Gossypium barbadense (AD2) 'Pima90' genome HEAU_v1

Overview
Analysis NameGossypium barbadense (AD2) 'Pima90' genome HEAU_v1
MethodPacBio RSII; Illumina HiSeq; FALCON 1.0
Source (v1)
Date performed2022-01-12

We assembled 2.29 Gb and 2.21 Gb of the NDM8 and Pima90 genomes, respectively (Table 1). To accomplish this, we obtained 205.18 Gb and 200.62 Gb long reads of NDM8 and Pima90 genomes, respectively, representing 180.38-fold coverage depth in total on the basis of single-molecule real-time (SMRT) sequencing. The initial assembly corrected by Illumina paired-end data (233.75-fold coverage in total) resulted in contigs with an N50 size of 15.28 Mb for NDM8 and 9.65 Mb for Pima90. Subsequently, these corrected contigs were connected to 754 superscaffolds for NDM8 and 909 for Pima90 using a total of 232.90-fold 10x Genomics linked-read data. Finally, we constructed chromosome-scale scaffolds using more than 125-fold Hi-C interacting unique paired-end data from each cotton genome. The final assemblies included 353 scaffolds for NDM8 and 309 for Pima90, resulting in contig and scaffold N50 values of 13.15 Mb and 107.67 Mb for NDM8 and 9.24 Mb and 102.45 Mb for Pima90. A total of 99.57% and 99.75% of genomes were anchored onto pseudochromosomes in NDM8 and Pima90, respectively, and the very few gaps (0.003% in NDM8 and 0.06% in Pima90) indicated the contiguity of the sequences. High mapping ratios (99.16% in the two genomes) and low error assembly site ratios (1.87 × 10−7 in NDM8 and 2.95 × 10−7 in Pima90) indicated the accuracy of the genomes. Besides, 96.1% and 95.9% of 1,440 embryophyta Benchmarking Universal Single-Copy Orthologs (BUSCOs) present in NDM8 and Pima90, respectively, showed the integrity of the genomes.

Table 1. Global summary of the final genome assemblies for NDM8 and Pima90

Summary of Assembly Gossypium hirsutum NDM8 Gossypium barbadense Pima90
Assembled genome size (Mb) 2,291.77 2,210.14
A-subgenome (Mb) 1,438.06 1,381.46
D-subgenome (Mb) 843.88 823.21
Anchoring (%) 99.57 99.75
Number of contigs 1,030 1,160
Contig N50 (Mb) 13.15 9.24
Scaffold N50 (Mb) 107.67 102.45
Gap ratio (%) 0.003 0.06
GC content (%) 34.36 34.17
Repeat ratio (%) 62.10 61.85
Predicted PCG model number 80,124 79,613
Average gene length (bp) 2,931.27 2,894.70
Average coding sequence length per gene (bp) 1,088.90 1,094.24
Average exon number per gene 4.76 4.77
BUSCOs (%) 9.61 9.59

Publication: Ma, et al. High-quality genome assembly and resequencing of modern cotton cultivars provide resources for crop improvement. Nature Genetics 53:1385–1391 (2021)

Properties
Additional information about this analysis:
Property NameValue
JBrowse URLhttps://www.cottongen.org/jbrowse/index.html?data=data/AD2_HEAU_P90_v1&loc=
Analysis Typewhole_genome
Assembly

The chromosomes (pseudomolecules) for Gossypium barbadenseHEAU-Pima90 genome. These files belong to the Gossypium barbadense(AD2) 'Pima90' genome HEAU_v1

Chromosomes (FASTA format) G.barbadense_Pima90.genome.fasta
Contact
Functional Analysis

Functional annotation files for the Gossypium barbadense HEAU Genome v1.0 are available for download below. The Gossypium barbadense HEAU 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 HEAU-Pima90_v1_genes2GO.xlsx.gz
IPR assignments from InterProScan HEAU-Pima90_v1_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways HEAU-Pima90_v1_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs HEAU-Pima90_v1_KEGG-pathways.xlsx.gz

 

Genes

The predicted gene model, their alignments and proteins for Gossypium barbadense'(AD2)' Pima90 genome. These files belong to the Gossypium barbadense (AD2) 'Pima90' genome HEAU_v1

Predicted gene models with exons (GFF3 format) G.barbadensse_HEAU_AD2-Pima90.gff3.gz
Coding sequences, CDS (FASTA format) G.barbadensse_HEAU_AD2-Pima90.transcripts.fa.gz
Protein sequences (FASTA format) G.barbadensse_HEAU_AD2-Pima90.protein.fa.gz
Homology

Homology of the Gossypium barbadense HEAU 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-9 was used for the NCBI nr (Release 2021-09) and 1e-6  for the Arabidoposis proteins (Araport11), UniProtKB/SwissProt (Release 2021-09), and UniProtKB/TrEMBL (Release 2021-09) databases. The best hit reports are available for download in Excel format. 

 

Protein Homologs

G.barbadense HEAU Genome v1.0 proteins with NCBI nr homologs (EXCEL file) HEAU-Pima90_v1_vs_nr.xlsx.gz
G.barbadense HEAU Genome v1.0 proteins with NCBI nr (FASTA file) HEAU-Pima90_v1_vs_nr_hit.fasta.gz
G.barbadense HEAU Genome v1.0 proteins without NCBI nr (FASTA file) HEAU-Pima90_v1_vs_nr_noHit.fasta.gz
G.barbadense HEAU Genome v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) HEAU-Pima90_v1_vs_tair.xlsx.gz
G.barbadense HEAU Genome v1.0 proteins with arabidopsis (Araport11) (FASTA file) HEAU-Pima90_v1_vs_tair_hit.fasta.gz
G.barbadense HEAU Genome v1.0 proteins without arabidopsis (Araport11) (FASTA file) HEAU-Pima90_v1_vs_tair_noHit.fasta.gz
G.barbadense HEAU Genome v1.0 proteins with SwissProt homologs (EXCEL file) HEAU-Pima90_v1_vs_swissprot.xlsx.gz
G.barbadense HEAU Genome v1.0 proteins with SwissProt (FASTA file) HEAU-Pima90_v1_vs_swissprot_hit.fasta.gz
G.barbadense HEAU Genome v1.0 proteins without SwissProt (FASTA file) HEAU-Pima90_v1_vs_swissprot_noHit.fasta.gz
G.barbadense HEAU Genome v1.0 proteins with TrEMBL homologs (EXCEL file) HEAU-Pima90_v1_vs_trembl.xlsx.gz
G.barbadense HEAU Genome v1.0 proteins with TrEMBL (FASTA file) HEAU-Pima90_v1_vs_trembl_hit.fasta.gz
G.barbadense HEAU Genome v1.0 proteins without TrEMBL (FASTA file) HEAU-Pima90_v1_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 barbadense HEAU me 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_HEAU_AD2_SNP
CottonGen RFLP markers mapped to genome G.barbadense_HEAU_AD2_RFLP
CottonGen SSR markers mapped to genome G.barbadense_HEAU_AD2_SSR
CottonGen InDel markers mapped to genome G.barbadense_HEAU_AD2_InDel

 

Publications

Ma Z, Zhang Y, Wu L, Zhang G, Sun Z, Li Z, Jiang Y, Ke H, Chen B, Liu Z, Gu Q, Wang Z, Wang G, Yang J, Wu J, Yan Y, Meng C, Li L, Li X, Mo S, Wu N, Ma L, Chen L, Zhang M, Si A, Yang Z, Wang N, Wu L, Zhang D, Cui Y, Cui J, Lv X, Li Y, Shi R, Duan Y, Tian S, Wang X. High-quality genome assembly and resequencing of modern cotton cultivars provide resources for crop improvement. Nature genetics. 2021 Aug 09; 53:1385–1391.

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_HEAU_AD2_g.arboreum_cottongen_reftransV1
G. barbadense CottonGen RefTrans v1 G.barbadense_HEAU_AD2_g.barbadense_cottongen_reftransV1
G. barbadense CottonGen RefTrans v1 G.barbadense_HEAU_AD2_g.hirsutum_cottongen_reftransV1
G. raimondii CottonGen RefTrans v1 G.barbadense_HEAU_AD2_g.raimondii_cottongen_reftransV1