Gossypium hirsutum (AD1) 'TX-1000' genome CRI_v1
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Overview
Three allotetraploid cotton genomes (Gossypium ekmanianum [(AD)6, Ge], Gossypium stephensii [(AD)7, Gs], and one early form of domesticated Gossypium hirsutum, race punctatum [(AD)1, Ghp].) were sequenced and assembled using a combination of sequencing technologies, including single-molecule realtime (PacBio), paired-end Illumina sequencing, and chromatin conformation capture (Hi-C). An initial assembly was generated via FALCON (22) using at least 20.83 million PacBio long reads for each cotton species and subsequently corrected using Illumina paired-end data (average 120-fold coverage). These megabase assemblies (N50 of 1.57, 1.23, and 11.49 Mb for Ge, Gs, and Ghp, respectively) were combined with Hi-C interaction information to produce chromosome-scale scaffolds, yielding final assemblies of 2.34, 2.29, and 2.29 Gb for Ge, Gs, and Ghp, respectively. These high-quality assemblies had scaffold N50 values of more than 107 Mb (Table 1), with 99% of bases anchored onto chromosomes and with 99% of mapped Illumina reads covering about 97% of the genomes. Nearly all of the 1,614 Embryophyta benchmarking universal single-copy orthologs (BUSCOs, embryophyta_odb10) were complete in the Ge (99.2%), Gs (97.4%), and Ghp (99.3%) assemblies and the long terminal repeat (LTR) assembly index (LAI score 13.7 in Ge, 12.8 in Gs, and 12.7 in Ghp) further indicated that these three assemblies could be considered "reference quality". Table 1: Features of three tetraploid cotton assemblies
Assembly
The chromosomes (pseudomolecules) for Gossypium hirsutum race punctatum accession no. Punctatum 25 (TX-1000) genome. These files belong to the Gossypium hirsutum (AD1) 'TX-1000' genome CRI_v1
Contact
Functional Analysis
Functional annotation files for the Gossypium hirsutum CRI Genome v1.0 are available for download below. The Gossypium hirsutum CRI 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
Genes
The predicted gene model, their alignments and proteins for Gossypium hirsutum race punctatum accession no. Punctatum 25 (TX-1000) genome. These files belong to the Gossypium hirsutum (AD1) 'TX-1000' genome CRI_v1
Homology
Homology of the Gossypium hirsutum CRI 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
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 CRI v1.0 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.
Publication
Peng R, Xu Y, Tian S, Unver T, Liu Z, Zhou Z, Cai X, Wang K, Wei Y, Liu Y, Wang H, Hu G, Zhang Z, Grover CE, Hou Y, Wang Y, Li P, Wang T, Lu Q, Wang Y, Conover JL, Ghazal H, Wang Q, Zhang B, Van Montagu M, Van de Peer Y, Wendel JF, Liu F. Evolutionary divergence of duplicated genomes in newly described allotetraploid cottons.. Proceedings of the National Academy of Sciences of the United States of America. 2022 Sep 27; 119(39):e2208496119. 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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