Chromosome-scale genome assembly of a Japanese chili pepper landrace, Capsicum annuum ‘Takanotsume’

日本を代表するトウガラシ「鷹の爪」の全ゲノムを解読 --多様なトウガラシを生み出すための基盤に--. 京都大学プレスリリース. 2023-01-12.Here, we report the genome sequence of a popular Japanese chili pepper landrace, Capsicum annuum ‘Takanotsume’. We used long-read sequencing and optical mapping, together with the genetic mapping technique, to obtain the chromosome-scale genome assembly of ‘Takanotsume’. The assembly consists of 12 pseudomolecules, which corresponds to the basic chromosome number of C. annuum, and is 3, 058.5 Mb in size, spanning 97.0% of the estimated genome size. A total of 34, 324 high-confidence genes were predicted in the genome, and 83.4% of the genome assembly was occupied by repetitive sequences. Comparative genomics of linked-read sequencing-derived de novo genome assemblies of two Capsicum chinense lines and whole-genome resequencing analysis of Capsicum species revealed not only nucleotide sequence variations but also genome structure variations (i.e., chromosomal rearrangements and transposon-insertion polymorphisms) between ‘Takanotsume’ and its relatives. Overall, the genome sequence data generated in this study will accelerate the pan-genomics and breeding of Capsicum, and facilitate the dissection of genetic mechanisms underlying the agronomically important traits of ‘Takanotsume’

Genome-wide study on the polysomic genetic factors conferring plasticity of flower sexuality in hexaploid persimmon

Sexuality is one of the fundamental mechanisms that work towards maintaining genetic diversity within a species. In diploid persimmons (Diospyros spp.), separated sexuality, the presence of separate male and female individuals (dioecy), is controlled by the Y chromosome-encoded small-RNA gene, OGI. On the other hand, sexuality in hexaploid Oriental persimmon (Diospyros kaki) is more plastic, with OGI-bearing genetically male individuals, able to produce both male and female flowers (monoecy). This is thought to be linked to the partial inactivation of OGI by a retrotransposon insertion, resulting in DNA methylation of the OGI promoter region. To identify the genetic factors regulating branch sexual conversion, genome-wide correlation/association analyses were conducted using ddRAD-Seq data from an F-1 segregating population, and using both quantitative and diploidized genotypes, respectively. We found that allelic ratio at the Y-chromosomal region, including OGI, was correlated with male conversion based on quantitative genotypes, suggesting that OGI can be activated in cis in a dosage-dependent manner. Genome-wide association analysis based on diploidized genotypes, normalized for the effect of OGI allele dosage, detected three fundamental loci associated with male conversion. These loci underlie candidate genes, which could potentially act epigenetically for the activation of OGI expression

Identification of bovine seminal plasma proteins with an activity to normalize endometrial epidermal growth factor concentrations in repeat breeder cows

Epidermal growth factor (EGF) concentrations in the bovine uterus show two peaks on Days 2-4 and 13-14 during the estrous cycle in normal cows; however, these peaks were not found in about 70% of Holstein repeat breeder cows. We have demonstrated the effect of seminal plasma (SP) to normalize the endometrial EGF concentrations on Day 3 and restore fertility in repeat breeder cows. The objective of this study was to identify SP protein(s) with the activity of normalizing the endometrial EGF concentrations. Semen was collected from 5 Holstein bulls and pooled SP obtained from 30 ejaculates were used for this study. The SP protein were separated by gel filtration and 2-dimensional electrophoresis. SP fractions with molecular weight of 16-29 kDa and pI5.8-7.0 showed an activity to normalize the endometrial EGF concentrations on Day 3. Then, protein spots in these area on electrophoresis gels were extracted and subjected to liquid chromatography with tandem mass spectrometry analysis. Twelve protein spots that include four spots of osteopontin (OPN) with different molecular weights and isoelectric points were identified. Protein extracts of one of these OPN spots normalized the endometrial EGF concentrations on Day 3 in 41.9% of repeat breeder cows. The present results indicated that OPN may be the molecule responsible for the activity normalizing the EGF concentrations on Day 3 in the endometrium of repeat breeder cows

Time Course of Acute Vertebral Fractures: A Prospective Multicenter Cohort Study

To date, it is still unclear how fresh osteoporotic vertebral fractures (OVFs) affect the patient’s quality of life and low back pain during a follow-up period of more than 1 year. In the previous trial, women with fresh OVF were randomized to rigid or soft brace for 12 weeks, then both groups were followed for the subsequent 48 weeks. In women completing this trial at our affiliated hospitals, we conducted a follow-up study to investigate the long-term course of an acute vertebral fracture in terms of pain and quality of life. When comparing visual analog scale scores for low back pain and European Quality of Life-5 Dimensions Questionnaire scores between consecutive time points, a significant difference was found between 0 and 12 weeks, but not between 12 and 48 weeks or between 48 weeks and final follow-up. A total 25% had residual low back pain at the final follow-up. A stepwise logistic regression analysis identified age and previous vertebral fracture as predictors of residual low back pain at the final follow-up. Therefore, the degree of low back pain and impairment of the quality of life improved by 12 weeks after injury and did not change thereafter until a mean follow-up of 5.3 years

DataSheet_1_A self-compatible pear mutant derived from γ-irradiated pollen carries an 11-Mb duplication in chromosome 17.zip

Self-compatibility is a highly desirable trait for pear breeding programs. Our breeding program previously developed a novel self-compatible pollen-part Japanese pear mutant (Pyrus pyrifolia Nakai), ‘415-1’, by using γ-irradiated pollen. ‘415-1’ carries the S-genotype S4dS5S5, with “d” indicating a duplication of S5 responsible for breakdown of self-incompatibility. Until now, the size and inheritance of the duplicated segment was undetermined, and a reliable detection method was lacking. Here, we examined genome duplications and their inheritance in 140 F1 seedlings resulting from a cross between ‘515-20’ (S1S3) and ‘415-1’. Amplicon sequencing of S-RNase and SFBB18 clearly detected S-haplotype duplications in the seedlings. Intriguingly, 30 partially triploid seedlings including genotypes S1S4dS5, S3S4dS5, S1S5dS5, S3S5dS5, and S3S4dS4 were detected among the 140 seedlings. Depth-of-coverage analysis using ddRAD-seq showed that the duplications in those individuals were limited to chromosome 17. Further analysis through resequencing confirmed an 11-Mb chromosome duplication spanning the middle to the end of chromosome 17. The duplicated segment remained consistent in size across generations. The presence of an S3S4dS4 seedling provided evidence for recombination between the duplicated S5 segment and the original S4haplotype, suggesting that the duplicated segment can pair with other parts of chromosome 17. This research provides valuable insights for improving pear breeding programs using partially triploid individuals.</p