A spontaneous white panicle mutant was found from the F6 progenies of an indica/japonica cross. The mu-tant exhibits white stripes on its basal leaves while the pani-cles, rachis and pedicel are milky white colored at...A spontaneous white panicle mutant was found from the F6 progenies of an indica/japonica cross. The mu-tant exhibits white stripes on its basal leaves while the pani-cles, rachis and pedicel are milky white colored at flowering stage. Genetic analysis in an F2 population from the cross of Zhi7/white panicle mutant indicates that the white panicle phenotype is controlled by a single recessive nuclear gene, tentatively termed as wp(t). Using microsatellite markers, the wp(t) gene was anchored between the markers of SSR101 and SSR63.9 with a map distance of 2.3 and 0.8 cM, respec-tively, and co-segregated with the marker of SSR17 on rice chromosome 1.展开更多
粗茎秦艽Gentiana crassicaulis Duthie ex Burk.为中药“秦艽”的基原植物之一,而同为龙胆属秦艽组的西藏秦艽Gentiana tibetica King ex Hook.f.、粗壮秦艽Gentiana robusta King ex Hook.f.为其近缘的非国家药典品种。因存在较大的...粗茎秦艽Gentiana crassicaulis Duthie ex Burk.为中药“秦艽”的基原植物之一,而同为龙胆属秦艽组的西藏秦艽Gentiana tibetica King ex Hook.f.、粗壮秦艽Gentiana robusta King ex Hook.f.为其近缘的非国家药典品种。因存在较大的种内形态变异,粗茎秦艽与西藏秦艽、粗壮秦艽间表现出较高的形态相似性,且存在一定的同域分布,为粗茎秦艽的鉴定带来了一定的难度。为有效鉴定中药秦艽国家药典品种粗茎秦艽与其近缘的非药典品种,本文基于前期测定的粗茎秦艽、粗壮秦艽叶绿体基因组序列,首次测定西藏秦艽叶绿体基因组序列,筛选分子标记并构建这三个物种的分子鉴定方法。结果如下:①获得西藏秦艽叶绿体基因组序列,长度为148765 bp,大单拷贝区(LSC)、小单拷贝区(SSC)分别为81163 bp和17070 bp,反向重复区(IR)为25266 bp;②粗茎秦艽、西藏秦艽、粗壮秦艽的叶绿体基因组结构一致;粗茎秦艽与西藏秦艽的重复序列、SSR分布情况一致,两个物种间叶绿体基因组变异位点数仅为9;③筛选同时对这三个物种有效鉴定的单核苷酸多态性位点(SNP),并验证稳定性;④建立SNP双峰检测方法,对各物种及混合样品进行有效鉴定。本工作可为粗茎秦艽及其近缘物种的DNA分子鉴定,以及相关藏药品种的整理等工作提供基础资料。展开更多
Understanding consistencies and discrepancies in characterizing diversity and quantity of phytoplankton is essential for better modeling ecosystem change.In this study,eukaryotic phytoplankton in the Pearl River Estua...Understanding consistencies and discrepancies in characterizing diversity and quantity of phytoplankton is essential for better modeling ecosystem change.In this study,eukaryotic phytoplankton in the Pearl River Estuary,South China Sea were investigated using nuclear 18S rRNA and plastid 16S or 23S rRNA genes and pigment analysis.It was found that 18S abundance poorly explained the variations in total chlorophyll a(Chl-a).However,the ratios of log-transformed 18S abundance to Chl-a in the major phytoplankton groups were generally environment dependent,suggesting that the ratio has potential as an indicator of the physiological state of phytoplankton.The richness of 18S-based operational taxonomic units was positively correlated with the richness of 16S-based amplicon sequence variants of the whole phytoplankton community,but insignifcant or weak for individual phytoplankton groups.Overall,the 18S based,rather than the 16S based,community structure had a greater similarity to pigment-based estimations.Relative to the pigment data,the proportion of haptophytes in the 18S dataset,and diatoms and cryptophytes in the 16S dataset,were underestimated.This study highlights that 18S metabarcoding tends to refect biomass-based community organization of eukaryotic phytoplankton.Because there were lower copy numbers of plastid 16S than 18S per genome,metabarcoding of 16S probably approximates cell abundance-based community organization.Changes in biomass organization of the pigment-based community were sensitive to environmental changes.Taken together,multiple methodologies are recommended to be applied to more accurately profle the diversity and community composition of phytoplankton in natural ecosystems.展开更多
Phaeocystis globosa is an important harmful algal bloom causative species distributing widely in temperate and tropical coastal waters in the world.The morphological,physiological,and biochemical characteristics are d...Phaeocystis globosa is an important harmful algal bloom causative species distributing widely in temperate and tropical coastal waters in the world.The morphological,physiological,and biochemical characteristics are different among geographic strains,which can not be distinguished with nuclear ribosomal DNA markers at present.Therefore,the genetic distance and phylogeographic relationships of nuclear 28S rDNA D1–D2 and ITS regions,and three chloroplast intergenic spacers(petN-trnS1,trnM1-psbA,and rbcS-rpl27)were analyzed and compared among 13 strains of P.globosa isolated from the Pacific Ocean and Atlantic Ocean in this study.In addition,the nucleotide polymorphisms of 28S rDNA D1–D2,ITS,and rbcS-rpl27 regions were evaluated in two P.globosa strains.The various levels of nucleotide polymorphism were in the nuclear 28S rDNA D1–D2 region and ITS region,but no polymorphism was in the chloroplast rbcS-rpl27 intergenic spacer.A reasonable intraspecific phylogeographic relationship was presented by rbcS-rpl27 intergenic spacer,which had the strongest distinction to geographic strains compared to those of 28S rDNA D1–D2 and ITS regions.In the phylogenetic tree of rbcS-rpl27 intergenic spacer,the two strains from the North Sea of the Atlantic Ocean were divided firstly from the species of P.globosa,and then formed an independent clade,while the other Atlantic strains and all of Pacific strains joined up to build the other clade.It was implied that at least two genetically distant populations of P.globosa existed in the Atlantic coastal regions.This study provided a high-resolution chloroplast marker to analyze intraspecific phylogeographic populations of P.globosa,and preliminarily clarified the genetic relationships of the Pacific and Atlantic strains of P.globosa.展开更多
Rapid and reliable identification of olive plants using DNA markers has been attempted in the past but the selection of polymorphic regions for discrimination at varietal level remained obscure. Recent sequencing of p...Rapid and reliable identification of olive plants using DNA markers has been attempted in the past but the selection of polymorphic regions for discrimination at varietal level remained obscure. Recent sequencing of plastid genome of the olive flaunts high resolution Cp markers for olive DNA fingerprinting. Using this information, we designed a combination of chloroplast markers to amplify genes recruited in photosynthesis, ribosomal and NADH energy metabolism for varietal identification of olive plants. Concatenated DNA sequences of more than 100 unknown and 10 reference plants samples were analyzed using various bioinformatics and phylogenetic tools. Conserved blocks of nucleotide sequences were detected in multiple alignments. Phylogenetic reconstruction differentiated the unknown plants into various clusters with known varieties. Further narrowing down of the samples through UPGMA tree clearly separated the plants into Arbosana, Frantoio and Koroneiki as the major varieties. Multiple alignments of these clusters revealed important variety specific SNPs including G and T nucleotides at specific positions. Sequence identifying at intra cultivar level was more than 98.79% while it dropped to 97%, and even to 96% at inter varietal level. Furthermore, a neighbor net network analysis separated these three clusters, thus validating the results of UPGMA tree. Over all, out of 100 plants samples, 49 plants were identified that fall into 10 varieties including Arbosana, Carolea, Chetoui, Coratina, Domat, Frantoio, Gemlik, Koroneiki,Leccino and Moraiolo. The maximum number of known plants belongs to Frantoio and Gemlik (8 each). The least number of samples was identified from Carolea, Domat and Moraiolo with 2 samples each. However, 51 plants could not be identified, as plants were not clustered with any of reference control. Our results have implications in on-farm conservation of olive germplasm and provision of genuine material for multiplication of authentic varieties. This strategy can be extended to varietal ident展开更多
The chloroplast is a pivotal organelle in plant cells and eukaryotic algae to carry out photosynthesis, which provides the primary source of the world＇s food. The expression of foreign genes in chloroplasts offers se...The chloroplast is a pivotal organelle in plant cells and eukaryotic algae to carry out photosynthesis, which provides the primary source of the world＇s food. The expression of foreign genes in chloroplasts offers several advantages over their expression in the nucleus： high-level expression, transgene stacking in operons and a lack of epigenetic interference allowing stable transgene expression. In addition, transgenic chloroplasts are generally not transmitted through pollen grains because of the cytoplasmic localization. In the past two decades, great progress in chloroplast engineering has been made. In this paper, we review and highlight recent studies of chloroplast engineering, including chloroplast transformation procedures, controlled expression of plastid transgenes in plants, the expression of foreign genes for improvement of plant traits, the production of biopharmaceuticals, metabolic pathway engineering in plants, plastid transformation to study RNA editing, and marker gene excision system.展开更多
文摘A spontaneous white panicle mutant was found from the F6 progenies of an indica/japonica cross. The mu-tant exhibits white stripes on its basal leaves while the pani-cles, rachis and pedicel are milky white colored at flowering stage. Genetic analysis in an F2 population from the cross of Zhi7/white panicle mutant indicates that the white panicle phenotype is controlled by a single recessive nuclear gene, tentatively termed as wp(t). Using microsatellite markers, the wp(t) gene was anchored between the markers of SSR101 and SSR63.9 with a map distance of 2.3 and 0.8 cM, respec-tively, and co-segregated with the marker of SSR17 on rice chromosome 1.
文摘粗茎秦艽Gentiana crassicaulis Duthie ex Burk.为中药“秦艽”的基原植物之一,而同为龙胆属秦艽组的西藏秦艽Gentiana tibetica King ex Hook.f.、粗壮秦艽Gentiana robusta King ex Hook.f.为其近缘的非国家药典品种。因存在较大的种内形态变异,粗茎秦艽与西藏秦艽、粗壮秦艽间表现出较高的形态相似性,且存在一定的同域分布,为粗茎秦艽的鉴定带来了一定的难度。为有效鉴定中药秦艽国家药典品种粗茎秦艽与其近缘的非药典品种,本文基于前期测定的粗茎秦艽、粗壮秦艽叶绿体基因组序列,首次测定西藏秦艽叶绿体基因组序列,筛选分子标记并构建这三个物种的分子鉴定方法。结果如下:①获得西藏秦艽叶绿体基因组序列,长度为148765 bp,大单拷贝区(LSC)、小单拷贝区(SSC)分别为81163 bp和17070 bp,反向重复区(IR)为25266 bp;②粗茎秦艽、西藏秦艽、粗壮秦艽的叶绿体基因组结构一致;粗茎秦艽与西藏秦艽的重复序列、SSR分布情况一致,两个物种间叶绿体基因组变异位点数仅为9;③筛选同时对这三个物种有效鉴定的单核苷酸多态性位点(SNP),并验证稳定性;④建立SNP双峰检测方法,对各物种及混合样品进行有效鉴定。本工作可为粗茎秦艽及其近缘物种的DNA分子鉴定,以及相关藏药品种的整理等工作提供基础资料。
基金This work was supported by the National Natural Science Foundation of China(nos.41976128 and 31970486)the Innovation Group Project of Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai)(no.311021004).
文摘Understanding consistencies and discrepancies in characterizing diversity and quantity of phytoplankton is essential for better modeling ecosystem change.In this study,eukaryotic phytoplankton in the Pearl River Estuary,South China Sea were investigated using nuclear 18S rRNA and plastid 16S or 23S rRNA genes and pigment analysis.It was found that 18S abundance poorly explained the variations in total chlorophyll a(Chl-a).However,the ratios of log-transformed 18S abundance to Chl-a in the major phytoplankton groups were generally environment dependent,suggesting that the ratio has potential as an indicator of the physiological state of phytoplankton.The richness of 18S-based operational taxonomic units was positively correlated with the richness of 16S-based amplicon sequence variants of the whole phytoplankton community,but insignifcant or weak for individual phytoplankton groups.Overall,the 18S based,rather than the 16S based,community structure had a greater similarity to pigment-based estimations.Relative to the pigment data,the proportion of haptophytes in the 18S dataset,and diatoms and cryptophytes in the 16S dataset,were underestimated.This study highlights that 18S metabarcoding tends to refect biomass-based community organization of eukaryotic phytoplankton.Because there were lower copy numbers of plastid 16S than 18S per genome,metabarcoding of 16S probably approximates cell abundance-based community organization.Changes in biomass organization of the pigment-based community were sensitive to environmental changes.Taken together,multiple methodologies are recommended to be applied to more accurately profle the diversity and community composition of phytoplankton in natural ecosystems.
基金Supported by the National Key Research and Development Plan Project,the Sino-Australian Centre for Healthy Coasts(No.2016YFE0101500)the Science&Technology Basic Resources Investigation Program(No.2018FY100206)the National Natural Science Foundation of China(Nos.41576121,41776127)。
文摘Phaeocystis globosa is an important harmful algal bloom causative species distributing widely in temperate and tropical coastal waters in the world.The morphological,physiological,and biochemical characteristics are different among geographic strains,which can not be distinguished with nuclear ribosomal DNA markers at present.Therefore,the genetic distance and phylogeographic relationships of nuclear 28S rDNA D1–D2 and ITS regions,and three chloroplast intergenic spacers(petN-trnS1,trnM1-psbA,and rbcS-rpl27)were analyzed and compared among 13 strains of P.globosa isolated from the Pacific Ocean and Atlantic Ocean in this study.In addition,the nucleotide polymorphisms of 28S rDNA D1–D2,ITS,and rbcS-rpl27 regions were evaluated in two P.globosa strains.The various levels of nucleotide polymorphism were in the nuclear 28S rDNA D1–D2 region and ITS region,but no polymorphism was in the chloroplast rbcS-rpl27 intergenic spacer.A reasonable intraspecific phylogeographic relationship was presented by rbcS-rpl27 intergenic spacer,which had the strongest distinction to geographic strains compared to those of 28S rDNA D1–D2 and ITS regions.In the phylogenetic tree of rbcS-rpl27 intergenic spacer,the two strains from the North Sea of the Atlantic Ocean were divided firstly from the species of P.globosa,and then formed an independent clade,while the other Atlantic strains and all of Pacific strains joined up to build the other clade.It was implied that at least two genetically distant populations of P.globosa existed in the Atlantic coastal regions.This study provided a high-resolution chloroplast marker to analyze intraspecific phylogeographic populations of P.globosa,and preliminarily clarified the genetic relationships of the Pacific and Atlantic strains of P.globosa.
文摘Rapid and reliable identification of olive plants using DNA markers has been attempted in the past but the selection of polymorphic regions for discrimination at varietal level remained obscure. Recent sequencing of plastid genome of the olive flaunts high resolution Cp markers for olive DNA fingerprinting. Using this information, we designed a combination of chloroplast markers to amplify genes recruited in photosynthesis, ribosomal and NADH energy metabolism for varietal identification of olive plants. Concatenated DNA sequences of more than 100 unknown and 10 reference plants samples were analyzed using various bioinformatics and phylogenetic tools. Conserved blocks of nucleotide sequences were detected in multiple alignments. Phylogenetic reconstruction differentiated the unknown plants into various clusters with known varieties. Further narrowing down of the samples through UPGMA tree clearly separated the plants into Arbosana, Frantoio and Koroneiki as the major varieties. Multiple alignments of these clusters revealed important variety specific SNPs including G and T nucleotides at specific positions. Sequence identifying at intra cultivar level was more than 98.79% while it dropped to 97%, and even to 96% at inter varietal level. Furthermore, a neighbor net network analysis separated these three clusters, thus validating the results of UPGMA tree. Over all, out of 100 plants samples, 49 plants were identified that fall into 10 varieties including Arbosana, Carolea, Chetoui, Coratina, Domat, Frantoio, Gemlik, Koroneiki,Leccino and Moraiolo. The maximum number of known plants belongs to Frantoio and Gemlik (8 each). The least number of samples was identified from Carolea, Domat and Moraiolo with 2 samples each. However, 51 plants could not be identified, as plants were not clustered with any of reference control. Our results have implications in on-farm conservation of olive germplasm and provision of genuine material for multiplication of authentic varieties. This strategy can be extended to varietal ident
基金supported by the Ministry of Science and Technology of China (863 Projects) (No.2007AA100505 and 2005AA206150)
文摘The chloroplast is a pivotal organelle in plant cells and eukaryotic algae to carry out photosynthesis, which provides the primary source of the world＇s food. The expression of foreign genes in chloroplasts offers several advantages over their expression in the nucleus： high-level expression, transgene stacking in operons and a lack of epigenetic interference allowing stable transgene expression. In addition, transgenic chloroplasts are generally not transmitted through pollen grains because of the cytoplasmic localization. In the past two decades, great progress in chloroplast engineering has been made. In this paper, we review and highlight recent studies of chloroplast engineering, including chloroplast transformation procedures, controlled expression of plastid transgenes in plants, the expression of foreign genes for improvement of plant traits, the production of biopharmaceuticals, metabolic pathway engineering in plants, plastid transformation to study RNA editing, and marker gene excision system.
