The highbush blueberry（Vaccinium corymbosum）,Duke,was used to construct a de novo transcriptome sequence library and to perform data statistical analysis.Mega 4,CLC Sequence Viewer 6 software,and quantitative PCR we...The highbush blueberry（Vaccinium corymbosum）,Duke,was used to construct a de novo transcriptome sequence library and to perform data statistical analysis.Mega 4,CLC Sequence Viewer 6 software,and quantitative PCR were employed for bioinformatics and expression analyses of the basic helix-loop-helix（BHLH）transcription factors of the sequencing library.The results showed that 28.38 gigabytes of valid data were obtained from transcriptome sequencing and were assembled into 108 033 unigenes.Functional annotation showed that 32 244 unigenes were annotated into Clusters of Orthologous Groups（COG）and Gene Ontology（GO）databases,whereas the rest of the 75 789 unigenes had no matching information.By using COG and GO classification tools,sequences with annotation information were divided into 25 and 52 categories,respectively,which involved transport and metabolism,transcriptional regulation,and signal transduction.Analysis of the transcriptome library identified a total of 59 BHLH genes.Sequence analysis revealed that 55 genes of that contained a complete BHLH domain.Furthermore,phylogenetic analysis showed that BHLH genes of blueberry（Duke）could be divided into 13 sub-groups.PCR results showed that 45 genes were expressed at various developmental stages of buds,stems,leaves,flowers,and fruits,suggesting that the function of BHLH was associated with the development of different tissues and organs of blueberry,Duke.The present study would provided a foundation for further investigations on the classification and functions of the blueberry BHLH family.展开更多
Basic helix-loop-helix （bHLH） transcription factors regulate the differentiation of various tissues in a vast diversity of species. The bHLH protein Atonal was first identified as a proneural gene involved in the fo...Basic helix-loop-helix （bHLH） transcription factors regulate the differentiation of various tissues in a vast diversity of species. The bHLH protein Atonal was first identified as a proneural gene involved in the formation of mechanosensory cells and photoreceptor cells in Drosophila （larman et al., 1993, 1994）. Atonal is expressed in sensory organ precursors and is required and sufficient for the development of chordotonal organs （Jar- man et al., 1993）. Moreover, Atonal expression is observed in the developing eye and is essential for the differentiation of R8 photoreceptors, which are the first photoreceptors that appear during development. Atonal is not involved in the formation of other photoreceptors （R1-R7） directly. However, R8 photore- ceptors recruit other photoreceptors from the surrounding cells （Jarman et al., 1994）.展开更多
Genome-wide identification and comparative gene-famiy analyses have commonly been performed to investigate spedesspecif ic evolution Inked to various traits and molecular pathways.However,most previous studies have be...Genome-wide identification and comparative gene-famiy analyses have commonly been performed to investigate spedesspecif ic evolution Inked to various traits and molecular pathways.However,most previous studies have been Smited to gene screening h a single reference genome,faiing to account for the gene presence/absence variations(gPAVs)in a species.Here,we propose an innovative pangenome-based approach for gene-family analyses based on orthologous gene groups(OGGs).Usng the basic heix-bop-helix(bH_H)transcription factor family in barley as an example,we identified 161-176 bHLHs in 20 barley genomes,which can be classified into 201 OGGs.These 201 OGGs were further dassif jed into 140 core,12 softcore,29 shell,and 20 Ihe-spedfic/cloud bHLHs,reveaing the complete profile of bHLH genes in barley.Using a genome-scanning approach,we overcame the genome annotation bias and identified an average of 15 un-amotated core bHLHs per barley genome We found that whole-genome/segmental duplicates are predominant mechanisms contrixiting to the expansion of most core/softcore bHLHs,whereas dispensable bHLHs are more Ikely to result from small-scale dupication events.Interestingly,we noticed that the dispensable bHLHs tend to be enriched in the specific subfamiSes SF13,SF27,and SF28,rn plying the potentially based expansion of specific bHLHs h barley.We found that 50%of the bHLHs con tan at least 1 intact transposon element(TE)within the 2-kb upstream-to-downstream region.bHLHs with copy-number variations(CWs)have 1.48 TEs on average,sigrif icantiy more than core bhLHs without CNVs(1.36),supporting a potential role ofTEs in bHLH expansion.Analyses of selection pressure showed that dispensablebHLHs have experienced dearrelaxation of selection compared with core bHLHs,consistent with their conservation patterns.We also integrated the pangenome data with recently avaiable barley pantranscrip-tome data from 5 tissues and discovered apparent transcriptional divergence within and across bHLH sifofamiies.We conclude that pangenome-based gene-family analyses can better describe the previously untapped,genu'ne evolutionary status of bHLHs and provide novel insights into bHLH evolution in barley.We expect that this study wil inspire similar analyses in many other gene famiies and species.展开更多
Basic helix-loop-helix(bHLH)transcription factors play an important role in a wide range of metabolic and developmental processes in eukaryotes,and bHLH proteins also participate in immune responses,especially in plan...Basic helix-loop-helix(bHLH)transcription factors play an important role in a wide range of metabolic and developmental processes in eukaryotes,and bHLH proteins also participate in immune responses,especially in plants.However,their roles in insects upon entomopathogen infection are unknown.In this study,54 bHLH genes in 41 families were identified in a polyphagous pest,Spodoptera litura,including a new bHLH gene in group B,which is specifically present in Lepidoptera and was thus named Lep.The conserved amino acids in the bHLH domain,structural architecture,and chromosomal distribution of bHLH genes in S.litura were analyzed.The bHLH genes in Plutella xylostella and Apis mellifera were also updated,and genome-wide comparison and phylogenetic analysis of bHLH members in 5 holometabolous insects were performed.The expression profiles of S.litura bHLH(SlbHLH)genes in 3 tissues at different developmental stages and their responses to S.litura nucleopolyhedrovirus(SpltNPV),Nomuraea rileyi(Nr),and Bacillus thuringiensis(Bt)infection were investigated.More SlbHLHs in group B were expressed and differentially expressed during pathogen infections,and SlbHLHs tended to be downregulated in the midgut of S.litura larvae after B.thuringiensis treatment.Our study provides an overview of bHLH family members in S.litura and their responses to different pathogens used for pest biocontrol.These findings on bHLH members may contribute to uncovering the mechanism of host-pathogen interaction.展开更多
PAR1 is an atypical basic-helix-loop-helix （bHLH） protein that negatively regulates the shade avoidance syndrome in Arabidopsis thaliana acting as a transcriptional cofactor. Consistently with this function, PAR1 ha...PAR1 is an atypical basic-helix-loop-helix （bHLH） protein that negatively regulates the shade avoidance syndrome in Arabidopsis thaliana acting as a transcriptional cofactor. Consistently with this function, PAR1 has to be in the nucleus to display biological activity. Previous structure-function analyses revealed that the N-terminal region of PAR1 drives the protein to the nucleus. However, truncated forms of PAR1 lacking this region still display biological activity, implying that PAR1 has additional mechanisms to localize into the nucleus. In this work, we compared the primary structure of PAR1 and various related and unrelated plant bHLH proteins, which led us to suggest that PAR1 contains a non-canonical nuclear localization signal （NLS） in the N-terminal region. By overexpressing truncated and mutated derivatives of PAR1, we have also investigated the importance of other regions of PAR1, such as the acidic and the extended HLH dimerization domains, for its nuclear localization. We found that, in the absence of the N-terminal region, a functional HLH domain is required for nuclear localization. Our results suggest the existence of a dual mechanism for PAR1 nuclear localization： （1） one mediated by the N-terminal non-consensus NLS and （2） a second one that involves interaction with other proteins via the dimerization domain,展开更多
基金supported by the National Natural Science Foundation of China (31301754)the Chinese Academy of Agricultural Sciences-Agricultural Science and Technology Innovation Program (CAAS-ASTIP)the Cultivation Plan for Youth Agricultural Science and Technology Innovative Talents of Liaoning Province, China (2015059)
文摘The highbush blueberry（Vaccinium corymbosum）,Duke,was used to construct a de novo transcriptome sequence library and to perform data statistical analysis.Mega 4,CLC Sequence Viewer 6 software,and quantitative PCR were employed for bioinformatics and expression analyses of the basic helix-loop-helix（BHLH）transcription factors of the sequencing library.The results showed that 28.38 gigabytes of valid data were obtained from transcriptome sequencing and were assembled into 108 033 unigenes.Functional annotation showed that 32 244 unigenes were annotated into Clusters of Orthologous Groups（COG）and Gene Ontology（GO）databases,whereas the rest of the 75 789 unigenes had no matching information.By using COG and GO classification tools,sequences with annotation information were divided into 25 and 52 categories,respectively,which involved transport and metabolism,transcriptional regulation,and signal transduction.Analysis of the transcriptome library identified a total of 59 BHLH genes.Sequence analysis revealed that 55 genes of that contained a complete BHLH domain.Furthermore,phylogenetic analysis showed that BHLH genes of blueberry（Duke）could be divided into 13 sub-groups.PCR results showed that 45 genes were expressed at various developmental stages of buds,stems,leaves,flowers,and fruits,suggesting that the function of BHLH was associated with the development of different tissues and organs of blueberry,Duke.The present study would provided a foundation for further investigations on the classification and functions of the blueberry BHLH family.
基金supported by grants from the Ministry of Education,Culture,Sports,Science and Technology in Japan and Naito Foundation to TCthe Japan Society for the Promotion of Science to MO and TC
文摘Basic helix-loop-helix （bHLH） transcription factors regulate the differentiation of various tissues in a vast diversity of species. The bHLH protein Atonal was first identified as a proneural gene involved in the formation of mechanosensory cells and photoreceptor cells in Drosophila （larman et al., 1993, 1994）. Atonal is expressed in sensory organ precursors and is required and sufficient for the development of chordotonal organs （Jar- man et al., 1993）. Moreover, Atonal expression is observed in the developing eye and is essential for the differentiation of R8 photoreceptors, which are the first photoreceptors that appear during development. Atonal is not involved in the formation of other photoreceptors （R1-R7） directly. However, R8 photore- ceptors recruit other photoreceptors from the surrounding cells （Jarman et al., 1994）.
基金supported by the Australia Grain Research and Development Corporation(9176507).
文摘Genome-wide identification and comparative gene-famiy analyses have commonly been performed to investigate spedesspecif ic evolution Inked to various traits and molecular pathways.However,most previous studies have been Smited to gene screening h a single reference genome,faiing to account for the gene presence/absence variations(gPAVs)in a species.Here,we propose an innovative pangenome-based approach for gene-family analyses based on orthologous gene groups(OGGs).Usng the basic heix-bop-helix(bH_H)transcription factor family in barley as an example,we identified 161-176 bHLHs in 20 barley genomes,which can be classified into 201 OGGs.These 201 OGGs were further dassif jed into 140 core,12 softcore,29 shell,and 20 Ihe-spedfic/cloud bHLHs,reveaing the complete profile of bHLH genes in barley.Using a genome-scanning approach,we overcame the genome annotation bias and identified an average of 15 un-amotated core bHLHs per barley genome We found that whole-genome/segmental duplicates are predominant mechanisms contrixiting to the expansion of most core/softcore bHLHs,whereas dispensable bHLHs are more Ikely to result from small-scale dupication events.Interestingly,we noticed that the dispensable bHLHs tend to be enriched in the specific subfamiSes SF13,SF27,and SF28,rn plying the potentially based expansion of specific bHLHs h barley.We found that 50%of the bHLHs con tan at least 1 intact transposon element(TE)within the 2-kb upstream-to-downstream region.bHLHs with copy-number variations(CWs)have 1.48 TEs on average,sigrif icantiy more than core bhLHs without CNVs(1.36),supporting a potential role ofTEs in bHLH expansion.Analyses of selection pressure showed that dispensablebHLHs have experienced dearrelaxation of selection compared with core bHLHs,consistent with their conservation patterns.We also integrated the pangenome data with recently avaiable barley pantranscrip-tome data from 5 tissues and discovered apparent transcriptional divergence within and across bHLH sifofamiies.We conclude that pangenome-based gene-family analyses can better describe the previously untapped,genu'ne evolutionary status of bHLHs and provide novel insights into bHLH evolution in barley.We expect that this study wil inspire similar analyses in many other gene famiies and species.
基金This research was funded by grants from the National Key R&D Program of China(No,2019YFD1002100)National Natural Science Foundation of China(No.31901941 and No.31970474)+1 种基金Natural Science Foun-dation of Guangdong Province(No.202102020966)China Postdoctoral Science Foundation(No.2020M682752).The authors are grateful for the generous gift of S.litura nucleopolyhedrovirus(SpItNPV)from Professor Kai Yang at Sun Yat-Sen University,Nomuruea rileyi(Nr06)from Professor Xusheng Liu at Central China Normal University,and Bacillus thuringiensis(WB9)from Professor Xiong Guan at Fujian Agriculture and Forestry University.
文摘Basic helix-loop-helix(bHLH)transcription factors play an important role in a wide range of metabolic and developmental processes in eukaryotes,and bHLH proteins also participate in immune responses,especially in plants.However,their roles in insects upon entomopathogen infection are unknown.In this study,54 bHLH genes in 41 families were identified in a polyphagous pest,Spodoptera litura,including a new bHLH gene in group B,which is specifically present in Lepidoptera and was thus named Lep.The conserved amino acids in the bHLH domain,structural architecture,and chromosomal distribution of bHLH genes in S.litura were analyzed.The bHLH genes in Plutella xylostella and Apis mellifera were also updated,and genome-wide comparison and phylogenetic analysis of bHLH members in 5 holometabolous insects were performed.The expression profiles of S.litura bHLH(SlbHLH)genes in 3 tissues at different developmental stages and their responses to S.litura nucleopolyhedrovirus(SpltNPV),Nomuraea rileyi(Nr),and Bacillus thuringiensis(Bt)infection were investigated.More SlbHLHs in group B were expressed and differentially expressed during pathogen infections,and SlbHLHs tended to be downregulated in the midgut of S.litura larvae after B.thuringiensis treatment.Our study provides an overview of bHLH family members in S.litura and their responses to different pathogens used for pest biocontrol.These findings on bHLH members may contribute to uncovering the mechanism of host-pathogen interaction.
文摘PAR1 is an atypical basic-helix-loop-helix （bHLH） protein that negatively regulates the shade avoidance syndrome in Arabidopsis thaliana acting as a transcriptional cofactor. Consistently with this function, PAR1 has to be in the nucleus to display biological activity. Previous structure-function analyses revealed that the N-terminal region of PAR1 drives the protein to the nucleus. However, truncated forms of PAR1 lacking this region still display biological activity, implying that PAR1 has additional mechanisms to localize into the nucleus. In this work, we compared the primary structure of PAR1 and various related and unrelated plant bHLH proteins, which led us to suggest that PAR1 contains a non-canonical nuclear localization signal （NLS） in the N-terminal region. By overexpressing truncated and mutated derivatives of PAR1, we have also investigated the importance of other regions of PAR1, such as the acidic and the extended HLH dimerization domains, for its nuclear localization. We found that, in the absence of the N-terminal region, a functional HLH domain is required for nuclear localization. Our results suggest the existence of a dual mechanism for PAR1 nuclear localization： （1） one mediated by the N-terminal non-consensus NLS and （2） a second one that involves interaction with other proteins via the dimerization domain,
