Auxin signaling and its components(Auxin/Indole-3-Acetic Acid(Aux/IAA))are critical for plant growth and development.Here,we performed a genome-wide annotation and identified twenty-one Aux/IAA genes in strawberry(Fra...Auxin signaling and its components(Auxin/Indole-3-Acetic Acid(Aux/IAA))are critical for plant growth and development.Here,we performed a genome-wide annotation and identified twenty-one Aux/IAA genes in strawberry(Fragaria vesca).Most FveIAAs were located on chromosomes 1,2,4,5,and 6,while no FveIAAs were found in chromosomes 3 and 7.Phylogenetic analysis divided these genes into nine subfamilies.Most FveIAAs contained the DNA-binding and Aux/IAA domains,as well as motifs I-IV.There were 2-6 exons in the FveIAA genes based on the gene structure analysis.Also,we found that four pairs of FveIAA genes underwent segment duplications.Moreover,four pairs of orthologous genes were observed between strawberry and Arabidopsis.Cis-element analysis in the promoter region indicated that FveIAAs may be involved in light,phytohormones,stress responses,and growth processes.Prediction of protein-protein interaction revealed that 17 of 21 FveIAA proteins were involved in the auxin-related signaling pathways.Additionally,FveIAAs showed tissue-specific expression and responded to IAA treatment.Thus,this systematic annotation of the FveIAA family would provide a fundamental basis for further functional and evolutionary analysis and to understanding the role of FveIAAs in strawberry growth and development.展开更多
Cultivated strawberry(Fragaria×ananassa)originated from four diploid ancestors:F.vesca,F.viridis,F.iinumae and F.nipponica.Among them,F.vesca is the dominant subgenome for cultivated strawberry.It is not well und...Cultivated strawberry(Fragaria×ananassa)originated from four diploid ancestors:F.vesca,F.viridis,F.iinumae and F.nipponica.Among them,F.vesca is the dominant subgenome for cultivated strawberry.It is not well understood how differences in gene expression between diploid and octoploid strawberry contribute to differences during fruit development.In this study,we used comprehensive transcriptomic analyses of F.vesca and F.×ananassa to investigate gene expression at the different stages of fruit development.In total,we obtained 3508(turning stage)and 3958(red stage)differentially expressed genes with pairwise comparisons between diploid and octoploid.The genes involved in flavonoid biosynthesis were almost upregulated in the turning stages of octoploid,and we also discovered a ripe fruit-specific module associated with several flavonoid biosynthetic genes,including FveMYB10,FveMYB9/11,and Fve RAP,using weighted gene coexpression network analysis(WGCNA).Furthermore,we identified the species-specific regulated networks in the octoploid and diploid fruit.Notably,we found that the WAK and F-box genes were enriched in the octoploid and diploid fruits,respectively.This study elucidates new findings on flavonoid biosynthesis and fruit size of strawberry with important implications for future molecular breeding in cultivated strawberry.展开更多
Auxin signaling plays a significant role in the whole process of plant growth and development from embryogenesis to senescence.Auxin response factors(ARFs) are reported to regulate the expression of auxin response gen...Auxin signaling plays a significant role in the whole process of plant growth and development from embryogenesis to senescence.Auxin response factors(ARFs) are reported to regulate the expression of auxin response genes by binding to auxin response elements.ARF is the most critical transcription factor family which has been released in most species,but few reports in strawberry.In this study,the structure characterization of 12 FvARF genes in strawberry,their expression patterns at different development stages,different organizations,and different indole-3-acetic acid(IAA) treatments were analyzed.The expression of 12 FvARFs was found in all experiment tissues and showed almost the same trend during fruit development.All FvARFs respond to the treatment of IAA.Our study provides comprehensive information on ARF family in strawberry,including gene structures,chromosome locations,phylogenetic relationships and expression patterns.The information on FvARF genes paves the way for future research on strawberry ARF genes.展开更多
Small RNAs(sRNAs) are vital regulators of gene expression and involved in various biological processes. Among them, micro RNAs(mi RNAs) and phased small interfering RNAs(phasi RNAs) have been well defined and studied ...Small RNAs(sRNAs) are vital regulators of gene expression and involved in various biological processes. Among them, micro RNAs(mi RNAs) and phased small interfering RNAs(phasi RNAs) have been well defined and studied in the past decades. A bunch of scripts or pipelines were developed to annotate mi RNAs and phasi RNAs. However, some computational annotations are rough and without careful manual check,resulting in low quality annotation. In this study, 19 public strawberry(Fragaria vesca) s RNA sequencing data from nine different tissues were collected to annotate mi RNAs and PHAS loci in F. vesca. After bioinformatics analysis and careful manual checking, 167 known mi RNAs, 27 mi RNA*s with notable abundance, 54 novel mi RNAs were accurately annotated. The terms of two mi RNAs were corrected from mi R477 b and mi R5225 using mi RN47 and mi R3627 h, respectively. Besides 21 nucleotides(nt) mi R390, eleven mi RNAs with a length of 22-nt are in charge of triggering the biogenesis of 21-nt phasi RNAs from 110 PHAS loci in strawberry. In particular, we found several PHAS loci were targeted by two different mi RNAs(similar to the "two-hit" model) and the phasi RNA generating region located between two target sites. We speculate that one target site is in control of triggering phasi RNA biogenesis and the other target site define the boundary of the region of phasi RNA biogenesis,which likely provide an accurate way for phasi RNA generation. Overall, we provided a comprehensive and accurate annotation of mi RNAs and PHAS loci in the F. vesca genome.展开更多
基金supported by the Natural Science Foundation of China(31701935)the Agricultural technology R&D Project of Xi’an City(20NYYF0037)+2 种基金the Natural Science Foundation of Chongqing(cstc2020jcyjmsxmX1064)We also gratefully thank funding from the Plant Biotechnology and Germplasm Conservation Project(XAWLKYTD017)Key Disciplines of Botany of Xi’an City(103060002).
文摘Auxin signaling and its components(Auxin/Indole-3-Acetic Acid(Aux/IAA))are critical for plant growth and development.Here,we performed a genome-wide annotation and identified twenty-one Aux/IAA genes in strawberry(Fragaria vesca).Most FveIAAs were located on chromosomes 1,2,4,5,and 6,while no FveIAAs were found in chromosomes 3 and 7.Phylogenetic analysis divided these genes into nine subfamilies.Most FveIAAs contained the DNA-binding and Aux/IAA domains,as well as motifs I-IV.There were 2-6 exons in the FveIAA genes based on the gene structure analysis.Also,we found that four pairs of FveIAA genes underwent segment duplications.Moreover,four pairs of orthologous genes were observed between strawberry and Arabidopsis.Cis-element analysis in the promoter region indicated that FveIAAs may be involved in light,phytohormones,stress responses,and growth processes.Prediction of protein-protein interaction revealed that 17 of 21 FveIAA proteins were involved in the auxin-related signaling pathways.Additionally,FveIAAs showed tissue-specific expression and responded to IAA treatment.Thus,this systematic annotation of the FveIAA family would provide a fundamental basis for further functional and evolutionary analysis and to understanding the role of FveIAAs in strawberry growth and development.
基金the Program for High-level University Construction of the Fujian Agriculture and Forestry University,China(612014028)the Natural Science Foundation of Fujian Province,China(2018J01700)Rural Revitalization Service Team of Fujian Agriculture and Forestry University,China(11899170125)。
文摘Cultivated strawberry(Fragaria×ananassa)originated from four diploid ancestors:F.vesca,F.viridis,F.iinumae and F.nipponica.Among them,F.vesca is the dominant subgenome for cultivated strawberry.It is not well understood how differences in gene expression between diploid and octoploid strawberry contribute to differences during fruit development.In this study,we used comprehensive transcriptomic analyses of F.vesca and F.×ananassa to investigate gene expression at the different stages of fruit development.In total,we obtained 3508(turning stage)and 3958(red stage)differentially expressed genes with pairwise comparisons between diploid and octoploid.The genes involved in flavonoid biosynthesis were almost upregulated in the turning stages of octoploid,and we also discovered a ripe fruit-specific module associated with several flavonoid biosynthetic genes,including FveMYB10,FveMYB9/11,and Fve RAP,using weighted gene coexpression network analysis(WGCNA).Furthermore,we identified the species-specific regulated networks in the octoploid and diploid fruit.Notably,we found that the WAK and F-box genes were enriched in the octoploid and diploid fruits,respectively.This study elucidates new findings on flavonoid biosynthesis and fruit size of strawberry with important implications for future molecular breeding in cultivated strawberry.
基金financially supported by the National Natural Science Foundation of China(31872069)the Natural Science Foundation of Liaoning Province,China(201602659)+1 种基金the Liaoning BaiQianWan Talents Program,China(2016921067)the Program for Excellent Talents in University of Liaoning Province,China(LJQ2014069)
文摘Auxin signaling plays a significant role in the whole process of plant growth and development from embryogenesis to senescence.Auxin response factors(ARFs) are reported to regulate the expression of auxin response genes by binding to auxin response elements.ARF is the most critical transcription factor family which has been released in most species,but few reports in strawberry.In this study,the structure characterization of 12 FvARF genes in strawberry,their expression patterns at different development stages,different organizations,and different indole-3-acetic acid(IAA) treatments were analyzed.The expression of 12 FvARFs was found in all experiment tissues and showed almost the same trend during fruit development.All FvARFs respond to the treatment of IAA.Our study provides comprehensive information on ARF family in strawberry,including gene structures,chromosome locations,phylogenetic relationships and expression patterns.The information on FvARF genes paves the way for future research on strawberry ARF genes.
基金supported by the National Natural Science Foundation of China(Grant No.31872063)。
文摘Small RNAs(sRNAs) are vital regulators of gene expression and involved in various biological processes. Among them, micro RNAs(mi RNAs) and phased small interfering RNAs(phasi RNAs) have been well defined and studied in the past decades. A bunch of scripts or pipelines were developed to annotate mi RNAs and phasi RNAs. However, some computational annotations are rough and without careful manual check,resulting in low quality annotation. In this study, 19 public strawberry(Fragaria vesca) s RNA sequencing data from nine different tissues were collected to annotate mi RNAs and PHAS loci in F. vesca. After bioinformatics analysis and careful manual checking, 167 known mi RNAs, 27 mi RNA*s with notable abundance, 54 novel mi RNAs were accurately annotated. The terms of two mi RNAs were corrected from mi R477 b and mi R5225 using mi RN47 and mi R3627 h, respectively. Besides 21 nucleotides(nt) mi R390, eleven mi RNAs with a length of 22-nt are in charge of triggering the biogenesis of 21-nt phasi RNAs from 110 PHAS loci in strawberry. In particular, we found several PHAS loci were targeted by two different mi RNAs(similar to the "two-hit" model) and the phasi RNA generating region located between two target sites. We speculate that one target site is in control of triggering phasi RNA biogenesis and the other target site define the boundary of the region of phasi RNA biogenesis,which likely provide an accurate way for phasi RNA generation. Overall, we provided a comprehensive and accurate annotation of mi RNAs and PHAS loci in the F. vesca genome.
