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....本研究报道了两个珍珠粟（pearl millet，学名*Cenchrus americanus*）品系的白金级无间隙染色体参考基因组组装结果：易感独脚金（Striga）的SOSAT-C88-P10（简称P10）以及抗独脚金的29Aw（简称Aw）。本研究的初衷源于根寄生杂草Striga hermontica对珍珠粟产量造成的严重危害——独脚金需依赖宿主释放的独脚金内酯（strigolactones, SLs）完成种子萌发。 上述基因组资源可为珍珠粟的高级基因组学研究提供有力支撑，助力表型性状、遗传多样性及环境适应性相关研究。此外，对P10与29Aw基因组开展比较分析，可为鉴定独脚金抗性的遗传决定因子奠定基础，进而推动抗逆珍珠粟品系的培育。 如需了解本研究中基因组注释部分的详细流程，请参考以下GitHub仓库：https://github.com/mjfi2sb3/millet-genome-annotation。 # 两个珍珠粟（*Cenchrus americanus*）基因组的染色体级组装、功能注释及转录组 ## 数据与文件结构说明 ### 基因组组装与数据 最终组装文件分别为适用于AwK的**Awk_genome_assmb_FINAL_v1.fasta.gz**，以及适用于P10K的**P10K_genome_assmb_FINAL_v1.fasta.gz**。上述组装文件（已完成染色体命名标准化）已用于基于MAKER（MAKER pipeline）流程的基因结构注释。 #### 其他组装相关文件： **Awk_assmb_files.tar.gz**与**P10k_assmb_files.tar.gz**为压缩包，包含我们使用Juicer工具（juicer tool）的输出结果：该工具依托OmniC测序数据，对初始hifiasm组装工具（hifiasm assembler tool）得到的HiFi组装结果进行支架组装。此类压缩包内含AGP文件、等效BED文件、断点报告，以及保留原始染色体命名的FASTA文件（请勿将其用于基因结构注释）。 #### 基因组原始数据： ##### AwK： * PacBio HiFi（SequelII平台）： 1. AWK_2....