Gossypium anomalum (B1) genome JAAS_v1.2_a1.1
|
Overview
About the assembly We generated 82.68 Gb (~64×) of high-quality long reads using the Pacbio SMART platform. After correction using 132.61 Gb (~103×) Illumina paired-end data, the long Pacbio reads were assembled into 611 contigs that captured 1.20 Gb of the G. anomalum genome, and of which 363 were too short (total length of Journal Pre-proof 9.35 Mb) to be then validated and scaffolded using BioNano optical maps. A total of 249,816,916 valid high-throughput chromosome conformation capture (Hi-C) valid reads were used to categorize, order, and orient these scaffolds. The final assembly comprised 364 scaffolds (N50 = 99.19 Mb), spanning 1.21 Gb and accounting for ~93.66% of the estimated genome (total size 1.29 Gb based on K-mer distribution analysis and 1.35 Gb by flow cytometry analysis), of which 351 were short scaffolds (total length of 9.58 Mb), and 13 super-scaffolds represent the complete set of G. anomalum pseudo-chromosomes and comprised 99.21% of the total assembled sequence. Publication
Assembly
The chromosomes (pseudomolecules) and scaffolds for Gossypium anomalum (B1) genome. This file belongs to the JAAS Assembly v1.2
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 anomalum JAAS Genome v1.2 are available for download below. The Gossypium anomalum JAAS Genome v1.2 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 anomalum (B1) genome. These files belong to the JAAS Assembly v1.2_a1.1
Homology
Homology of the Gossypium anomalum JAAS Genome v1.2 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 anomalum JAAS me 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. anomalum genome assembly. Alignments with an alignment length of 97% and 90% identify were preserved. The available files are in GFF3 format.
Links
|