Gossypium australe (G2) genome CRI assembly v1.1

Overview
Analysis NameGossypium australe (G2) genome CRI assembly v1.1
MethodPacBio Sequel and MECAT v. 1.0
SourceGCA_005393395.2_CCRI_HENU_Gaus_1.1
Date performed2019-10-06

About the assembly

The Gossypium australe PA1801(G2-lz) genome was sequenced and assembled with a combination of four technologies: Pacbio single-molecule real-time (SMRT) sequencing, paired-end sequencing, optical mapping (DLS) and Illumina short-read Hi-C. Assembly with these complementary data types proceeded in a stepwise fashion, producing progressively improved assemblies stored under NCBI BioProject PRJNA513946.

 Assembly Summary G. australe
 Total sequence length 1,743,386,794
 Total ungapped length 1,728,043,998  
 Gaps between scaffolds 0
 Number of scaffolds 564
 Scaffold N50 143,600,552
 Scaffold L50 6
 Number of contigs 2,352
 Contig N50 1,901,092
 Contig L50 254
 Total number of chromosomes and plasmids  13
 Number of component sequences (WGS or clone) 564

Publication

Cai, Y., Cai, X., Wang, Q., Wang, P., Zhang, Y., Cai, C., Xu, Y., Wang, K., Zhou, Z., Wang, C., Geng, S., Li, B., Dong, Q., Hou, Y., Wang, H., Ai, P., Liu, Z., Yi, F., Sun, M., An, G., Cheng, J., Zhang, Y., Shi, Q., Xie, Y., Shi, X., Chang, Y., Huang, F., Chen, Y., Hong, S., Mi, L., Sun, Q., Zhang, L., Zhou, B., Peng, R., Zhang, X. and Liu, F. (2019) Genome sequencing of the Australian wild diploid species Gossypium austral highlights disease resistance and delayed gland morphogenesis. Plant Biotechnol. J., https://doi.org/10.1111/pbi.13249

Assembly

The chromosomes (pseudomolecules) and scaffolds for G. australe genome. These files belong to the CRI-G2 Assembly v1.1

Chromosomes & scaffolds (FASTA format) G.australe_CRI-G2_assembly_v1.1.fasta.gz
Genes

The predicted gene model, their alignments and proteins for G. australe genome. These files belong to the CRI-G2 Assembly 1.1

Predicted gene models with exons (GFF3 format) G.australe_CRI-G2_v1.1_functional.gff.gz
Coding sequences, CDS (FASTA format) G.australe_CRI-G2_v1.1_cds.fasta.gz
Protein sequences (FASTA format) G.australe_CRI-G2_v1.1_pep.fasta.gz
mRNA sequences (FASTA format) G.australe_CRI-G2_v1.1_mRNA.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 Gossypium australe 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.australe_CRI-G2_v1.1.0_SNP
CottonGen InDel markers mapped to genome G.australe_CRI-G2_v1.1.0_InDel
CottonGen RFLP markers mapped to genome G.australe_CRI-G2_v1.1.0_RFLP
CottonGen SSR markers mapped to genome G.australe_CRI-G2_v1.1.0_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. australe 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. australe_CRI-TM1-v1.0_g.arboreum_cottongen_reftransV1
G. barbadense CottonGen RefTrans v1 G. australe_CRI-TM1-v1.0_g.barbadense_cottongen_reftransV1
G. australe CottonGen RefTrans v1 G. australe_CRI-TM1-v1.0_g.hirsutum_cottongen_reftransV1
G. raimondii CottonGen RefTrans v1 G. australe_CRI-TM1-v1.0_g.raimondii_cottongen_reftransV1
Homology

Homology of the Gossypium australe CRI 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 australe CRI Genome v1.1 proteins with NCBI nr homologs (EXCEL file) G2_CRI_v1.1_vs_nr.xlsx.gz
Gossypium australe CRI Genome v1.1 proteins with NCBI nr (FASTA file) G2_CRI_v1.1_vs_nr_hit.fasta.gz
Gossypium australe CRI Genome v1.1 proteins without NCBI nr (FASTA file) G2_CRI_v1.1_vs_nr_noHit.fasta.gz
Gossypium australe CRI Genome v1.1 proteins with arabidopsis (Araport11) homologs (EXCEL file) G2_CRI_v1.1_vs_tair.xlsx.gz
Gossypium australe CRI Genome v1.1 proteins with arabidopsis (Araport11) (FASTA file) G2_CRI_v1.1_vs_tair_hit.fasta.gz
Gossypium australe CRI Genome v1.1 proteins without arabidopsis (Araport11) (FASTA file) G2_CRI_v1.1_vs_tair_noHit.fasta.gz
Gossypium australe CRI Genome v1.1 proteins with SwissProt homologs (EXCEL file) G2_CRI_v1.1_vs_swissprot.xlsx.gz
Gossypium australe CRI Genome v1.1 proteins with SwissProt (FASTA file) G2_CRI_v1.1_vs_swissprot_hit.fasta.gz
Gossypium australe CRI Genome v1.1 proteins without SwissProt (FASTA file) G2_CRI_v1.1_vs_swissprot_noHit.fasta.gz
Gossypium australe CRI Genome v1.1 proteins with TrEMBL homologs (EXCEL file) G2_CRI_v1.1_vs_trembl.xlsx.gz
Gossypium australe CRI Genome v1.1 proteins with TrEMBL (FASTA file) G2_CRI_v1.1_vs_trembl_hit.fasta.gz
Gossypium australe CRI Genome v1.1 proteins without TrEMBL (FASTA file) G2_CRI_v1.1_vs_trembl_noHit.fasta.gz

 

Functional Analysis

Functional annotation files for the Gossypium australe CRI Genome v1.1 are available for download below. The Gossypium australe CRI 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 G2_CRI_v1.1_genes2GO.xlsx.gz
IPR assignments from InterProScan G2_CRI_v1.1_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways G2_CRI_v1.1_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs G2_CRI_v1.1_KEGG-pathways.xlsx.gz