Gossypium hirsutum (AD1) genome ZJU-Improved Assembly v2.1 & Annotation a1.0

Overview
Analysis NameGossypium hirsutum (AD1) genome ZJU-Improved Assembly v2.1 & Annotation a1.0
MethodDeNovoMAGIC3, BioNano, Hi-C, and POPSEQ
SourceG. hirsutum (AD1) TM1 genome ZJU-Improved v2.1-a1.0
Date performed2019-03-14

About the assembly

An improved de novo assembled genome of Texas Marker-1 (TM-1) was produced by using the software package DenovoMAGIC3 (NRGene, Nes Ziona, Israel).  Thereafter, the initial scaffolds were further corrected and merged using optical mapping data (BioNano Genomics).  Finally, three-dimensional proximity information obtained by Hi-C and our updated ultra-dense genetic map with single-nucleotide polymorphisms (SNPs) was used to check, order and orient these super-scaffolds. 

Summary of Improved Assembly  
Sequenced genome size (Mb) 2295.26
Contig N50 (kb) 113.02
Scaffold N50 (Mb) 15.51
Scaffold L50 (Mb) 48
Longest Scaffold (Mb) 41.92
Gap size (Mb) 27.36
Annotated protein-coding genes 72,761
TE proportion (%) 63.89
Complete BUSCOs 97.5
Fragmented (%) 0.42
Missing (%) 2.29
Duplicated copy (%) 93.61

 

Publication

Hu et al. Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton.

Assembly

The chromosomes (pseudomolecules) and scaffolds for G. hrisutum 'TM-1' genome. These files belong to the ZJU Improved Assembly v2.1

Chromosomes & scaffolds (FASTA format) G.hirsutum_ZJU-AD1_assembly_v2.1.fasta.gz
Genes

The predicted gene model, their alignments and proteins for G. hirsutum 'TM-1' genome. These files belong to the ZJU Improved Assembly v2.1 & Annotation a1.0

Predicted gene models with exons (GFF3 format) G.hirsutum_ZJU-AD1_v2.1_a1.0_functional.gff.gz
Coding sequences, CDS (FASTA format) G.hirsutum_ZJU-AD1_v2.1_a1.0_cds.fasta.gz
Protein sequences (FASTA format) G.hirsutum_ZJU-AD1_v2.1_a1.0_pep.fasta.gz
Downloads

All annotation files are available for download by selecting the desired data type in the left-hand "Resources" side bar.  Each data type page will provide a description of the available files and links do download.  Alternatively, you can use the FTP repository for bulk download.

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 G. arboreum genome 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 G.hirsutum_AD1_ZJU_v2.1_SNP
CottonGen InDel markers mapped to genome G.hirsutum_AD1_ZJU_v2.1_InDel
CottonGen RFLP markers mapped to genome G.hirsutum_AD1_ZJU_v2.1_RFLP
CottonGen SSR markers mapped to genome G.hirsutum_AD1_ZJU_v2.1_SSR

 

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. hirsutum 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 G.hirsutum_ZJU_v2.1_g.arboreum_cottongen_reftransV1
G. barbadense CottonGen RefTrans v1 G.hirsutum_ZJU_v2.1_g.barbadense_cottongen_reftransV1
G. hirsutum CottonGen RefTrans v1 G.hirsutum_ZJU_v2.1_g.hirsutum_cottongen_reftransV1
G. raimondii CottonGen RefTrans v1 G.hirsutum_ZJU_v2.1_g.raimondii_cottongen_reftransV1
Functional Analysis

Functional annotation files for the Gossypium hirsutum ZJU Genome v2.1 are available for download below. The Gossypium hirsutum ZJU Genome 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 AD1_ZJU_v2.1_genes2GO.xlsx.gz
IPR assignments from InterProScan AD1_ZJU_v2.1_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways AD1_ZJU_v2.1_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs AD1_ZJU_v2.1_KEGG-pathways.xlsx.gz

 

Homology

Homology of the Gossypium hirsutumZJU Genome v2.1 proteins was determined by pairwise sequence comparison using the blastp algorithm against various protein databases. An expectation value cutoff less than 1e-9 was used for the NCBI nr (Release 2018-05) and 1e-6  for the Arabidoposis proteins (TAIR10), UniProtKB/SwissProt (Release 2019-01), and UniProtKB/TrEMBL (Release 2019-01) databases. The best hit reports are available for download in Excel format. 

 

Protein Homologs

Gossypium hirsutum v2.0 proteins with NCBI nr homologs (EXCEL file) AD1_ZJU_v2.1_vs_nr.xlsx.gz
Gossypium hirsutum ZJU v2.1 proteins with NCBI nr (FASTA file) AD1_ZJU_v2.1_vs_nr_hit.fasta.gz
Gossypium hirsutum ZJU v2.1 proteins without NCBI nr (FASTA file) AD1_ZJU_v2.1_vs_nr_noHit.fasta.gz
Gossypium hirsutum v2.0 proteins with arabidopsis (TAIR10) homologs (EXCEL file) AD1_ZJU_v2.1_vs_tair.xlsx.gz
Gossypium hirsutum ZJU v2.1 proteins with arabidopsis (TAIR10) (FASTA file) AD1_ZJU_v2.1_vs_tair_hit.fasta.gz
Gossypium hirsutum ZJU v2.1 proteins without arabidopsis (TAIR10) (FASTA file) AD1_ZJU_v2.1_vs_tair_noHit.fasta.gz
Gossypium hirsutum ZJU v2.1 proteins with SwissProt homologs (EXCEL file) AD1_ZJU_v2.1_vs_swissprot.xlsx.gz
Gossypium hirsutum ZJU v2.1 proteins with SwissProt (FASTA file) AD1_ZJU_v2.1_vs_swissprot_hit.fasta.gz
Gossypium hirsutum ZJU v2.1 proteins without SwissProt (FASTA file) AD1_ZJU_v2.1_vs_swissprot_noHit.fasta.gz
Gossypium hirsutum ZJU v2.1 proteins with TrEMBL homologs (EXCEL file) AD1_ZJU_v2.1_vs_trembl.xlsx.gz
Gossypium hirsutum ZJU v2.1 proteins with TrEMBL (FASTA file) AD1_ZJU_v2.1_vs_trembl_hit.fasta.gz
Gossypium hirsutum ZJU v2.1 proteins without TrEMBL (FASTA file) AD1_ZJU_v2.1_vs_trembl_noHit.fasta.gz