PepperBase: a integrated genomics resource database for pepper
PepperBase is a comprehensive genomics resource database for pepper. It integrates the first gap-free genome assembly for cultivated pepper Zunla-1 (Capsicum annuum L.), along with related genomic, transcriptomic, and epigenomic data. PepperBase also provides various user-friendly tools for convenient access to these genomics resources.
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Phenotypic Diversity of Capsicum annuum L.
Among the five domesticated species in Capsicum genus, Capsicum annuum L. is the most widely cultivated and frequently utilized species in breeding programmes. C. annuum L. encompasses rich variation in fruit shape, size, weight, orientation, and level of pungency, making it the most diverse of cultivated peppers.
Circos diagram of genomic features of Zunla-1_v3.0
A total of 39,085 protein-coding genes were predicted. TEs accounted for 84.58% (2.61 Gb) of the Zunla-1 pepper genome assembly. TEs were enriched near the centromeric regions of the chromosomes, while their density generally decreased towards the telomeric regions.
Genomics Comparison between v3.0 and v2.0 of Zunla-1
The collinear relationship between Zunla-1_3.0 and Zunla-1_2.0 is shown with the potential large inversions highlighted. The total size of the 12 chromosomes in Zunla-1_v3.0 was 430.34 Mb larger than that in Zunla-1_v2.0. There are 1,102,798 gaps in the Zunla-1_v2.0, while no gap exists in the Zunla-1_v3.0. Positioning of the centromeres also has been greatly improved in Zunal-1_v3.0.
Statistics of the genome assembly of Zunla-1_v3.0
A total of 103.54 Gb (~35×) of HiFi long reads were generated for Zunla-1 and assemblied into 85 contigs with a total size of 3.08 Gb and a contig N50 of 167.63 Mb. With the assistance of the Hi-C data, 99.94% of the assembled sequences were successfully anchored into 12 pseudo-chromosomes.
News
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The ONT full-length transcriptome data and DNA methylation data has been integrated into PepperBase. ( 2024-04-25 ) - The prototype version of PepperBase has been set up ! ( 2024-03-02 )
