Centella asiatica L.,a medicinal herb,has attracted substantial interest in research as well as commercial domains due to its bioactive compounds which include the pentacyclic triterpenoid centellosides,and in additio...Centella asiatica L.,a medicinal herb,has attracted substantial interest in research as well as commercial domains due to its bioactive compounds which include the pentacyclic triterpenoid centellosides,and in addition,hydroxy.In addition,hydroxycinnamic acid conjugates as well as flavonoids.The latter is the major class of secondary plant metabolites and comprises various subclasses,including anthocyanidins.Anthocyanins are rarely reported in extracts from C.asiatica and differ structurally due to a flavylium(2-phenylchromenylium)ion that carries a positive charge at the oxygen atom of the C-ring of the basic flavonoid structure.Callus of C.asiatica was initiated and propagated on synthetic media and subjected to different light regimes.White callus resulted from white fluorescent illumination,while purple callus developed in response to white light emitting diode(LED)illumination.To profile the metabolites responsible for the intense purple coloration,methanolic extracts were prepared from the two cell lines.Total phenolic,flavonoid,and anthocyanin content were determined and indicated(i)very low levels of flavonoids and anthocyanins in white callus and(ii)that anthocyanins dominate the flavonoid content of the purple callus.Extracts were subjected to untargeted ultra-high-performance liquid chromatography coupled to high-definition mass spectrometry(UHPLC–MS)to profile newly synthesized anthocyanins.Metabolite annotation was based on accurate mass determination and characteristic fragmentation patterns.Here,the reprogramming of the metabolome of white C.asiatica callus due to LED illumination is reported and the profiles of cryptic anthocyanins as well as putative flavonoid and caffeoylquinic acid co-pigments in purple callus are described.展开更多
The identification and understanding of cryptic intraspecific evolutionary units(lineages) are crucial for planning effective conservation strategies aimed at preserving genetic diversity in endangered species.However...The identification and understanding of cryptic intraspecific evolutionary units(lineages) are crucial for planning effective conservation strategies aimed at preserving genetic diversity in endangered species.However, the factors driving the evolution and maintenance of these intraspecific lineages in most endangered species remain poorly understood. In this study, we conducted resequencing of 77 individuals from 22 natural populations of Davidia involucrata, a “living fossil” dove tree endemic to central and southwest China. Our analysis revealed the presence of three distinct local lineages within this endangered species, which emerged approximately 3.09 and 0.32 million years ago. These divergence events align well with the geographic and climatic oscillations that occurred across the distributional range.Additionally, we observed frequent hybridization events between the three lineages, resulting in the formation of hybrid populations in their adjacent as well as disjunct regions. These hybridizations likely arose from climate-driven population expansion and/or long-distance gene flow. Furthermore, we identified numerous environment-correlated gene variants across the total and many other genes that exhibited signals of positive evolution during the maintenance of two major local lineages. Our findings shed light on the highly dynamic evolution underlying the remarkably similar phenotype of this endangered species. Importantly, these results not only provide guidance for the development of conservation plans but also enhance our understanding of evolutionary past for this and other endangered species with similar histories.展开更多
The genus Silurus,an important group of catfish,exhibits heterogeneous distribution in Eurasian freshwater systems.This group includes economically important and endangered species,thereby attracting considerable scie...The genus Silurus,an important group of catfish,exhibits heterogeneous distribution in Eurasian freshwater systems.This group includes economically important and endangered species,thereby attracting considerable scientific interest.Despite this interest,the lack of a comprehensive phylogenetic framework impedes our understanding of the mechanisms underlying the extensive diversity found within this genus.Herein,we analyzed 89 newly sequenced and 20 previously published mitochondrial genomes(mitogenomes)from 13 morphological species to reconstruct the phylogenetic relationships,biogeographic history,and species diversity of Silurus.Our phylogenetic reconstructions identified eight clades,supported by both maximum-likelihood and Bayesian inference.Sequence-based species delimitation analyses yielded multiple molecular operational taxonomic units(MOTUs)in several taxa,including the Silurus asotus complex(four MOTUs)and Silurus microdorsalis(two MOTUs),suggesting that species diversity is underestimated in the genus.A reconstructed time-calibrated tree of Silurus species provided an age estimate of the most recent common ancestor of approximately 37.61 million years ago(Ma),with divergences among clades within the genus occurring between 11.56 Ma and 29.44 Ma,and divergences among MOTUs within species occurring between 3.71 Ma and 11.56 Ma.Biogeographic reconstructions suggested that the ancestral area for the genus likely encompassed China and the Korean Peninsula,with multiple inferred dispersal events to Europe and Central and Western Asia between 21.78 Ma and 26.67 Ma and to Japan between 2.51 Ma and 18.42 Ma.Key factors such as the Eocene-Oligocene extinction event,onset and intensification of the monsoon system,and glacial cycles associated with sea-level fluctuations have likely played significant roles in shaping the evolutionary history of the genus Silurus.展开更多
Dumasia taxonomy and classification have long been problematic.Species within this genus have few morphological differences and plants without flowers or fruits are difficult to accurately identify.In this study,we ev...Dumasia taxonomy and classification have long been problematic.Species within this genus have few morphological differences and plants without flowers or fruits are difficult to accurately identify.In this study,we evaluated the ability of six DNA barcoding sequences,one nuclear(ITS)and five chloroplast regions(trnH-psbA,matK,rbcL,trnL-trnF,psbB-psbF),to efficiently identify Dumasia species.Most single markers or their combinations identify obvious barcoding gaps between intraspecific and interspecific genetic variation.Most combined analyses including ITS showed good species resolution and identification efficiency.We therefore suggest that ITS alone or a combination of ITS with any cpDNA marker are most suitable for DNA barcoding of Dumasia.The phylogenetic analyses clearly indicated that Dumasia yunnanensis is not monophyletic and is separated as two independent branches,which may result from cryptic differentiation.Our results demonstrate that molecular data can deepen the comprehension of taxonomy of Dumasia and provide an efficient approach for identification of the species.展开更多
The Paramesotriton caudopunctatus species group is mainly distributed in the karst mountain ecosystems of Guizhou, China. Although some species have been included in previous phylogenetic studies, the evolutionary rel...The Paramesotriton caudopunctatus species group is mainly distributed in the karst mountain ecosystems of Guizhou, China. Although some species have been included in previous phylogenetic studies, the evolutionary relationships and divergence-time of members of this species group as a whole remain unexplored. In this study, we report the sequencing of one protein coding mitochondrial gene fragment(ND2) and one nuclear gene(POMC), and use a combination of phylogenetic analyses and coalescent simulations to explore the cryptic diversity and evolutionary history of the P. caudopunctatus species group. Phylogenetic relationships revealed that the P. caudopunctatus species group is composed of two major groups, i. e., East Clade and Western-South Clade. The divergence-time and ancestral area estimation suggested that the P. caudopunctatus species group likely originated in the Doupeng Mountains in Guizhou, China at 12.34 Ma(95% HPD: 8.30–14.73), and intraspecific divergence began at about 2.17 Ma(95% HPD: 1.39–2.97). This timing coincides with the orogenesis of the Miaoling Mountains during the Late Miocene to early Pleistocene. The delimitation of species in the P. caudopunctatus species group supports the existence of the currently identified species, and consensus was confirmed across methods for the existence of least to two cryptic species within what has been traditionally considered to be P. caudopunctatus species group. This study is of significance for understanding the species formation, dispersal, and diversity of the tailed amphibians in the karst mountains ecosystem of Guizhou and the role of the Miaoling Mountains as a geographical barrier to species dispersal.展开更多
Objective:To examine the taxonomic boundaries in the Stellantchasmus populations in different hosts and reveal the cryptic speciation of the Stellantchasmus in Thailand based on both morphological and molecular approa...Objective:To examine the taxonomic boundaries in the Stellantchasmus populations in different hosts and reveal the cryptic speciation of the Stellantchasmus in Thailand based on both morphological and molecular approaches.Methods:Stellantchasmus falcatus(S.falcatus) s.l.was collected from different hosts throughout Thailand.The worms were examined and measured.The nuclear ITS2 gene and the mitochondrial COI gene were used to investigate the S.falcatus s.l.from Dermogenus pusillus and Liza subviridis.Results:Stellantchasmus was one of food-borne trematode that widely distribute throughout Thailand.The comparison of S.falcatus s.l.from Dermogenus pusillus and Liza subviridis indicated a genetic divergence of nuD NA with 3.6% and mtD NA with 19.3%,respectively.Morphological characteristics were fairly different in the ratio of body size,length of prepharynx,and ratio of organ size.Conclusions:Our results provide initial evidence that S.falcatus s.l.from different hosts tend to be a different species based on both molecular and morphological characters.Cryptic species complexes are generally found among parasites that tend to have large populations and/or rapid evolution.The degree of genetic diversity existing would suggest the practice of targeted regimes to design and minimize these lections of anthelmintic resistance in the future.展开更多
Sparids are of considerable economic importance in marine fishery and aquaculture in China, and the species diversity of this group is considered relatively high. However, the accurate species identification and delim...Sparids are of considerable economic importance in marine fishery and aquaculture in China, and the species diversity of this group is considered relatively high. However, the accurate species identification and delimitation of sparids in China remain unaddressed. In this study, we used mitochondrial cytochrome oxidase subunit ?(COI) and 16S ribosomal RNA(16S) genes to conduct DNA barcoding and species delimitation in eleven sparid species from the coastal waters of China. Based on Kimura-2 parameter genetic distances, the mean intraspecific/interspecific variation for COI and 16S were calculated as 0.004/0.152 and 0.002/0.072, respectively. All the conspecific individuals formed monophyletic clusters in neighbour-joining trees of both markers. An obvious barcoding gap was detected for each species, and a common genetic threshold of 1.3% sequence divergence was defined for species delimitation in both markers. Although the sequence variation of 16S was generally lower than that of COI, the results indicated that sparid species could be ef fectively and accurately identified and delimited by COI as well as 16S. Thus, we propose that the COI gene serve as the standard DNA barcode for sparids, and that the 16S gene could also be an ideal candidate barcode. Moreover, each of the six sparid species( Argyrops spinifer, Rhabdosargus sarba, Dentex hypselosomus, Acanthopagrus latus, Acanthopagrus australis and Acanthopagrus berda) showed high intraspecific divergence(>1.3% genetic threshold) with the remarkable geographic lineages in the Indo-West Pacific oceans, which supported that potential unrecognized cryptic species were in them. The potential cryptic diversity revealed here might be primarily attributed to the allopatric divergences caused by the long-term geographic isolation between the Indian and West Pacific oceans or between the opposite sides of the Indian Ocean. The results further suggest that a revision of taxonomic status of these species is required, followed by development of a biodiversity conservation strategy.展开更多
Background: The Brown Hawk Owl complex is said to consist of three species,the Brown Boobook(Ninox scutulata),the Chocolate Boobook(Ninox randi) and the Northern Boobook(Ninox japonica),which includes the nominate mig...Background: The Brown Hawk Owl complex is said to consist of three species,the Brown Boobook(Ninox scutulata),the Chocolate Boobook(Ninox randi) and the Northern Boobook(Ninox japonica),which includes the nominate migratory lineage Ninox japonica japonica and a mitochondrially distinct lineage of taxonomically uncertain status that has been recorded year-round at least in Taiwan.Overlap in ranges during migration and morphological similarity have led to difficulties in distinguishing the Brown Boobook from the Northern Boobook.Methods: PCR of cytochrome-b and Sanger sequencing of Ninox samples from Singapore and Brunei were used to determine sample identity.Results: Two out of four Singaporean samples and the Brunei sample were identified as Northern Boobooks.This is the first official record of this species in Singapore and represents a considerable range extension for the species.Further,the samples belong to the mitochondrially distinct lineage previously characterized in resident Taiwan Residents populations rather than to the well-known nominate migratory lineage.Conclusions: Our data show that the mitochondrial signature previously documented in resident Taiwan Residents populations of the Northern Boobook extends to migratory populations.This cryptic lineage may be more widespread in its breeding quarters,extending to the Chinese and Russian mainland,in which case the name florensis would apply to it.Further genetic and bioacoustic investigation is required to resolve the taxonomic status of this lineage.展开更多
The sweetpotato whitefly Bemisia tabaci（Homoptera：Aleyrodidae）is a destructive pest of agriculture and horticulture worldwide.Recent phylogenetic analysis using mitochondrial cytochrome oxidase 1 sequences indicate...The sweetpotato whitefly Bemisia tabaci（Homoptera：Aleyrodidae）is a destructive pest of agriculture and horticulture worldwide.Recent phylogenetic analysis using mitochondrial cytochrome oxidase 1 sequences indicates that this whitefly is a species complex including at least 24 morphologically indistinguishable but genetically distinct cryptic species.In this study,the inter-species crosses of Middle East-Asia Minor 1（MEAM1）,Mediterranean（MED）and Asia II 7 cryptic species,which were referred to as B,Q and Cv biotypes before,were conducted in two different devices,leaf cages（7 cm3）and cylinder cages（280 cm3）,and at three temperatures of 22,30 and 38°C.Results indicated that no female progeny were produced in the reciprocal cross between MEAM1×Asia II 7,between MED×Asia II 7 cryptic species neither in leaf cage nor in cylinder cages,while 0.81 and 1.37% of females in the offspring were recorded in the reciprocal cross between MEAM1×MED in leaf cage experiments.Approximately 0.95-0.98% female progeny were recorded in the reciprocal cross between MEAM1×MED at 30°C,0.77% female progeny were recorded in the single cross direction between MEAM1 × MED at 22°C,and no female progeny were found in their reciprocal cross at 38°C in leaf cage.Our findings indicated that neither space dimension nor temperature have a significant effect on the hybridization of different B.tabaci cryptic species.展开更多
Emerging evidence demonstrates that cryptic translation from RNAs previously annotated as noncoding might generate microproteins with oncogenic functions.However,the importance and underlying mechanisms of these micro...Emerging evidence demonstrates that cryptic translation from RNAs previously annotated as noncoding might generate microproteins with oncogenic functions.However,the importance and underlying mechanisms of these microproteins in alternative splicing-driven tumor progression have rarely been studied.Here,we show that the novel protein TPM3P9,encoded by the lncRNA tropomyosin 3 pseudogene 9,exhibits oncogenic activity in clear cell renal cell carcinoma(ccRCC)by enhancing oncogenic RNA splicing.Overexpression of TPM3P9 promotes cell proliferation and tumor growth.Mechanistically,TPM3P9 binds to the RRM1 domain of the splicing factor RBM4 to inhibit RBM4-mediated exon skipping in the transcription factor TCF7L2.This results in increased expression of the oncogenic splice variant TCF7L2-L,which activates NF-κB signaling via its interaction with SAM68 to transcriptionally induce RELB expression.From a clinical perspective,TPM3P9 expression is upregulated in cancer tissues and is significantly correlated with the expression of TCF7L2-L and RELB.High TPM3P9 expression or low RBM4 expression is associated with poor survival in patients with ccRCC.Collectively,our findings functionally and clinically characterize the“noncoding RNA”-derived microprotein TPM3P9 and thus identify potential prognostic and therapeutic factors in renal cancer.展开更多
Identifying cryptic species poses a substantial challenge to both biologists and naturalists due to morphological similarities.Bemisia tabaci is a cryptic species complex containing more than 44 putative species;sever...Identifying cryptic species poses a substantial challenge to both biologists and naturalists due to morphological similarities.Bemisia tabaci is a cryptic species complex containing more than 44 putative species;several of which are currently among the world's most destructive crop pests.Interpreting and delimiting the evolution of this species complex has proved problematic.To develop a comprehensive framework for species delimitation and identification,we evaluated the performance of distinct data sources both individually and in combination among numerous samples of the B.tabaci species complex acquired worldwide.Distinct datasets include full mitogenomes,single-copy nuclear genes,restriction site-associated DNA sequencing,geographic range,host speciation,and reproductive compatibility datasets.Phylogenetically,our well-supported topologies generated from three dense molecular markers highlighted the evolutionary divergence of species of the B.tabaci complex and suggested that the nuclear markers serve as a more accurate representation of B.tabaci species diversity.Reproductive compatibility datasets facilitated the identification of at least 17 different cryptic species within our samples.Native geographic range information provides a complementary assessment of species recognition,while the host range datasets provide low rate of delimiting resolution.We further summarized different data performances in species classification when compared with reproductive compatibility,indicating that combination of mtCOI divergence,nuclear markers,geographic range provide a complementary assessment of species recognition.Finally,we represent a model for understanding and untangling the cryptic species complexes based on the evidence from this study and previously published articles.展开更多
The probiotic bacterium Escherichia coli Nissle 1917(EcN)holds significant promise for use in clinical and biological industries.However,the reliance on antibiotics to maintain plasmid-borne genes has overshadowed its...The probiotic bacterium Escherichia coli Nissle 1917(EcN)holds significant promise for use in clinical and biological industries.However,the reliance on antibiotics to maintain plasmid-borne genes has overshadowed its benefits.In this study,we addressed this issue by engineering the endogenous cryptic plasmids pMUT1 and pMUT2.The non-essential elements were removed to create more stable derivatives pMUT1NR△and pMUT2HBC△.Synthetic promoters by integrating binding motifs on sigma factors were further constructed and applied for expression of Bacteroides thetaiotaomicron heparinaseⅢand the biosynthesis of ectoine.Compared to traditional antibiotic-dependent expression systems,our newly constructed antibiotic-free expression systems offer considerable advantages for clinical and synthetic biology applications.展开更多
The mountains of Southwest China comprise a significant large mountain range and biodiversity hotspot imperiled by global climate change.The high species diversity in this mountain system has long been attributed to a...The mountains of Southwest China comprise a significant large mountain range and biodiversity hotspot imperiled by global climate change.The high species diversity in this mountain system has long been attributed to a complex set of factors,and recent large-scale macroevolutionary investigations have placed a broad timeline on plant diversification that stretches from 10 million years ago(Mya)to the present.Despite our increasing understanding of the temporal mode of speciation,finer-scale populationlevel investigations are lacking to better refine these temporal trends and illuminate the abiotic and biotic influences of cryptic speciation.This is largely due to the dearth of organismal sampling among closely related species and populations,spanning the incredible size and topological heterogeneity of this region.Our study dives into these evolutionary dynamics of speciation using genomic and ecomorphological data of Stellera chamaejasme L.We identified four previously unrecognized cryptic species having indistinct morphological traits and large metapopulation of evolving lineages,suggesting a more recent diversification(~2.67-0.90 Mya),largely influenced by Pleistocene glaciation and biotic factors.These factors likely influenced allopatric speciation and advocated cyclical warming–cooling episodes along elevational gradients during the Pleistocene.The study refines the evolutionary timeline to be much younger than previously implicated and raises the concern that projected future warming may influence the alpine species diversity,necessitating increased conservation efforts.展开更多
文摘Centella asiatica L.,a medicinal herb,has attracted substantial interest in research as well as commercial domains due to its bioactive compounds which include the pentacyclic triterpenoid centellosides,and in addition,hydroxy.In addition,hydroxycinnamic acid conjugates as well as flavonoids.The latter is the major class of secondary plant metabolites and comprises various subclasses,including anthocyanidins.Anthocyanins are rarely reported in extracts from C.asiatica and differ structurally due to a flavylium(2-phenylchromenylium)ion that carries a positive charge at the oxygen atom of the C-ring of the basic flavonoid structure.Callus of C.asiatica was initiated and propagated on synthetic media and subjected to different light regimes.White callus resulted from white fluorescent illumination,while purple callus developed in response to white light emitting diode(LED)illumination.To profile the metabolites responsible for the intense purple coloration,methanolic extracts were prepared from the two cell lines.Total phenolic,flavonoid,and anthocyanin content were determined and indicated(i)very low levels of flavonoids and anthocyanins in white callus and(ii)that anthocyanins dominate the flavonoid content of the purple callus.Extracts were subjected to untargeted ultra-high-performance liquid chromatography coupled to high-definition mass spectrometry(UHPLC–MS)to profile newly synthesized anthocyanins.Metabolite annotation was based on accurate mass determination and characteristic fragmentation patterns.Here,the reprogramming of the metabolome of white C.asiatica callus due to LED illumination is reported and the profiles of cryptic anthocyanins as well as putative flavonoid and caffeoylquinic acid co-pigments in purple callus are described.
基金supported by the Second Tibetan Plateau Scientific Expedition and Research program (No. 2019QZKK0502)Strategic Priority Research Program of Chinese Academy of Sciences (No. XDB31010300)+1 种基金Fundamental Research Funds for the Central UniversitiesInternational Collaboration 111 Program (BP0719040)。
文摘The identification and understanding of cryptic intraspecific evolutionary units(lineages) are crucial for planning effective conservation strategies aimed at preserving genetic diversity in endangered species.However, the factors driving the evolution and maintenance of these intraspecific lineages in most endangered species remain poorly understood. In this study, we conducted resequencing of 77 individuals from 22 natural populations of Davidia involucrata, a “living fossil” dove tree endemic to central and southwest China. Our analysis revealed the presence of three distinct local lineages within this endangered species, which emerged approximately 3.09 and 0.32 million years ago. These divergence events align well with the geographic and climatic oscillations that occurred across the distributional range.Additionally, we observed frequent hybridization events between the three lineages, resulting in the formation of hybrid populations in their adjacent as well as disjunct regions. These hybridizations likely arose from climate-driven population expansion and/or long-distance gene flow. Furthermore, we identified numerous environment-correlated gene variants across the total and many other genes that exhibited signals of positive evolution during the maintenance of two major local lineages. Our findings shed light on the highly dynamic evolution underlying the remarkably similar phenotype of this endangered species. Importantly, these results not only provide guidance for the development of conservation plans but also enhance our understanding of evolutionary past for this and other endangered species with similar histories.
基金National Natural Science Foundation of China(32000306)Project of Innovation Team of Survey and Assessment of the Pearl River Fishery Resources(2023TD-10)Natural Science Foundation of Shaanxi Province(2023-JC-YB-325)。
文摘The genus Silurus,an important group of catfish,exhibits heterogeneous distribution in Eurasian freshwater systems.This group includes economically important and endangered species,thereby attracting considerable scientific interest.Despite this interest,the lack of a comprehensive phylogenetic framework impedes our understanding of the mechanisms underlying the extensive diversity found within this genus.Herein,we analyzed 89 newly sequenced and 20 previously published mitochondrial genomes(mitogenomes)from 13 morphological species to reconstruct the phylogenetic relationships,biogeographic history,and species diversity of Silurus.Our phylogenetic reconstructions identified eight clades,supported by both maximum-likelihood and Bayesian inference.Sequence-based species delimitation analyses yielded multiple molecular operational taxonomic units(MOTUs)in several taxa,including the Silurus asotus complex(four MOTUs)and Silurus microdorsalis(two MOTUs),suggesting that species diversity is underestimated in the genus.A reconstructed time-calibrated tree of Silurus species provided an age estimate of the most recent common ancestor of approximately 37.61 million years ago(Ma),with divergences among clades within the genus occurring between 11.56 Ma and 29.44 Ma,and divergences among MOTUs within species occurring between 3.71 Ma and 11.56 Ma.Biogeographic reconstructions suggested that the ancestral area for the genus likely encompassed China and the Korean Peninsula,with multiple inferred dispersal events to Europe and Central and Western Asia between 21.78 Ma and 26.67 Ma and to Japan between 2.51 Ma and 18.42 Ma.Key factors such as the Eocene-Oligocene extinction event,onset and intensification of the monsoon system,and glacial cycles associated with sea-level fluctuations have likely played significant roles in shaping the evolutionary history of the genus Silurus.
基金We thank Dr.Zhi-qiang Lu and Mr.Yi Fu for help during the field survey.We are grateful to Dr.Ovidiu Paun for very helpful comments on earlier drafts of this manuscript.We thank Dr.Shu-feng Li for the distributional map,as well as Dr.Bing Liu,Dr.Ren-bin Zhu,and Mr.Yi Fu for their photos of some Dumasia species.The first author thanks Dr.Wen-bin Yu,Dr.Pei-liang Liu,Dr.Xue-li Zhao,and Dr.Zhu-qiu Song for their help during the writing process.Additional thanks go to Dr.Richard T.Corlett,Raymond Porter and Mr Yuan-qiong Zhang for polishing this work.The authors would also like to express gratitude to two anonymous reviewers for their valuable comments on the manuscript.This work was financially supported by the Second Tibetan Plateau Scientific Expedition and Research(STEP)program(2019QZKK0502)National Natural Science Foundation of China(NSFC 41861008)the 135 Karst‘breakthrough’project Grant 2017XTBG-T03.
文摘Dumasia taxonomy and classification have long been problematic.Species within this genus have few morphological differences and plants without flowers or fruits are difficult to accurately identify.In this study,we evaluated the ability of six DNA barcoding sequences,one nuclear(ITS)and five chloroplast regions(trnH-psbA,matK,rbcL,trnL-trnF,psbB-psbF),to efficiently identify Dumasia species.Most single markers or their combinations identify obvious barcoding gaps between intraspecific and interspecific genetic variation.Most combined analyses including ITS showed good species resolution and identification efficiency.We therefore suggest that ITS alone or a combination of ITS with any cpDNA marker are most suitable for DNA barcoding of Dumasia.The phylogenetic analyses clearly indicated that Dumasia yunnanensis is not monophyletic and is separated as two independent branches,which may result from cryptic differentiation.Our results demonstrate that molecular data can deepen the comprehension of taxonomy of Dumasia and provide an efficient approach for identification of the species.
基金supported by the programs of the Strategic Priority Research Program B of the Chinese Academy of Sciences (CAS) (No. XDB31000000)the National Natural Science Foundation of China (Grant No. 31460091)+2 种基金the Na tional Animal Collection Resource Center, China (Grant No. 2005DKA21402)the Application of Amphibian Natural Antioxidant Peptides as Cosmetic Raw Material Antioxidants (QKZYD [2020]4002)the National Top Discipline Construction Project of Guizhou Province,Geography in Guizhou Normal University (No. 85 2017 Qianjiao Keyan Fa)。
文摘The Paramesotriton caudopunctatus species group is mainly distributed in the karst mountain ecosystems of Guizhou, China. Although some species have been included in previous phylogenetic studies, the evolutionary relationships and divergence-time of members of this species group as a whole remain unexplored. In this study, we report the sequencing of one protein coding mitochondrial gene fragment(ND2) and one nuclear gene(POMC), and use a combination of phylogenetic analyses and coalescent simulations to explore the cryptic diversity and evolutionary history of the P. caudopunctatus species group. Phylogenetic relationships revealed that the P. caudopunctatus species group is composed of two major groups, i. e., East Clade and Western-South Clade. The divergence-time and ancestral area estimation suggested that the P. caudopunctatus species group likely originated in the Doupeng Mountains in Guizhou, China at 12.34 Ma(95% HPD: 8.30–14.73), and intraspecific divergence began at about 2.17 Ma(95% HPD: 1.39–2.97). This timing coincides with the orogenesis of the Miaoling Mountains during the Late Miocene to early Pleistocene. The delimitation of species in the P. caudopunctatus species group supports the existence of the currently identified species, and consensus was confirmed across methods for the existence of least to two cryptic species within what has been traditionally considered to be P. caudopunctatus species group. This study is of significance for understanding the species formation, dispersal, and diversity of the tailed amphibians in the karst mountains ecosystem of Guizhou and the role of the Miaoling Mountains as a geographical barrier to species dispersal.
基金supported by National Research Council of Thailand(NRCT)to CW(grant number 2559A10402051,2016)The Thailand Research Fund to NN(grant number TRG5880053)
文摘Objective:To examine the taxonomic boundaries in the Stellantchasmus populations in different hosts and reveal the cryptic speciation of the Stellantchasmus in Thailand based on both morphological and molecular approaches.Methods:Stellantchasmus falcatus(S.falcatus) s.l.was collected from different hosts throughout Thailand.The worms were examined and measured.The nuclear ITS2 gene and the mitochondrial COI gene were used to investigate the S.falcatus s.l.from Dermogenus pusillus and Liza subviridis.Results:Stellantchasmus was one of food-borne trematode that widely distribute throughout Thailand.The comparison of S.falcatus s.l.from Dermogenus pusillus and Liza subviridis indicated a genetic divergence of nuD NA with 3.6% and mtD NA with 19.3%,respectively.Morphological characteristics were fairly different in the ratio of body size,length of prepharynx,and ratio of organ size.Conclusions:Our results provide initial evidence that S.falcatus s.l.from different hosts tend to be a different species based on both molecular and morphological characters.Cryptic species complexes are generally found among parasites that tend to have large populations and/or rapid evolution.The degree of genetic diversity existing would suggest the practice of targeted regimes to design and minimize these lections of anthelmintic resistance in the future.
基金Supported by the National Natural Science Foundation of China(Nos.31372532,41006084,41276166)the Project for Outstanding Young Teachers in Higher Education of Guangdong,China(No.Yq2013093)
文摘Sparids are of considerable economic importance in marine fishery and aquaculture in China, and the species diversity of this group is considered relatively high. However, the accurate species identification and delimitation of sparids in China remain unaddressed. In this study, we used mitochondrial cytochrome oxidase subunit ?(COI) and 16S ribosomal RNA(16S) genes to conduct DNA barcoding and species delimitation in eleven sparid species from the coastal waters of China. Based on Kimura-2 parameter genetic distances, the mean intraspecific/interspecific variation for COI and 16S were calculated as 0.004/0.152 and 0.002/0.072, respectively. All the conspecific individuals formed monophyletic clusters in neighbour-joining trees of both markers. An obvious barcoding gap was detected for each species, and a common genetic threshold of 1.3% sequence divergence was defined for species delimitation in both markers. Although the sequence variation of 16S was generally lower than that of COI, the results indicated that sparid species could be ef fectively and accurately identified and delimited by COI as well as 16S. Thus, we propose that the COI gene serve as the standard DNA barcode for sparids, and that the 16S gene could also be an ideal candidate barcode. Moreover, each of the six sparid species( Argyrops spinifer, Rhabdosargus sarba, Dentex hypselosomus, Acanthopagrus latus, Acanthopagrus australis and Acanthopagrus berda) showed high intraspecific divergence(>1.3% genetic threshold) with the remarkable geographic lineages in the Indo-West Pacific oceans, which supported that potential unrecognized cryptic species were in them. The potential cryptic diversity revealed here might be primarily attributed to the allopatric divergences caused by the long-term geographic isolation between the Indian and West Pacific oceans or between the opposite sides of the Indian Ocean. The results further suggest that a revision of taxonomic status of these species is required, followed by development of a biodiversity conservation strategy.
基金funded by the National University of Singapore(NUS)Faculty of Science and Department of Biological Sciences through grants WBS R-154-000-570-133 and R-154-000-583-651,respectively
文摘Background: The Brown Hawk Owl complex is said to consist of three species,the Brown Boobook(Ninox scutulata),the Chocolate Boobook(Ninox randi) and the Northern Boobook(Ninox japonica),which includes the nominate migratory lineage Ninox japonica japonica and a mitochondrially distinct lineage of taxonomically uncertain status that has been recorded year-round at least in Taiwan.Overlap in ranges during migration and morphological similarity have led to difficulties in distinguishing the Brown Boobook from the Northern Boobook.Methods: PCR of cytochrome-b and Sanger sequencing of Ninox samples from Singapore and Brunei were used to determine sample identity.Results: Two out of four Singaporean samples and the Brunei sample were identified as Northern Boobooks.This is the first official record of this species in Singapore and represents a considerable range extension for the species.Further,the samples belong to the mitochondrially distinct lineage previously characterized in resident Taiwan Residents populations rather than to the well-known nominate migratory lineage.Conclusions: Our data show that the mitochondrial signature previously documented in resident Taiwan Residents populations of the Northern Boobook extends to migratory populations.This cryptic lineage may be more widespread in its breeding quarters,extending to the Chinese and Russian mainland,in which case the name florensis would apply to it.Further genetic and bioacoustic investigation is required to resolve the taxonomic status of this lineage.
基金funded by the National Basic Research Program of China(2009CB119203)the National NaturalScience Foundation of China(31071732)the Foundation of Lingnan Fruit Innovation Team of GuangdongProvince,China(2009-14)
文摘The sweetpotato whitefly Bemisia tabaci（Homoptera：Aleyrodidae）is a destructive pest of agriculture and horticulture worldwide.Recent phylogenetic analysis using mitochondrial cytochrome oxidase 1 sequences indicates that this whitefly is a species complex including at least 24 morphologically indistinguishable but genetically distinct cryptic species.In this study,the inter-species crosses of Middle East-Asia Minor 1（MEAM1）,Mediterranean（MED）and Asia II 7 cryptic species,which were referred to as B,Q and Cv biotypes before,were conducted in two different devices,leaf cages（7 cm3）and cylinder cages（280 cm3）,and at three temperatures of 22,30 and 38°C.Results indicated that no female progeny were produced in the reciprocal cross between MEAM1×Asia II 7,between MED×Asia II 7 cryptic species neither in leaf cage nor in cylinder cages,while 0.81 and 1.37% of females in the offspring were recorded in the reciprocal cross between MEAM1×MED in leaf cage experiments.Approximately 0.95-0.98% female progeny were recorded in the reciprocal cross between MEAM1×MED at 30°C,0.77% female progeny were recorded in the single cross direction between MEAM1 × MED at 22°C,and no female progeny were found in their reciprocal cross at 38°C in leaf cage.Our findings indicated that neither space dimension nor temperature have a significant effect on the hybridization of different B.tabaci cryptic species.
基金supported by the National Key Research and Development Program of China(2022YFA1304604,2020YFE0202200)the Fundamental Research Funds for the Central Universities(21624109)+3 种基金the Young Scientists Fund of the National Natural Science Foundation of China(82303050)the Guangdong Natural Science Foundation(2022A1515012388)the Natural Science Foundation of Guangdong Province(2023A1515011901)the Guangdong Basic and Applied Basic Research Foundation(2022A1515111106).
文摘Emerging evidence demonstrates that cryptic translation from RNAs previously annotated as noncoding might generate microproteins with oncogenic functions.However,the importance and underlying mechanisms of these microproteins in alternative splicing-driven tumor progression have rarely been studied.Here,we show that the novel protein TPM3P9,encoded by the lncRNA tropomyosin 3 pseudogene 9,exhibits oncogenic activity in clear cell renal cell carcinoma(ccRCC)by enhancing oncogenic RNA splicing.Overexpression of TPM3P9 promotes cell proliferation and tumor growth.Mechanistically,TPM3P9 binds to the RRM1 domain of the splicing factor RBM4 to inhibit RBM4-mediated exon skipping in the transcription factor TCF7L2.This results in increased expression of the oncogenic splice variant TCF7L2-L,which activates NF-κB signaling via its interaction with SAM68 to transcriptionally induce RELB expression.From a clinical perspective,TPM3P9 expression is upregulated in cancer tissues and is significantly correlated with the expression of TCF7L2-L and RELB.High TPM3P9 expression or low RBM4 expression is associated with poor survival in patients with ccRCC.Collectively,our findings functionally and clinically characterize the“noncoding RNA”-derived microprotein TPM3P9 and thus identify potential prognostic and therapeutic factors in renal cancer.
基金Peter Sseruwagi and Joseph Ndunguru,Mikocheni Agriculture Research Institute,Tanzania,for collecting samples from Uganda.J.N.C.is supported by grants(AGL2013-48913-C2-1-R and AGL2016-75819-C2-2-R)from the Ministerio de Economia y Competitividad(MINECO,Spain)co-financed by ERDF.E.F.O.is a recipient of a"Juan de la Cierva-Incorporacion"postdoctoral contract from MINECO.
文摘Identifying cryptic species poses a substantial challenge to both biologists and naturalists due to morphological similarities.Bemisia tabaci is a cryptic species complex containing more than 44 putative species;several of which are currently among the world's most destructive crop pests.Interpreting and delimiting the evolution of this species complex has proved problematic.To develop a comprehensive framework for species delimitation and identification,we evaluated the performance of distinct data sources both individually and in combination among numerous samples of the B.tabaci species complex acquired worldwide.Distinct datasets include full mitogenomes,single-copy nuclear genes,restriction site-associated DNA sequencing,geographic range,host speciation,and reproductive compatibility datasets.Phylogenetically,our well-supported topologies generated from three dense molecular markers highlighted the evolutionary divergence of species of the B.tabaci complex and suggested that the nuclear markers serve as a more accurate representation of B.tabaci species diversity.Reproductive compatibility datasets facilitated the identification of at least 17 different cryptic species within our samples.Native geographic range information provides a complementary assessment of species recognition,while the host range datasets provide low rate of delimiting resolution.We further summarized different data performances in species classification when compared with reproductive compatibility,indicating that combination of mtCOI divergence,nuclear markers,geographic range provide a complementary assessment of species recognition.Finally,we represent a model for understanding and untangling the cryptic species complexes based on the evidence from this study and previously published articles.
基金financially supported by the National Natural Science Foundation of China(32370066,32000058)the Fundamental Research Funds for the Central Universities(JUSRP622003)+1 种基金National First-class Discipline Program of Light Industry Technology and Engineering(QGJC20230202)the Postgraduate Research&Practice Innovation Program of Jiangsu Province(KYCX23_2487).
文摘The probiotic bacterium Escherichia coli Nissle 1917(EcN)holds significant promise for use in clinical and biological industries.However,the reliance on antibiotics to maintain plasmid-borne genes has overshadowed its benefits.In this study,we addressed this issue by engineering the endogenous cryptic plasmids pMUT1 and pMUT2.The non-essential elements were removed to create more stable derivatives pMUT1NR△and pMUT2HBC△.Synthetic promoters by integrating binding motifs on sigma factors were further constructed and applied for expression of Bacteroides thetaiotaomicron heparinaseⅢand the biosynthesis of ectoine.Compared to traditional antibiotic-dependent expression systems,our newly constructed antibiotic-free expression systems offer considerable advantages for clinical and synthetic biology applications.
基金funded by the Second Tibetan Plateau Scientific Expedition and Research(STEP)program(2019QZKK0502)the Key Projects of the Joint Fund of the National Natural Science Foundation of China(U23A20149)+4 种基金the Research Fund for International Young Scientists of the National Natural Science Foundation of China(32150410356)National Natural Science Foundation of China(32322006)the Young Academic and Technical Leader Raising Foundation of Yunnan Province(2019HB039)the International Association for Plant Taxonomy(IAPT)Research grant(421064806)supported by the“CAS President's International Fellowship Initiative”(PIFI)postdoctoral fel owship(2021PB0034)。
文摘The mountains of Southwest China comprise a significant large mountain range and biodiversity hotspot imperiled by global climate change.The high species diversity in this mountain system has long been attributed to a complex set of factors,and recent large-scale macroevolutionary investigations have placed a broad timeline on plant diversification that stretches from 10 million years ago(Mya)to the present.Despite our increasing understanding of the temporal mode of speciation,finer-scale populationlevel investigations are lacking to better refine these temporal trends and illuminate the abiotic and biotic influences of cryptic speciation.This is largely due to the dearth of organismal sampling among closely related species and populations,spanning the incredible size and topological heterogeneity of this region.Our study dives into these evolutionary dynamics of speciation using genomic and ecomorphological data of Stellera chamaejasme L.We identified four previously unrecognized cryptic species having indistinct morphological traits and large metapopulation of evolving lineages,suggesting a more recent diversification(~2.67-0.90 Mya),largely influenced by Pleistocene glaciation and biotic factors.These factors likely influenced allopatric speciation and advocated cyclical warming–cooling episodes along elevational gradients during the Pleistocene.The study refines the evolutionary timeline to be much younger than previously implicated and raises the concern that projected future warming may influence the alpine species diversity,necessitating increased conservation efforts.
