CCCH型锌指蛋白基因以基因家族的形式存在，在信号转导调控、形态发生和逆境应答等诸多生物学过程中起着重要作用。为给该基因的克隆及功能研究提供参考信息，本研究针对二穗短柄草的基因组序列，运用多种生物信息学方法在全基因组范围...CCCH型锌指蛋白基因以基因家族的形式存在，在信号转导调控、形态发生和逆境应答等诸多生物学过程中起着重要作用。为给该基因的克隆及功能研究提供参考信息，本研究针对二穗短柄草的基因组序列，运用多种生物信息学方法在全基因组范围对CCCH型锌指蛋白基因进行了鉴定分析。结果表明，二穗短柄草共有61个含CCCH基序的蛋白质，它们的基因 DNA序列全长825~13 288 bp，内含子数量0~13个，编码区全长498~4 944 bp，编码165~1 007个氨基酸；共检测到145个CCCH基序，以C X8 C X5 C X3 H和C X7 C X5 C X3 H最为常见；基因不均等地分布在5条染色体上，其中2号染色体分布最多，有21个，5号染色体分布最少，仅4个；系统发育分析表明，61个成员可分为8组。展开更多
CCCH(C3 H) Zinc finger(Znf) transcription factors(TFs), as a novel type of Znf gene, regulate the expression of genes by binding to their mRNAs and play important roles in plant growth and development and abiotic stre...CCCH(C3 H) Zinc finger(Znf) transcription factors(TFs), as a novel type of Znf gene, regulate the expression of genes by binding to their mRNAs and play important roles in plant growth and development and abiotic stress resistance.Longan(Dimocarpous longan) is a tropical/subtropical fruit tree of great economic importance in Southeast Asia.However, genomic information on C3 H and their functions in longan are still unknown. In this study, a comprehensive analysis of the longan C3 H(DlC3 H) gene family was carried out. A total of 49 DlC3 H genes in three clades were identified from the longan genome database. Characteristics of the genes were analyzed with respect to gene structure,motif composition, phylogenetic tree and potential functions. The analysis of alternative splicing(AS) events suggested that AS events in DlC3 H genes were related to the transformation from longan non-embryonic to embryonic cultures.Promoter analysis indicated that most of the DlC3 H genes included cis-acting elements associated with hormones and stresses responses. Quantitative real-time PCR(qRT-PCR) analysis indicated that 26 of the 49 DlC3 Hs, which possess methyl jasmonate(MeJA) and abscisic acid(ABA) responsive cis-acting elements, showed differential expression patterns under treatment with ABA, MeJA and their endogenous inhibitors, suggesting that DlC3 Hs might be involved in the ABA and MeJA signaling pathways. The expression profiles of 17 of the 49 DlC3 Hs in non-embryonic callus and three tissues of embryonic cultures showed that only five of the 17 DlC3 Hs had the same expression trends as the FPKM trends in transcriptome data;the expression levels of DlC3 H07/14/16/36/49 in embryogenic callus and DlC3 H04/38 in globular embryos were high, suggesting that they have different functions in embryonic development. Further, we verified that DlC3 H01/03/05/11/19/39 were regulated by sRNAs by a modified 5’ RLM-RACE method. This study provides the first systematic analysis of C3 H genes in longan, and found that C3 H genes may be involved in hormone and stress responses, and somatic embryogenesis. Our preliminary investigation may provide clues to further studies on the characteristics and functions of this family in longan.展开更多
文摘CCCH型锌指蛋白基因以基因家族的形式存在，在信号转导调控、形态发生和逆境应答等诸多生物学过程中起着重要作用。为给该基因的克隆及功能研究提供参考信息，本研究针对二穗短柄草的基因组序列，运用多种生物信息学方法在全基因组范围对CCCH型锌指蛋白基因进行了鉴定分析。结果表明，二穗短柄草共有61个含CCCH基序的蛋白质，它们的基因 DNA序列全长825~13 288 bp，内含子数量0~13个，编码区全长498~4 944 bp，编码165~1 007个氨基酸；共检测到145个CCCH基序，以C X8 C X5 C X3 H和C X7 C X5 C X3 H最为常见；基因不均等地分布在5条染色体上，其中2号染色体分布最多，有21个，5号染色体分布最少，仅4个；系统发育分析表明，61个成员可分为8组。
基金funded by the National Natural Science Foundation of China(31672127 and 31572088)the Scientific Research Foundation of Horticulture College of Fujian Agriculture and Forestry University,China(2018S02)+1 种基金the Construction of Plateau Discipline of Fujian Province,China(102/71201801101)the Project of Fujian Academy of Agricultural Sciences,China(AB2017-4)。
文摘CCCH(C3 H) Zinc finger(Znf) transcription factors(TFs), as a novel type of Znf gene, regulate the expression of genes by binding to their mRNAs and play important roles in plant growth and development and abiotic stress resistance.Longan(Dimocarpous longan) is a tropical/subtropical fruit tree of great economic importance in Southeast Asia.However, genomic information on C3 H and their functions in longan are still unknown. In this study, a comprehensive analysis of the longan C3 H(DlC3 H) gene family was carried out. A total of 49 DlC3 H genes in three clades were identified from the longan genome database. Characteristics of the genes were analyzed with respect to gene structure,motif composition, phylogenetic tree and potential functions. The analysis of alternative splicing(AS) events suggested that AS events in DlC3 H genes were related to the transformation from longan non-embryonic to embryonic cultures.Promoter analysis indicated that most of the DlC3 H genes included cis-acting elements associated with hormones and stresses responses. Quantitative real-time PCR(qRT-PCR) analysis indicated that 26 of the 49 DlC3 Hs, which possess methyl jasmonate(MeJA) and abscisic acid(ABA) responsive cis-acting elements, showed differential expression patterns under treatment with ABA, MeJA and their endogenous inhibitors, suggesting that DlC3 Hs might be involved in the ABA and MeJA signaling pathways. The expression profiles of 17 of the 49 DlC3 Hs in non-embryonic callus and three tissues of embryonic cultures showed that only five of the 17 DlC3 Hs had the same expression trends as the FPKM trends in transcriptome data;the expression levels of DlC3 H07/14/16/36/49 in embryogenic callus and DlC3 H04/38 in globular embryos were high, suggesting that they have different functions in embryonic development. Further, we verified that DlC3 H01/03/05/11/19/39 were regulated by sRNAs by a modified 5’ RLM-RACE method. This study provides the first systematic analysis of C3 H genes in longan, and found that C3 H genes may be involved in hormone and stress responses, and somatic embryogenesis. Our preliminary investigation may provide clues to further studies on the characteristics and functions of this family in longan.
