Gossypium hirsutum (AD1) 'TM-1' genome HAU_v2.0
Overview
About the Assembly We assembled the TM-1 and 3-79 genomes with Canu (version 2.1.1), which included correction, trimming, and assembly in three steps. We performed these steps manually. First, ONT reads and PacBio reads from both genomes were corrected and trimmed using Canu with default parameters (correctedErrorRate = 0.045 for PacBio reads; correctedErrorRate = 0.144 for Nanopore reads). Trimmed highquality reads from ONT (~40x) and PacBio (~40x) were delivered as input to Canu using a mix of formats with default parameters. To improve base quality, we aligned Illumina paired-end reads (~50x) to contigs using BWA–MEM and polished them with Pilon (version 1.23) (–fix bases –mindepth 10 –minmq 30). High-quality paired-end Hi-C reads based on DpnII for G. hirsutum TM-1 and G. barbadense 3-79 were mapped to the two contig-scale assemblies using Juicer (version 1.6). The original contigs were organized into chromosomes with the 3D-DNA pipeline (version 180 419) (-r 2 -i 15000 –buildgapped- map). Finally, we used Juicebox Assembly Tools (v1.11.08) to manually correct and refine the connections. Summary of assemblies of G. hirsutum and G. barbadense genome
Assembly
The chromosomes (pseudomolecules) and scaffolds for G. hrisutum 'TM-1' genome. These files belong to the Gossypium hirsutum (AD1) 'TM-1' genome HAU_v2.0
Functional Annotation
Functional annotation files for the Gossypium hirsutum TM-1 Genome v2.0 are available for download below. The Gossypium hirsutum TM-1 Genome v2.0 proteins were analyzed using InterProScan in order to assign InterPro domains and Gene Ontology (GO) terms. Pathways analysis was performed using the KEGG Automatic Annotation Server (KAAS). Downloads
Genes
The predicted gene model, their alignments and proteins for G. hirsutum 'TM-1' genome. These files belong to the Gossypium hirsutum (AD1) 'TM-1' genome HAU_v2.0
Publication
Chang, Xing, Xin He, Jianying Li, Zhenping Liu, Ruizhen Pi, Xuanxuan Luo, Ruipeng Wang et al. "High-quality Gossypium hirsutum and Gossypium barbadense genome assemblies reveal the landscape and evolution of centromeres." Plant Communications 5, no. 2 (2024). doi.org/10.1016/j.xplc.2023.100722 |