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.
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.
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▶ 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.
▶ Genome
▷ 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.
Germplasm
