| 1 | Updated annotation of the wild strawberry Fragaria vesca V4 genome显示文摘The diploid strawberry Fragaria vesca serves as an ideal model plant for cultivated strawberry(Fragaria×ananassa,8x)and the Rosaceae family.The F.vesca genome was initially published in 2011 using older technologies.Recently,a new and greatly improved F.vesca genome,designated V4,was published.However,the number of annotated genes is remarkably reduced in V4(28,588 genes)compared to the prior annotations(32,831 to 33,673 genes).Additionally,the annotation of V4(v4.0.a1)implements a new nomenclature for gene IDs(FvH4_XgXXXXX),rather than the previous nomenclature(geneXXXXX).Hence,further improvement of the V4 genome annotation and assigning gene expression levels under the new gene IDs with existing transcriptome data are necessary to facilitate the utility of this high-quality F.vesca genome V4.Here,we built a new and improved annotation,v4.0.a2,for F.vesca genome V4.The new annotation has a total of 34,007 gene models with 98.1%complete Benchmarking Universal Single-Copy Orthologs(BUSCOs).In this v4.0.a2 annotation,gene models of 8,342 existing genes are modified,9,029 new genes are added,and 10,176 genes possess alternatively spliced isoforms with an average of 1.90 transcripts per locus.Transcription factors/regulators and protein kinases are globally identified.Interestingly,the transcription factor family FAr-red-impaired Response 1(FAR1)contains 82 genes in v4.0.a2 but only two members in v4.0.a1.Additionally,the expression levels of all genes in the new annotation across a total of 46 different tissues and stages are provided.Finally,miRNAs and their targets are reanalyzed and presented.Altogether,this work provides an updated genome annotation of the F.vesca V4 genome as well as a comprehensive gene expression atlas with the new gene ID nomenclature,which will greatly facilitate gene functional studies in strawberry and other evolutionarily related plant species. | Yongping Li Mengting Pi Qi Gao Zhongchi Liu Chunying Kang | 2019 | Horticulture Research2019，6，1： | 2 |
| 3 | The MADS-box gene FveSEP3 plays essential roles in flower organogenesis and fruit development in woodland strawberry显示文摘Flower and fruit development are two key steps for plant reproduction.The ABCE model for flower development has been well established in model plant species;however,the functions of ABCE genes in fruit crops are less understood.In this work,we identi fied an EMS mutant named R27 in woodland strawberry(Fragaria vesca),showing the conversion of petals,stamens,and carpels to sepaloid organs in a semidominant inheritance fashion.Mapping by sequencing revealed that the class E gene homolog FveSEP3(FvH4_4g23530)possessed the causative mutation in R27 due to a G to E amino acid change in the conserved MADS domain.Additional fvesep3^(CR) mutants generated by CRISPR/Cas9 displayed similar phenotypes to fvesep3-R27.Overexpressing wild-type or mutated FveSEP3 in Arabidopsis suggested that the mutation in R27 might cause a dominant-negative effect.Further analyses indicated that FveSEP3 physically interacted with each of the ABCE proteins in strawberry.Moreover,both R27 and fvesep3^(CR) mutants exhibited parthenocarpic fruit growth and delayed fruit ripening.Transcriptome analysis revealed that both common and specific differentially expressed genes were identi fied in young fruit at 6-7 days post anthesis(DPA)of fvesep3 and pollinated wild type when compared to unpollinated wild type,especially those in the auxin pathway,a key hormone regulating fruit set in strawberry.Together,we provided compelling evidence that FveSEP3 plays predominant E functions compared to other E gene homologs in flower development and that FveSEP3 represses fruit growth in the absence of pollination and promotes fruit ripening in strawberry. | Mengting Pi Shaoqiang Hu Laichao Cheng Ruhan Zhong Zhuoying Cai Zhongchi Liu Jia-Long Yao Chunying Kang | 2021 | Horticulture Research2021，8，1： | 1 |
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