目的:探究正常肺组织、肺腺癌癌旁和肺腺癌中所有基因的表达水平趋势,寻找特征性基因并进行实验验证。方法:下载加州大学圣克鲁斯分校(University of California,Santa Cruz,UCSC)数据中心中癌症基因组图谱(the cancer genome atlas,TC...目的:探究正常肺组织、肺腺癌癌旁和肺腺癌中所有基因的表达水平趋势,寻找特征性基因并进行实验验证。方法:下载加州大学圣克鲁斯分校(University of California,Santa Cruz,UCSC)数据中心中癌症基因组图谱(the cancer genome atlas,TCGA)和基因型-组织表达项目(genotype-tissue expression,GTEX)的整合数据,采用R语言分析所有基因的表达趋势,寻找特征性基因,提取癌旁和肿瘤组织共同高表达的基因集,进行GO和KEGG分析富集情况,鉴定最显著的通路中在肺组织和癌旁及肺腺癌中变化最大的基因。通过细胞生物学实验验证候选基因在肿瘤中的作用。结果:整合数据显示存在一群正常组织中低表达但在肺腺癌癌旁和肺腺癌中高表达的基因(DEGS2、PIGY、FUCA、GM2A),GO分析显示该基因群富集最显著的通路是膜脂质代谢过程,对该通路基因和符合趋势的基因取交集,发现DEGS2在癌旁和癌组织中升高最明显,升高倍数达3.27倍。实验证实,敲除DEGS224 h后细胞迁移能力下降,72 h后细胞活性下降55.0%。结论:DEGS2在癌旁和肺腺癌中呈高表达,其表达能促进肺腺癌的增殖和迁移,从而进一步驱动从癌旁组织到癌的发展。展开更多
【目的】绿原酸是杜仲叶片质量评价的指标性成分,具有抗菌消炎、抗氧化、抗肿瘤及抗肝炎等多种药用价值。本研究在鉴定和挖掘参与调控杜仲叶片绿原酸生物合成的代谢通路及关键基因,为进一步深入解析杜仲叶片绿原酸形成的分子机制提供参...【目的】绿原酸是杜仲叶片质量评价的指标性成分,具有抗菌消炎、抗氧化、抗肿瘤及抗肝炎等多种药用价值。本研究在鉴定和挖掘参与调控杜仲叶片绿原酸生物合成的代谢通路及关键基因,为进一步深入解析杜仲叶片绿原酸形成的分子机制提供参考。【方法】以内蒙古自治区包头市4月、7月和10月的杜仲叶片为材料,通过高效液相色谱法(HPLC)测定不同时期的杜仲叶片绿原酸含量,利用转录组测序的方法鉴定差异表达基因。【结果】杜仲叶片绿原酸含量从4月至7月再到10月,随着叶片发育呈现先上升后下降趋势。通过转录组测序共得到58.06 Gb Clean data,鉴定到11 689个基因,在T1 vs T2、T1 vs T3和T2 vs T3 3组比较中,下调表达基因数量均高于上调表达基因数量。KEGG富集分析和GO富集分析,均有绿原酸合成相关富集。Kmeans趋势表达将基因划分为10个模块,其中Class4、Class8和Class10中的基因表达量变化趋势与绿原酸含量变化趋势相一致,从Class4、Class8和Class10中鉴定出2个酶,9个基因与绿原酸生物合成相关,实时荧光定量PCR(qRT-PCR)结果与RNA-seq结果一致。【结论】杜仲叶片中绿原酸含量随着叶片发育呈现先增加后降低趋势。展开更多
【目的】探究蓝鸟睡莲切花在瓶插过程中的花茎生理变化并进行转录组测序分析,为揭示睡莲在瓶插过程中花茎弯曲的分子机制及培育抗茎秆弯曲睡莲品种提供理论依据。【方法】以蓝鸟睡莲为试验材料进行切花瓶插,每天固定时间测定瓶插睡莲的...【目的】探究蓝鸟睡莲切花在瓶插过程中的花茎生理变化并进行转录组测序分析,为揭示睡莲在瓶插过程中花茎弯曲的分子机制及培育抗茎秆弯曲睡莲品种提供理论依据。【方法】以蓝鸟睡莲为试验材料进行切花瓶插,每天固定时间测定瓶插睡莲的生理指标,根据睡莲弯茎程度分为4个时期,截取花茎4个时期弯茎样本(分别标记为Dor‐sal_1、Dorsal_2、Dorsal_3和Dorsal_4),测定不同样本中可溶性糖和淀粉含量,基于转录组测序技术筛选差异表达基因(DEG),对DEGs进行GO功能注释分析、KEGG信号通路富集分析和K-means分析,挖掘导致睡莲切花弯茎的关键代谢通路及关键基因,并通过实时荧光定量PCR验证基因相对表达量与转录组数据的一致性。【结果】睡莲的吸水量、失水量、水分平衡值均呈先上升后下降的变化趋势,睡莲花茎的平均伸长量为4.45 cm,占原始长度的17.8%。Dorsal_1和Dorsal_2样本中淀粉含量无显著差异(P>0.05),但二者均显著高于Dorsal_3和Dorsal_4(P<0.05,下同),且Dorsal_3样本中淀粉含量显著高于Dorsal_4。Dorsal_1 vs Dorsal_2组、Dorsal_1 vs Dorsal_3组、Dorsal_1 vs Dorsal_4组、Dorsal_2 vs Dorsal_3组、Dorsal_3 vs Dorsal_4组DEGs数分别为5149、6903、5483、2456和269个,其中下调表达基因分别为2826、3822、3068、1313和113个,上调表达基因分别为2323、3081、2415、1143和156个。4个不同弯茎时期样本间共有112个DEGs。GO功能注释和KEGG信号通路富集分析结果显示,睡莲弯茎中DEGs主要富集在与光合作用、细胞壁合成和植物激素与信号转导等相关的生物途径中。K-means分析结果显示,DEGs被聚类为9类(Class 1~Class 9),通过Class 1与Venn图共筛选出25个DEGs,Class 5筛选到19个调控睡莲弯茎相关基因。实时荧光定量PCR验证结果显示,DEGs相对表达量与转录组数据基因表达基本一致。【结论】水分、淀粉和可溶性糖含量以及光照响应、植物激素、细胞壁形成与分解等因素的相互作用共同导致睡莲弯茎。推测与生长素及细胞壁结构相关的基因是影响睡莲弯茎的关键基因群。展开更多
[目的]探究枸杞果实不同发育时期转录水平上的基因表达变化,筛选类胡萝卜素生物合成相关差异表达基因(DEGs),为揭示枸杞果实在不同发育阶段类胡萝卜素含量差异的分子机制及枸杞分子育种提供理论参考。[方法]通过Illumina NovaSeq 6000...[目的]探究枸杞果实不同发育时期转录水平上的基因表达变化,筛选类胡萝卜素生物合成相关差异表达基因(DEGs),为揭示枸杞果实在不同发育阶段类胡萝卜素含量差异的分子机制及枸杞分子育种提供理论参考。[方法]通过Illumina NovaSeq 6000高通量测序技术,分析青果期(YD)、转色期(ZD)和成熟期(XD)的杞鑫1号枸杞果实转录谱,以|log_(2)Fold Change|≥1,且错误发现率(FDR)<0.05为标准筛选DEGs,结合KEGG、GO、KOG、NR等数据库注释信息和PubMed数据库文献,筛选出与类胡萝卜素代谢合成相关的DEGs。测定不同发育期枸杞果实类胡萝卜素含量。采用实时荧光定量PCR验证8个DEGs转录组数据的可靠性。[结果]YD vs ZD组、YD vs XD组和ZD vs XD组中DEGs总数分别为6480、1497和7781个,其中分别有3946、827和2888个DEGs上调表达,2534、670和4893个下调表达。3个果实发育期共有234个DEGs。GO功能注释结果显示,在YD vs ZD组、YD vs XD组和ZD vs XD组,分别有1700、579和1657个DEGs被注释到生物过程(BP)、细胞组分(CC)和分子功能(MF)三大功能类别。3个比较组的KEGG信号通路均主要集中在代谢途径和次生代谢物生物合成过程中。从YD vs ZD组、YD vs XD组和ZD vs XD组3个比较组中分别挖掘到50、18和68个与功效成分相关的DEGs,参与类胡萝卜素合成途径的DEGs有34个,其中在YD vs ZD组、YD vs XD和ZD vs XD组分别富集到12、5和17个。杞鑫1号枸杞3个发育时期的果实均含有类胡萝卜素,随杞鑫1号枸杞果实发育,类胡萝卜素含量整体呈先下降后增加的变化趋势,YD、ZD和XD果实中类胡萝卜素含量分别为0.35、0.25和1.20 mg/g。PSY、PDS、ZDS、CHYB和Z-ISO 5个类胡萝卜素合成途径关键酶基因在YD和XD的表达量均高于100。类胡萝卜素合成代谢的关键酶基因PSY、PDS、ZDS和CHYB高表达,而类胡萝卜素分解代谢相关酶基因ZEP和NCED低表达。8个DEGs在杞鑫1号果实中的相对表达量与转录组测序结果基本一致。[结论]在杞鑫1号枸杞青果期和成熟期,类胡萝卜代谢途径中类胡萝卜素合成途径的关键酶基因PSY、PDS、ZDS、CHYB高水平表达而类胡萝卜素分解代谢相关的基因ZEP、NCED表达量较低,这些基因协同促进杞鑫1号枸杞成熟期果实中玉米黄质、β-胡萝卜素等类胡萝卜素的大量合成。展开更多
Rapid growth is an innovative trait of woody bamboos that has been widely studied.However,the genetic basis and evolution of this trait are poorly understood.Taking advantage of genomic resources of 11 representative ...Rapid growth is an innovative trait of woody bamboos that has been widely studied.However,the genetic basis and evolution of this trait are poorly understood.Taking advantage of genomic resources of 11 representative bamboos at different ploidal levels,we integrated morphological,physiological,and transcriptomic datasets to investigate rapid growth.In particular,these bamboos include two large-sized and a small-sized woody species,compared with a diploid herbaceous species.Our results showed that gibberellin A1 was important for the rapid shoot growth of the world's largest bamboo,Dendrocalamus sinicus,and indicated that two gibberellins(GAs)-related genes,KAO and SLRL1,were key to the rapid shoot growth and culm size in woody bamboos.The expression of GAs-related genes exhibited significant subgenome asymmetry with subgenomes A and C demonstrating expression dominance in the large-sized woody bamboos while the generally submissive subgenomes B and D dominating in the small-sized species.The subgenome asymmetry was found to be correlated with the subgenome-specific gene structure,particularly UTRs and core promoters.Our study provides novel insights into the molecular mechanism and evolution of rapid shoot growth following allopolyploidization in woody bamboos,particularly via subgenome asymmetry.These findings are helpful for understanding of how polyploidization in general and subgenome asymmetry in particular contributed to the origin of innovative traits in plants.展开更多
Global warming is primarily characterized by asymmetric temperature increases,with greater temperature rises in winter/spring and at night compared to summer/autumn and the daytime.We investigated the impact of winter...Global warming is primarily characterized by asymmetric temperature increases,with greater temperature rises in winter/spring and at night compared to summer/autumn and the daytime.We investigated the impact of winter night warming on the top expanded leaves of the spring wheat cultivar Yangmai 18 and the semi-winter wheat cultivar Yannong 19 during the 2020-2021 growing season.Results showed that the night-time mean temperature in the treatment group was 1.27°C higher than the ambient temperature,and winter night warming increased the yields of both wheat cultivars,the activities of sucrose synthase and sucrose phosphate synthase after anthesis,and the biosynthesis of sucrose and soluble sugars.Differentially expressed genes(DEGs)were identified using criteria of P-value<0.05 and fold change>2,and they were subjected to Gene Ontology(GO)annotation and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analyses.Genes differentially expressed in wheat leaves treated with night warming were primarily associated with starch and sucrose metabolism,amino acid biosynthesis,carbon metabolism,plant hormone signal transduction,and amino sugar and nucleotide sugar metabolism.Comparisons between the groups identified 14 DEGs related to temperature.These results highlight the effects of winter night warming on wheat development from various perspectives.Our results provide new insights into the molecular mechanisms of the response of wheat to winter night warming and the candidate genes involved in this process.展开更多
文摘目的:探究正常肺组织、肺腺癌癌旁和肺腺癌中所有基因的表达水平趋势,寻找特征性基因并进行实验验证。方法:下载加州大学圣克鲁斯分校(University of California,Santa Cruz,UCSC)数据中心中癌症基因组图谱(the cancer genome atlas,TCGA)和基因型-组织表达项目(genotype-tissue expression,GTEX)的整合数据,采用R语言分析所有基因的表达趋势,寻找特征性基因,提取癌旁和肿瘤组织共同高表达的基因集,进行GO和KEGG分析富集情况,鉴定最显著的通路中在肺组织和癌旁及肺腺癌中变化最大的基因。通过细胞生物学实验验证候选基因在肿瘤中的作用。结果:整合数据显示存在一群正常组织中低表达但在肺腺癌癌旁和肺腺癌中高表达的基因(DEGS2、PIGY、FUCA、GM2A),GO分析显示该基因群富集最显著的通路是膜脂质代谢过程,对该通路基因和符合趋势的基因取交集,发现DEGS2在癌旁和癌组织中升高最明显,升高倍数达3.27倍。实验证实,敲除DEGS224 h后细胞迁移能力下降,72 h后细胞活性下降55.0%。结论:DEGS2在癌旁和肺腺癌中呈高表达,其表达能促进肺腺癌的增殖和迁移,从而进一步驱动从癌旁组织到癌的发展。
文摘【目的】绿原酸是杜仲叶片质量评价的指标性成分,具有抗菌消炎、抗氧化、抗肿瘤及抗肝炎等多种药用价值。本研究在鉴定和挖掘参与调控杜仲叶片绿原酸生物合成的代谢通路及关键基因,为进一步深入解析杜仲叶片绿原酸形成的分子机制提供参考。【方法】以内蒙古自治区包头市4月、7月和10月的杜仲叶片为材料,通过高效液相色谱法(HPLC)测定不同时期的杜仲叶片绿原酸含量,利用转录组测序的方法鉴定差异表达基因。【结果】杜仲叶片绿原酸含量从4月至7月再到10月,随着叶片发育呈现先上升后下降趋势。通过转录组测序共得到58.06 Gb Clean data,鉴定到11 689个基因,在T1 vs T2、T1 vs T3和T2 vs T3 3组比较中,下调表达基因数量均高于上调表达基因数量。KEGG富集分析和GO富集分析,均有绿原酸合成相关富集。Kmeans趋势表达将基因划分为10个模块,其中Class4、Class8和Class10中的基因表达量变化趋势与绿原酸含量变化趋势相一致,从Class4、Class8和Class10中鉴定出2个酶,9个基因与绿原酸生物合成相关,实时荧光定量PCR(qRT-PCR)结果与RNA-seq结果一致。【结论】杜仲叶片中绿原酸含量随着叶片发育呈现先增加后降低趋势。
文摘【目的】探究蓝鸟睡莲切花在瓶插过程中的花茎生理变化并进行转录组测序分析,为揭示睡莲在瓶插过程中花茎弯曲的分子机制及培育抗茎秆弯曲睡莲品种提供理论依据。【方法】以蓝鸟睡莲为试验材料进行切花瓶插,每天固定时间测定瓶插睡莲的生理指标,根据睡莲弯茎程度分为4个时期,截取花茎4个时期弯茎样本(分别标记为Dor‐sal_1、Dorsal_2、Dorsal_3和Dorsal_4),测定不同样本中可溶性糖和淀粉含量,基于转录组测序技术筛选差异表达基因(DEG),对DEGs进行GO功能注释分析、KEGG信号通路富集分析和K-means分析,挖掘导致睡莲切花弯茎的关键代谢通路及关键基因,并通过实时荧光定量PCR验证基因相对表达量与转录组数据的一致性。【结果】睡莲的吸水量、失水量、水分平衡值均呈先上升后下降的变化趋势,睡莲花茎的平均伸长量为4.45 cm,占原始长度的17.8%。Dorsal_1和Dorsal_2样本中淀粉含量无显著差异(P>0.05),但二者均显著高于Dorsal_3和Dorsal_4(P<0.05,下同),且Dorsal_3样本中淀粉含量显著高于Dorsal_4。Dorsal_1 vs Dorsal_2组、Dorsal_1 vs Dorsal_3组、Dorsal_1 vs Dorsal_4组、Dorsal_2 vs Dorsal_3组、Dorsal_3 vs Dorsal_4组DEGs数分别为5149、6903、5483、2456和269个,其中下调表达基因分别为2826、3822、3068、1313和113个,上调表达基因分别为2323、3081、2415、1143和156个。4个不同弯茎时期样本间共有112个DEGs。GO功能注释和KEGG信号通路富集分析结果显示,睡莲弯茎中DEGs主要富集在与光合作用、细胞壁合成和植物激素与信号转导等相关的生物途径中。K-means分析结果显示,DEGs被聚类为9类(Class 1~Class 9),通过Class 1与Venn图共筛选出25个DEGs,Class 5筛选到19个调控睡莲弯茎相关基因。实时荧光定量PCR验证结果显示,DEGs相对表达量与转录组数据基因表达基本一致。【结论】水分、淀粉和可溶性糖含量以及光照响应、植物激素、细胞壁形成与分解等因素的相互作用共同导致睡莲弯茎。推测与生长素及细胞壁结构相关的基因是影响睡莲弯茎的关键基因群。
文摘[目的]探究枸杞果实不同发育时期转录水平上的基因表达变化,筛选类胡萝卜素生物合成相关差异表达基因(DEGs),为揭示枸杞果实在不同发育阶段类胡萝卜素含量差异的分子机制及枸杞分子育种提供理论参考。[方法]通过Illumina NovaSeq 6000高通量测序技术,分析青果期(YD)、转色期(ZD)和成熟期(XD)的杞鑫1号枸杞果实转录谱,以|log_(2)Fold Change|≥1,且错误发现率(FDR)<0.05为标准筛选DEGs,结合KEGG、GO、KOG、NR等数据库注释信息和PubMed数据库文献,筛选出与类胡萝卜素代谢合成相关的DEGs。测定不同发育期枸杞果实类胡萝卜素含量。采用实时荧光定量PCR验证8个DEGs转录组数据的可靠性。[结果]YD vs ZD组、YD vs XD组和ZD vs XD组中DEGs总数分别为6480、1497和7781个,其中分别有3946、827和2888个DEGs上调表达,2534、670和4893个下调表达。3个果实发育期共有234个DEGs。GO功能注释结果显示,在YD vs ZD组、YD vs XD组和ZD vs XD组,分别有1700、579和1657个DEGs被注释到生物过程(BP)、细胞组分(CC)和分子功能(MF)三大功能类别。3个比较组的KEGG信号通路均主要集中在代谢途径和次生代谢物生物合成过程中。从YD vs ZD组、YD vs XD组和ZD vs XD组3个比较组中分别挖掘到50、18和68个与功效成分相关的DEGs,参与类胡萝卜素合成途径的DEGs有34个,其中在YD vs ZD组、YD vs XD和ZD vs XD组分别富集到12、5和17个。杞鑫1号枸杞3个发育时期的果实均含有类胡萝卜素,随杞鑫1号枸杞果实发育,类胡萝卜素含量整体呈先下降后增加的变化趋势,YD、ZD和XD果实中类胡萝卜素含量分别为0.35、0.25和1.20 mg/g。PSY、PDS、ZDS、CHYB和Z-ISO 5个类胡萝卜素合成途径关键酶基因在YD和XD的表达量均高于100。类胡萝卜素合成代谢的关键酶基因PSY、PDS、ZDS和CHYB高表达,而类胡萝卜素分解代谢相关酶基因ZEP和NCED低表达。8个DEGs在杞鑫1号果实中的相对表达量与转录组测序结果基本一致。[结论]在杞鑫1号枸杞青果期和成熟期,类胡萝卜代谢途径中类胡萝卜素合成途径的关键酶基因PSY、PDS、ZDS、CHYB高水平表达而类胡萝卜素分解代谢相关的基因ZEP、NCED表达量较低,这些基因协同促进杞鑫1号枸杞成熟期果实中玉米黄质、β-胡萝卜素等类胡萝卜素的大量合成。
基金supported by the Key Project of Natural Science Foundation of Yunnan Province (202401AS070082)the National Natural Science Foundation of China (grants 32120103003 and 31970355)
文摘Rapid growth is an innovative trait of woody bamboos that has been widely studied.However,the genetic basis and evolution of this trait are poorly understood.Taking advantage of genomic resources of 11 representative bamboos at different ploidal levels,we integrated morphological,physiological,and transcriptomic datasets to investigate rapid growth.In particular,these bamboos include two large-sized and a small-sized woody species,compared with a diploid herbaceous species.Our results showed that gibberellin A1 was important for the rapid shoot growth of the world's largest bamboo,Dendrocalamus sinicus,and indicated that two gibberellins(GAs)-related genes,KAO and SLRL1,were key to the rapid shoot growth and culm size in woody bamboos.The expression of GAs-related genes exhibited significant subgenome asymmetry with subgenomes A and C demonstrating expression dominance in the large-sized woody bamboos while the generally submissive subgenomes B and D dominating in the small-sized species.The subgenome asymmetry was found to be correlated with the subgenome-specific gene structure,particularly UTRs and core promoters.Our study provides novel insights into the molecular mechanism and evolution of rapid shoot growth following allopolyploidization in woody bamboos,particularly via subgenome asymmetry.These findings are helpful for understanding of how polyploidization in general and subgenome asymmetry in particular contributed to the origin of innovative traits in plants.
基金supported by the Natural Science Foundation of Anhui Province,China(2008085qc118)the National Natural Science Foundation of China(U19A2021)+1 种基金the Major Science and Technology Special Project of Anhui Province,China(S202003a06020035)the Jiangsu Collaborative Innovation Center for Modern Crop Production,China(JCIC-MCP)。
文摘Global warming is primarily characterized by asymmetric temperature increases,with greater temperature rises in winter/spring and at night compared to summer/autumn and the daytime.We investigated the impact of winter night warming on the top expanded leaves of the spring wheat cultivar Yangmai 18 and the semi-winter wheat cultivar Yannong 19 during the 2020-2021 growing season.Results showed that the night-time mean temperature in the treatment group was 1.27°C higher than the ambient temperature,and winter night warming increased the yields of both wheat cultivars,the activities of sucrose synthase and sucrose phosphate synthase after anthesis,and the biosynthesis of sucrose and soluble sugars.Differentially expressed genes(DEGs)were identified using criteria of P-value<0.05 and fold change>2,and they were subjected to Gene Ontology(GO)annotation and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analyses.Genes differentially expressed in wheat leaves treated with night warming were primarily associated with starch and sucrose metabolism,amino acid biosynthesis,carbon metabolism,plant hormone signal transduction,and amino sugar and nucleotide sugar metabolism.Comparisons between the groups identified 14 DEGs related to temperature.These results highlight the effects of winter night warming on wheat development from various perspectives.Our results provide new insights into the molecular mechanisms of the response of wheat to winter night warming and the candidate genes involved in this process.
