Gossypium arboreum (A2) 'ZB-1' genome ZSTU_v1
|
Overview
About the assembly Recent advancements in plant regeneration and synthetic polyploid creation have been documented in Gossypium arboreum ZB-1. These developments make ZB-1 a potential model within the Gossypium genus for investigating gene function and polyploidy. This work generated the sequence and annotation of the ZB-1 genome. The contig-level genome was constructed using the PacBio high-fidelity reads, encompassing 81 contigs with an N50 length of 112.12 Mb. The Hi-C data assisted the construction of the chromosome-level genome, which consists of 13 pseudo-chromosomes and 39 un-anchored contigs, with a total length of about 1.67 Gb. Repetitive sequences accounted for about 69.7% of the genome in length. Based on ab initio and evidence-based prediction, we have identified 48,021 protein-coding genes in the ZB-1 genome. Comparative genomics analysis revealed conserved gene content and arrangement between ZB-1 and G. arboreum SXY1. The single nucleotide polymorphism occurrence rate between ZB-1 and SXY1 was about 0.54 per 1,000 nucleotides. This study enriched the genomic resources for further exploration into cotton regeneration and polyploidy mechanisms. Table 1. Statistics of the Gossypium arboreum ZB-1 genome assembly
Publication Sun R et al., Chromosome-level genome assembly and annotation of a potential model organism Gossypium arboreum ZB-1. Scientific Data. 2024 Jun 12;11(1):620.
Assembly
The chromosomes (pseudomolecules) and scaffolds for Gossypium arboreum (A2) 'ZB-1' genome. This file belongs to the ZSTU G. arboreum Assembly v1.0
Contact
Sun, Yu-Qiang; Yu, Dong-Liang Functional Analysis
Functional annotation files for the Gossypium arboreum 'ZB-1' ZSTU v1.0.a1 protein sequences are available for download below. Protein sequences were analyzed using InterProScan v5.72 to assign InterPro domains and Gene Ontology (GO) terms. Pathway analysis was performed using the KEGG Automatic Annotation Server (KAAS) v2.1. Downloads
Genes
The predicted gene model, their alignments and proteins etc. for Gossypium arboreum(A2) 'ZB-1' genome. These files belong to the ZSTU G. arboreum Assembly v1.0
*_cds_from_genomic.fna.gz & *_rna_from_genomic.fna.gz (info from the link of NCBI): FASTA sequences of individual features annotated on the genomic records. The sequences are based solely on the genome sequence and annotated feature at a particular location. They may differ from the product sequences found in the *_rna.fna.gz and *_protein.faa.gz files which may be based on transcript or other data sources and include mismatches, indels, or additional sequence not found at a particular genomic location. Homology
Homology of the Gossypium arboreum 'ZB-1' ZSTU v1.0.a1 protein sequences was determined by pairwise sequence comparison using the BLASTp algorithm against various protein databases. An E-value cutoff of 10-6 was applied for Arabidopsis thaliana (Araport11, 2022-09), UniProtKB/Swiss-Prot (Release date: 2026-01-28), and UniProtKB/TrEMBL (Release date: 2026-01-28) databases. The best-hit reports are available for download in Excel format. Protein Homologs
Markers
Marker alignments were performed by the CottonGen Team of the Main Bioinformatics Lab (WSU). The alignment tool 'BLAT' was used to map marker sequences from CottonGen to the Gossypium arboreum 'ZB-1' ZSTU v1.0 assembly. Markers required 90% identity over 97% of their length. For SSRs & RFLPs, gap size was restricted to 1000 bp or less with ewer than 2 gaps. For dbSNPs and indels, gap size was restricted to 2 bp with fewer than 2 gaps. The available files are in GFF3 format. Markers available in CottonGen are linked to JBrowse.
Links
|
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||