Gossypium hirsutum (AD1) 'TM-1' genome WHU_v1
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Overview
About the assembly The new assembly of Gossypium hirsutum genome (genetic standard line TM-1) was released from the Institute for Advanced Studies, Wuhan University, Wuhan, China (IAS-WHU). The assembly were sequenced using high-depth SMRT long reads resulting in 81.6-fold genome coverage (~205 Gb). The genome assembly was corrected by using accurate Illumina paired-end reads. The resulting assembled genome size was 2,290 Mb with 99.17% of all sequences anchored on 26 chromosomes (A-subgenome, 1,449 Mb; D-subgenome, 822 Mb). The N50 of the new assembled genome is 5,020 kb, with significantly fewer gaps compared with previously published genome assemblies. The new genome assembly has substantial improvements with high completeness and accuracy. In addition, the new assembly filled a lot of genome gaps existed in previous assemblies. The new assembly also showed high congruence and good collinear relationships in quantity among cotton genomes. Our continuing efforts to assemble the high-resolution and chromosome-scale G. hirsutum reference genome will further facilitate the translation of genomics to cotton breeding and genetics.
Publication Huang, G. et al., Genome sequence of Gossypium herbaceum and genome updates of Gossypium arboreum and Gossypium hirsutum provide insights into cotton A-genome evolution. Nature Genetics. 2020. doi.org/10.1038/s41588-020-0607-4 Assembly
The chromosomes (pseudomolecules) and scaffolds for Gossypium hirsutum (AD1) 'TM1' genome. These files belong to the WHU Updated Assembly v1.0
Downloads
All annotation files are available for download by selecting the desired data type in the left-hand side bar. Each data type page will provide a description of the available files and links do download. Functional Analysis
Functional annotation files for the Gossypium hirsutum WHU Genome v1.0 are available for download below. The Gossypium hirsutum WHU 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
Genes
The predicted gene model, their alignments and proteins for Gossypium hirsutum (AD1) 'TM1' genome. These files belong to the WHU Assembly v1.0
Homology
Homology of the Gossypium hirsutum WHU 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 2018-05) and 1e-6 for the Arabidoposis proteins (Araport11), 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
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 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.
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.
Links
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