LettuceGDB currently harbors two cultivar (Salinas and YL1) reference genomes and all related annotations. Considering the abundant lettuce cultivars, a pan-genome consisting of other four representative cultivars including looseleaf, romaine, butterhead and wild lettuce (L. serriola) has been initialized and these data will be released in the near future.
LettuceGDB has a collection of 1,333 germplasms from 49 countries, and this germplasm collection contains all most all representatives of lettuces. Whole-genome resequencing was performed on 1,048 of them and based on these data, the genetic relationship and structure, evolutionary relationship of different cultivars has been sorted out.
We manually recorded 13 phenotypes of 1,333 germplasms at five locations while multiple high-throughput phenomic platforms were employed to record the phenotypes of these germplasms. Among these records, several agronomical and morphological traits such as leaf types, growth cycle related to bolting and flowering time, etc., have been detailed analyzed.
Whole genome re-sequencing datasets of 1048 strains 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 promoters, CDSs, etc., also have been sorted out. The figure displays the phylogenetic relationship of these 1048 strains via 300k SNPs.
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...
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.
▶ Guo Z, Li B, Du J, Shen F, Zhao Y, Deng Y, Kuang Z, Tao Y, Wan M, Lu X, Wang D, Wang Y, Han Y, Wei J, Li L, Guo X, Zhao C, Yang X. LettuceGDB: The community database for lettuce genetics and omics. Plant Commun. 2022. 12:100425.
▷ Crisphead lettuce (Lactuca sativa cv. Salinas): The data were generated by Compositae Genome Project and the Lettuce Genome Sequencing Project. To Lettuce Genome Resource and the Michelmore lab. Cite: Reyes-Chin-Wo, S., Wang, Z., Yang, X., Kozik, A., Arikit, S., Song, C., Xia, L., Froenicke, L., Lavelle, D.O., Truco, M.J., et al. (2017). Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce. Nat Commun 8:14953.
Original data from NCBI Genome GCF_002870075.3_Lsat_Salinas_v8
▷ Stem lettuce (Lactuca sativa var. angustana): Data originally generated by the LettuceGDB team. Raw data have been deployed in the BIG Data Center, PRJCA007442.
▷ Prickly lettuce (Lactuca serriola L.): Data originally generated by the LettuceGDB team, who is working on performing subsequent assembly and annotation.
LettuceGDB harbors a core pan-genome of representative lettuces, including prickly lettuce (Lactuca serriola, the closest wild relative of cultivated lettuce) and other five typical lettuce cultivars, Stem, Crisphead, Butterhead, Romaine, and Looseleaf. For each of them, the chromosome-scale whole genome sequence with detailed annotation is first released while the previous version of Crisphead (Reyes-Chin-Wo, et al., 2017) is also provided. The figure displays the genome information of Stem lettuce by Circos.
In LettuceGDB, 1,333 germplasms are collected from 49 countries on five continents except for Antarctica. This germplasm collection contains all most all types of lettuces. Briefly, the proportions of each type are Butterhead (237 or 18.1%), Crisphead (239 or 18.2%), Romaine (202 or 15.4%), Stem (85 or 6.5%), Oil, Looseleaf (285 or 21.7%), hybrid strains (184 or 14.0%), and wild relatives (81 or 6.1%).
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.
1048 strains via whole genome re-sequencing datasets were used to perform DNA polymorphic analysis. The genetic variation including single nucleotide polymorphisms (SNPs) and structural variation (deletions and inversions) focuses on those with important aspects of lettuce diversity. The figure displays the phylogenetic relationship of these 1048 strains via 300k SNPs.
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.
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.