Dataset Information

Chromosome-scale genome assembly of a Japanese chili pepper landrace, Capsicum annuum 'Takanotsume'.

ABSTRACT: 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'.

SUBMITTER: Shirasawa K

PROVIDER: S-EPMC9886071 | biostudies-literature | 2023 Feb

REPOSITORIES: biostudies-literature

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Chromosome-scale genome assembly of a Japanese chili pepper landrace, Capsicum annuum 'Takanotsume'.

Shirasawa Kenta K Hosokawa Munetaka M Yasui Yasuo Y Toyoda Atsushi A Isobe Sachiko S

DNA research : an international journal for rapid publication of reports on genes and genomes 20230201 1

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 pre ...[more]

PMID: 36566389

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Project description:Red chili pepper (Capsicum annuum L.), which belongs to the Solanaceae family, contains a variety of phytochemicals with health-promoting properties including capsaicinoids, phenolics and fatty acids. Red chili pepper is one of the most consumed vegetables in Korea and occupies the largest cultivated area among spices. In this study, the ethanolic extracts from two Korean local cultivars, namely Subicho and Eumseong, were analyzed using a hybrid trapped ion mobility Q-TOF mass spectrometer equipped with a UPLC system, and their phytochemical profiles were then compared with those of a common phytophthora disease-resistant cultivar called Dokbulwang, which is extensively used for red chili pepper powder in public spaces across Korea. Utilizing high-resolution ion-mobility Q-TOF MS analysis, 458 and 192 compounds were identified from the three different red chili peppers in positive and negative ion modes, respectively, by matching with a reference spectral library. Principal component analysis revealed clear distinctions among the three cultivars, allowing us to identify key phytochemical components responsible for discriminating the local cultivars from the public cultivar. Furthermore, the assessment of total flavonoid, phenolic, and antioxidant activity in the red pepper extracts, highlighted their diverse molecular and chemical profiles. Despite the higher total flavonoid and phenolic content values observed in the public cultivar, the radical scavenging rate was higher in the local cultivars, particularly in Subicho. This suggest the presence of stronger antioxidant compounds in the local cultivar, indicating their potential health benefits due to their rich content of bioactive compounds. Notably, the local cultivars exhibited significantly higher proportions of organic compounds (more than four times) and terpenoids (more than two times) compared to the public cultivar. Specifically, higher levels of five major capsaicinoid compounds were found in the local cultivars when compared to the public cultivar. The observed disparities in phytochemical composition and antioxidant activities indicate the molecular diversity present among these cultivars. Further exploration of the bioactive compounds in these local cultivars could prove invaluable for the development of native crops, potentially leading to the discovery of novel sources of bioactive molecules for various applications in health and agriculture.

Dataset Information

Chromosome-scale genome assembly of a Japanese chili pepper landrace, Capsicum annuum 'Takanotsume'.

Publications

Chromosome-scale genome assembly of a Japanese chili pepper landrace, Capsicum annuum 'Takanotsume'.

Similar Datasets

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