A chromosome-scale reference genome of Lobularia maritima, an ornamental plant with high stress tolerance

Abstract

Lobularia maritima (L.) Desv. is an ornamental plant cultivated across the world. It belongs to the family Brassicaceae and can tolerate dry, poor and contaminated habitats. Here, we present a chromosome-scale, high-quality genome assembly of L. maritima based on integrated approaches combining Illumina short reads and Hi–C chromosome conformation data. The genome was assembled into 12 pseudochromosomes with a 197.70 Mb length, and it includes 25,813 protein-coding genes. Approximately 41.94% of the genome consists of repetitive sequences, with abundant long terminal repeat transposable elements. Comparative genomic analysis confirmed that L. maritima underwent a species-specific whole-genome duplication (WGD) event ~22.99 million years ago. We identified ~1900 species-specific genes, 25 expanded gene families, and 50 positively selected genes in L. maritima. Functional annotations of these genes indicated that they are mainly related to stress tolerance. These results provide new insights into the stress tolerance of L. maritima, and this genomic resource will be valuable for further genetic improvement of this important ornamental plant.

Evaluation of Halophyte Biopotential as an Unused Natural Resource: The Case of Lobularia maritima

“…Recent studies have shown that L. maritima genome is ~197.70 Mb in size, with 88.31% (174.59 Mb) of the sequences assigned to 12 pseudochromosomes [ 9 ]. The L. maritima genome is smaller than that of other Brassicaceae species; it contains 25,813 genes and large numbers of repetitive elements [ 9 ].…”

“…Recent studies have shown that L. maritima genome is ~197.70 Mb in size, with 88.31% (174.59 Mb) of the sequences assigned to 12 pseudochromosomes [ 9 ]. The L. maritima genome is smaller than that of other Brassicaceae species; it contains 25,813 genes and large numbers of repetitive elements [ 9 ]. The adaptive divergence of a species from closely related species is frequently linked to gene families with significantly enlarged or contracted copy numbers [ 43 ].…”

“…Several interesting genes with a demonstrated influence on salt tolerance have recently been isolated from this species. A total of 319 stress-related genes belonging to twenty-five gene families were found to be significantly enriched in L. maritima genome, which might have facilitated its adaptation to harsh environments [ 9 ]. These genes are primarily involved in the responses of L. maritima to (i) molecules of bacterial and fungal origin, (ii) insects, (iii) wounding stress, and (iv) heavy metals and abiotic stresses [ 9 ] ( Figure 2 ).…”

“…Therefore, this review aims to shed light on halophytes—species capable of surviving harsh environmental conditions—and to describe the Mediterranean plant Lobularia maritima , an example of a perennial, diploid (2 = 24) herbaceous halophyte of the family Brassicaceae, commonly known as sweet alyssum, in terms of its composition and pharmacological potential [ 6 , 7 , 8 , 9 ].…”

Idahoa and Subularia: Hidden polyploid origins of two enigmatic genera of crucifers

“…Since the pioneering studies demonstrating the paleotetraploidy of the Arabidopsis genome and the mesohexaploidy of the “diploid” Brassica and Brassiceae species (The Arabidopsis Genome Initiative, 2000; Lysak et al, 2005; Parkin et al, 2005), many other clade‐ or genus‐specific mesopolyploid events have been discovered in Brassicaceae (e.g., Mandáková et al, 2010, 2017a; Kagale et al, 2014; Geiser et al, 2016; Huang et al, 2020; Guo et al, 2021). Mesopolyploid genomes have diploidized genomes with low chromosome number and often biased subgenome fractionation.…”