Gossypium hirsutum (AD1) 'UA48' genome HGS_v1.1

Overview
Analysis NameGossypium hirsutum (AD1) 'UA48' genome HGS_v1.1
MethodPacBio Sequel II, Illumina NovaSeq, MECAT v. 1.3
Source (v1.0, a1.1)
Date performed2024-05-15

About the UA48 Assembly

Main assembly consisted of 93.70x of PACBIO coverage (8,899 bp average read size), and was assembled using MECAT and the resulting sequence was polished using ARROW. A total of 108,262 unique, non-repetitive, non-overlapping 1 KB syntenic markers were generated using the v2.0 G. hirsutum var. TM1 genome (genome release and aligned to the polished G. hirsutum var. UA48 assembly. Contig breaks were identified as an abrupt change in linkage group. A total of 56 breaks were made. The broken contigs were then ordered, oriented, and assembled into 26 chromosomes using the version 2.0 G. hirsutum syntenic markers. A total of 925 joins were made during this process. The HiC library was aligned to the integrated chromosomes, and several minor rearrangements were made. Adjacent alternative haplotypes were identified on the joined contig set. AltHap regions were collapsed using the longest common substring between the two haplotypes. A total of 334 adjacent altHaps were collapsed. Care was taken to ensure that telomere was properly oriented in the chromosomes, and the resulting sequence was screened for retained vector and/or contaminants. A total of 98.2% of the assembled sequence is contained in the chromosomes. Finally, Homozygous SNPs and INDELs were corrected in the release sequence using ~68x of illumina reads (2x150, 400bp insert).

Genome Information

UA48  
Assembly Source Phytozome genome ID: 569 
Assembly Version / Annotation Version v1.0 / a1.1
Total Scaffold Length (bp) 2,293,500,691
Number of Scaffolds 860
Min. Number of Scaffolds containing half of assembly (L50) 10
Shortest Scaffold from L50 set (N50) 105,664,978
Total Contig Length (bp) 2,287,690,691
Number of Contigs 1,441
Min. Number of Contigs containing half of assembly (L50) 84
Shortest Contig from L50 set (N50) 8,142,815
Number of Protein-coding Transcripts 113,741
Number of Protein-coding Genes 77,237
Percentage of Eukaryote BUSCO Genes 99
Percentage of Embroyphyte BUSCO Genes 98.3

Publication

Sreedasyam, A., Lovell, J.T., Mamidi, S. et al. Genome resources for three modern cotton lines guide future breeding efforts. Nat. Plants 10, 1039–1051 (2024). https://doi.org/10.1038/s41477-024-01713-z

Assembly

The chromosomes (pseudomolecules) for G. hrisutum UA48 genome. These files belong to the HGS (Phytozome) Assembly v1.0

Chromosomes (FASTA format) G.hirsutum_HGS-AD1_UA48_assembly_v1.fa.gz
Functional Analysis

Functional annotation files for the Gossypium hirsutum UA48 Genome v1.0 are available for download below. The Gossypium hirsutum UA48 Genome v1.0 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

GO assignments from InterProScan GhirsutumUA48_569_v1.1_genes2GO.xlsx.gz
IPR assignments from InterProScan GhirsutumUA48_569_v1.1_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs GhirsutumUA48_569_v1.1_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways GhirsutumUA48_569_v1.1_KEGG-pathways.xlsx.gz
Genes

The predicted gene model, their alignments, and proteins for G. hirsutum 'UA48' genome. These files belong to the HGS (Phytozome) Assembly v1.0

Predicted gene models with exons (GFF3 format) G.hirsutum_UA48_v1.1_gff3.gz
Predicted gene models (GFF3 format) G.hirsutum_UA48_v1.1_gene_gff3.gz
Protein-coding Transcripts, CDS sequences (FASTA format) G.hirsutum_UA48_v1.1_cds.fa.gz  
Protein sequences (FASTA format) G.hirsutum_UA48_v1.1_protein.fa.gz
Protein-coding Gene sequences (FASTA format) G.hirsutum_UA48_v1.1_gene.fa.gz  
Homology

Homology of the Gossypium hirsutum UA48 genome v1.0 proteins was determined by pairwise sequence comparison using the blastp algorithm against various protein databases. An expectation value cutoff less than 1e-6  for the Arabidoposis proteins (Araport11, 2022-09), UniProtKB/SwissProt (Release 2024-03), and UniProtKB/TrEMBL (Release 2024-03) databases. The best hit reports are available for download in Excel format. 

Protein Homologs

G.hirsutum UA48 Genome v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) GhirsutumUA48_v1.1_vs_tair.xlsx.gz
G.hirsutum UA48 Genome v1.0 proteins with arabidopsis (Araport11) (FASTA file) GhirsutumUA48_v1.1_vs_tair_hit.fasta.gz
G.hirsutum UA48 Genome v1.0 proteins without arabidopsis (Araport11) (FASTA file) GhirsutumUA48_v1.1_vs_tair_noHit.fasta.gz
G.hirsutum UA48 Genome v1.0 proteins with SwissProt homologs (EXCEL file) GhirsutumUA48_v1.1_vs_swissprot.xlsx.gz
G.hirsutum UA48 Genome v1.0 proteins with SwissProt (FASTA file) GhirsutumUA48_v1.1_vs_swissprot_hit.fasta.gz
G.hirsutum UA48 Genome v1.0 proteins without SwissProt (FASTA file) GhirsutumUA48_v1.1_vs_swissprot_noHit.fasta.gz
G.hirsutum UA48 Genome v1.0 proteins with TrEMBL homologs (EXCEL file) GhirsutumUA48_v1.1_vs_trembl.xlsx.gz
G.hirsutum UA48 Genome v1.0 proteins with TrEMBL (FASTA file) GhirsutumUA48_v1.1_vs_trembl_hit.fasta.gz
G.hirsutum UA48 Genome v1.0 proteins without TrEMBL (FASTA file) GhirsutumUA48_v1.1_vs_trembl_noHit.fasta.gz
Markers
Marker alignments were performed by the CottonGen Team of Main Bioinformatics Lab at WSU. The alignment tool 'BLAT' was used to map marker sequences from CottonGen to the Gossypium hirsutum UA48 v1.0 assembly. Markers required 90% identity over 97% of their length. For SSRs & RFLPs, gap size was restricted to 1000bp or less with less than 2 gaps. For dbSNPs and Indels gap size was restricted to 2bp with less than 2 gaps. The available files are in GFF3 format. Markers available in CottonGen are linked to JBrowse.
 
CottonGen SNP markers mapped to genome AD1_GhirsutumUA48_569_v1.1_SNP
CottonGen RFLP markers mapped to genome AD1_GhirsutumUA48_569_v1.1_RFLP
CottonGen SSR markers mapped to genome AD1_GhirsutumUA48_569_v1.1_SSR
CottonGen InDel markers mapped to genome AD1_GhirsutumUA48_569_v1.1_InDel
Transcript Alignments
Transcript alignments were performed by the CottonGen Team of Main Bioinformatics Lab at WSU. The alignment tool 'BLAT' was used to map transcripts to the G. Ghirsutum UA48 genome assembly. Alignments with an alignment length of 97% and 90% identify were preserved. The available files are in GFF3 format.
G. arboreum CottonGen RefTrans v1 AD1_GhirsutumUA48_569_v1.1_g.arboreum_cottongen_reftransV1
G. hirsutum CottonGen RefTrans v1 AD1_GhirsutumUA48_569_v1.1_g.hirsutum_cottongen_reftransV1
G. barbadense CottonGen RefTrans v1 AD1_GhirsutumUA48_569_v1.1_g.barbadense_cottongen_reftransV1
G. raimondii CottonGen RefTrans v1 AD1_GhirsutumUA48_569_v1.1_g.raimondii_cottongen_reftransV1