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HollyGTD currently hosts three fully sequenced and assembled genomes of one evergreen tree species Ilex latifolia and two deciduous tree species I. asprella and I. polyneura and their related annotation information. More de novo sequenced and assembled genomes of some important holly species in the near future would facilitate both the scientific research and breeding programs to produce novel ornamental cultivars, healthy beverages ...
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HollyGTD provides information (including references and type information) for a total of 1400 scientific names, and this list contains almost all the current known species of hollies. In addition, the wild images and micromorphology photos including pollen grains, pyrenes, and leaf epidermis are also integrate in this content.
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Whole genome re-sequencing datasets of 114 hollies were used to perform DNA variant analysis. Tens millions of single nucleotide polymorphisms (SNPs) and millions of structural variation (deletions and inversions) have been detected, and their impacts corresponding to different regions of genes such as CDSs, UTRs, etc., also have been sorted out.
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ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) is a technique used in molecular biology to assess genome-wide chromatin accessibility. In LettuceGDB, 1482 accessible regions were detected by ATAC-Seq, 490 of them were located in gene regions. Among these, more than 45.5% were located within 3 kb upstream...
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In terms of parsing 21 deeply sequenced small RNA libraries in different tissues (root, leaf, stem, flower), and five PARE-Seq libraries, current microRNAome of LettuceGDB contains 157 miRNA loci belonging to 76 families, 9 cluster and 3629 miRNA targets. In addition, for each specific microRNA, detailed annotations including sequences, structures, expression pattern, etc., were presented in a single webpage.
Lastest News
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2023-05-10
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2023-05-04
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2023-02-01
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2022-11-01
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2022-10-01
Summary
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- Gene number: 35,218
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- Gene number: 32,838
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- Gene number: 39,215
Citation
▶ HollyGTD: An integrated database for holly (Aquifoliaceae) genome and taxonomy. In preparation.
▶ Genome
▷ Ilex latifolia: Xu, K.W., Wei, X.F., Lin, C.X., Zhang, M., Zhang, Q., Zhou, P., Fang, Y.M., Xue, J.Y., and Duan, Y.F. (2022). The chromosome-level holly (Ilex latifolia) genome reveals key enzymes in triterpenoid saponin biosynthesis and fruit color change. Front Plant Sci 13, 982323.
▷ Ilex polyneura: Yao, X., Lu, Z., Song, Y., Hu, X., and Corlett, R.T. (2022). A chromosome-scale genome assembly for the holly (Ilex polyneura) provides insights into genomic adaptations to elevation in Southwest China. Hortic Res 9.
▷ Ilex asprella: Kong, B.L., Nong, W., Wong, K.H., Law, S.T., So, W.L., Chan, J.J., Zhang, J., Lau, T.D., Hui, J.H., and Shaw, P.C. (2022). Chromosomal level genome of Ilex asprella and insight into antiviral triterpenoid pathway. Genomics 114, 110366.
Phenotype
Combined with genome-wide association studies (GWAS), phenomics is a powerful tool to dissect the genetic basis of crop traits. Currently, a high-throughput lettuce phenotyping facility was employed to record the phenotype 1,048 strains, including images of top view, shapes of leaves, 3D structure of whole plants, etc. More traits and relative information will be released in the near future.
ATAC-Seq
ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) is a technique used in molecular biology to assess genome-wide chromatin accessibility. In LettuceGDB, 1482 accessible regions were detected by ATAC-Seq, 490 of them were located in gene regions. Among these, more than 45.5% were located within 3 kb upstream of a transcriptional start site (TSS), 28.4% were located in introns, 26.1% were located in exons. The accessible regions identified are mostly enriched around the TSS, which is consistent with these regions containing cis-regulatory elements in Lettuce.
miRNA
MiRNAome of stem lettuce contains 82 miRNA loci (MIRs) belonging to 41 families, 1 cluster and 2,831 predicted miRNA-target pairs. In addition, 16 deeply sequenced small RNA libraries belong to 3 tissues (leaf, root, stem) were used in quantification of miRNA expression patterns, and 3 PARE-Seq libraries were employed to validate predicted miRNA-target pairs.
Tools
