Brett Pike, Anders Gonçalves da Silva, Wilson Terán
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Four haplotype-resolved genome assemblies and a reference-free 66-haplotype pangenome graph for Cannabis sativa.
We present 4 haplotype-resolved, chromosome scale diploid assemblies of cannabis, assembled from ONT R9.4.1 reads via a novel pipeline based on Hi-C phasing. These assemblies, while low in QV, offer contiguity and genic content comparable to recent HiFi assemblies. Along with a trio-binned assembly previously produced by us and 56 haplotypes selected from the Salk Institute Cannabis Pangenome project, we use these assemblies to create a reference-free pangenome graph. Within a total length of 6.48 Gb, it contains 162.14 M nodes, 228.27 M edges, 14.87 M SNPs, and 6.40 M indels. By optimizing parameters within the Pangenome Graph Builder (PGGB), we avoid many spurious connections among repeat elements, reduce processing time, and arrive at a data structure that visibly recapitulates the linear nature of plant chromosomes. Via k-mer analysis, we corroborate that more genotypes are needed to close the cannabis pangenome, and that, in particular, the region of origin likely remains undersampled.
期刊介绍：
Scientific Data is an open-access journal focused on data, publishing descriptions of research datasets and articles on data sharing across natural sciences, medicine, engineering, and social sciences. Its goal is to enhance the sharing and reuse of scientific data, encourage broader data sharing, and acknowledge those who share their data.
The journal primarily publishes Data Descriptors, which offer detailed descriptions of research datasets, including data collection methods and technical analyses validating data quality. These descriptors aim to facilitate data reuse rather than testing hypotheses or presenting new interpretations, methods, or in-depth analyses.
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