Genome assembly of the popular Korean soybean cultivar Hwangkeum

Involvement of the GH38 Family Exoglycosidase α-Mannosidase in Strawberry Fruit Ripening

Exoglycosidase enzymes hydrolyze the N-glycosylations of cell wall enzymes, releasing N-glycans that act as signal molecules and promote fruit ripening. Vesicular exoglycosidase α-mannosidase enzymes of the GH38 family (EC 3.2.1.24; α-man) hydrolyze N-glycans in non-reduced termini. Strawberry fruit (Fragaria × ananassa) is characterized by rapid softening as a result of cell wall modifications during the fruit ripening process. Enzymes acting on cell wall polysaccharides explain the changes in fruit firmness, but α-man has not yet been described in F. × ananassa, meaning that the indirect effects of N-glycan removal on its fruit ripening process are unknown. The present study identified 10 GH38 α-man sequences in the F. × ananassa genome with characteristic conserved domains and key residues. A phylogenetic tree built with the neighbor-joining method and three groups of α-man established, of which group I was classified into three subgroups and group III contained only Poaceae spp. sequences. The real-time qPCR results demonstrated that FaMAN genes decreased during fruit ripening, a trend mirrored by the total enzyme activity from the white to ripe stages. The analysis of the promoter regions of these FaMAN genes was enriched with ripening and phytohormone response elements, and contained cis-regulatory elements related to stress responses to low temperature, drought, defense, and salt stress. This study discusses the relevance of α-man in fruit ripening and how it can be a useful target to prolong fruit shelf life.

Vitis labrusca genome assembly reveals diversification between wild and cultivated grapevine genomes

Wild grapevines are important genetic resources in breeding programs to confer adaptive fitness traits and unique fruit characteristics, but the genetics underlying these traits, and their evolutionary origins, are largely unknown. To determine the factors that contributed to grapevine genome diversification, we performed comprehensive intragenomic and intergenomic analyses with three cultivated European (including the PN40024 reference genome) and two wild North American grapevine genomes, including our newly released Vitis labrusca genome. We found the heterozygosity of the cultivated grapevine genomes was twice as high as the wild grapevine genomes studied. Approximately 30% of V. labrusca and 48% of V. vinifera Chardonnay genes were heterozygous or hemizygous and a considerable number of collinear genes between Chardonnay and V. labrusca had different gene zygosity. Our study revealed evidence that supports gene gain-loss events in parental genomes resulted in the inheritance of hemizygous genes in the Chardonnay genome. Thousands of segmental duplications supplied source material for genome-specific genes, further driving diversification of the genomes studied. We found an enrichment of recently duplicated, adaptive genes in similar functional pathways, but differential retention of environment-specific adaptive genes within each genome. For example, large expansions of NLR genes were discovered in the two wild grapevine genomes studied. Our findings support variation in transposable elements contributed to unique traits in grapevines. Our work revealed gene zygosity, segmental duplications, gene gain-and-loss variations, and transposable element polymorphisms can be key driving forces for grapevine genome diversification.

GlPS1 overexpression accumulates coumarin secondary metabolites in transgenic Arabidopsis

The dried root of Glehnia littoralis is a traditional Chinese herbal medicine mainly used to treat lung diseases and plays an important role in fighting coronavirus disease 2019 pneumonia in China. This study focused on the key enzyme gene GlPS1 for furanocoumarin synthesis in G. littoralis. In the 35S:GlPS1 transgenic Arabidopsis study, the Arabidopsis thaliana-overexpressing GlPS1 gene was more salt-tolerant than Arabidopsis in the blank group. Metabolomics analysis showed 30 differential metabolites in Arabidopsis, which overexpressed the GlPS1 gene. Twelve coumarin compounds were significantly upregulated, and six of these coumarin compounds were not detected in the blank group. Among these differential coumarin metabolites, isopimpinellin and aesculetin have been annotated by the Kyoto Encyclopedia of Genes and Genomes and isopimpinellin was not detected in the blank group. Through structural comparison, imperatorin was formed by dehydration and condensation of zanthotoxol and a molecule of isoprenol, and the difference between them was only one isoprene. Results showed that the GlPS1 gene positively regulated the synthesis of coumarin metabolites in A. thaliana and at the same time improved the salt tolerance of A. thaliana.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s11240-022-02427-w.

Genetic and Genomic Resources for Soybean Breeding Research

Soybean (Glycine max) is a legume species of significant economic and nutritional value. The yield of soybean continues to increase with the breeding of improved varieties, and this is likely to continue with the application of advanced genetic and genomic approaches for breeding. Genome technologies continue to advance rapidly, with an increasing number of high-quality genome assemblies becoming available. With accumulating data from marker arrays and whole-genome resequencing, studying variations between individuals and populations is becoming increasingly accessible. Furthermore, the recent development of soybean pangenomes has highlighted the significant structural variation between individuals, together with knowledge of what has been selected for or lost during domestication and breeding, information that can be applied for the breeding of improved cultivars. Because of this, resources such as genome assemblies, SNP datasets, pangenomes and associated databases are becoming increasingly important for research underlying soybean crop improvement.

Genome assembly of the JD17 soybean provides a new reference genome for comparative genomics

Cultivated soybean (Glycine max) is an important source for protein and oil. Many elite cultivars with different traits have been developed for different conditions. Each soybean strain has its own genetic diversity, and the availability of more high-quality soybean genomes can enhance comparative genomic analysis for identifying genetic underpinnings for its unique traits. In this study, we constructed a high-quality de novo assembly of an elite soybean cultivar Jidou 17 (JD17) with chromosome contiguity and high accuracy. We annotated 52,840 gene models and reconstructed 74,054 high-quality full-length transcripts. We performed a genome-wide comparative analysis based on the reference genome of JD17 with 3 published soybeans (WM82, ZH13, and W05), which identified 5 large inversions and 2 large translocations specific to JD17, 20,984-46,912 presence-absence variations spanning 13.1-46.9 Mb in size. A total of 1,695,741-3,664,629 SNPs and 446,689-800,489 Indels were identified and annotated between JD17 and them. Symbiotic nitrogen fixation genes were identified and the effects from these variants were further evaluated. It was found that the coding sequences of 9 nitrogen fixation-related genes were greatly affected. The high-quality genome assembly of JD17 can serve as a valuable reference for soybean functional genomics research.