Chromosome-level assembly of two pearl millet (Cenchrus americanus) genomes, functional annotation and transcriptomes

We present platinum-grade reference genome assemblies, featuring gapless chromosomes, for two pearl millet lines: the Striga-susceptible SOSAT-C88-P10 (P10) and the resistant 29Aw (Aw). This study was motivated by the severe impact of the root parasitic weed Striga hermontica on pearl millet yield, with Striga relying on host-released strigolactones (SLs) for seed germination. These resources enable advanced genomic investigations in pearl millet, facilitating research on phenotypic traits, diversity, and adaptation. Additionally, comparative analysis between P10 and 29Aw genomes can pave the way for identifying genetic determinants of Striga resistance, contributing to the development of resilient pearl millet lines., For a detailed workflow of the genome annotation part of the work, please refer to the following github repo: https://github.com/mjfi2sb3/millet-genome-annotation, , # Chromosome-level assembly of two pearl millet (*Cenchrus americanus*) genomes, functional annotation and transcriptomes.

## Description of the data and file structure

**Genome assemblies & data**

The final assemblies are: **Awk_genome_assmb_FINAL_v1.fasta.gz** and **P10K_genome_assmb_FINAL_v1.fasta.gz** for AwK and P10K, respectively. These are the assemblies (with finalised chromosome names) that were used in the gene structure annotation using the MAKER pipeline.

***Other assembly related files:***

**Awk_assmb_files.tar.gz** and **P10k_assmb_files.tar.gz** are tarballs that contain the output from the juicer tool that we used to scaffold the initial hifiasm (assembler tool) HiFi-based assemblies using OmniC data. These tarballs contain: an agp file, an equivalent bed file, a break point report, and the fasta file with the original chromosome names (do not use with gene structure annotation).

***Genomic Raw Data:***

***AwK:***

* PacBio HiFi (SequelII):

1. AWK_2....