and 18 in Psa. junceaL. secalinusL. racemosus (PI 531811) and L. racemosus (PI 531812), respectively, and the number of pSc250-family hybridization signals were 17 and 24 in Psa. juncea and L. secalinus, respectively, but no signal was detected in two L. racemosus samples. The distribution of retrotransposon sequences on the chromosomes of three detected species was basically dispersed, and the distribution of chromosome sequences in Leymus species showed a tendency of homogenity. Especially, clone sequences pPj-44 and pPj-28 showed significant differences in signal distribution between Psa. juncea and Leymus species, suggesting sequence expansion and contraction, respectively, during allopolyploidization, and clone sequence pPj-77 only differentiated the hybridization intensity of 10 chromosomes from the rest of the chromosomes in one L. racemosus(PI 531812). The results suggested the repeats of Psa. juncea evolved rapidly and had homogenous diffusion during the polypoid formation of Leymus species and the repeat composition might be significant different among different Leymus species.

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