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De Novo Genome Assembly of the Japanese Wheat Cultivar Norin 61 Highlights Functional Variation in Flowering Time and Fusarium-Resistant Genes in East Asian Genotypes.

ABSTRACT: Bread wheat is a major crop that has long been the focus of basic and breeding research. Assembly of its genome has been difficult because of its large size and allohexaploid nature (AABBDD genome). Following the first reported assembly of the genome of the experimental strain Chinese Spring (CS), the 10+ Wheat Genomes Project was launched to produce multiple assemblies of worldwide modern cultivars. The only Asian cultivar in the project is Norin 61, a representative Japanese cultivar adapted to grow across a broad latitudinal range, mostly characterized by a wet climate and a short growing season. Here, we characterize the key aspects of its chromosome-scale genome assembly spanning 15 Gb with a raw scaffold N50 of 22 Mb. Analysis of the repetitive elements identified chromosomal regions unique to Norin 61 that encompass a tandem array of the pathogenesis-related 13 family. We report novel copy-number variations in the B homeolog of the florigen gene FT1/VRN3, pseudogenization of its D homeolog and the association of its A homeologous alleles with the spring/winter growth habit. Furthermore, the Norin 61 genome carries typical East Asian functional variants different from CS, ranging from a single nucleotide to multi-Mb scale. Examples of such variation are the Fhb1 locus, which confers Fusarium head-blight resistance, Ppd-D1a, which confers early flowering, Glu-D1f for Asian noodle quality and Rht-D1b, which introduced semi-dwarfism during the green revolution. The adoption of Norin 61 as a reference assembly for functional and evolutionary studies will enable comprehensive characterization of the underexploited Asian bread wheat diversity.

SUBMITTER: Shimizu KK

PROVIDER: S-EPMC7991897 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundChikungunya virus (CHIKV) is a re-emerging mosquito-borne virus which causes epidemics of fever, severe joint pain and rash. Between 2005 and 2010, the East/Central/South African (ECSA) genotype was responsible for global explosive outbreaks across India, the Indian Ocean and Southeast Asia. From late 2013, Asian genotype CHIKV has caused outbreaks in the Americas. The characteristics of cross-antibody efficacy and epitopes are poorly understood.Methodology/principal findingsWe characterized human immune sera collected during two independent outbreaks in Malaysia of the Asian genotype in 2006 and the ECSA genotype in 2008-2010. Neutralizing capacity was analyzed against representative clinical isolates as well as viruses rescued from infectious clones of ECSA and Asian CHIKV. Using whole virus antigen and recombinant E1 and E2 envelope glycoproteins, we further investigated antibody binding sites, epitopes, and antibody titers. Both ECSA and Asian sera demonstrated stronger neutralizing capacity against the ECSA genotype, which corresponded to strong epitope-antibody interaction. ECSA serum targeted conformational epitope sites in the E1-E2 glycoprotein, and E1-E211K, E2-I2T, E2-H5N, E2-G118S and E2-S194G are key amino acids that enhance cross-neutralizing efficacy. As for Asian serum, the antibodies targeting E2 glycoprotein correlated with neutralizing efficacy, and I2T, H5N, G118S and S194G altered and improved the neutralization profile. Rabbit polyclonal antibody against the N-terminal linear neutralizing epitope from the ECSA sequence has reduced binding capacity and neutralization efficacy against Asian CHIKV. These findings imply that the choice of vaccine strain may impact cross-protection against different genotypes.Conclusion/significanceImmune serum from humans infected with CHIKV of either ECSA or Asian genotypes showed differences in binding and neutralization characteristics. These findings have implications for the continued outbreaks of co-circulating CHIKV genotypes and effective design of vaccines and diagnostic serological assays.

Project description:This study assess the population diversity and temporal variability of caused by Fusarium oxysporum f. sp. vasinfectum (FOV) races/genotypes infecting cotton cultivars with either FOV or Meloidogyne incognita resistance. All plants sampled demonstrated typical symptoms of FOV including wilting, chlorosis and necrosis of the leaves, and discoloration of the vascular tissue in the stem. A diverse population of FOV was characterized. Eight races/genotypes of FOV were collected throughout the three site years. FOV race 1 was the most predominant in all tests (AUDPC=101.1); statistically higher numbers of isolates from LA-108 (AUDPC=59.9), race 8 (AUDPC=47.5), and race 2 (AUDPC=38.6) were also found compared to other races and genotypes collected. FOV race 1, race 2, race 8, and 108 were the most virulent races identified. The genotypes MDS-12, LA-110, and LA-127/140 were found in all tests but at a low incidence, and LA-112 was only found in trace amounts. MDS-12, LA-110, LA-112, and LA-127/140 produced less disease pressure. FOV race 4 which is highly virulent and present in California and Texas was not found in Alabama. A positive correlation was observed between the accumulation of growing degree days and FOV race 1, race 2, race 8, LA-108, and LA-110. Later symptom expression influenced by seasonal heat partially mitigates damage allowing cotton to produce bolls though they may be reduced in number and lint quality. Plant resistance to the FOV as expressed in these cultivars appears to provide better protection than M. incognita resistance. PhytoGen 72, which is resistant to FOV races/genotypes had low levels of FOV infection even though it sustained a high level of M. incognita root population density. The M. incognita resistant cultivars Deltapine 1558NR B2RF and PhytoGen 480 W3FE supported a lower nematode population density, however, FOV disease incidence was not reduced. FOV races/genotypes did not vary significantly between the nematode resistant and nematode susceptible cultivars.

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De Novo Genome Assembly of the Japanese Wheat Cultivar Norin 61 Highlights Functional Variation in Flowering Time and Fusarium-Resistant Genes in East Asian Genotypes.

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