Gossypium hirsutum (AD1) TM-1 genome ZJU-Improved v2.1_a1
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.
The chromosomes (pseudomolecules) and scaffolds for G. hrisutum 'TM-1' genome. These files belong to the ZJU Improved Assembly v2.1
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
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.
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.
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.
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).
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.