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1. Genome-wide identification and expression analysis of the polyamine biosynthesis gene in sweet orange (Citrus sinensis) | |||
WuHao,Liu Jihong | |||
Agronomy 28 April 2017 | |||
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Abstract:Polyamines (PAs) are low molecular weight, aliphatic polycations found in the cells of all living organisms. And in plants, a growing number of evidences support that PAs play important roles in abiotic stresses. In this study, a total of 18 polyamine biosynthesis genes which belong to 10 kinds of different polyamine biosynthesis enzymes were isolated from the entire citrus genome and a further analysis including the chromosomal locations, phylogenetic relationships, functional annotations, promoter analysis, and gene structures were performed. Tissue specific expression of these genes was detected in root, stem, leaf, pulp, peel, and callus. The polyamine biosynthesis gene displayed various responses to exogenous polyamines (putrescine, spermidine, spermine) and ABA treatments, and were differentially altered by abiotic stresses, including cold and salt. And the change patterns of three main polyamines during cold stress in leaves and callus were characterized. The comprehensive analysis of polyamine biosynthesis gene is helpful to exploit strategies to improve plant tolerance to multiple environmental stresses. | |||
TO cite this article:WuHao,Liu Jihong. Genome-wide identification and expression analysis of the polyamine biosynthesis gene in sweet orange (Citrus sinensis)[OL].[28 April 2017] http://en.paper.edu.cn/en_releasepaper/content/4730680 |
2. Superoxide dismutase multigene family in longan somatic embryo: a comparison of the CuZn-SODs, Fe- SODs, and Mn-SOD gene structures,splicing, phylogeny, promoters and expression | |||
Lin Yuling,Lai Zhongxiong | |||
Agronomy 04 December 2012 | |||
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Abstract: Superoxide dismutases (SODs) encoded by a multigene family are important antioxidant enzymes that guard against superoxide toxicity. To date, no systematic characterization of this gene family has been conducted and their functions are not completely clear in plant embryos. 20 full-length cDNAs, encoding cytoplasmic CSD1a and DlCSD1b, chloroplast DlCSD2a and DlFSD1a, plastidic DlFSD1b and mitochondrial DlMSD, respectively, were obtained from longan embryogenic callus (EC) by RT-PCR and RACE. Each member contained multiple polyadenylation sites. The genomic structures of DlCSD1a, DlCSD1b, DlCSD2a, DlFSD1a, DlFSD1b and DlMSD genes consisted eight, six, seven, six, seven and five introns, respectively, and their introns lengths varied greatly. In addition, seven variants with different splicing modes were cloned, showing their functional diversity during longan somatic emrbyogenesis (SE). Further, each type of SOD gene had multiple transcription start sites (TSS), and the choice of TSS in SODs only affected the length of the 5'UTR, but not created protein diversity. Meanwhile, the promoters of DlCSD1a, DlCSD2a, DlFSD1a and DlMSD were isolated, which contained lots of cis-acting elements in response to light, GA, auxin, JA, MeJA, dehydration, coldness, wounding, etc. Comprehensive analysis of the expression profiles showed that the different types of SOD showed different spatial and temporal expression modes and played a key role especially at the middle and later developmental stages during longan SE. This study provided the comprehensive analysis of the whole SOD gene family from plants SE for the first time, including cloning of the full-length cDNAs, gene structures, alternatively spliced variants, phylogeny, TSS, isolation of promoters, and expression patterns, and these comparisons could provide a multifaceted view on diverse functions of the SOD isoforms during longan somatic embryos formation. | |||
TO cite this article:Lin Yuling,Lai Zhongxiong. Superoxide dismutase multigene family in longan somatic embryo: a comparison of the CuZn-SODs, Fe- SODs, and Mn-SOD gene structures,splicing, phylogeny, promoters and expression[OL].[ 4 December 2012] http://en.paper.edu.cn/en_releasepaper/content/4498654 |
3. Analyses of global transcriptomics and metabolic network on longan (Dimocarpus longan Lour.) embryogenic callus by Illumina paired-end sequencing | |||
Lai Zhongxiong,Lin Yuling | |||
Agronomy 05 February 2012 | |||
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Abstract:Background: Longan, a famous tropical/subtropical woody fruit in Southeast Asia. However, progress in the molecular mechanism of longan embryogenesis influencing yield and quality is slow by lack of transcriptomic and genomic information. Illumina second generation sequencing is suitable for generating enormous transcript sequences for functional genomic analysis for non-model species with un-sequenced genomes such as longan.Results: Longan EC(embryogenic callus) cDNA library was sequenced by Illumina HiSeq2000. The total of 64,876,258 clean reads with 5.84 Gb nucleotides were assembled into 68,925 unigenes with mean length of 448 bp, and ≥1000 bp unigenes accounted for 8.26 %. Based on BLASTx, 40,634 unigenes had significant similarity with Nr and Swiss-Prot databases. 38,845 and 17,118 annotated unigenes were respectively assigned to GO categories with 43 sub-categories and COG group with 25 sub-groups. Additionally, 17,306 unigenes were assigned to 199 KEGG pathways, which were well represented by Metabolic pathways, Plant-pathogen interaction, Biosynthesis of secondary metabolites, and Genetic information processing. Analyses of the unigenes (≥1000 bp) revealed that not only as many as 328 unigenes concerning embryogenesis-related genes such as EMB, PPR, MEE but also many unigenes concerning reproductive growth such as flowering, gametophyte genesis and fertility, and vegetative growth such as root and shoot growth, expressed in EC, which differed remarkably from the in vivo embryogenesis reported before. Conclusions: This research firstly provided a global transcriptome dataset of longan EC. The results showed that the expressed genes of EC were that much and so various, which suggested that EC almost reflect the whole profile of S.E., even seem to be the epitome of the whole plant on the molecular level. In a word, this dataset provided a new insight into molecular mechanism of embryogenesis in longan even in other plants. | |||
TO cite this article:Lai Zhongxiong,Lin Yuling. Analyses of global transcriptomics and metabolic network on longan (Dimocarpus longan Lour.) embryogenic callus by Illumina paired-end sequencing[OL].[ 5 February 2012] http://en.paper.edu.cn/en_releasepaper/content/4465149 |
4. Selection of reliable reference genes for expression studies by reverse transcription quantitative real-time PCR in litchi under different experimental conditions | |||
ZHONG Haiying,CHEN Jianwen,LI Caiqin,WU Jianyang,CHEN Lei,CHEN Jianye,LU Wangjin,LI Jianguo | |||
Agronomy 21 March 2011 | |||
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Abstract:Reverse transcription quantitative real-time PCR (RT-qPCR), a sensitive technique for quantifying gene expression, depends on the stability of the reference gene(s) used for data normalization. Only a few studies on reference genes have been done in fruit trees and none in litchi. In the present work, seven frequently used candidate reference genes, including actin (ACTIN), glyceraldehyde-3-phosphate-dehydrogenase (GADPH), elongation factor 1-alpha (EF-1α), poly ubiquitin enzyme (UBQ), α-tubulin (TUA), β-tubulin (TUB) and RNA polymerase II transcription factor (RPII) were evaluated for their expression stability in litchi. Seventy-eight samples, including different varieties, tissues, organs, developmental stages and treatments, such as NAA, shading, and girdling plus defoliation, were addressed in this analysis. Our results showed that GAPDH was the most suitable reference gene among all the tested samples, different organs and NAA treatment. ACTIN was stably expressed in varieties and fruit developmental stages. RPII and UBQ exhibited the better expression stability in tissues. EF-1α was the most stable gene in shading and girdling plus defoliation treatments. Moreover, using combination of two genes as reference genes might improve the reliability of gene expression by RT-qPCR in litchi. The better combination was GAPDH + EF-1α or GAPDH + ACTIN for all the examined samples. In addition, the validated reference genes were further relied when used to quantify the expression of an interested gene, LcARF13 under different experimental conditions. These results firstly provide guidelines for reference genes selection under different experimental conditions and a foundation for more accurate and widespread use of RT-qPCR in litchi. | |||
TO cite this article:ZHONG Haiying,CHEN Jianwen,LI Caiqin, et al. Selection of reliable reference genes for expression studies by reverse transcription quantitative real-time PCR in litchi under different experimental conditions[OL].[21 March 2011] http://en.paper.edu.cn/en_releasepaper/content/4417495 |
5. Isolation and Characterization of Homolog PtLEAFY promoter in Trifoliate Orange (Poncirus trifoliata L. Raf. ) | |||
Mei Li,Zhang Jinzhi,Li Zhimin,Hu Chungen | |||
Agronomy 19 January 2009 | |||
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Abstract:Abstract The long juvenile phase for 6 to 8 years in woody plants has become a serious obstacle for genetic analysis and breeding practice. In order to understand the flower transition mechanism in woody plants, DNA sequence of a LEAFY homologue in trifoliate orange (Poncirus trifoliata L. Raf.) was isolated and characterized. A chimeric expression construct PtLEAFY::GUS indicated the promoter from woody plant acted its role in Arabidopsis thiliana from 7-day old shoot apical meristem to rosette leaves. These findings concluded that PtLEAFY promoter from woody plants had immediate function in annual plants and may potential provide the specific promoter of shoot apical meristem . | |||
TO cite this article:Mei Li,Zhang Jinzhi,Li Zhimin, et al. Isolation and Characterization of Homolog PtLEAFY promoter in Trifoliate Orange (Poncirus trifoliata L. Raf. )[OL].[19 January 2009] http://en.paper.edu.cn/en_releasepaper/content/28042 |
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