Gossypium hirsutum (AD1) 'UA48' genome HGS_v1.1

Overview
Analysis NameGossypium hirsutum (AD1) 'UA48' genome HGS_v1.1
MethodPacBio Sequel II, Illumina NovaSeq, MECAT v. 1.3
Source (v1.0, a1.1)
Date performed2024-05-15

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  
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

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