Gossypium bickii (G1) genome JZU_v1
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Overview
About the assembly This is about Gossypium bickii (G1) genome assembly. Through the K-mer distribution analysis, the genome size was estimated to be 1,706.79 Mb with 0.18% heterozygosity and 74.19% repetitive sequences. For the initial assembly, a total of 248.64 Gb of PacBio long reads were generated, which was approximately 142.08-fold genome coverage, to assemble a genome of 1,765.96 Mb with 1,574 contigs and a contig N50 of 4.62 Mb. The assembled contigs were then polished by aligning PacBio long reads to the initial assembly. To increase the consensus accuracy of the assembly, the initial assembly was also corrected using 299.22 Gb high-quality Illumina reads, which was about 176.01-fold genome coverage. To construct the chromosome-level genome, a total of 277.57 Gb high-quality Hi-C fragments, which was about 163.27-fold genome coverage with 915.85 million read pairs, were used to categorize and order the assembled contigs. The Hi-C heatmap shows 13 distinct chromosomal groups. Finally, approximately 1,704.25 Mb of assembly (96.51% of the total assembled genome size) were anchored into 13 pseudochromosomes with 445 scaffolds and a scaffold N50 of 133.90 Mb, which captured 1766.07 Mb of the G1-genome.
Publication - Sheng K, Sun Y, Liu M, Cao Y, Han Y, Li C, Muhammad U, Daud MK, Wang W, Li H, Samrana S, Hui Y, Zhu S*, Chen J*, Zhao T*. A reference-grade genome assembly for Gossypium bickii and insights into its genome evolution and formation of pigment glands and gossypol Volume 4, Issue 1, 9 January 2023, 100421. Assembly
The chromosomes (pseudomolecules) and scaffolds for Gossypium bickii (G1) genome. This file belongs to the ZJU Assembly v1.0
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 bickii ZJU Genome v1.0 are available for download below. The Gossypium bickii ZJU 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 bickii (G1) genome. These files belong to the ZJU Assembly v1.0
Homology
Homology of the Gossypium bickii ZJU 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 bickii ZJU 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.
Publication
Sheng K, Sun Y, Liu M, Cao Y, Han Y, Li C, Muhammad U, Daud MK, Wang W, Li H, Samrana S, Hui Y, Zhu S, Chen J, Zhao T. A reference-grade genome assembly for Gossypium bickii and insights into its genome evolution and formation of pigment glands and gossypol. Plant communications. 2022 online: doi: 10.1016/j.xplc.2022.100421 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. bickii 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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