Chromosome-level genome assembly of bunching onion illuminates genome evolution and flavor formation in Allium crops

Abstract

The Allium genus is cultivated globally as vegetables, condiments, or medicinal plants and is characterized by large genomes and strong pungency. However, the genome evolution and genomic basis underlying their unique flavor formation remain poorly understood. Herein, we report an 11.27-Gb chromosome-scale genome assembly for bunching onion (A. fistulosum). The uneven bursts of long-terminal repeats contribute to diversity in genome constituents, and dispersed duplication events largely account for gene expansion in Allium genomes. The extensive duplication and differentiation of alliinase and lachrymatory factor synthase manifest as important evolutionary events during flavor formation in Allium crops. Furthermore, differential selective preference for flavor-related genes likely lead to the variations in isoalliin content in bunching onions. Moreover, we reveal that China is the origin and domestication center for bunching onions. Our findings provide insights into Allium genome evolution, flavor formation and domestication history and enable future genome-assisted breeding of important traits in these crops.

Apostasia Mitochondrial Genome Analysis and Monocot Mitochondria Phylogenomics

“…Compared with other species of Asparagales, the mitogenome size of A. shenzhenica is moderate. However, the mitogenome size is remarkably smaller than that of G. elata [10], but larger than those of A. cepa, A. officinalis, and H. citrina [26][27][28]. The overall GC content is 44.4%, which is similar to that of other species of Asparagales (42.9-46.7%) (Table 4).…”

Annotation of the Turnera subulata (Passifloraceae) Draft Genome Reveals the S-Locus Evolved after the Divergence of Turneroideae from Passifloroideae in a Stepwise Manner

“…Transposable elements (TE) are one of the driving forces of evolution, altering gene expression patterns [ 46 , 47 , 48 ], chromatin accessibility [ 45 , 49 , 50 ], and gene duplication and evolution [ 26 , 47 ]. It has been proposed that TEs may be the main driving force for genome evolution in several species, including Moso bamboo [ 51 ], Pinus tabuliformis [ 52 ], and Allium fistulosum [ 53 ]. The general importance of TE in the evolution of novel structures, such as fiber cells in cotton [ 46 ], flavor in onion [ 53 ], and self-compatibility in species of Capsella [ 54 ], may suggest they should be of interest in studies related to the evolution of the S -genes of distylous species.…”

“…It has been proposed that TEs may be the main driving force for genome evolution in several species, including Moso bamboo [ 51 ], Pinus tabuliformis [ 52 ], and Allium fistulosum [ 53 ]. The general importance of TE in the evolution of novel structures, such as fiber cells in cotton [ 46 ], flavor in onion [ 53 ], and self-compatibility in species of Capsella [ 54 ], may suggest they should be of interest in studies related to the evolution of the S -genes of distylous species. This is especially true considering that the S -loci of Primula [ 6 ], Turnera [ 3 ], and Linum [ 4 ] accumulate TEs.…”

Turning Garlic into a Modern Crop: State of the Art and Perspectives

“…We are currently witnessing a revolution in the number of sequenced genomes for Allium species, with available sequences for the genomes of garlic [ 85 ], onion [ 87 ] and bunching onion [ 88 ]. Garlic was the first Allium species to have a chromosome-scale genome assembly, which was achieved through a combination of PacBio, Illumina and ONT sequencing technologies, as well as 10X Genomic libraries and Hi-C technology.…”

“…The large number of transposable elements (which account for 76% of the genome size) contribute to its large size and their insertions often affect the expression of other genes. The large size of the garlic genome has been attributed to the expansion of gypsy -type LTR retrotransposons [ 88 ]. In fact, 4219 garlic genes were found to be disrupted by transposon insertions, including an orthologue of the floral homeotic gene APETALA2 .…”