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 identification of other plant species.展开更多
Bulbophyllum is the largest genus in Orchidaceae with a pan tropical distribution.Due to highly significant diversifications,it is considered to be one of the most taxonomically and phylogenetically complex taxa.The d...Bulbophyllum is the largest genus in Orchidaceae with a pan tropical distribution.Due to highly significant diversifications,it is considered to be one of the most taxonomically and phylogenetically complex taxa.The diversification pattern and evolutionary adaptation of chloroplast genomes are poorly understood in this species-rich genus,and suitable molecular markers are necessary for species determination and phylogenetic analysis.A natural Asian section Macrocaulia was selected to estimate the interspecific divergence of chloroplast genomes in this study.Here,we sequenced the complete chloroplast genome of four Bulbophyllum species,including three species from section Macrocaulia.The four chloroplast genomes had a typical quadripartite structure with a genome size ranged from 156,182 to 158,524 bp.The chloroplast genomes included 113 unique genes encoding 79 proteins,30 tRNAs and 4 rRNAs.Comparison of the four chloroplast genomes showed that the three species from section Macrocaulia had similar structure and gene contents,and shared a number of indels,which mainly contribute to its monophyly.In addition,interspecific divergence level was also great.Several exclusive indels and polymorphism SSR loci might be used for taxonomical identification and determining interspecific polymorphisms.A total of 20 intergenic regions and three coding genes of the most variable hotspot regions were proposed as candidate effective molecular markers for future phylogenetic relationships at different taxonomical levels and species divergence in Bulbophyllum.All of chloroplast genes in four Bulbophyllum species were under purifying selection,while 13 sites within six genes exhibited sitespecific selection.A whole chloroplast genome phylogenetic analysis based on Maximum Likelihood,Bayesian and Parsimony methods all supported the monophyly of section Macrocaulia and the genus of Bulbophyllum.Our findings provide valuable molecular markers to use in accurately identifying species,clarifying taxonomy,and resolving the phylogeny and evolution of the genus Bulbophyllum.The molecular markers developed in this study will also contribute to further research of conservation of Bulbophyllum species.展开更多
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 identification of other plant species.
基金supported by the National Natural Science Foundation of China(No.31870183,No.U1702235)Southeast Asia Biodiversity Research Institute,Chinese Academy of Sciences(Y4ZK111B01)。
文摘Bulbophyllum is the largest genus in Orchidaceae with a pan tropical distribution.Due to highly significant diversifications,it is considered to be one of the most taxonomically and phylogenetically complex taxa.The diversification pattern and evolutionary adaptation of chloroplast genomes are poorly understood in this species-rich genus,and suitable molecular markers are necessary for species determination and phylogenetic analysis.A natural Asian section Macrocaulia was selected to estimate the interspecific divergence of chloroplast genomes in this study.Here,we sequenced the complete chloroplast genome of four Bulbophyllum species,including three species from section Macrocaulia.The four chloroplast genomes had a typical quadripartite structure with a genome size ranged from 156,182 to 158,524 bp.The chloroplast genomes included 113 unique genes encoding 79 proteins,30 tRNAs and 4 rRNAs.Comparison of the four chloroplast genomes showed that the three species from section Macrocaulia had similar structure and gene contents,and shared a number of indels,which mainly contribute to its monophyly.In addition,interspecific divergence level was also great.Several exclusive indels and polymorphism SSR loci might be used for taxonomical identification and determining interspecific polymorphisms.A total of 20 intergenic regions and three coding genes of the most variable hotspot regions were proposed as candidate effective molecular markers for future phylogenetic relationships at different taxonomical levels and species divergence in Bulbophyllum.All of chloroplast genes in four Bulbophyllum species were under purifying selection,while 13 sites within six genes exhibited sitespecific selection.A whole chloroplast genome phylogenetic analysis based on Maximum Likelihood,Bayesian and Parsimony methods all supported the monophyly of section Macrocaulia and the genus of Bulbophyllum.Our findings provide valuable molecular markers to use in accurately identifying species,clarifying taxonomy,and resolving the phylogeny and evolution of the genus Bulbophyllum.The molecular markers developed in this study will also contribute to further research of conservation of Bulbophyllum species.
