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

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.

Chloroplast genomic resources for phylogeny and DNA barcoding: a case study on Fritillaria.

The genus Fritillaria comprises approximately 130 perennial herbaceous species. In the Pharmacopoeia of the People's Republic of China, the bulbs of 11 Fritillaria species are used in Chinese herbal medicines. However, the traditional methods of morphological classification cannot accurately identify closely related species of Fritillaria. Previous studies have attempted to identify these species with universal molecular markers, but insufficient phylogenetic signal was available. In this study, the complete chloroplast genomes of eight Fritillaria species were compared. The length of the eight Fritillaria chloroplast genomes ranges from 151,009 bp to 152,224 bp. A total of 136 SSR loci were identified, including 124 polymorphic SSR loci. For large repeat sequences, 108 repeat loci and four types of repeats were observed. Ten highly variable regions were identified as potential molecular markers. These SSRs, large repeat sequences and highly variable regions provide important information for the development of genetic markers and DNA fingerprints. Phylogenetic analyses showed that the topological structures of all data sets (except the IR regions) were in complete agreement and well resolved. Overall, this study provides comprehensive chloroplast genomic resources, which will be valuable for future studies of evolution and species identification in Fritillaria.

Relationship between cytoplasmic male sterility and SPL-like gene expression in stem mustard.

We studied how mitochondria-nuclear interactions may give rise to cytoplasmic male sterility (CMS) in stem mustard exhibiting abnormal microsporogenesis. In this system, expression of SPL-like, the counterpart of the Arabidopsis nuclear gene SPOROCYTELESS, is specifically lost in buds of CMS plants. When mitochondrial-specific inhibitors were applied to wild-type fertile stem mustard plants, expression of SPL-like was repressed to some extent. As a consequence, the shape and vigor of pollen grains were severely affected, whereas the fertility of pistils remained unaltered. Thereby, we suggest that a probable pathway responsible for CMS in stem mustard involves mitochondrial retrograde regulation, with SPL-like as a target nuclear gene for a mitochondrial signal.