Through huge effort the whole team made, The Lettuce Genome Database (LettuceGDB) was online and the team released its version 1.0 on Nov 1st 2021. Cheers!
Basic informatin
· Database Name: Lettuce Genome Database (LettuceGDB).
· Short Description: A comprehensive omics database for cutting-edge research and breeding in lettuce
Data in LettuceGDB
· Data available from current LettuceGDB includes the information on two cultivar genomes. One is a crisphead variety (L. sativa cv. Salinas) while the other one, a variety of stem lettuce (L. sativa cv. YL1), is de novo assembled and firstly released by our Lettuce Breeding Group (LBG). All information related to these two genomes, including detailed genomic annotations, can be downloaded through the Download tool.
· The Genotype data are re-sequencing data of different Lactuca accessions. The LBG generated re-sequencing data of 1,048 accessions including 900 various cultivars and over 100 wild relatives. These data include 70,792,508 SNPs and 5,869,237 InDels, which affecting more than 35,000 annotated gene loci.
· LettuceGDB provides basic information of 1,313 germplasms which collected from 49 countries. The Phenotype data is divided into two categories. The first category is manually recorded through multi-sites planting and growth cycles in the past years. These data include 26 characteristics such as multiple important agronomic traits. The second category of phenotypic records were obtained by high-throughput phenotypic platforms.
· The transcriptome information mainly comes from Zhang’s work (Zhang L et al,. 2017), which contains the leaf transcriptome of 240 Lactuca accessions, as well as the transcriptomic data of stem lettuce sequenced by our LBG. We summarizes the expression information of genes in different varieties and wild relatives.
· miRNAome mainly includes two batches of datasets, 31 sRNA-Seq datasets from different tissues and 5 PARE-Seq datasets. The current miRNAome includes 157 high confident miRNA genes and other annotations such as genomic positions and sequences, secondary structures, target genes by both prediction and experimental validation from PARE-Seq datasets, conservation, etc., and this part of data is also mirrored with the Plant MicroRNA Encyclopedia (PmiREN2.0).
· LettuceGDB contains 4,120 metabolites from 50 lettuce germplasms belonging to six types of lettuce, which were obtained based on the liquid chromatography-tandem mass spectrometry (LC-MS/MS) method. Among the detectable compounds, 533 of them are annotated, which are divided into ten groups, including alkaloids, amino acids and derivatives, flavonoids, lignans and coumarins, lipids, nucleotides and derivatives, organic acids, phenolic acids, terpenoids and others.
· The current type of epigenetic data are relatively limited, only the datasets from a study from our LBG. ATAC-Seq (Assay for Transposase-Accessible Chromatin with high-throughput sequencing) was employed to test the differences of transposase accessible areas of chromatin in leaf before and after heat treatment.
Features of LettuceGDB
· LettuceGDB provides many convenient accesses, powerful search engines and easy-to-use ways to download data.
· Users can browse detailed information of germplasms in interactive map, compile and compare phenotypic data using visualization tools, fetch polymorph information via a powerful search engine, and gain plentiful epigenomic resources.
· LettuceGDB also provides eight helpful tools, Search Gene, Blast, JBrowse, Primer Design, Gene expression, Homologs, Gene Annotation, Literature, by which users can explore more useful information in a customized way.
Taken together, we believe LettuceGDB integrates and compiles resourceful omics data for both scientific research and breeding practices in lettuce. It is a comprehensive functional database amenable for data mining and database-driven exploration.
If you meet any troubles or find any bugs when you visit LettuceGDB, please email to Contact@LettuceGDB.com, post requests in LettuceGDB forum or you can contact us directly by: Address: No.9 zhonglu shuguanghuayuan, Haidian District, Beijing, China, 100097; Tel: +86-10-51503774.
LettuceGDB team
Nov.1st 2021
Germplasm