A comprehensive and integrated database could provide coherent information to users and advance either scientific or practical progresses. Holly Genome & Taxonomy Database (HollyGTD), which integrates the holly data from public databases with the data produced by our group. The HollyGTD combines a variety of multi-omics data (genome, re-sequencing, and transcriptome) and taxonomic resources with a wealth of phenotypic images. In addition, HollyGTD offers a couple of easy-to-use access functions/interfaces and eight built-in tools for data analysis, for instance, Blast, JBrowse, Search Gene, Tissue Expression, Gene Annotation, Phylogenetic Tree, Primer Design, and Literature. Therefore, we believe that HollyGTD, a comprehensive database with useful data on genome, genotype, and taxonomy, may represent a valuable resource for the entire holly research community.
1. Click on “FTP Download” to obtain assembly and annotation files. 2. Click on “Blast” then jump to Blast interface.
Taxonomy Search Box 1. Search box: three arguments for searching taxonomy by Scientific name, Authority or REF. 2. Result box: showcase for filtered taxonomy. 3. Download file including all taxonomy information.
Two search modes are available in Genotype page, search by gene identifier or by range (of the chromosome).
1. Users could input a gene name, e.g. lla01G000030, then select a variant type and effect type. The option “Effect Type” includes all, intergenic, promoter, intron, exon, 5’ UTR, 3’ UTR.
2. Users could input a range of genome, including chromosome (Chr), start position and end position. Then select a variant type and effect type as above.
3. The result table showcase the variants among 114 resequencing data.
4. Download a TSV (Tab-separated values) file including the selected polymorph information.
1. Searching gene by inputting a gene id. e.g. Ila01G000010.
2. Obtaining the sequences of queried gene, including CDS and protein.
3. An interactive mode of gene structure. Blue boxes represent exons. Black lines represent introns. An arrow indicates transcription direction. Double-stranded DNA sequences corresponding to horizontal scroll bar exhibit in the black box.
1. Search box: inputting a gene name, e.g. Ila01G000010.
2. Bar chart showing the average expression level of queried gene in green fruit, red fruit and leaves of different developmental stages.
3. Heat map showing the expression level of queried gene in 21 RNA-seq libraries.
InterproScan was implemented to annotate gene from three holly genomes. Users just need to input a gene id, then click on button "Search".
Users can select and filter branches to obtain specific holly in the phylogenetic trees. The phylogenetic tree was obtained from Yang’s research (Yang et al., 2023).
Yang, Y., Jiang, L., Liu, E.-D., Liu, W.-L., Chen, L., Kou, Y.-X., et al. (2023). Time to update the sectional classification of Ilex (Aquifoliaceae): New insights from Ilex phylogeny, morphology, and distribution. J. Syst. Evol. doi: 10.1111/jse.12935
Primer3 is a widely used program for designing PCR primers (PCR = "Polymerase Chain Reaction"). PCR is an essential and ubiquitous tool in genetics and molecular biology. Primer3 can also design hybridization probes and sequencing primers.
PCR is used for many different goals. Consequently, primer3 has many different input parameters that you control and that tell primer3 exactly what characteristics make good primers for your goals.
HollyGTD integrates a modified version of primer3, by which users only need to input a gene id before selecting mRNA in the pull-down menu (see red box). Then, clicking on the button “Get sequence”, the sequences will be filled in automatically.
1. Searching box for literature regarding to holly: User could search studies related to holly from over 800 publications by four options, including year, author, title, and journal.
2. Result table: Clicking on a title, then jumping to the full text of this paper.
Tools