Gossypium barbadense (AD2) Hai7124 genome ZJU Assembly v1.1 & Annotation a1

Overview
Analysis NameGossypium barbadense (AD2) Hai7124 genome ZJU Assembly v1.1 & Annotation a1
MethodDeNovoMAGIC3, BioNano, Hi-C, and POPSEQ
SourceG. barbadense (AD2) Hai7124 genome ZJU v1.1-a1
Date performed2019-03-14

About the assembly

We adopted a hierarchical approach to perform the chromosome-scale assembly. The 800 Gb high-quality data (>330× genome coverage) generated from a series of PCR-free libraries, mate paired-end read (MP) libraries and 10× GemCode library were assembled using the software package DenovoMAGIC3 (NRGene, Nes Ziona, Israel). Initially, the assembly of G. barbadense cv. Hai7124 that captured 2.23 Gb was generated. Thereafter, the initial scaffolds were further corrected and merged using optical mapping data (BioNano Genomics). Finally, we used three-dimensional proximity information obtained by Hi-C and our updated ultra-dense genetic map with 6,165,057 single-nucleotide polymorphisms (SNPs) to check, order and orient these super-scaffolds. A total of 115 erroneously assembled loci were detected and corrected.

Summary of Improved Assembly  
Sequenced genome size (Mb) 2224.98
Contig N50 (kb) 77.66
Scaffold N50 (Mb) 23.44
Scaffold L50 (Mb) 20
Longest Scaffold (Mb) 101.65
Gap size (Mb) 32.46
Annotated protein-coding genes 75,071
TE proportion (%) 62.15
Complete BUSCOs 97.29
Fragmented (%) 0.35
Missing (%) 2.15
Duplicated copy (%) 93.82

 

Publication

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

Properties
Additional information about this analysis:
Property NameValue
Analysis Typewhole_genome
JBrowse URLhttps://www.cottongen.org/jbrowse/index.html?data=
JBrowse URLhttps://www.cottongen.org/jbrowse/index.html?data=data/Gb_ZJU_v1.1&
Short NameZJU-AD2_v1.1
Assembly

The chromosomes (pseudomolecules) and scaffolds for G. barbadense 'Hai7124' genome. These files belong to the ZJU assembly v1.1

Chromosomes & scaffolds (FASTA format) G.barbadense_ZJU-AD2_assembly_v1.1.fasta.gz
Genes

The predicted gene model, their alignments and proteins for G. barbadense 'Hai7124' genome. These files belong to the ZJU assembly v1.1 & annotation a1

Predicted gene models with exons (GFF3 format) G.barbadense_ZJU-AD2_v1.1_a1.0_functional.gff.gz
Coding sequences, CDS (FASTA format) G.barbadense_ZJU-AD2_v1.1_a1.0_cds.fasta.gz
Protein sequences (FASTA format) G.barbadense_ZJU-AD2_v1.1_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.barbadense_AD2_ZJU_v1.1_SNP
CottonGen InDel markers mapped to genome G.barbadense_AD2_ZJU_v1.1_InDel
CottonGen RFLP markers mapped to genome G.barbadense_AD2_ZJU_v1.1_RFLP
CottonGen SSR markers mapped to genome G.barbadense_AD2_ZJU_v1.1_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.barbadense 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.barbadense_ZJU_v1.1_g.arboreum_cottongen_reftransV1
G. barbadense CottonGen RefTrans v1 G.barbadense_ZJU_v1.1_g.barbadense_cottongen_reftransV1
G. hirsutum CottonGen RefTrans v1 G.barbadense_ZJU_v1.1_g.hirsutum_cottongen_reftransV1
G. raimondii CottonGen RefTrans v1 G.barbadense_ZJU_v1.1_g.raimondii_cottongen_reftransV1
Functional Analysis

Functional annotation files for the Gossypium barbadense ZJU Genome v1.1 are available for download below. The Gossypium barbadense 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 AD2_ZJU_v1.1_genes2GO.xlsx.gz
IPR assignments from InterProScan AD2_ZJU_v1.1_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways AD2_ZJU_v1.1_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs AD2_ZJU_v1.1_KEGG-pathways.xlsx.gz

 

Homology

Homology of the Gossypium barbadense ZJU Genome v1.1 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 barbadense ZJU v1.1 proteins with NCBI nr homologs (EXCEL file) AD2_ZJU_v1.1_vs_nr.xlsx.gz
Gossypium barbadense ZJU v1.1 proteins with NCBI nr (FASTA file) AD2_ZJU_v1.1_vs_nr_hit.fasta.gz
Gossypium barbadense ZJU v1.1 proteins without NCBI nr (FASTA file) AD2_ZJU_v1.1_vs_nr_noHit.fasta.gz
Gossypium barbadense ZJU v1.1 proteins with arabidopsis (TAIR10) homologs (EXCEL file) AD2_ZJU_v1.1_vs_tair.xlsx.gz
Gossypium barbadense ZJU v1.1 proteins with arabidopsis (TAIR10) (FASTA file) AD2_ZJU_v1.1_vs_tair_hit.fasta.gz
Gossypium barbadense ZJU v1.1 proteins without arabidopsis (TAIR10) (FASTA file) AD2_ZJU_v1.1_vs_tair_noHit.fasta.gz
Gossypium barbadense ZJU v1.1 proteins with SwissProt homologs (EXCEL file) AD2_ZJU_v1.1_vs_swissprot.xlsx.gz
Gossypium barbadense ZJU v1.1 proteins with SwissProt (FASTA file) AD2_ZJU_v1.1_vs_swissprot_hit.fasta.gz
Gossypium barbadense ZJU v1.1 proteins without SwissProt (FASTA file) AD2_ZJU_v1.1_vs_swissprot_noHit.fasta.gz
Gossypium barbadense ZJU v1.1 proteins with TrEMBL homologs (EXCEL file) AD2_ZJU_v1.1_vs_trembl.xlsx.gz
Gossypium barbadense ZJU v1.1 proteins with TrEMBL (FASTA file) AD2_ZJU_v1.1_vs_trembl_hit.fasta.gz
Gossypium barbadense ZJU v1.1 proteins without TrEMBL (FASTA file) AD2_ZJU_v1.1_vs_trembl_noHit.fasta.gz