Gossypium hirsutum (AD1) 'YM11' genome XAAS_v1
Overview
To characterize genomes corresponding to upland cotton with cold tolerance features that are suitable for the Xinjiang climate, YM11, an accession with elite cold tolerance and adaptation to the climate of Xinjiang, was selected for genome de novo assembly. The sprouted seeds of YM11 (pure lines) were uniformly planted in seedling trays and then placed in a greenhouse at a 12 h/12 h day/night regime, 32 ◦C/27 ◦C accordingly. The planting medium was a mixture of peat soil, perlite, and vermiculite at a ratio of 3:1:1. During the three-leaf stage, the seedlings were uniformly placed in an artificial climate chamber at 4 ◦C with a light-to-dark cycle of 14 h:10 h and illumination intensity of 1500~2000 lx for cold stress treatment. The sampling time was set at 0 h and 6 h. Transcriptome sequencing (RNA-seq) and metabolome analysis were performed at the two-time points with three and six biological replicates, respectively. Approximately 2 g of leaves from each biological replicate were frozen in liquid nitrogen immediately, ground into fine powder, and then transferred to a -80 ◦C refrigerator for storage. In particular, two replicated samples (~1 g) at both 0 h and 6 h from the same tissue used in RNA-seq were selected for the CUT&Tag assay. In addition, approximately 5 g young leaves of YM11 were sampled to extract genomic DNA for genome assembly, and a collection of YM11 root, stem, leaf, flower, and boll mixed samples from the field was used to conduct RNA-seq for transcriptome-assisted genome annotation. Global statistics of the genome assembly of YM11.
Assembly
The chromosomes (pseudomolecules) for Gossypium hirsutum cv 'Yuan Mian 11' genome. These files belong to the Gossypium hirsutum (AD1) 'YM11' genome XAAS_v1
Genes
The predicted gene model, their alignments and proteins for Gossypium hirsutum cv 'Yuan Mian 11' genome. These files belong to the Gossypium hirsutum (AD1) 'YM11' genome XAAS_v1
Homology
Homology of the Gossypium hirsutum YM11 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-6 for the Arabidoposis proteins (Araport11, 2022-09), UniProtKB/SwissProt (Release 2023-07), and UniProtKB/TrEMBL (Release 2023-07) 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 YM11 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
Wang J, Liang Y, Gong Z, Zheng J, Li Z, Zhou G, Xu Y, Li X. Genomic and epigenomic insights into the mechanism of cold response in upland cotton (Gossypium hirsutum). Plant physiology and biochemistry: PPB. 2023 Nov 25; 206:108206. 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 YM11 genome assembly. Alignments with an alignment length of 97% and 90% identify were preserved. The available files are in GFF3 format.
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