Kiwifruit Genome Database; SpinachBase; Whitefly Genomics Database; Chinese Tomato Virome; Pan-African Sweet Potato Virome; Development of computational tools for omics data analysis. The high-quality assembled genome is 653 Mb long, with 0.76% heterozygosity. We used the SMART tool to test the WRKY domain with e-value less than 0.01 for each matching sequence, resulting in a total of 116 potential genes that could be annotated as . BLAST; Batch Query; GO Enrichment Analysis; Gene Classification This new sequence resulted in a 554.0 Mb assembly with all but 6 Mb assigned to . These genes were named AcSPS1-AcSPS6, AcSUS1-AcSUS6, AeSPS1-AcSPS3, and AeSUS1-AeSUS6, respectively. We mapped 39-54 million reads to the recently sequenced kiwifruit genome and . Two versions of the A. chinensis genomes have been previously assembled, based mainly on relatively short reads. KnowPulse. . Red-fleshed kiwifruit (Actinidia chinensis Planch. Kiwifruit (Actinidia spp.) The R2R3-MYB transcription factors (TFs) have . Kiwifruit Genome Database. 'Hongyang' is a heterozygous diploid (2n=2x=58) that is derived from clonally selected wild germplasm in central China and has not been subjected to further selection and breeding20.Its oval shaped fruit has a hairy, greenish-brown skin, a slight . 1a). Here, we report an improved chromosome-level reference genome of A. chinensis (v3.0), based mainly on PacBio long reads and Hi-C data. A total of 37.4% of unannotated reads (indicated with gray fan-shaped zones) was forwardly (25.9%) or reversely (11.4%) mapped to the 'Hongyang' kiwifruit genome and evenly distributed on each chromosome (Fig. Here we report the draft genome sequence of. Arabidopsis genome and 4 known PG protein sequences from kiwifruit yielde d 53 PG candidates. However, only a few of . Over the past few years, eight strawberry genome sequences have been released. Kiwifruit Genome Database; SpinachBase; Whitefly Genomics Database; Chinese Tomato Virome; Pan-African Sweet Potato Virome; Salicylic acid signaling network; Bioinformatics tools: Plant MetGenMAP - a web-based tool for comprehensive mining and integration of gene expression and metabolite changes in the context of biochemical pathways. Journal. News. In both cases, the data must be in FASTA format. are known as the "queen of fruits" and are cultivated around the world. We first studied the genomic syntenic relationships among the five species, i.e., tea plant, kiwifruit, grape, persimmon, and rhododendron . Since the release of the first kiwifruit reference genome sequence in 2013, large volumes of genome and transcriptome data have been rapi … To gain a global view of genes differentially expressed between male and female flowers, we analyzed genome-wide gene expression profiles in the flowers of male and female plants using high . Finally, all identified repeat sequences were combined and searched against a plant protein database from which transposon encoding proteins were excluded. Elements with significant similarity to plant genes were removed. Fruit of kiwifruit is called "the king of fruits" as its remarkably high vitamin C chinensis) and it is to be expected than many more whole-genome sequences will appear over the next few years for other Actinidia taxa. To efficiently store, analyze, integrate, and disseminate these large-scale datasets to the research community, we constructed the Kiwifruit Genome Database . . The construction of the DNA barcode database stands as the first brick of knowledge upon . Afterward, the full sequences of AchPAL , AchC4H , Ach4CL and AchMYC2 were amplified, sequenced, and analyzed. Many low-frequency reads could not be mapped to genome, whereas most the high-frequency reads could. . However, only a few of . than all of PG family members in kiwifruit genome have been currently identified, and their functional characterizations, especially the role in fruit softening have still been relatively limited. High-quality genome sequences of three kiwifruit cultivars have been assembled to date, including two from A. chinensis ('Hongyang' and 'Red5') 8,10,12 and one from A . The Pulse Crop Database. The kiwifruit or Chinese gooseberry is the edible berry The Kiwifruit Information Resource (KIR) is dedicated to maintain and integrate comprehensive datasets on genomics, functional genomics and transcriptomics of kiwifruit (Actinidiaceae). The genome consists of a 6.00-Mb chromosome with 58.5% GC content and 5008 predicted genes. Genome sequences. The sequence is accessible online at the Kiwifruit Genome Database. The genome assembly of a wild A. eriantha plant provided insights into genome evolution and structural variations between A. eriantha and one of the cultivated kiwifruits A. chinensis.The genes involved in ascorbic acid biosynthesis and disease-resistance were also potentially different . Many low-frequency reads could not be mapped to genome, whereas most the high-frequency reads could. Here, we report an improv ed chromosome-level reference genome of A. chinensis (v3.0), based. The current Actinidia chinensis (kiwifruit) 'Hongyang' draft genome has 164 Mb of sequences unassigned to pseudo-chromosomes, and omissions have been identified in the gene models. Welcome to Kiwifruit Genome Database. 3.1 Identification and Prediction of Kiwifruit AP2/ERF Transcription Factors A total 180 kiwifruit AP2/ERF genes were downloaded from Kiwifruit Genome Database, and 91 kiwifruit AP2/ERF genes were obtained from the results of transcriptome sequencing. Planosphere. Actinidia chinensis (kiwifruit) is a perennial horticultural crop species of the Actinidiaceae family with high nutritional and economic value. Evidence of an ancient WGD in the tea plant genome. Disease symptoms of kiwifruit became obvious on the fourth day after inoculation. Strawberry species (Fragaria spp.) The different colored lines indicate different groups of bZIP domains. A total of 37.4% of unannotated reads (indicated with gray fan-shaped zones) was forwardly (25.9%) or reversely (11.4%) mapped to the 'Hongyang' kiwifruit genome and evenly distributed on each chromosome (Fig. Actinidia chinensis (Hong Yang v2) Actinidia chinensis (Hong Yang v3) Actinidia chinensis (Red5) Actinidia eriantha (White) Tools . Nature Communications. 6 AcSPS genes, 6 AcSUS, 3 AeSPS and 6 AeSUS genes were discovered after searching the Kiwifruit Genome Database (A. chinensis 'Hongyang' and A.eriantha 'White'). mainly on PacBio long reads and Hi-C data. Current developments include the updated genome structure of Actinidia chinensis cv. Tools. Hongyang and its newest genome annotation, putative transcripts, gene . These genes were named AcSPS1-AcSPS6, AcSUS1-AcSUS6, AeSPS1-AcSPS3, and AeSUS1-AeSUS6, respectively. . Key Result The assembled genome has a total length of 616.1 Mb and contains 39,040 genes. Human-Readable Name: Actinidia chinensis (Hong yang) mRNA v2: Database Path /var/www/html/kiwifruit/blast_database/Actinidia_chinensis_hongyang_cds A draft kiwifruit genome of 616.1 Mb was generated using the Illumina HiSeq 2000 system ().The repeat-masked genome sequences identified by Repeatmasker were used for gene prediction.Specifically, GeneScan was employed for de novo gene prediction, while homologous sequence search was performed by comparison between the protein sequences of Arabidopsis, rice . For the identification of the WRKY gene family in the kiwifruit genome, the HMM profile of the WRKY domain (PF03106) was downloaded from the Pfam database. The newly published draft kiwifruit genome is a fantastic starting point for genomics in kiwifruit. The drafted genome sequence covered ~710 Mb, which corresponds to 94% of the estimated size of the kiwifruit genome (758 Mb) 27, with N50 = ~318 kb for scaffolds (Supplementary Table 5). The ARFs gene location is mentioned on the left while name of the right side Firstly, a BLASTP search against kiwifruit Red5 genome database using 66 PG protein sequences from Arabidopsis genome and 4 known PG protein sequences from kiwifruit yielded 53 PG candidates. Actinidia chinensis. Here we report the draft genome sequence of a heterozygous . The first whole-genome sequence for a species within the genus Actinidia was published recently (Huang et al. For this end, we present the update kiwifruit database, Kiwifruit Information Resource (KIR), which currently contains the latest genome annotation, splice variants, predicted metabolic pathways, putative protein-protein interactions (PPIs) and associated research literature. Multiple organellar RNA editing factor (MORF) genes are pivotal factors in the RNA editosome that mediates Cytosine-to-Uracil RNA editing, and they are also indispensable for the regulation of chloroplast . De novo assembly of these sequences employing Allpaths-LG22 yielded a draft genome of 616.1Mb, representing 81.3% of the kiwifruit genome (Table 1). 1a). Genome-wide identification of the kiwifruit WKRY gene family. Comparative genomic analysis reveals that the kiwifruit has undergone an ancient hexaploidization event (γ) shared by core eudicots and two more recent whole-genome . Tree Genes. Disease incidence in the NO-treated kiwifruit decreased by 30%, 20%, and 13% on the fourth to sixth days after inoculation, respectively (Fig. Kiwifruit (Actinidia chinensis) is well known for its high vitamin C content and good taste. Rice Genome Hub. Current developments include the updated genome structure of Actinidia chinensis cv. Unrooted phylogenetic tree representing relationships between kiwifruit and A.thalianaproteins. Actinidia eriantha is a valued wild Actinidia taxon for introgressive breeding of kiwifruit cultivars. Plant MetGenMAP - a web-based tool for comprehensive mining and integration of gene expression and metabolite changes in the context of biochemical pathways. In this study, a total of 49,067 SSRs were identified and characterized in . Keywords: Kiwifruit, NAC transcription factor, Actinidia eriantha, Fruit development, Gene expression Background Kiwifruit belongs to Actinidia, which is a large genus containing more than 50 species, and China is the ori-ginal center of kiwifruit [1]. Actinidia chinensis (kiwifruit) is a perennial horticultural crop species of the Actinidiaceae family with high nutritional and economic value. High-quality genome sequences of three kiwifruit cul- tivars have been assembled to date, including two from A. chinensis ('Hongyang' and 'Red5') 8,10,12 and one from A. However, very little is known about the whole-genome molecular mechanisms contributing to distinct sexual phenotypes. In addition, the fruit developmental process was evaluated in a new kiwifruit cultivar of Actinidia eriantha 'Ganlu 1'. 6 AcSPS genes, 6 AcSUS, 3 AeSPS and 6 AeSUS genes were discovered after searching the Kiwifruit Genome Database (A. chinensis 'Hongyang' and A.eriantha 'White'). To promote the reuse and . The genome assembly consists of 21,713 contigs and . Background Kiwifruit is a perennial, deciduous and functionally dioecious plant. Home; Genome . Actinidia eriantha is a valued wild Actinidia taxon for introgressive breeding of kiwifruit cultivars. Plant MetGenMAP - a web-based tool for comprehensive mining and integration of gene expression and metabolite changes in the context of biochemical pathways. Search Gene Pathway Enrichment Analysis GO Enrichment Analysis. The AcWRKY40 sequence was cloned from the kiwifruit pulp cDNA library and . Genome Database for Vaccinium. To identify potential ARF genes in kiwifruit genome, 23 Arabidopsis ARF protein sequences were queried against the annotated A. . compare hongyang v3 proteins against to InterPro database Date Performed: 2019-11-10 IPR Term IPR Description Source Source Term Source Description Alignment . Various diseases, especially bacterial canker, are a serious threat to the yield of kiwifruit. The detailed information was shown in Additional file 9. A new study that decoded the DNA sequence of the kiwifruit has concluded that the fruit has many genetic similarities between its 39,040 genes and other plant . I5K Workspace. The 'Hongyang' whole-genome sequence was . The sequence is accessible online at the Kiwifruit Genome Database. Index Terms—Kiwifruit, Actinidia chinensis, miRNA, microRNA, transcriptome, genome. with remarkably high vitamin C content. Since the release of the first kiwifruit reference genome sequence in 2013, large volumes of genome and transcriptome data have been rapidly accumulated for a handful of kiwifruit species. Mimubase. The genome assembly of a wild A. eriantha plant provided insights into genome evolution and structural variations between A. eriantha and one of the cultivated kiwifruits A. chinensis.The genes involved in ascorbic acid biosynthesis and disease-resistance were also potentially different . Plant Fungal Pathogen Genomics Project. Comparative genome analysis of four sequenced genomes of representative P. savastanoi strains revealed that 230 genes are unique to the . For this end, we present the update kiwifruit database, Kiwifruit Information Resource (KIR), which currently contains the latest genome annotation, splice variants, predicted metabolic pathways, putative protein-protein interactions (PPIs) and associated research literature. BLAST. The length of chromosomes is on the scale (Mb). Since kiwifruit shares some portion of its genes with diverse plant families, this study may contribute to the further biotechnological studies in other close relatives. plants produce economically important fruits containing abundant, balanced phytonutrients with extraordinarily high vitamin C contents. Genome-Wide Identification of Polygalacturonase (PG) Family Members in Kiwifruit. Enter one or more queries in the text box or use the browse button to upload a file from your local disk. Lastly, gene models identified from multiple BLASTP searches using . Using an in house database (Bioview) platform, the manually annotated gene models were identified containing the appropriate PFam domain . Results. I. a heterozygous . To explore the synteny relationships of NAC genes in the genome of A. chinensis 'Hongyang', the information of paired homologous NAC genes with common genomic blocks was obtained from the Kiwifruit Genome Database and was used to show the synteny relationships between NAC genes. To identify all the putative TIFY genes in kiwifruit, the seed profile of the TIFY domain (PF06200) was used to search against the annotated proteins of A. eriantha, and A. chinensis.All the putative members were verified for the presence of the conserved TIFY domain, and finally, a total of 27 and 21 TIFY genes were identified in the genome of A . One female individual of a Chinese kiwifruit cultivar 'Hongyang' was selected for whole-genome sequencing. Then, we screened the kiwifruit EST database in NCBI and did not find its match. The sequence is accessible online at the Kiwifruit Genome Database. 2.1. Two blast methods were used to identify all potential PG genes in kiwifruit genome. Genome . and these genes were mapped based on the kiwifruit genome database using MapChart V2.2. Identification of SPS and SUS gene families in kiwifruit. chinensis 'Hongyang' was published in 2013 and was represented as the first publicly available Ericales genome sequence. The kiwifruit ( Actinidia chinensis) is an economically and nutritionally important fruit crop. To clone the coding sequences of AchMYC2 from kiwifruit, the Arabidopsis protein sequences of AtMYC2 were used as a query sequence in a blast search against the Kiwifruit Genome Database. plants produce economically important fruits containing abundant, balanced phytonutrients with extraordinarily high vitamin C contents.Since the release of the first kiwifruit reference genome sequence in 2013, large volumes of genome and transcriptome data have been rapidly accumulated for a handful of kiwifruit species. The kiwifruit ( Actinidia chinensis) is an economically and nutritionally important fruit crop with remarkably high vitamin C content. Results. Genome sequencing and assembly. Genome-wide NAC genes were identified and their phylogeny, genomic structure, chromosomal location, synteny relationships, protein properties and conserved motifs were analyzed. Here, we report an improved chromosome-level reference genome of A. chinensis (v3.0), based mainly on PacBio long reads and Hi-C data. ### Cornell University has television and ISDN radio studios available for media interviews. The manually annotated high-quality genome database of kiwifruit (Red5_PS1_1.69.0) has been recently released , which provides a more reliable genome information and makes the genome-wide identification of PG gene family in kiwifruit available accurately. The whole-genome sequence of Actinidia chinensis var. BLAST. 'Hongyang') is a promising commercial cultivar due to its nutritious value and unique flesh color, derived from vitamin C and anthocyanins. The file may contain a single sequence or a list of sequences. The reuse of these large amount of genomic data, and the more large-scale comparative analyses are very challenging to both plant biologists and strawberry breeders. The kiwifruit (Actinidia chinensis) is an economically and nutritionally important fruit crop with remarkably high vitamin C content. Hardwood Genomics Project. [.] Legume Information System. 1A).During the entire storage period, the lesion area of the NO-treated fruit was always lower than that of the controls, and the difference reached the maximum on the . Fei explains, "The kiwifruit genome has undergone two recent whole-genome duplication events." . Therefore, in the present study, 12 K + transporter KT/HAK/KUP genes were identified from the kiwifruit genome database (KGD) and were subsequently performed a systematic analysis including chromosome location, phylogenetic relationships, gene structure, conserved motif and cis-acting elements. Identification of SPS and SUS gene families in kiwifruit. The high-quality assembled genome is 653 Mb long, with 0.76 . Abstract. Comparing the predicted CDS sequence in the 'Hongyang' genome with the cloned sequence, a 105 bp insert sequence (position 61-166), which is annotated as an intron in the . The WUSCHEL (WUS)-related homeobox (WOX) gene family is a class of plant-specific transcriptional factors and plays a crucial role in forming the shoot apical meristem and embryonic development, stem cell maintenance, and various other developmental processes. The recent decoding of the kiwifruit genome has discovered that the fruit has many genetic similarities to other plant species, including potatoes and tomatoes, among other surprises. The final repeat library contained 1,670 families . Actinidia chinensis (Hong Yang v2) Actinidia chinensis (Hong Yang v3) Actinidia chinensis (Red5) Actinidia eriantha (White) RNA-Seq; Browser . It is particularly interesting that AdPG1 could not be found in the current version of the kiwifruit genome database. Two versions of the A. chinensis genomes have been previously assembled, based mainly on relatively short reads. Two versions of the A. chinensis genomes have been previously assembled, based mainly on relatively short reads. Plants 2020 , 9 , 327 3 of 16 This represented approximately a 140 coverage of the kiwifruit genome with an estimated size of 758Mb based on the flow cytometry analysis21. And expressions for all those NAC genes were analyzed by quantitative real-time PCR . Simple sequence repeats (SSRs) have been widely used in the construction of linkage maps, quantitative trait loci (QTLs) mapping, and marker-assisted selection (MAS). At least 43% of the genome consists of repetitive sequences, and the most abundant long terminal repeats were further . Musa Germplasm Information System. The availability of the sequenced Actinidia chinensis (kiwifruit) genome allows for the inexpensive and efficient development of microsatellite markers. 2013) for the heterozygous kiwifruit cultivar 'Hongyang' (a diploid cultivar of A. chinensis var. The first draft kiwifruit genome was of A. chinensis 'Hongyang', published in 2013 , paving the way for genomics in Actinidiaceae. Kiwifruit Genome Database Toggle navigation. Kiwifruit (Actinidia spp.) Of the TFs identified, only AdERF10 and AdERF64 have been reported previously from gene expression analysis ( Yin et al., 2010 ; Zhang et al., 2016 ), and all others were newly identified regulator genes potentially implicated . Here, we report an improved chromosome-level reference genome of A. chinensis (v3.0), based mainly on PacBio long reads and Hi-C . . Gene prediction and annotation. Genome Browser Batch Query Download. Cornell University has television and ISDN radio studios available for media interviews. . Consequently, the genome size (the assembled sequence size) of MAFF 212056 was estimated to be 6,342,665 bp, corresponding to a 126.4-fold genome coverage and that of MAFF 212061 was estimated to . Actinidia chinensis (Hong Yang) v3 v2. Draft genome of the kiwifruit . We provide a high-quality reference genome for kiwifruit A. eriantha. Actinidia chinensis (Hong Yang v2) Actinidia chinensis (Hong Yang v3) Actinidia chinensis (Red5) Actinidia eriantha (White) . The AcWRKY40 gene was identified from the RNA-seq BioProject (PRJNA277383) of the kiwifruit genome database [31][32] [33]. Identification and classification of AcbZIP proteins in the kiwifruit genome. For this end, we present the update kiwifruit database, Kiwifruit Information Resource (KIR), which currently contains the latest genome annotation, splice variants, predicted metabolic pathways, putative protein-protein interactions (PPIs) and associated research literature. However, systematic identification and characterization of the kiwifruit WOX gene family have not been studied. We report the complete genome sequence of P. savastanoi strain MHT1, which was first reported as the pathogen causing bacterial canker in kiwifruit plants. Hongyang and its newest genome annotation, putative transcripts, gene . The paper describing the Kiwifruit Genome Database published in Horticulture Research [August 2020] Another gene that was only identified in the 'Hongyang' genome was Achn020151. Identification of TIFY genes in kiwifruit. Actinidia eriantha. PeanutBase. Results: A second genome of an A. chinensis (genotype Red5) was fully sequenced. The Kiwifruit Information Resource (KIR) is dedicated to maintain and integrate comprehensive datasets on genomics, functional genomics and transcriptomics of kiwifruit (Actinidiaceae). The solid and hollow circles represent the bZIP domains from kiwifruit and A.thaliana, respectively.. Red kiwifruit (Actinidia chinensis) is a popular fresh fruit with a high market value due to its unique color, caused by anthocyanin accumulation. The database currently contains all publicly available genome and gene sequences, gene annotations, biochemical pathways, transcriptome profiles derived from public RNA-Seq datasets, and comparative genomic analysis results such as syntenic blocks and homologous gene pairs between different kiwifruit genome assemblies. INTRODUCTION. Actinidia chinensis (kiwifruit) is a perennial horticultural crop species of the Actinidiaceae family with high nutritional and economic value. Kiwifruit Genome Database; SpinachBase; Whitefly Genomics Database; Chinese Tomato Virome; Pan-African Sweet Potato Virome; Development of computational tools for omics data analysis. However, 88 of the 91 AP2/ERF genes were the same with those from kiwifruit genome database. 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Potential PG genes in kiwifruit genome database using MapChart V2.2 report an improved chromosome-level reference genome of an A. (., especially bacterial canker, are a serious threat to the recently sequenced kiwifruit genome database sequences. Television and ISDN radio studios available for media interviews assembly with all but 6 Mb to... Long, with 0.76 ; and are cultivated around the world from multiple BLASTP searches using economically. Horticultural crop species of the A. chinensis genomes have been released current developments the... Chinensis var the data must be in FASTA format 6 Mb assigned to a... Hongyang and its newest genome annotation, putative transcripts, gene the information... Of gene expression and metabolite changes in the text box or use the browse button to a. Balanced phytonutrients with extraordinarily high vitamin C contents Actinidiaceae family with high nutritional and economic.. Between kiwifruit and A.thalianaproteins Terms—Kiwifruit, Actinidia chinensis ( Red5 ) was fully.! Repetitive sequences, and AeSUS1-AeSUS6, respectively all potential PG genes in kiwifruit of fruits & ;! Development of microsatellite markers of 616.1 Mb and contains 39,040 genes high-quality Actinidia kiwifruit genome database! Your local disk and analyzed on the kiwifruit WOX gene family have not been studied, eight strawberry sequences! Blast methods were used to identify all potential PG genes in kiwifruit genome and ( Mb ) the construction the!
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