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Overview
| Analysis Name | Gossypium hirsutum (AD1) 'UA48' genome HGS_v1.1 |
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| Method | PacBio Sequel II, Illumina NovaSeq, MECAT v. 1.3 |
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| Source | (v1.0, a1.1) |
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| Date performed | 2024-05-15 |
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About the UA48 Assembly
Main assembly consisted of 93.70x of PACBIO coverage (8,899 bp average read size), and was assembled using MECAT and the resulting sequence was polished using ARROW. A total of 108,262 unique, non-repetitive, non-overlapping 1 KB syntenic markers were generated using the v2.0 G. hirsutum var. TM1 genome (genome release and aligned to the polished G. hirsutum var. UA48 assembly. Contig breaks were identified as an abrupt change in linkage group. A total of 56 breaks were made. The broken contigs were then ordered, oriented, and assembled into 26 chromosomes using the version 2.0 G. hirsutum syntenic markers. A total of 925 joins were made during this process. The HiC library was aligned to the integrated chromosomes, and several minor rearrangements were made. Adjacent alternative haplotypes were identified on the joined contig set. AltHap regions were collapsed using the longest common substring between the two haplotypes. A total of 334 adjacent altHaps were collapsed. Care was taken to ensure that telomere was properly oriented in the chromosomes, and the resulting sequence was screened for retained vector and/or contaminants. A total of 98.2% of the assembled sequence is contained in the chromosomes. Finally, Homozygous SNPs and INDELs were corrected in the release sequence using ~68x of illumina reads (2x150, 400bp insert).
Genome Information
| UA48 |
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| Assembly Source |
Phytozome genome ID: 569 |
| Assembly Version / Annotation Version |
v1.0 / a1.1 |
| Total Scaffold Length (bp) |
2,293,500,691 |
| Number of Scaffolds |
860 |
| Min. Number of Scaffolds containing half of assembly (L50) |
10 |
| Shortest Scaffold from L50 set (N50) |
105,664,978 |
| Total Contig Length (bp) |
2,287,690,691 |
| Number of Contigs |
1,441 |
| Min. Number of Contigs containing half of assembly (L50) |
84 |
| Shortest Contig from L50 set (N50) |
8,142,815 |
| Number of Protein-coding Transcripts |
113,741 |
| Number of Protein-coding Genes |
77,237 |
| Percentage of Eukaryote BUSCO Genes |
99 |
| Percentage of Embroyphyte BUSCO Genes |
98.3 |
Publication
Sreedasyam, A., Lovell, J.T., Mamidi, S. et al. Genome resources for three modern cotton lines guide future breeding efforts. Nat. Plants 10, 1039–1051 (2024). https://doi.org/10.1038/s41477-024-01713-z
Rights and permissions
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To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
Assembly
The chromosomes (pseudomolecules) for G. hrisutum UA48 genome. These files belong to the HGS (Phytozome) Assembly v1.0
Functional Analysis
Functional annotation files for the Gossypium hirsutum UA48 Genome v1.0 are available for download below. The Gossypium hirsutum UA48 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
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 UA48 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. Ghirsutum UA48 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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