The draft of stem lettuce genome released

On the end year of 2018, we initialized the project of sequencing the cultivar, stem lettuce.

Stem lettuce (Lactuca sativa var. angustana), also called Chinese lettuce, is a cultivar of lettuce grown primarily for its thick stem or its leaves. It is used as a vegetable and is especially popular in China and east Asian, where the stem is interchangeably called qingsun (Chinese: 青笋) or wosun (Chinese: 莴笋).

To produce a high-quality stem lettuce reference genome, we generated a de novo assembly of stem lettuce ‘Yanling1’ (YL1) composed of 280 assembled scaffolds and arranged into 9 pseudomolecules, which represent the 9 chromosomes of lettuce. This assembly resulted from a combination of short (Illumina) and long sequencing reads (PacBio), along with scaffolding based on optical maps (BioNano) and chromosome conformation capture (HiC) (Table 1). This chromosome-scale assembly was complemented by a detailed de novo annotation of genes based on RNA sequencing (RNA-seq) data, TE annotation and small RNA alignments.

Table 1. Assembly of stem lettuce. Note: Stage 1^a: the assembly generated only by PacBio data; Stage 2^b: the assembly generated by PacBio and Bionano data; Stage 3^c: the assembly generated by PacBio, Bionano and HiC data.