Gossypium barbadense (AD2) 'Yuma' genome HAU_v1
Overview
We selected 12 representative G. barbadense accessions from around the world, including 7 primitively domesticated accessions from South America, 2 Sea Island landrace accessions from the Caribbean region, and 3 cultivated accessions. An average of 63.1 GB of high-fidelity (HiFi) reads were generated for the 12 accessions. These were initially assembled via HiFiasm into individual genomes ranging from 2.21 to 2.25GB in size (Table 1) and with contig N50 ranging from 55.0 Mb to 102.7 Mb (average = 70.4 Mb), longer than the previously published genome of G. barbadense. These 98.40% (range 97.48% to 98.93%) assembled contigs were further anchored and ordered into 26 pseudo-chromosomes based on the 3-79 reference genome. Assembly completeness was high for all assemblies, which contained more than 99.5% complete BUSCOs, and the LTR Assembly Index (LAI) scores ranged from 13.78 to 15.18 per genome, which is considered reference quality according to LAI scores (Table 1). Table 1. Statistics of the genomic assembly and annotation of 12 G. barbadense accessions
Assembly
The chromosomes (pseudomolecules) for Gossypium barbadense 'Yuma' genome. These files belong to the Gossypium barbadense (AD2) ' Yuma' genome HAU_v1.
Functional Analysis
Functional annotation files for the Gossypium barbadense Yuma Genome v1.0 are available for download below. The Gossypium barbadense Yuma 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 barbadense ' Yuma.' genome. These files belong to the Gossypium barbadense (AD2) ' Yuma' genome HAU_v1
Homology
Homology of the Gossypium barbadense Yuma 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 barbadense Yuma 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.
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. barbadense Yuma 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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