本研究利用MISA软件筛选火龙果转录组测序获得的108 127条Unigenes,共检测出7 622个EST-SSR位点,其发生频率为6.02%,平均每9.00 kb出现1个位点。单核苷酸重复类型占优势,占总EST-SSR位点的56.59%,其次是二核苷酸和三核苷酸,分别占28.4%...本研究利用MISA软件筛选火龙果转录组测序获得的108 127条Unigenes,共检测出7 622个EST-SSR位点,其发生频率为6.02%,平均每9.00 kb出现1个位点。单核苷酸重复类型占优势,占总EST-SSR位点的56.59%,其次是二核苷酸和三核苷酸,分别占28.4%和14.04%;其它特性重复类型数量较少,所占比例均不足1%。二核苷酸重复基元类型中以AG/CT、AC/GT为优势重复基元,分别占总SSR位点数目的25.37%和2.02%;三核苷酸重复基元类型以AAG/CCT为主,占总SSR位点数目的 3.13%。设计合成125对EST-SSR引物,并随机选取8份形态学差异明显的火龙果种质提取基因组DNA,进行PCR扩增,采用琼脂糖凝胶电泳和10%聚丙烯变性凝胶电泳检测方法对引物进行初步检测,筛选出32对扩增条带锐利清晰的引物。选取38份火龙果种质对筛选出的引物进行多态性检测,获得16对多态性较好的引物,共扩增出47个多态性位点,多态信息含量(polymorphism information content, PIC)范围为0.243～0.667,平均多态性信息含量(polymorphism information content, PIC)为0.459,平均观测等位基因数(number of alleles, Na)为3,平均香农信息指数(Shannon's information index, I)为0.891;利用引物C31931、C13719和C32141等8种引物组合可以有效区分38份火龙果种质,构建其DNA的EST-SSR指纹图谱;UPGMA聚类分析,以0.62为阈值,可将38份火龙果种质分为3类:第一类包括红肉与粉红肉种质,第二类为白肉种质,第三类为蛇鞭柱属的2个种质。本研究基于火龙果转录组测序序列开发了一批具有高度多态性潜力的SSR引物,该引物可有效地将38份火龙果种质区分开来。因此,基于火龙果转录组测序开发的EST-SSR标记,可为火龙果种质鉴定、亲缘关系分析及遗传图谱构建等提供更丰富的标记来源。展开更多
The Chinese tree shrew(Tupaia belangeri chinensis),a member of the mammalian order Scandentia,exhibits considerable similarities with primates,including humans,in aspects of its nervous,immune,and metabolic systems.Th...The Chinese tree shrew(Tupaia belangeri chinensis),a member of the mammalian order Scandentia,exhibits considerable similarities with primates,including humans,in aspects of its nervous,immune,and metabolic systems.These similarities have established the tree shrew as a promising experimental model for biomedical research on cancer,infectious diseases,metabolic disorders,and mental health conditions.Herein,we used metatranscriptomic sequencing to analyze plasma,as well as oral and anal swab samples,from 105 healthy asymptomatic tree shrews to identify the presence of potential zoonotic viruses.In total,eight mammalian viruses with complete genomes were identified,belonging to six viral families,including Flaviviridae,Hepeviridae,Parvovirinae,Picornaviridae,Sedoreoviridae,and Spinareoviridae.Notably,the presence of rotavirus was recorded in tree shrews for the first time.Three viruses-hepacivirus 1,parvovirus,and picornavirus-exhibited low genetic similarity(<70%)with previously reported viruses at the whole-genome scale,indicating novelty.Conversely,three other viruses-hepacivirus 2,hepatovirus A and hepevirus-exhibited high similarity(>94%)to known viral strains.Phylogenetic analyses also revealed that the rotavirus and mammalian orthoreovirus identified in this study may be novel reassortants.These findings provide insights into the diverse viral spectrum present in captive Chinese tree shrews,highlighting the necessity for further research into their potential for crossspecies transmission.展开更多
Background Four-chambered stomach including the forestomachs(rumen,reticulum,and omasum)and abomasum allows ruminants convert plant fiber into high-quality animal products.The early development of this four-chambered ...Background Four-chambered stomach including the forestomachs(rumen,reticulum,and omasum)and abomasum allows ruminants convert plant fiber into high-quality animal products.The early development of this four-chambered stomach is crucial for the health and well-being of young ruminants,especially the immune development.However,the dynamics of immune development are poorly understood.Results We investigated the early gene expression patterns across the four-chambered stomach in Hu sheep,at 5,10,15,and 25 days of age.We found that forestomachs share similar gene expression patterns,all four stomachs underwent widespread activation of both innate and adaptive immune responses from d 5 to 25,whereas the metabolic function were significantly downregulated with age.We constructed a cell landscape of the four-chambered stomach using single-cell sequencing.Integrating transcriptomic and single-cell transcriptomic analyses revealed that the immune-associated module hub genes were highly expressed in T cells,monocytes and macrophages,as well as the defense-associated module hub genes were highly expressed in endothelial cells in the four-stomach tissues.Moreover,the non-immune cells such as epithelial cells play key roles in immune maturation.Cell communication analysis predicted that in addition to immune cells,non-immune cells recruit immune cells through macrophage migration inhibitory factor signaling in the forestomachs.Conclusions Our results demonstrate that the immune and defense responses of four stomachs are quickly developing with age in lamb's early life.We also identified the gene expression patterns and functional cells associated with immune development.Additionally,we identified some key receptors and signaling involved in immune regulation.These results help to understand the early life immune development at single-cell resolution,which has implications to develop nutritional manipulation and health management strategies based on specific targets including key receptors and signaling pathways.展开更多
Seedless citrus has become one of the breeding goals due to its high edible ratio and convenience in fresh consumption and processing.In this study, the ‘Hongjiangcheng' sweet orange(WT) and its seedless mutant(M...Seedless citrus has become one of the breeding goals due to its high edible ratio and convenience in fresh consumption and processing.In this study, the ‘Hongjiangcheng' sweet orange(WT) and its seedless mutant(MT) after cobalt-60 radiation were selected to study the formation metabolism of citrus seedless phenotype. Compared with WT, the MT had altered primary metabolite contents, as indicated by GC-MS analysis. The mature pollen of the MT was mostly distorted and shrunken, and the orange mutant exhibited significantly lower fertility than the WT. Through pollination experiments and paraffin sectioning of the MT, we observed self-compatibility during pollen tube germination in situ, in combination with the absence of natural parthenocarpy and arrested zygotic embryo development at the fourth week after pollination. From transcriptomic analyses of ovules in the fourth week, 815 differentially expressed genes(DEGs) were identified.Furthermore, according to the annotation of gene function and qRT-PCR analysis, Cs4g10930, Cs5g21900 and orange1.1t02243 were identified as candidate genes that may govern the mechanism of seedlessness. Finally, Agrobacterium-mediated transformation verified that the overexpression of Cs4g10930 and Cs5g21900 in Newhall navel orange calli inhibited embryoid production. This study provides a better understanding of seedless formation in citrus and two key genes that may play an important role in the early selection of seedless lines in citrus breeding programs.展开更多
目的:基于转录组测序技术研究小鼠肾脏组织在适应高原低氧胁迫过程中的基因表达和相应的分子机制。方法:在海拔4200 m(高原肾脏实验组,high⁃altitude kidney test group,HKT)和海拔400 m(平原肾脏对照组,plain kidney control group,PKC...目的:基于转录组测序技术研究小鼠肾脏组织在适应高原低氧胁迫过程中的基因表达和相应的分子机制。方法:在海拔4200 m(高原肾脏实验组,high⁃altitude kidney test group,HKT)和海拔400 m(平原肾脏对照组,plain kidney control group,PKC)的环境下分别饲养C57BL/6小鼠,30 d后无菌取出小鼠肾脏组织用高通量测序技术(RNA⁃sequencing,RNA⁃Seq)进行转录组测序。将HKT组和PKC组的测序结果进行基因本体数据库(gene ontology,GO)注释分析和京都基因和基因组百科全书数据库(Kyoto encyclopedia of genes and genomes,KEGG)富集分析,并通过实时荧光定量PCR(real⁃time quantitative PCR,RT⁃qPCR)实验验证测序结果的可靠性。结果:相比于PKC组,HKT组中1349个基因表达上调(P<0.05),1658个基因表达下调(P<0.05)。其中催乳素受体(prolactin receptor,PRLR)、载脂蛋白E(apolipoprotein E,APOE)、载脂蛋白A4(apolipoprotein A4,APOA4)、细胞色素C(cytochrome C somatic,CYCS)、酰基辅酶A氧化酶2(acyl⁃coenzyme A oxidase 1,ACOX2)、细胞色素C氧化酶亚基5A(cytochrome C oxidase subunit 5A,COX5A)、细胞色素C氧化酶亚基5B(cytochrome C oxidase subunit 5B,COX5B)、细胞色素C氧化酶亚基7A(cytochrome C oxidase subunit 7A,COX7A)和热休克蛋白β⁃1(heat shock proteinβ⁃1,HSPB1)等基因显著富集。GO注释分析和KEGG富集分析结果显示,差异基因显著富集在细胞器内膜、线粒体内膜和线粒体蛋白复合物等部位,此外过氧化物酶体、氧化磷酸化、产热、碳代谢以及三羧酸循环等通路显著富集。结论:高原低氧刺激可能通过影响机体的能量代谢相关通路致使机体氧化应激、炎症反应和脂质代谢失衡。展开更多
Saccharina is one of the most important cold-water living marine brown algal genera. In this study we ana-lyzed the transcriptome of S. japonica, which belongs to the 1 000 Plants （OneKP） Project, by using a next-ge...Saccharina is one of the most important cold-water living marine brown algal genera. In this study we ana-lyzed the transcriptome of S. japonica, which belongs to the 1 000 Plants （OneKP） Project, by using a next-generation high-throughput DNA sequencing technique. About 5.16 GB of raw data were generated, and 65 536 scaffolds with an average length of 454 bp were assembled with SOAP de novo assembly method. In total, 19 040 unigenes were identified by BLAST;25 734 scaffolds were clustered into 37 Gene ontology functional groups;6 760 scaffolds were classified into 25 COG categories, as well as 2 665 scaffolds that were assigned to 306 KEGG pathways. Majority of the unigenes exhibited more similarities to algae including brown algae and diatom than other cyanobacteria, marine diatom, and plant. Saccharina japonica has the outstanding capability to accumulate halogen such as Br and I via halogenation processes from seawater. We acquired 42 different vanadium-dependent haloperoxidases （vHPO） in S. japonica transcriptome data, including 5 segments of vanadium-dependent iodoperoxidase （vIPO） and 37 segments of vanadium-de-pendent bromoperoxidase （vBPO）. Complicated analyses of identified fulllength S. japonica vBPO1 and S. japonica vBPO2 revealed the importance of vBPO among species of brown algae and the strong relationship between marine algal vBPOs and vIPOs. This study will enhance our understanding of the biological charac-teristics and economic values of S. japonica species.展开更多
The coding product of alginate-c5-mannuronan-epimerase gene （algG gene） can catalyze the conversion of mannuronate to guluronate and determine the M/G ratio of alginate. Most of the current knowledge about genes inv...The coding product of alginate-c5-mannuronan-epimerase gene （algG gene） can catalyze the conversion of mannuronate to guluronate and determine the M/G ratio of alginate. Most of the current knowledge about genes involved in the alginate biosynthesis comes from bacterial systems. In this article, based on some algal and bacterial algG genes registered on GenBank and EMBL databases, we predicted 94 algG genes open reading frame （ORF） sequences of brown algae from the 1 000 Plant Transcriptome Sequencing Project （OneKP）. By method of transcriptomic sequence analysis, gene structure and gene localization analysis, multiple sequence alignment and phylogenetic tree construction, we studied the algal algG gene family characteristics, the structure modeling and conserved motifs of AlgG protein, the origin of alginate biosyn-thesis and the variation incidents that might have happened during evolution in algae. Although there are different members in the algal algG gene family, almost all of them harbor the conserved epimerase region. Based on the phylogenetic analysis of algG genes, we proposed that brown algae acquired the alginate bio-synthesis pathway from an ancient bacterium by horizontal gene transfer （HGT）. Afterwards, followed by duplications, chromosome disorder, mutation or recombination during evolution, brown algal algG genes were divided into different types.展开更多
Phosphomannomutase （PMM;EC 5.4.2.8） is an enzyme that catalyzes the interconversion reaction between mannose-6-phosphate and mannose-1-phosphate. However, its systematic molecular and functional in-vestigations in a...Phosphomannomutase （PMM;EC 5.4.2.8） is an enzyme that catalyzes the interconversion reaction between mannose-6-phosphate and mannose-1-phosphate. However, its systematic molecular and functional in-vestigations in algae have not hitherto been reported. In this work, with the accomplishment of the 1 000 Plant Project （OneKP） in which more than 218 species of Chromista, including 19 marine phaeophytes, 22 marine rhodophytes, 171 chlorophytes, 5 cryptophytes, 4 haptophytes, and 5 glaucophytes were sequenced, we used a gene analysis method to analyze the PMM gene sequences in algae and confirm the existence of the PMM gene in the transcriptomic sequencing data of Rhodophyta and Ochrophyta. Our results showed that only one type of PMM with four conserved motifs exists in Chromista which is similar to human PMM. Moreover, the phylogenetic tree revealed that algae PMM possibly originated from archaea.展开更多
Tumors are complex ecosystems in which heterogeneous cancer cells interact with their microenvironment composed of diverse immune,endothelial,and stromal cells.Cancer biology had been studied using bulk genomic and ge...Tumors are complex ecosystems in which heterogeneous cancer cells interact with their microenvironment composed of diverse immune,endothelial,and stromal cells.Cancer biology had been studied using bulk genomic and gene expression profiling,which however mask the cellular diversity and average the variability among individual molecular programs.Recent advances in single-cell transcriptomic sequencing have enabled a detailed dissection of tumor ecosystems and promoted our understanding of tumorigenesis at single-cell resolution.In the present review,we discuss the main topics of recent cancer studies that have implemented singlecell RNA sequencing(scRNA-seq).To study cancer cells,scRNA-seq has provided novel insights into the cancer stem-cell model,treatment resistance,and cancer metastasis.To study the tumor microenvironment,scRNA-seq has portrayed the diverse cell types and complex cellular states of both immune and non-immune cells interacting with cancer cells,with the promise to discover novel targets for future immunotherapy.展开更多
文摘本研究利用MISA软件筛选火龙果转录组测序获得的108 127条Unigenes,共检测出7 622个EST-SSR位点,其发生频率为6.02%,平均每9.00 kb出现1个位点。单核苷酸重复类型占优势,占总EST-SSR位点的56.59%,其次是二核苷酸和三核苷酸,分别占28.4%和14.04%;其它特性重复类型数量较少,所占比例均不足1%。二核苷酸重复基元类型中以AG/CT、AC/GT为优势重复基元,分别占总SSR位点数目的25.37%和2.02%;三核苷酸重复基元类型以AAG/CCT为主,占总SSR位点数目的 3.13%。设计合成125对EST-SSR引物,并随机选取8份形态学差异明显的火龙果种质提取基因组DNA,进行PCR扩增,采用琼脂糖凝胶电泳和10%聚丙烯变性凝胶电泳检测方法对引物进行初步检测,筛选出32对扩增条带锐利清晰的引物。选取38份火龙果种质对筛选出的引物进行多态性检测,获得16对多态性较好的引物,共扩增出47个多态性位点,多态信息含量(polymorphism information content, PIC)范围为0.243～0.667,平均多态性信息含量(polymorphism information content, PIC)为0.459,平均观测等位基因数(number of alleles, Na)为3,平均香农信息指数(Shannon's information index, I)为0.891;利用引物C31931、C13719和C32141等8种引物组合可以有效区分38份火龙果种质,构建其DNA的EST-SSR指纹图谱;UPGMA聚类分析,以0.62为阈值,可将38份火龙果种质分为3类:第一类包括红肉与粉红肉种质,第二类为白肉种质,第三类为蛇鞭柱属的2个种质。本研究基于火龙果转录组测序序列开发了一批具有高度多态性潜力的SSR引物,该引物可有效地将38份火龙果种质区分开来。因此,基于火龙果转录组测序开发的EST-SSR标记,可为火龙果种质鉴定、亲缘关系分析及遗传图谱构建等提供更丰富的标记来源。
基金supported by the National Key R&D Program of China (2021YFC2300900,2021YFC2301300)Academic Promotion Programme of Shandong First Medical University (2019QL006)+2 种基金Natural Science Foundation of Shandong Province (ZR2020QH274)Yunnan Key Research and Development Program (202103AQ100001,202102AA310055)Key Program of Chinese Academy of Sciences (KJZD-SW-L11)。
文摘The Chinese tree shrew(Tupaia belangeri chinensis),a member of the mammalian order Scandentia,exhibits considerable similarities with primates,including humans,in aspects of its nervous,immune,and metabolic systems.These similarities have established the tree shrew as a promising experimental model for biomedical research on cancer,infectious diseases,metabolic disorders,and mental health conditions.Herein,we used metatranscriptomic sequencing to analyze plasma,as well as oral and anal swab samples,from 105 healthy asymptomatic tree shrews to identify the presence of potential zoonotic viruses.In total,eight mammalian viruses with complete genomes were identified,belonging to six viral families,including Flaviviridae,Hepeviridae,Parvovirinae,Picornaviridae,Sedoreoviridae,and Spinareoviridae.Notably,the presence of rotavirus was recorded in tree shrews for the first time.Three viruses-hepacivirus 1,parvovirus,and picornavirus-exhibited low genetic similarity(<70%)with previously reported viruses at the whole-genome scale,indicating novelty.Conversely,three other viruses-hepacivirus 2,hepatovirus A and hepevirus-exhibited high similarity(>94%)to known viral strains.Phylogenetic analyses also revealed that the rotavirus and mammalian orthoreovirus identified in this study may be novel reassortants.These findings provide insights into the diverse viral spectrum present in captive Chinese tree shrews,highlighting the necessity for further research into their potential for crossspecies transmission.
基金partially supported by the Natural Science Foundation of Zhejiang Province(Award number:D21C170001)the National Natural Science Foundation of China(Award number:31973000)。
文摘Background Four-chambered stomach including the forestomachs(rumen,reticulum,and omasum)and abomasum allows ruminants convert plant fiber into high-quality animal products.The early development of this four-chambered stomach is crucial for the health and well-being of young ruminants,especially the immune development.However,the dynamics of immune development are poorly understood.Results We investigated the early gene expression patterns across the four-chambered stomach in Hu sheep,at 5,10,15,and 25 days of age.We found that forestomachs share similar gene expression patterns,all four stomachs underwent widespread activation of both innate and adaptive immune responses from d 5 to 25,whereas the metabolic function were significantly downregulated with age.We constructed a cell landscape of the four-chambered stomach using single-cell sequencing.Integrating transcriptomic and single-cell transcriptomic analyses revealed that the immune-associated module hub genes were highly expressed in T cells,monocytes and macrophages,as well as the defense-associated module hub genes were highly expressed in endothelial cells in the four-stomach tissues.Moreover,the non-immune cells such as epithelial cells play key roles in immune maturation.Cell communication analysis predicted that in addition to immune cells,non-immune cells recruit immune cells through macrophage migration inhibitory factor signaling in the forestomachs.Conclusions Our results demonstrate that the immune and defense responses of four stomachs are quickly developing with age in lamb's early life.We also identified the gene expression patterns and functional cells associated with immune development.Additionally,we identified some key receptors and signaling involved in immune regulation.These results help to understand the early life immune development at single-cell resolution,which has implications to develop nutritional manipulation and health management strategies based on specific targets including key receptors and signaling pathways.
基金supported by the National Key Research and Development Program (Grant No. 2018YFD1000200)Special Fund for Basic Research Funds in Central Universities (Grant No. 2662018PY072)。
文摘Seedless citrus has become one of the breeding goals due to its high edible ratio and convenience in fresh consumption and processing.In this study, the ‘Hongjiangcheng' sweet orange(WT) and its seedless mutant(MT) after cobalt-60 radiation were selected to study the formation metabolism of citrus seedless phenotype. Compared with WT, the MT had altered primary metabolite contents, as indicated by GC-MS analysis. The mature pollen of the MT was mostly distorted and shrunken, and the orange mutant exhibited significantly lower fertility than the WT. Through pollination experiments and paraffin sectioning of the MT, we observed self-compatibility during pollen tube germination in situ, in combination with the absence of natural parthenocarpy and arrested zygotic embryo development at the fourth week after pollination. From transcriptomic analyses of ovules in the fourth week, 815 differentially expressed genes(DEGs) were identified.Furthermore, according to the annotation of gene function and qRT-PCR analysis, Cs4g10930, Cs5g21900 and orange1.1t02243 were identified as candidate genes that may govern the mechanism of seedlessness. Finally, Agrobacterium-mediated transformation verified that the overexpression of Cs4g10930 and Cs5g21900 in Newhall navel orange calli inhibited embryoid production. This study provides a better understanding of seedless formation in citrus and two key genes that may play an important role in the early selection of seedless lines in citrus breeding programs.
文摘目的:基于转录组测序技术研究小鼠肾脏组织在适应高原低氧胁迫过程中的基因表达和相应的分子机制。方法:在海拔4200 m(高原肾脏实验组,high⁃altitude kidney test group,HKT)和海拔400 m(平原肾脏对照组,plain kidney control group,PKC)的环境下分别饲养C57BL/6小鼠,30 d后无菌取出小鼠肾脏组织用高通量测序技术(RNA⁃sequencing,RNA⁃Seq)进行转录组测序。将HKT组和PKC组的测序结果进行基因本体数据库(gene ontology,GO)注释分析和京都基因和基因组百科全书数据库(Kyoto encyclopedia of genes and genomes,KEGG)富集分析,并通过实时荧光定量PCR(real⁃time quantitative PCR,RT⁃qPCR)实验验证测序结果的可靠性。结果:相比于PKC组,HKT组中1349个基因表达上调(P<0.05),1658个基因表达下调(P<0.05)。其中催乳素受体(prolactin receptor,PRLR)、载脂蛋白E(apolipoprotein E,APOE)、载脂蛋白A4(apolipoprotein A4,APOA4)、细胞色素C(cytochrome C somatic,CYCS)、酰基辅酶A氧化酶2(acyl⁃coenzyme A oxidase 1,ACOX2)、细胞色素C氧化酶亚基5A(cytochrome C oxidase subunit 5A,COX5A)、细胞色素C氧化酶亚基5B(cytochrome C oxidase subunit 5B,COX5B)、细胞色素C氧化酶亚基7A(cytochrome C oxidase subunit 7A,COX7A)和热休克蛋白β⁃1(heat shock proteinβ⁃1,HSPB1)等基因显著富集。GO注释分析和KEGG富集分析结果显示,差异基因显著富集在细胞器内膜、线粒体内膜和线粒体蛋白复合物等部位,此外过氧化物酶体、氧化磷酸化、产热、碳代谢以及三羧酸循环等通路显著富集。结论:高原低氧刺激可能通过影响机体的能量代谢相关通路致使机体氧化应激、炎症反应和脂质代谢失衡。
基金The National Natural Science Foundation of China under contract Nos 41206116,31140070 and 31271397Technology Project of Ocean and Fisheries of Guangdong Province under contract No.A201201E03+1 种基金the Fundamental Research Funds for the Central Universities under contract No.201262003the algal transcriptome sequencing was supported by OneKP Project(www.onekp.com)
文摘Saccharina is one of the most important cold-water living marine brown algal genera. In this study we ana-lyzed the transcriptome of S. japonica, which belongs to the 1 000 Plants （OneKP） Project, by using a next-generation high-throughput DNA sequencing technique. About 5.16 GB of raw data were generated, and 65 536 scaffolds with an average length of 454 bp were assembled with SOAP de novo assembly method. In total, 19 040 unigenes were identified by BLAST;25 734 scaffolds were clustered into 37 Gene ontology functional groups;6 760 scaffolds were classified into 25 COG categories, as well as 2 665 scaffolds that were assigned to 306 KEGG pathways. Majority of the unigenes exhibited more similarities to algae including brown algae and diatom than other cyanobacteria, marine diatom, and plant. Saccharina japonica has the outstanding capability to accumulate halogen such as Br and I via halogenation processes from seawater. We acquired 42 different vanadium-dependent haloperoxidases （vHPO） in S. japonica transcriptome data, including 5 segments of vanadium-dependent iodoperoxidase （vIPO） and 37 segments of vanadium-de-pendent bromoperoxidase （vBPO）. Complicated analyses of identified fulllength S. japonica vBPO1 and S. japonica vBPO2 revealed the importance of vBPO among species of brown algae and the strong relationship between marine algal vBPOs and vIPOs. This study will enhance our understanding of the biological charac-teristics and economic values of S. japonica species.
基金The National High Technology Research and Development Program of China under contract No.2012AA10A406the National Nat-ural Science Foundation of China under contract Nos 41206116,31140070 and 31271397+3 种基金Technology Project of Ocean and Fisheries of Guangdong Province under contract No.A201201E03the Fundamental Research Funds for the Central Universities under contract No.201262003China Post-doctoral Science Foundation under contract No.2011M501167the algal transcriptome sequencing was supported by 1KP Project(www.onekp.com)
文摘The coding product of alginate-c5-mannuronan-epimerase gene （algG gene） can catalyze the conversion of mannuronate to guluronate and determine the M/G ratio of alginate. Most of the current knowledge about genes involved in the alginate biosynthesis comes from bacterial systems. In this article, based on some algal and bacterial algG genes registered on GenBank and EMBL databases, we predicted 94 algG genes open reading frame （ORF） sequences of brown algae from the 1 000 Plant Transcriptome Sequencing Project （OneKP）. By method of transcriptomic sequence analysis, gene structure and gene localization analysis, multiple sequence alignment and phylogenetic tree construction, we studied the algal algG gene family characteristics, the structure modeling and conserved motifs of AlgG protein, the origin of alginate biosyn-thesis and the variation incidents that might have happened during evolution in algae. Although there are different members in the algal algG gene family, almost all of them harbor the conserved epimerase region. Based on the phylogenetic analysis of algG genes, we proposed that brown algae acquired the alginate bio-synthesis pathway from an ancient bacterium by horizontal gene transfer （HGT）. Afterwards, followed by duplications, chromosome disorder, mutation or recombination during evolution, brown algal algG genes were divided into different types.
基金The National High Technology Research and Development Program of China under contract No.2012AA10A406the National Nat-ural Science Foundation of China under contract Nos 41206116,31140070 and 31271397+3 种基金Technology Project of Ocean and Fisheries of Guangdong Province under contract No.A201201E03the Fundamental Research Funds for the Central Universities under contract No.201262003China Post-doctoral Science Foundation under contract No.2011M501167the algal transcriptome sequencing was supported by 1KP Project(www.onekp.com)
文摘Phosphomannomutase （PMM;EC 5.4.2.8） is an enzyme that catalyzes the interconversion reaction between mannose-6-phosphate and mannose-1-phosphate. However, its systematic molecular and functional in-vestigations in algae have not hitherto been reported. In this work, with the accomplishment of the 1 000 Plant Project （OneKP） in which more than 218 species of Chromista, including 19 marine phaeophytes, 22 marine rhodophytes, 171 chlorophytes, 5 cryptophytes, 4 haptophytes, and 5 glaucophytes were sequenced, we used a gene analysis method to analyze the PMM gene sequences in algae and confirm the existence of the PMM gene in the transcriptomic sequencing data of Rhodophyta and Ochrophyta. Our results showed that only one type of PMM with four conserved motifs exists in Chromista which is similar to human PMM. Moreover, the phylogenetic tree revealed that algae PMM possibly originated from archaea.
基金This work was financially supported by the National Science and Technology Major Project(2019YFC1315702)the Guangdong Province Key Research and Development Program(2019B020226002).
文摘Tumors are complex ecosystems in which heterogeneous cancer cells interact with their microenvironment composed of diverse immune,endothelial,and stromal cells.Cancer biology had been studied using bulk genomic and gene expression profiling,which however mask the cellular diversity and average the variability among individual molecular programs.Recent advances in single-cell transcriptomic sequencing have enabled a detailed dissection of tumor ecosystems and promoted our understanding of tumorigenesis at single-cell resolution.In the present review,we discuss the main topics of recent cancer studies that have implemented singlecell RNA sequencing(scRNA-seq).To study cancer cells,scRNA-seq has provided novel insights into the cancer stem-cell model,treatment resistance,and cancer metastasis.To study the tumor microenvironment,scRNA-seq has portrayed the diverse cell types and complex cellular states of both immune and non-immune cells interacting with cancer cells,with the promise to discover novel targets for future immunotherapy.
