The sugar transporter system of strawberry:genome-wide identification and expression correlation with fruit soluble sugar-related traits in a Fragaria×ananassa germplasm collection

Sugar from plant photosynthesis is a basic requirement for life activities.Sugar transporters are the proteins that mediate sugar allocation among or within source/sink organs.The transporters of the major facilitator superfamily(MFS)targeting carbohydrates represent the largest family of sugar transporters in many plants.Strawberry(Fragaria×ananassa Duchesne)is an important crop appreciated worldwide for its unique fruit flavor.The involvement of MFS sugar transporters(STs)in cultivated strawberry fruit sugar accumulation is largely unknown.In this work,we characterized the genetic variation associated with fruit soluble sugars in a collection including 154 varieties.Then,a total of 67 ST genes were identified in the v4.0 genome integrated with the v4.0.a2 protein database of F.vesca,the dominant subgenome provider for modern cultivated strawberry.Phylogenetic analysis updated the nomenclature of strawberry ST homoeologs.Both the chromosomal distribution and structural characteristics of the ST family were improved.Semi-RT-PCR analysis in nine tissues from cv.Benihoppe screened 34 highly expressed ST genes in fruits.In three varieties with dramatically differing fruit sugar levels,qPCR integrated with correlation analysis between ST transcript abundance and sugar content identified 13 sugar-correlated genes.The correlations were re-evaluated across 19 varieties,including major commercial cultivars grown in China.Finally,a model of the contribution of the sugar transporter system to subcellular sugar allocation in strawberry fruits was proposed.Our work highlights the involvement of STs in controlling strawberry fruit soluble sugars and provides candidates for the future functional study of STs in strawberry development and responses and a new approach for strawberry genetic engineering and molecular breeding.

Genome-wide characterization and expression analysis of WRKY family genes during development and resistance to Colletotrichum fructicola in cultivated strawberry(Fragaria×ananassa Duch.)

Based on the recently published whole-genome sequence of cultivated strawberry ’Camarosa’, in this study, 222FaWRKY genes were identified in the ’Camarosa’ genome. Phylogenetic analysis showed that the 222 FaWRKY candidate genes were classified into three groups, of which 41 were in group Ⅰ, 142 were in group Ⅱ, and 39 were in group Ⅲ. The 222 FaWRKY genes were evenly distributed among the seven chromosomes. The exon–intron structures and motifs of the WRKY genes had evolutionary diversity in different cultivated strawberry genomes. Regarding differential expression, the expression of FaWRKY133 was relatively high in leaves, while FaWRKY63 was specifically expressed in roots. FaWRKY207, 59, 46, 182, 156, 58, 39, 62 and 115 were up-regulated during achene development from the green to red fruit transition. FaWRK181, 166 and 211 were highly expressed in receptacles at the ripe fruit stage. One interesting finding was that Fa WRKY179 and 205 were significantly repressed after Colletotrichum fructicola inoculation in both ’Benihoppe’ and ’Sweet Charlie’ compared with Mock. The data reported here provide a foundation for further comparative genomics and analyses of the distinct expression patterns of FaWRKY genes in various tissues and in response to C. fructicola inoculation.

The different interactions of Colletotrichum gloeosporioides with two strawberry varieties and the involvement of salicylic acid

The disease symptoms recognized as‘Anthracnose’are caused by Colletotrichum spp.and lead to large-scale strawberry(Fragaria×ananassa Duchesne)losses worldwide in terms of both quality and production.Little is known regarding the mechanisms underlying the genetic variations in the strawberry–Colletotrichum spp.interaction.In this work,Colletotrichum gloeosporioides(C.gloeosporioides)infection was characterized in two varieties exhibiting different susceptibilities,and the involvement of salicylic acid(SA)was examined.Light microscopic observation showed that C.gloeosporioides conidia germinated earlier and faster on the leaf surface of the susceptible cultivar compared with the less-susceptible cultivar.Several PR genes were differentially expressed,with higher-amplitude changes observed in the less-susceptible cultivar.The less-susceptible cultivar contained a higher level of basal SA,and the SA levels increased rapidly upon infection,followed by a sharp decrease before the necrotrophic phase.External SA pretreatment reduced susceptibility and elevated the internal SA levels in both varieties,which were sharply reduced in the susceptible cultivar upon inoculation.The less-susceptible cultivar also displayed a more sensitive and marked increase in the transcripts of NB-LRR genes to C.gloeosporioides,and SA pretreatment differentially induced transcript accumulation in the two varieties during infection.Furthermore,SA directly inhibited the germination of C.gloeosporioides conidia;NB-LRR transcript accumulation in response to SA pretreatment was both dose-and cultivar-dependent.The results demonstrate that the less-susceptible cultivar showed reduced conidia germination.The contribution of SA might involve microbial isolate-specific sensitivity to SA,cultivar/tissue-specific SA homeostasis and signaling,and the sensitivity of R genes and the related defense network to SA and pathogens.

Auxin biosynthesis by the YUCCA6 flavin monooxygenase gene in woodland strawberry

Auxin has been regarded as the main signal molecule coordinating the growth and ripening of fruits in strawberry, the reference genomic system for Rosaceae. The mechanisms regulating auxin biosynthesis in strawberry are largely elusive. Recently, we demonstrated that two YUCCA genes are involved in flower and fruit development in cultivated strawberry. Here, we show that the woodland strawberry （Fragaria vesca L.） genome harbors nine loci for YUCCA genes and eight of them encode functional proteins. Transcription pattern in different plant organs was different for all eight FvYUCs. Functionality of the FvYUC6 gene was studied in transgenic strawberry over- expressing FvYUC6, which showed typical high-auxin pheno- types. Overexpression of FvYUC6 also delayed flowering and led to complete male sterility in F. vesta. Additionally, specific repression of FvYUC6 expression by RNA interference signifi- cantly inhibited vegetative growth and reduced plant fertility. The development of leaves, roots, flowers, and fruits was greatly affected in FvYUC6-repressed plants. Expression of a subset of auxin-responsive genes was well correlated with the changes of FvYUC6 transcript levels and free indole-3-acetic acid levels in transgenic strawberry. These observations are consistent with an important role of FvYUC6 in auxin synthesis, and support a main role of the gene product in vegetative and reproductive development in woodland strawberry.

Identification and classification of promoters using the attention mechanism based on long short-term memory

A promoter is a short region of DNA that can bind RNA polymerase and initiate gene transcription.It is usually located directly upstream of the transcription initiation site.DNA promoters have been proven to be the main cause of many human diseases,especially diabetes,cancer or Huntington’s disease.Therefore,the classification of promoters has become an interesting problem and has attracted the attention of many researchers in the field of bioinformatics.Various studies have been conducted in order to solve this problem,but their performance still needs further improvement.In this research,we segmented the DNA sequence in a k-mers manner,then trained the word vector model,inputted it into long short-term memory(LSTM)and used the attention mechanism to predict.Our method can achieve 93.45%and 90.59%cross-validation accuracy in the two layers,respectively.Our results are better than others based on the same data set,and provided some ideas for accurately predicting promoters.In addition,this research suggested that natural language processing can play a significant role in biological sequence prediction.