Carotenoids are important phytonutrients with antioxidant properties,and are widely used in foods and feedstuffs as Supplements.Astaxanthin,a red-colored ketocarotenoid,has strong antioxidant activity and thus can ben...Carotenoids are important phytonutrients with antioxidant properties,and are widely used in foods and feedstuffs as Supplements.Astaxanthin,a red-colored ketocarotenoid,has strong antioxidant activity and thus can benefit human health.However,astaxanthin is not produced in most higher plants.Here we report the bioengineering of astaxanthin biosynthesis in rice endosperm by introducing four synthetic genes,sZmPSY1,sPaCrtl,sCrBKT,and sHpBHY,which encode the enzymes phytoene synthase,phytoene desaturase,β-carotene ketolase,and β-carotene hydroxylase,respectively.Transgneic overexpression of two (sZmPSY1 and sPaCrtl),three (sZmPSY1,sPaCrtl and sCrBKT),and all these four genes driven by rice endosperm-specific promoters established the Carotenoid/ketocarotenoid/astaxanthin biosynthetic pathways in the endosperm and thus resulted in various types of germplasm,from the yellow-grained β-caro- tene-enriched Golden Rice to orange-red-grained Canthaxanthin Rice and Astaxanthin Rice,respectively. Grains Of Astaxanthin Rice were enriched with astaxanthin in the endosperm and had higher antioxidant activity.These results proved that introduction of a minimal set of four transgenes enables de novo biosynthesis of astaxanthin in therice endosperm.This work provides a Successful example for synthetic biology in plants and biofortification in crops;the biofortified rice products generated by this study could be consumed as health-promoting foods and processed tO produce dietary supplements.展开更多
The stress-associated protein （SAP） multigene family is conserved in both animals and plants. Its function in some an- imals and plants are known, but it is yet to be deciphered in wheat （Triticum aestivum L.）. We...The stress-associated protein （SAP） multigene family is conserved in both animals and plants. Its function in some an- imals and plants are known, but it is yet to be deciphered in wheat （Triticum aestivum L.）. We identified the wheat gene TaSAP17-D, a member of the SAP gene family with an AN1/AN1 conserved domain. Subcellular localization indicated that TaSAP17-D localized to the nucleus, cytoplasm, and cell membrane. Expression pattern analyses revealed that TaSAP17-D was highly expressed in seedlings and was involved in NaCI response, polyethylene glycol （PEG）, cold, and exogenous abscisic acid （ABA）. Constitutive expression of TaSAP17-D in transgenic Arabidopsis resulted in enhanced tolerance to salt stress, confirmed by improved multiple physiological indices and significantly upregulated marker genes related to salt stress response. Our results suggest that TaSAP17-D is a candidate gene that can be used to protect crop plants from salt stress.展开更多
For the very first time,morpho-anatomical features of both fruiting bodies as well as below-ground structures have been confronted with a newly produced multigene phylogeny of root symbiotic basidiomycetes using one o...For the very first time,morpho-anatomical features of both fruiting bodies as well as below-ground structures have been confronted with a newly produced multigene phylogeny of root symbiotic basidiomycetes using one of the most speciose genera of ectomycorrhizal fungi(Russula,Russulales)as an example.In this first of two papers,the authors focus more specifically on below-ground structures.Our five-gene phylogeny divides the genus in five main clades,here interpreted as representing seven subgenera,all significantly supported.Although more conserved than features of fruiting bodies,the anatomy of ectomycorrhiza does not allow for an unambiguous characterization of the main clades resolved by phylogenetic analysis,but the anatomy of ectomycorrhiza performs better to naturally classify the species of this genus.Features of fruiting bodies remain much more adequate for the delimitation of terminal clades and are irreplaceable for morphological species identification.Tropical taxa mostly nest in ancient lineages,but are also present in some terminal clades of otherwise temperate species groups.The shift from plectenchymatic to pseudoparenchymatic ECM outer mantle structures happened most likely already in the paleotropics,and is here hypothesized to have facilitated a major diversification of the genus with new hosts in the northern hemisphere.Available data as well as our own observations on below ground structures of several Lactifluus species suggests that this genus shares with Russula the absence of lactifers in ECM mantles and rhizomorphs,contrary to species of Lactarius where lactifers are always present.First observations on rhizomorphs of species in Multifurca confirm the presence of vessel-like and ladder-like hyphae,also found in the other agarioid genera of this family,while distinct lactifers are only present in the lactarioid,but not in russuloid members of this genus.展开更多
The rice （Oryza sativa L.） Xa3/Xa26 gene, conferring race-specific resistance to bacterial blight disease and encoding a leucine-rich repeat （LRR） receptor kinase-like protein, belongs to a multigene family consis...The rice （Oryza sativa L.） Xa3/Xa26 gene, conferring race-specific resistance to bacterial blight disease and encoding a leucine-rich repeat （LRR） receptor kinase-like protein, belongs to a multigene family consisting of tandem clustered homologous genes, colocalizing with several uncharacterized genes for resistance to bacterial blight or fungal blast. To provide more information on the expressional and biochemical characteristics of the Xa3/Xa26 family, we analyzed the family members. Four Xa3/Xa26 family members in the indica rice variety Teqing, which carries a bacterial blight resistance gene with a chromosomal location tightly linked to Xa3/Xa26, and five Xa3/Xa26 family members in the japonica rice variety Nipponbare, which carries at least one uncharacterized blast resistance gene, were constitutively expressed in leaf tissue. The result suggests that some of the family members may be candidates of these uncharacterized resistance genes. At least five putative N-glycosylation sites in the LRR domain of XA3/XA26 protein are not glycosylated. The XA3/XA26 and its family members MRKa and MRKc all possess the consensus sequences of paired cysteines, which putatively function in dimerization of the receptor proteins for signal transduction, immediately before the first LRR and immediately after the last LRR. However, no homo-dimer between the XA3/XA26 molecules or hetero-dimer between XA3/XA26 and MRKa or MRKc were formed, indicating that XA3/XA26 protein might function either as a monomer or a hetero-dimer formed with other protein outside of the XA3/XA26 family. These results provide valuable information for further extensive investigation into this multiple protein family.展开更多
Objective: This study aims to establish a method for highly parallel multiplexed detection of genetic mutations in Chinese lung cancer samples through Agena i PLEX chemistry and matrix-assisted laser desorption ioniza...Objective: This study aims to establish a method for highly parallel multiplexed detection of genetic mutations in Chinese lung cancer samples through Agena i PLEX chemistry and matrix-assisted laser desorption ionization time-of-flight analysis on Mass ARRAY mass spectrometry platform.Methods: We reviewed the related literature and data on lung cancer treatments. We also identified 99 mutation hot spots in 13 target genes closely related to the pathogenesis, drug resistance, and metastasis of lung cancer. A total of 297 primers, composed of99 paired forward and reverse amplification primers and 99 matched extension primers, were designed using Assay Design software. The detection method was established by analyzing eight cell lines and six lung cancer specimens. The proposed method was then validated through comparisons by using a Lung Carta^(TM) kit. The sensitivity and specificity of the proposed method were evaluated by directly sequencing EGFR and KRAS genes in 100 lung cancer cases.Results: The proposed method was able to detect multiplex genetic mutations in lung cancer cell lines. This finding was consistent with the observations on previously reported mutations. The proposed method can also detect such mutations in clinical lung cancer specimens. This result was consistent with the observations with Lung Carta^(TM) kit. However, an FGFR2 mutation was detected only through the proposed method. The measured sensitivity and specificity were 100% and 96.3%, respectively.Conclusions: The proposed Mass ARRAY technology-based multiplex method can detect genetic mutations in Chinese lung cancer patients. Therefore, the proposed method can be applied to detect mutations in other cancer tissues.展开更多
Objective:There are many hereditary breast cancer patients in China,and multigene panel testing has been a new paradigm of genetic testing for these patients and their relatives.However,the magnitude of breast cancer ...Objective:There are many hereditary breast cancer patients in China,and multigene panel testing has been a new paradigm of genetic testing for these patients and their relatives.However,the magnitude of breast cancer risks related to multiple breast cancer susceptibility genes are largely unknown in Chinese women.Methods:We screened pathogenic variants in 15 established or potential breast cancer susceptibility genes from 8,067 consecutive Chinese female breast cancer patients and 13,129 Chinese cancer-free female controls.These breast cancer patients were unselected for age at diagnosis or family history.Results:We found that pathogenic variants in TP53[odds ratio(OR):16.9,95%confidence interval(CI):5.2–55.2];BRCA2(OR:10.4,95%CI:7.6–14.2);BRCA1(OR:9.7,95%CI:6.3–14.8);and PALB2(OR:5.2,95%CI:3.0–8.8)were associated with a high risk of breast cancer.ATM,BARD1,CHEK2,and RAD51D were associated with a moderate risk of breast cancer with ORs ranging from 2-fold to 4-fold.In contrast,pathogenic variants of NBN,RAD50,BRIP1,and RAD51C were not associated with increased risk of breast cancer in Chinese women.The pathogenic variants of PTEN,CDH1,and STK11 were very rare,so they had a limited contribution to Chinese breast cancer.Patients with pathogenic variants of TP53,BRCA1,BRCA2,and PALB2 more often had earlyonset breast cancer,bilateral breast cancer,and a family history of breast cancer and/or any cancer.Conclusions:This study provided breast cancer risk assessment data for multiple genes in Chinese women,which is useful for genetic testing and clinical management of Chinese hereditary breast cancer.展开更多
Brown algae （Chromista, Ochrophyta, Phaeophyceae） are a large group of multicellular algae that play im-portant roles in the ocean＇s ecosystem and biodiversity. However, poor molecular bases for studying their phyl...Brown algae （Chromista, Ochrophyta, Phaeophyceae） are a large group of multicellular algae that play im-portant roles in the ocean＇s ecosystem and biodiversity. However, poor molecular bases for studying their phylogenetic evolutions and novel metabolic characteristics have hampered progress in the field. In this study, we sequenced the de novo transcriptome of 18 major species of brown algae in China, covering six orders and seven families, using the high-throughput sequencing platform Illumina HiSeq 2000. From the transcriptome data of these 18 species and publicly available genome data of Ectocarpus siliculosus and Phaeodactylum tricornutum, we identified 108 nuclear-generated orthologous genes and clarified the phy-logenetic relationships among these brown algae based on a multigene method. These brown algae could be separated into two clades：Clade Ishigeales-Dictyotales and Clade Ectocarpales-Laminariales-Desmares-tiale-Fucales. The former was at the base of the phylogenetic tree, indicating its early divergence, while the latter was divided into two branches, with Order Fucales diverging from Orders Ectocarpales, Laminariales, and Desmarestiale. In our analysis of taxonomy-contentious species, Sargassum fusiforme and Saccharina sculpera were found to be closely related to genera Sargassum and Saccharina, respectively, while Petalonia fascia showed possible relation to genus Scytosiphon. The study provided molecular evidence for the phylo-genetic taxonomy of brown algae.展开更多
African swine fever(ASF)is etiologically an acute,highly contagious and hemorrhagic disease caused by African swine fever virus(ASFV).Due to its genetic variation and phenotypic diversity,until now,no efficient commer...African swine fever(ASF)is etiologically an acute,highly contagious and hemorrhagic disease caused by African swine fever virus(ASFV).Due to its genetic variation and phenotypic diversity,until now,no efficient commercial vaccines or therapeutic options are available.The ASFV genome contains a conserved middle region and two flexible ends that code for five multigene families(MGFs),while the biological functions of the MGFs are not fully characterized.Here,ASFV MGF505-2R-deficient mutant ASFV-Δ2R was constructed based on a highly virulent genotype II field isolate ASFV CN/GS/2018 currently circulating in China.Transcriptomic profiling demonstrated that ASFV-Δ2R was capable of inducing a larger number of differentially expressed genes(DEGs)compared with ASFV CN/GS/2018.Hierarchical clustering of up-regulated DEGs revealed that ASFV-Δ2R induced the most dramatic expression of interferon-related genes and inflammatory and innate immune genes,as further validated by RT-qPCR.The GO and KEGG pathway analysis identified significantly enriched pathways involved in pathogen recognition and innate antiviral immunity.Conversely,pharmacological activation of those antiviral immune responses by exogenous cytokines,including type I/II IFNs,TNF-αand IL-1β,exerted combinatory effects and synergized in antiviral capacity against ASFV replication.Collectively,MGF505-2R is a newly identified inhibitor of innate immunity potentially implicated in immune evasion.展开更多
Recently the developed single guide(sg)RNA-guided clustered regularly interspaced short palindromic repeats/associated protein 9 nuclease(CRISPR/Cas9) technology has opened a new avenue for antiviral therapy. The CRIS...Recently the developed single guide(sg)RNA-guided clustered regularly interspaced short palindromic repeats/associated protein 9 nuclease(CRISPR/Cas9) technology has opened a new avenue for antiviral therapy. The CRISPR/Cas9 system uniquely allows targeting of multiple genome sites simultaneously. However, there are relatively few applications of CRISPR/Cas9 multigene editing to target insect viruses. To address the need for sustained delivery of a multiplex CRISPR/Cas9-based genome-editing vehicle against insect viruses, we developed a one-vector(pSL1180-Cas9-U6-sgRNA) system that expresses multiple sgRNA and Cas9 protein to excise Bombyx mori nucleopolyhedrovirus(BmNPV) in insect cells.We screened the immediate-early-1 gene(ie-1), the major envelope glycoprotein gene(gp64), and the late expression factor gene(lef-11), and identified multiple sgRNA editing sites through flow cytometry and viral DNA replication analysis. In addition, we constructed a multiplex editing vector(PSL1180-Cas9-sgIE1-sgLEF11-sgGP64, sgMultiple) to efficiently regulate multiplex gene-editing and inhibit BmNPV replication after viral infection. This is the first report of the application of a multiplex CRISPR/Cas9 system to inhibit insect virus replication. This multiplex system can significantly enhance the potential of CRISPR/Cas9-based multiplex genome engineering in insect virus.展开更多
Although the high degree of non-monophyly and parallel evolution has long been acknowledged within the mazaediate Caliciaceae(Lecanoromycetes,Ascomycota),a natural re-classification of the group has not yet been accom...Although the high degree of non-monophyly and parallel evolution has long been acknowledged within the mazaediate Caliciaceae(Lecanoromycetes,Ascomycota),a natural re-classification of the group has not yet been accomplished.Here we constructed a multigene phylogeny of the Caliciaceae-Physciaceae clade in order to resolve the detailed relationships within the group,to propose a revised classification,and to perform a dating study.The few characters present in the available fossil and the complex character evolution of the group affects the interpretation of morphological traits and thus influences the assignment of the fossil to specific nodes in the phylogeny,when divergence time analyses are carried out.Alternative fossil assignments resulted in very different time estimates and the comparison with the analysis based on a secondary calibration demonstrates that the most likely placement of the fossil is close to a terminal node rather than a basal placement in the Calicium clade.Our dating analysis show two successive events giving rise to main clades of mazaediate taxa within the Caliciaceae,in the Upper-Lower Cretaceous boundary and in the Paleocene.As a result of this study,Cyphelium is synonymized with Calicium,Acolium is resurrected,and the new genera Allocalicium and Pseudothelomma are described.Twelve new combinations are proposed:Acolium karelicum,Acolium marcianum,Allocalicium adaequatum,Calicium carolinianum,Calicium lecideinum,Calicium lucidum,Calicium notarisii,Calicium pinicola,Calicium trachyliodes,Pseudothelomma occidentale,Pseudothelomma ocellatum and Thelomma brunneum.A key for the mazaedium-producing Caliciaceae is included.展开更多
A new classification of the taxa formerly ascribed to Biannulariaceae(≡Catathelasmataceae),viz.Catathelasma(type),Callistosporium,Pleurocollybia,Macrocybe,Pseudolaccaria,Guyanagarika and Anupama is here proposed.Phyl...A new classification of the taxa formerly ascribed to Biannulariaceae(≡Catathelasmataceae),viz.Catathelasma(type),Callistosporium,Pleurocollybia,Macrocybe,Pseudolaccaria,Guyanagarika and Anupama is here proposed.Phylogenetic inference of the Tricholomatineae based on the analysis of a combined dataset of nuclear genes including ITS,18S and 28S rDNA,tef1 and rpb2 data supports significantly a monophyletic origin of the aforementioned genera with the exception of Catathelasma,which is significantly related with Bonomyces and Cleistocybe.Biannulariaceae is therefore emended to include the clade formed by Catathelasma,Bonomyces and Cleistocybe.Consequently,the new family Callistosporiaceae is proposed to name the clade containing Callistosporium(=Pleurocollybia)and related genera.Species of Callistosporium with distant lamellae,long hygrophoroid basidia and large amygdaliform spores are accommodated in the new genus Xero-phorus.Finally,the new species Callistosporium pseudofelleum and Macrocybe sardoa are described,Clitocybe hesleri and C.fellea are combined into Callistosporium and Pseudolaccaria,respectively,and Callistosporium olivascens var.donadinii is upgraded to species rank and combined into Xerophorus.展开更多
Anthostomella has long been regarded as a large,but polyphyletic genus in the family Xylariaceae,but species in this group generally lack phylogenetic data.In this study,14 anthostomella-like taxa collected from Italy...Anthostomella has long been regarded as a large,but polyphyletic genus in the family Xylariaceae,but species in this group generally lack phylogenetic data.In this study,14 anthostomella-like taxa collected from Italy,were studied using both morphology and molecular data.Single ascospore isolates were obtained and the asexual morphs of five taxa established.The phylogenetic relationships of the xylariaceous taxa were inferred using combined ITS,RPB2,βtubulin and LSU gene regions.We introduce new sequence data for 24 with included the 14 new anthostomella-like taxa.The subfamilies Hypoxyloideae and Xylarioideae within Xylariaceae were recognized as the two major clades with high bootstrap support.Within the two clades 21 subclades were resolved and the anthostomella-like taxa clustered in five of these subclades indicating that the genus is polyphyletic.Anthostomella sensu stricto comprised A.forlicesenica,A.formosa,A.helicofissa,A.rubicola and A.obesa.The A.formosa and A.rubicola collections morphologically closely resemble the type specimens and therefore we designate reference specimens.Three new species Anthostomella helicofissa,A.forlicesenica and A.obesa are also introduced.Four distinct lineages of anthostomella-like taxa correspondent to four new genera,Anthocanalis,Brunneiperidium,Lunatiannulus and Pyriformiascoma,which are also introduced,while one clustered in Astrocystis and is introduced as a new species.Keys to the new anthostomella-like genera and species examined in this study are provided.展开更多
Approximately 1 in 8 women will develop breast cancer during their lifetime and the risk factors include age, family history, and reproductive factors. In women with a family history of breast cancer, there is a propo...Approximately 1 in 8 women will develop breast cancer during their lifetime and the risk factors include age, family history, and reproductive factors. In women with a family history of breast cancer, there is a proportion in which a gene mutation can be the cause of the predisposition for breast cancer. A careful assessment of family and clinical history should be performed in these women in order to determine if a genetic counseling referral is indicated. In cases of hereditary breast cancer, genetic testing with a multigene panel can identify specific genetic mutations in over 100 genes. The most common genes mutated in hereditary breast cancer are the high-penetrance BRCA1 and BRCA2 genes. In addition, other mutations in high-penetrance genes in familial cancer syndromes and mutations in DNA repair genes can cause hereditary breast cancer. Mutations in low-penetrance genes and variants of uncertain signifcance may play a role in breast cancer development, but the magnitude and scope of risk in these cases remain unclear, thus the clinical utility of testing for these mutations is uncertain. In women with high-penetrance genetic mutations or lifetime risk of breast cancer 〉 20%, risk-reducing interventions, such as intensive screening, surgery, and chemoprevention, can decrease the incidence and mortality of breast cancer.展开更多
BACKGROUND Colonic adenomatous polyposis of unknown etiology(CPUE)is an adenomatous polyposis phenotype that resembles Familial Adenomatous Polyposis(FAP)even though no germline pathogenic variant is identified.AIM We...BACKGROUND Colonic adenomatous polyposis of unknown etiology(CPUE)is an adenomatous polyposis phenotype that resembles Familial Adenomatous Polyposis(FAP)even though no germline pathogenic variant is identified.AIM We sought to better characterize the clinical features and outcomes in a cohort of CPUE patients.METHODS This is a retrospective case series of patients 18 years old or older with adenomatous oligopolyposis(between 10-100 adenomas)and negative genetic testing,identified through the Hereditary Gastrointestinal Cancer Database at Massachusetts General Hospital,a tertiary academic referral center.A retrospective chart review was performed with a focus on demographics,alcohol and tobacco use,medication use,familial malignancy and polyp burden,genetic testing information,endoscopic surveillance data including the corresponding histopathology,colonic and extracolonic malignancies,mortality events,and their etiology.Spearman correlation and Pearson Chi-square test(or Fisher's exact test)were used for continuous and categorical variables respectively.RESULTS CPUE patients were primarily male(69%)and presented for genetic counseling at 63.7 years.Only 2 patients(2.9%)reported a first-degree relative with polyposis.During an average surveillance period of 12.3 years,0.5 colonoscopies per year were performed.Patients developed 2.3 new adenomas per year.4(5.7%)were diagnosed with colorectal cancer(CRC)at a mean age of 66 years,and 3 were diagnosed prior to the onset of oligopolyposis.7(10%)required colectomy due to advanced dysplasia or polyp burden.With respect to upper gastrointestinal manifestations,1 patient had a gastric adenoma,but there were no cases of gastric or small bowel polyposis.During surveillance,10(14%)patients died at a mean age of 72,and none were due to CRC.CONCLUSION CPUE is distinct from familial adenomatous polyposis(FAP)syndrome and the use of FAP surveillance guidelines may result in unnecessarily frequent upper and lower endoscopies.展开更多
Grapevine(Vitis vinifera L.)is an economically important fruit crop in the world,and China ranks first in the production of grapes with approximately 15%of the world’s total yield.However,diseases that cause the deat...Grapevine(Vitis vinifera L.)is an economically important fruit crop in the world,and China ranks first in the production of grapes with approximately 15%of the world’s total yield.However,diseases that cause the death of grapevine shoots pose a severe threat to the production of grapes.In this study,the fungus Neopestalotiopsis eucalypti was identified as a causal pathogen of grapevine shoot rot based on the morphology of conidia and a phylogenetic analysis.The phylogenetic analysis was performed with three isolates based on the combined sequence of internal transcribed spacer(ITS)region of ribosomal DNA,part of the translation elongation factor 1-alpha(Tef)and theβ-tubulin(Tub2)genes.The three isolates were all identified as N.eucalypti.Pathogenicity tests of the three fungal isolates were conducted on grapevines shoots in vitro and in vivo.The results showed that all three fungal isolates caused severe rot lesions on the inoculated grapevine shoots,and N.eucalypti was re-isolated from the inoculated grapevine shoots.Therefore,N.eucalypti was confirmed as a causal agent of the grapevine shoot rot.This is the first report of N.eucalypti causing grapevine shoot disease in China.展开更多
Understanding how many species exist and the processes by which they form remains a central topic of ecological and evolutionary biology,but represents a special challenge within microbial groups.The lichen-forming fu...Understanding how many species exist and the processes by which they form remains a central topic of ecological and evolutionary biology,but represents a special challenge within microbial groups.The lichen-forming fungi represent one of the best examples in which species evolution and diversity create patterns of high phenotypic plasticity coupled with wide geographic distributions.We sampled the lichen-forming species Tephromela atra and related species at a world-wide scale to reconstruct a phylogenetic hypothesis using three nuclear markers.Samples were also studied for morphological and chemical traits to assess how well the phenotypic relationships with species,previously segregated from T.atra,agrees with molecular data.We used a genealogical concordance approach and identified 15 monophyletic clades,which may represent independent lineages.By combining morphological and chemical characters,ecological preferences and geographic origin we distinguish six different species.Although subtle phenotypical traits are frequently used for describing previously cryptic species in fungi,the continuum of variability found in morphology and chemical patterns in T.atra prevents the description of new taxa with characteristic traits.We observed that phenotypic characters arise in parallel at local or regional scale but are not correlated with genetic isolation.Therefore,they are insufficient for characterizing species with broad geographic ranges within T.atra.展开更多
基金The National Natural Science Foundation of China (317717,40)Guangdong Province Public Interest Research and Capacity Building Special Fund (2016A020210084+2 种基金2015B020201002)and the Ministry of Agriculture of China (2016ZX080100012016ZX08009002).
文摘Carotenoids are important phytonutrients with antioxidant properties,and are widely used in foods and feedstuffs as Supplements.Astaxanthin,a red-colored ketocarotenoid,has strong antioxidant activity and thus can benefit human health.However,astaxanthin is not produced in most higher plants.Here we report the bioengineering of astaxanthin biosynthesis in rice endosperm by introducing four synthetic genes,sZmPSY1,sPaCrtl,sCrBKT,and sHpBHY,which encode the enzymes phytoene synthase,phytoene desaturase,β-carotene ketolase,and β-carotene hydroxylase,respectively.Transgneic overexpression of two (sZmPSY1 and sPaCrtl),three (sZmPSY1,sPaCrtl and sCrBKT),and all these four genes driven by rice endosperm-specific promoters established the Carotenoid/ketocarotenoid/astaxanthin biosynthetic pathways in the endosperm and thus resulted in various types of germplasm,from the yellow-grained β-caro- tene-enriched Golden Rice to orange-red-grained Canthaxanthin Rice and Astaxanthin Rice,respectively. Grains Of Astaxanthin Rice were enriched with astaxanthin in the endosperm and had higher antioxidant activity.These results proved that introduction of a minimal set of four transgenes enables de novo biosynthesis of astaxanthin in therice endosperm.This work provides a Successful example for synthetic biology in plants and biofortification in crops;the biofortified rice products generated by this study could be consumed as health-promoting foods and processed tO produce dietary supplements.
基金supported by the National Key Research and Development Program of China (2016YFD0100605)the Agricultural Science and Technology Innovation Program, China (ASTIP)
文摘The stress-associated protein （SAP） multigene family is conserved in both animals and plants. Its function in some an- imals and plants are known, but it is yet to be deciphered in wheat （Triticum aestivum L.）. We identified the wheat gene TaSAP17-D, a member of the SAP gene family with an AN1/AN1 conserved domain. Subcellular localization indicated that TaSAP17-D localized to the nucleus, cytoplasm, and cell membrane. Expression pattern analyses revealed that TaSAP17-D was highly expressed in seedlings and was involved in NaCI response, polyethylene glycol （PEG）, cold, and exogenous abscisic acid （ABA）. Constitutive expression of TaSAP17-D in transgenic Arabidopsis resulted in enhanced tolerance to salt stress, confirmed by improved multiple physiological indices and significantly upregulated marker genes related to salt stress response. Our results suggest that TaSAP17-D is a candidate gene that can be used to protect crop plants from salt stress.
文摘For the very first time,morpho-anatomical features of both fruiting bodies as well as below-ground structures have been confronted with a newly produced multigene phylogeny of root symbiotic basidiomycetes using one of the most speciose genera of ectomycorrhizal fungi(Russula,Russulales)as an example.In this first of two papers,the authors focus more specifically on below-ground structures.Our five-gene phylogeny divides the genus in five main clades,here interpreted as representing seven subgenera,all significantly supported.Although more conserved than features of fruiting bodies,the anatomy of ectomycorrhiza does not allow for an unambiguous characterization of the main clades resolved by phylogenetic analysis,but the anatomy of ectomycorrhiza performs better to naturally classify the species of this genus.Features of fruiting bodies remain much more adequate for the delimitation of terminal clades and are irreplaceable for morphological species identification.Tropical taxa mostly nest in ancient lineages,but are also present in some terminal clades of otherwise temperate species groups.The shift from plectenchymatic to pseudoparenchymatic ECM outer mantle structures happened most likely already in the paleotropics,and is here hypothesized to have facilitated a major diversification of the genus with new hosts in the northern hemisphere.Available data as well as our own observations on below ground structures of several Lactifluus species suggests that this genus shares with Russula the absence of lactifers in ECM mantles and rhizomorphs,contrary to species of Lactarius where lactifers are always present.First observations on rhizomorphs of species in Multifurca confirm the presence of vessel-like and ladder-like hyphae,also found in the other agarioid genera of this family,while distinct lactifers are only present in the lactarioid,but not in russuloid members of this genus.
基金Supported by the National Program on the Development of Basic Research in China and the National Natural Science Foundation of China. Publication of this paper is supported by the National Natural Science Foundation of China （30624808）.
文摘The rice （Oryza sativa L.） Xa3/Xa26 gene, conferring race-specific resistance to bacterial blight disease and encoding a leucine-rich repeat （LRR） receptor kinase-like protein, belongs to a multigene family consisting of tandem clustered homologous genes, colocalizing with several uncharacterized genes for resistance to bacterial blight or fungal blast. To provide more information on the expressional and biochemical characteristics of the Xa3/Xa26 family, we analyzed the family members. Four Xa3/Xa26 family members in the indica rice variety Teqing, which carries a bacterial blight resistance gene with a chromosomal location tightly linked to Xa3/Xa26, and five Xa3/Xa26 family members in the japonica rice variety Nipponbare, which carries at least one uncharacterized blast resistance gene, were constitutively expressed in leaf tissue. The result suggests that some of the family members may be candidates of these uncharacterized resistance genes. At least five putative N-glycosylation sites in the LRR domain of XA3/XA26 protein are not glycosylated. The XA3/XA26 and its family members MRKa and MRKc all possess the consensus sequences of paired cysteines, which putatively function in dimerization of the receptor proteins for signal transduction, immediately before the first LRR and immediately after the last LRR. However, no homo-dimer between the XA3/XA26 molecules or hetero-dimer between XA3/XA26 and MRKa or MRKc were formed, indicating that XA3/XA26 protein might function either as a monomer or a hetero-dimer formed with other protein outside of the XA3/XA26 family. These results provide valuable information for further extensive investigation into this multiple protein family.
基金supported by the Special Fund for Research in the Public Interest from the National Health and Family Planning Commission of PRC (Grant No. 201402031)the Key Lab System Project of the Guangdong Science and Technology Department (Grant No. 2012A061400006)the Special Fund for Research in the Public Interest and Capacity Building from the Guangdong Science and Technology Department (Grant No. 2014A020212225)
文摘Objective: This study aims to establish a method for highly parallel multiplexed detection of genetic mutations in Chinese lung cancer samples through Agena i PLEX chemistry and matrix-assisted laser desorption ionization time-of-flight analysis on Mass ARRAY mass spectrometry platform.Methods: We reviewed the related literature and data on lung cancer treatments. We also identified 99 mutation hot spots in 13 target genes closely related to the pathogenesis, drug resistance, and metastasis of lung cancer. A total of 297 primers, composed of99 paired forward and reverse amplification primers and 99 matched extension primers, were designed using Assay Design software. The detection method was established by analyzing eight cell lines and six lung cancer specimens. The proposed method was then validated through comparisons by using a Lung Carta^(TM) kit. The sensitivity and specificity of the proposed method were evaluated by directly sequencing EGFR and KRAS genes in 100 lung cancer cases.Results: The proposed method was able to detect multiplex genetic mutations in lung cancer cell lines. This finding was consistent with the observations on previously reported mutations. The proposed method can also detect such mutations in clinical lung cancer specimens. This result was consistent with the observations with Lung Carta^(TM) kit. However, an FGFR2 mutation was detected only through the proposed method. The measured sensitivity and specificity were 100% and 96.3%, respectively.Conclusions: The proposed Mass ARRAY technology-based multiplex method can detect genetic mutations in Chinese lung cancer patients. Therefore, the proposed method can be applied to detect mutations in other cancer tissues.
基金This study was supported by grants from the National Natural Science Foundation of China(Grant Nos.81772824,81372832,and 81974422).
文摘Objective:There are many hereditary breast cancer patients in China,and multigene panel testing has been a new paradigm of genetic testing for these patients and their relatives.However,the magnitude of breast cancer risks related to multiple breast cancer susceptibility genes are largely unknown in Chinese women.Methods:We screened pathogenic variants in 15 established or potential breast cancer susceptibility genes from 8,067 consecutive Chinese female breast cancer patients and 13,129 Chinese cancer-free female controls.These breast cancer patients were unselected for age at diagnosis or family history.Results:We found that pathogenic variants in TP53[odds ratio(OR):16.9,95%confidence interval(CI):5.2–55.2];BRCA2(OR:10.4,95%CI:7.6–14.2);BRCA1(OR:9.7,95%CI:6.3–14.8);and PALB2(OR:5.2,95%CI:3.0–8.8)were associated with a high risk of breast cancer.ATM,BARD1,CHEK2,and RAD51D were associated with a moderate risk of breast cancer with ORs ranging from 2-fold to 4-fold.In contrast,pathogenic variants of NBN,RAD50,BRIP1,and RAD51C were not associated with increased risk of breast cancer in Chinese women.The pathogenic variants of PTEN,CDH1,and STK11 were very rare,so they had a limited contribution to Chinese breast cancer.Patients with pathogenic variants of TP53,BRCA1,BRCA2,and PALB2 more often had earlyonset breast cancer,bilateral breast cancer,and a family history of breast cancer and/or any cancer.Conclusions:This study provided breast cancer risk assessment data for multiple genes in Chinese women,which is useful for genetic testing and clinical management of Chinese hereditary breast cancer.
基金The National Natural Science Foundation of China under contract Nos 31140070,31271397 and 41206116the algal transcrip-tome sequencing was supported by 1KP Project(www.onekp.com)
文摘Brown algae （Chromista, Ochrophyta, Phaeophyceae） are a large group of multicellular algae that play im-portant roles in the ocean＇s ecosystem and biodiversity. However, poor molecular bases for studying their phylogenetic evolutions and novel metabolic characteristics have hampered progress in the field. In this study, we sequenced the de novo transcriptome of 18 major species of brown algae in China, covering six orders and seven families, using the high-throughput sequencing platform Illumina HiSeq 2000. From the transcriptome data of these 18 species and publicly available genome data of Ectocarpus siliculosus and Phaeodactylum tricornutum, we identified 108 nuclear-generated orthologous genes and clarified the phy-logenetic relationships among these brown algae based on a multigene method. These brown algae could be separated into two clades：Clade Ishigeales-Dictyotales and Clade Ectocarpales-Laminariales-Desmares-tiale-Fucales. The former was at the base of the phylogenetic tree, indicating its early divergence, while the latter was divided into two branches, with Order Fucales diverging from Orders Ectocarpales, Laminariales, and Desmarestiale. In our analysis of taxonomy-contentious species, Sargassum fusiforme and Saccharina sculpera were found to be closely related to genera Sargassum and Saccharina, respectively, while Petalonia fascia showed possible relation to genus Scytosiphon. The study provided molecular evidence for the phylo-genetic taxonomy of brown algae.
基金supported by grants from the National Key R&D Program of China(2021YFD1801300)the Key-Area Research and Development Program of Guangdong Province(grant number 2019B020211003)+2 种基金the Chinese Academy of Agricultural Science and Technology Innovation Project(grants number CAAS-ZDRW202006 and CAAS-ASTIP-2021-LVRI)Technology Major Projects of Gansu Province(20ZD7A006 and NCC0006)as well as funding from the director of Lanzhou Veterinary Research Institute(LVRI-SZJJ-202106).
文摘African swine fever(ASF)is etiologically an acute,highly contagious and hemorrhagic disease caused by African swine fever virus(ASFV).Due to its genetic variation and phenotypic diversity,until now,no efficient commercial vaccines or therapeutic options are available.The ASFV genome contains a conserved middle region and two flexible ends that code for five multigene families(MGFs),while the biological functions of the MGFs are not fully characterized.Here,ASFV MGF505-2R-deficient mutant ASFV-Δ2R was constructed based on a highly virulent genotype II field isolate ASFV CN/GS/2018 currently circulating in China.Transcriptomic profiling demonstrated that ASFV-Δ2R was capable of inducing a larger number of differentially expressed genes(DEGs)compared with ASFV CN/GS/2018.Hierarchical clustering of up-regulated DEGs revealed that ASFV-Δ2R induced the most dramatic expression of interferon-related genes and inflammatory and innate immune genes,as further validated by RT-qPCR.The GO and KEGG pathway analysis identified significantly enriched pathways involved in pathogen recognition and innate antiviral immunity.Conversely,pharmacological activation of those antiviral immune responses by exogenous cytokines,including type I/II IFNs,TNF-αand IL-1β,exerted combinatory effects and synergized in antiviral capacity against ASFV replication.Collectively,MGF505-2R is a newly identified inhibitor of innate immunity potentially implicated in immune evasion.
基金supported by grants from the National Natural Science Foundation of China (Nos. 31872427 and 31572466)China Agriculture Research System (CARS-18)+1 种基金Chongqing Special Postdoctoral Science Foundation (XmT2018020)China Postdoctoral Science Foundation (2018M633309)
文摘Recently the developed single guide(sg)RNA-guided clustered regularly interspaced short palindromic repeats/associated protein 9 nuclease(CRISPR/Cas9) technology has opened a new avenue for antiviral therapy. The CRISPR/Cas9 system uniquely allows targeting of multiple genome sites simultaneously. However, there are relatively few applications of CRISPR/Cas9 multigene editing to target insect viruses. To address the need for sustained delivery of a multiplex CRISPR/Cas9-based genome-editing vehicle against insect viruses, we developed a one-vector(pSL1180-Cas9-U6-sgRNA) system that expresses multiple sgRNA and Cas9 protein to excise Bombyx mori nucleopolyhedrovirus(BmNPV) in insect cells.We screened the immediate-early-1 gene(ie-1), the major envelope glycoprotein gene(gp64), and the late expression factor gene(lef-11), and identified multiple sgRNA editing sites through flow cytometry and viral DNA replication analysis. In addition, we constructed a multiplex editing vector(PSL1180-Cas9-sgIE1-sgLEF11-sgGP64, sgMultiple) to efficiently regulate multiplex gene-editing and inhibit BmNPV replication after viral infection. This is the first report of the application of a multiplex CRISPR/Cas9 system to inhibit insect virus replication. This multiplex system can significantly enhance the potential of CRISPR/Cas9-based multiplex genome engineering in insect virus.
基金supported by grants from the Swedish Research Council(VR 621-2009-5372 and VR 621-2012-3990)。
文摘Although the high degree of non-monophyly and parallel evolution has long been acknowledged within the mazaediate Caliciaceae(Lecanoromycetes,Ascomycota),a natural re-classification of the group has not yet been accomplished.Here we constructed a multigene phylogeny of the Caliciaceae-Physciaceae clade in order to resolve the detailed relationships within the group,to propose a revised classification,and to perform a dating study.The few characters present in the available fossil and the complex character evolution of the group affects the interpretation of morphological traits and thus influences the assignment of the fossil to specific nodes in the phylogeny,when divergence time analyses are carried out.Alternative fossil assignments resulted in very different time estimates and the comparison with the analysis based on a secondary calibration demonstrates that the most likely placement of the fossil is close to a terminal node rather than a basal placement in the Calicium clade.Our dating analysis show two successive events giving rise to main clades of mazaediate taxa within the Caliciaceae,in the Upper-Lower Cretaceous boundary and in the Paleocene.As a result of this study,Cyphelium is synonymized with Calicium,Acolium is resurrected,and the new genera Allocalicium and Pseudothelomma are described.Twelve new combinations are proposed:Acolium karelicum,Acolium marcianum,Allocalicium adaequatum,Calicium carolinianum,Calicium lecideinum,Calicium lucidum,Calicium notarisii,Calicium pinicola,Calicium trachyliodes,Pseudothelomma occidentale,Pseudothelomma ocellatum and Thelomma brunneum.A key for the mazaedium-producing Caliciaceae is included.
文摘A new classification of the taxa formerly ascribed to Biannulariaceae(≡Catathelasmataceae),viz.Catathelasma(type),Callistosporium,Pleurocollybia,Macrocybe,Pseudolaccaria,Guyanagarika and Anupama is here proposed.Phylogenetic inference of the Tricholomatineae based on the analysis of a combined dataset of nuclear genes including ITS,18S and 28S rDNA,tef1 and rpb2 data supports significantly a monophyletic origin of the aforementioned genera with the exception of Catathelasma,which is significantly related with Bonomyces and Cleistocybe.Biannulariaceae is therefore emended to include the clade formed by Catathelasma,Bonomyces and Cleistocybe.Consequently,the new family Callistosporiaceae is proposed to name the clade containing Callistosporium(=Pleurocollybia)and related genera.Species of Callistosporium with distant lamellae,long hygrophoroid basidia and large amygdaliform spores are accommodated in the new genus Xero-phorus.Finally,the new species Callistosporium pseudofelleum and Macrocybe sardoa are described,Clitocybe hesleri and C.fellea are combined into Callistosporium and Pseudolaccaria,respectively,and Callistosporium olivascens var.donadinii is upgraded to species rank and combined into Xerophorus.
基金The authors appreciate the financial support and postgraduate scholarship provided by State Key Laboratory of Mycology,Institute of Microbiology,Chinese Academy of Sciences,Beijing and the Mushroom Research Foundation,Chiang Mai,Thailand.The authors gratefully thank Dr Shaun Pennycook from Landcare Research University of Auckland,New Zealand for nomenclature advice on the proposed names.
文摘Anthostomella has long been regarded as a large,but polyphyletic genus in the family Xylariaceae,but species in this group generally lack phylogenetic data.In this study,14 anthostomella-like taxa collected from Italy,were studied using both morphology and molecular data.Single ascospore isolates were obtained and the asexual morphs of five taxa established.The phylogenetic relationships of the xylariaceous taxa were inferred using combined ITS,RPB2,βtubulin and LSU gene regions.We introduce new sequence data for 24 with included the 14 new anthostomella-like taxa.The subfamilies Hypoxyloideae and Xylarioideae within Xylariaceae were recognized as the two major clades with high bootstrap support.Within the two clades 21 subclades were resolved and the anthostomella-like taxa clustered in five of these subclades indicating that the genus is polyphyletic.Anthostomella sensu stricto comprised A.forlicesenica,A.formosa,A.helicofissa,A.rubicola and A.obesa.The A.formosa and A.rubicola collections morphologically closely resemble the type specimens and therefore we designate reference specimens.Three new species Anthostomella helicofissa,A.forlicesenica and A.obesa are also introduced.Four distinct lineages of anthostomella-like taxa correspondent to four new genera,Anthocanalis,Brunneiperidium,Lunatiannulus and Pyriformiascoma,which are also introduced,while one clustered in Astrocystis and is introduced as a new species.Keys to the new anthostomella-like genera and species examined in this study are provided.
文摘Approximately 1 in 8 women will develop breast cancer during their lifetime and the risk factors include age, family history, and reproductive factors. In women with a family history of breast cancer, there is a proportion in which a gene mutation can be the cause of the predisposition for breast cancer. A careful assessment of family and clinical history should be performed in these women in order to determine if a genetic counseling referral is indicated. In cases of hereditary breast cancer, genetic testing with a multigene panel can identify specific genetic mutations in over 100 genes. The most common genes mutated in hereditary breast cancer are the high-penetrance BRCA1 and BRCA2 genes. In addition, other mutations in high-penetrance genes in familial cancer syndromes and mutations in DNA repair genes can cause hereditary breast cancer. Mutations in low-penetrance genes and variants of uncertain signifcance may play a role in breast cancer development, but the magnitude and scope of risk in these cases remain unclear, thus the clinical utility of testing for these mutations is uncertain. In women with high-penetrance genetic mutations or lifetime risk of breast cancer 〉 20%, risk-reducing interventions, such as intensive screening, surgery, and chemoprevention, can decrease the incidence and mortality of breast cancer.
文摘BACKGROUND Colonic adenomatous polyposis of unknown etiology(CPUE)is an adenomatous polyposis phenotype that resembles Familial Adenomatous Polyposis(FAP)even though no germline pathogenic variant is identified.AIM We sought to better characterize the clinical features and outcomes in a cohort of CPUE patients.METHODS This is a retrospective case series of patients 18 years old or older with adenomatous oligopolyposis(between 10-100 adenomas)and negative genetic testing,identified through the Hereditary Gastrointestinal Cancer Database at Massachusetts General Hospital,a tertiary academic referral center.A retrospective chart review was performed with a focus on demographics,alcohol and tobacco use,medication use,familial malignancy and polyp burden,genetic testing information,endoscopic surveillance data including the corresponding histopathology,colonic and extracolonic malignancies,mortality events,and their etiology.Spearman correlation and Pearson Chi-square test(or Fisher's exact test)were used for continuous and categorical variables respectively.RESULTS CPUE patients were primarily male(69%)and presented for genetic counseling at 63.7 years.Only 2 patients(2.9%)reported a first-degree relative with polyposis.During an average surveillance period of 12.3 years,0.5 colonoscopies per year were performed.Patients developed 2.3 new adenomas per year.4(5.7%)were diagnosed with colorectal cancer(CRC)at a mean age of 66 years,and 3 were diagnosed prior to the onset of oligopolyposis.7(10%)required colectomy due to advanced dysplasia or polyp burden.With respect to upper gastrointestinal manifestations,1 patient had a gastric adenoma,but there were no cases of gastric or small bowel polyposis.During surveillance,10(14%)patients died at a mean age of 72,and none were due to CRC.CONCLUSION CPUE is distinct from familial adenomatous polyposis(FAP)syndrome and the use of FAP surveillance guidelines may result in unnecessarily frequent upper and lower endoscopies.
基金the financial support from the earmarked fund for China Agriculture Research System(CARS-27)
文摘Grapevine(Vitis vinifera L.)is an economically important fruit crop in the world,and China ranks first in the production of grapes with approximately 15%of the world’s total yield.However,diseases that cause the death of grapevine shoots pose a severe threat to the production of grapes.In this study,the fungus Neopestalotiopsis eucalypti was identified as a causal pathogen of grapevine shoot rot based on the morphology of conidia and a phylogenetic analysis.The phylogenetic analysis was performed with three isolates based on the combined sequence of internal transcribed spacer(ITS)region of ribosomal DNA,part of the translation elongation factor 1-alpha(Tef)and theβ-tubulin(Tub2)genes.The three isolates were all identified as N.eucalypti.Pathogenicity tests of the three fungal isolates were conducted on grapevines shoots in vitro and in vivo.The results showed that all three fungal isolates caused severe rot lesions on the inoculated grapevine shoots,and N.eucalypti was re-isolated from the inoculated grapevine shoots.Therefore,N.eucalypti was confirmed as a causal agent of the grapevine shoot rot.This is the first report of N.eucalypti causing grapevine shoot disease in China.
基金LM,MG and TS are grateful to the Austrian Science Foundation for financial support(LM for FWF Herta-Firnberg Project T481-B20,TS for FWF P25237)SPO is supported by the grant CTM2012-38222-C02-02 from the Spanish Ministry of Economy and Competitiveness.Program.
文摘Understanding how many species exist and the processes by which they form remains a central topic of ecological and evolutionary biology,but represents a special challenge within microbial groups.The lichen-forming fungi represent one of the best examples in which species evolution and diversity create patterns of high phenotypic plasticity coupled with wide geographic distributions.We sampled the lichen-forming species Tephromela atra and related species at a world-wide scale to reconstruct a phylogenetic hypothesis using three nuclear markers.Samples were also studied for morphological and chemical traits to assess how well the phenotypic relationships with species,previously segregated from T.atra,agrees with molecular data.We used a genealogical concordance approach and identified 15 monophyletic clades,which may represent independent lineages.By combining morphological and chemical characters,ecological preferences and geographic origin we distinguish six different species.Although subtle phenotypical traits are frequently used for describing previously cryptic species in fungi,the continuum of variability found in morphology and chemical patterns in T.atra prevents the description of new taxa with characteristic traits.We observed that phenotypic characters arise in parallel at local or regional scale but are not correlated with genetic isolation.Therefore,they are insufficient for characterizing species with broad geographic ranges within T.atra.
