Data Source
The Sanwen Huang lab at Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences. Data downloaded from Sol Genomics


Genome Overview
A high-accuracy and gapless linear reference genome is as critical as the backbone of a graph pangenome. To this end, we assembled a state-of-the-art backbone genome (tomato cv. Heinz 1706, Build SL5.0) using high-fidelity (HiFi) long reads and high-throughput chromosome conformation capture (Hi-C) long-range scaffolding....We performed the annotation of SL5.0 (ITAG5.0), predicting 36,648 protein-coding genes. (from Nature606, 527-534 (2022))

Genome Information
Assembly Source:
AGI_CAAS_Shenzhen
Assembly Version:
SL5.0
Annotation Source:
AGI_CAAS_Shenzhen
Annotation Version:
ITAG5.0
Total Scaffold Length (bp):
801,812,098
Number of Scaffolds:
13
Min. Number of Scaffolds containing half of assembly (L50):
6
Shortest Scaffold from L50 set (N50):
67,567,563
Total Contig Length (bp):
801,782,098
Number of Contigs:
73
Min. Number of Contigs containing half of assembly (L50):
9
Shortest Contig from L50 set (N50):
41,697,488
Number of Protein-coding Transcripts:
43,752
Number of Protein-coding Genes:
36,648
Percentage of Eukaryote BUSCO Genes:
94.7
Percentage of Embroyphyte BUSCO Genes:
93.5


Reference Publication(s)
Zhou, Y., Zhang, Z., Bao, Z., Li, H., Lyu, Y., Zan, Y., … Huang, S. (2022). Graph pangenome captures missing heritability and empowers tomato breeding. Nature, 606(7914), 527–534. https://doi.org/10.1038/s41586-022-04808-9

https://phytozome-next.jgi.doe.gov/info/Slycopersicum_ITAG5_0