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ARS Home » Plains Area » Lubbock, Texas » Cropping Systems Research Laboratory » Plant Stress and Germplasm Development Research » Research » Publications at this Location » Publication #413796
Research Project: Development of Climate Resilient Germplasm and Management Tools for Sustainable Row Crop Production

Location: Plant Stress and Germplasm Development Research

Title: Illumina short reads used to generate a composite genome and characterize Fusarium isolates from cotton roots in Uzbekistan

Author
item Jobe, Timothy
item Ulloa, Mauricio
item FOKAR, MOHAMED - Texas Tech University
item SHUKHRAT, SHERMATOV - Uzbekistan Academy Of Sciences
item BURIEV, ZABARDAST - Uzbekistan Academy Of Sciences
item ABDURAKHMONOV, IBROKHIM - Uzbekistan Academy Of Sciences

Submitted to: National Center for Biotechnology Information (NCBI)
Publication Type: Other
Publication Acceptance Date: 5/17/2024
Publication Date: 9/19/2024
Citation: Jobe, T.O., Ulloa, M., Fokar, M., Shukhrat, S., Buriev, Z., Abdurakhmonov, I.Y. 2024. Illumina short reads used to generate a composite genome and characterize Fusarium isolates from cotton roots in Uzbekistan. National Center for Biotechnology Information (NCBI).

Interpretive Summary:

Technical Abstract: Fusarium wilt is a global disease caused by Fusarium oxysporum (FO) which is responsible for sizeable crop losses annually and is found in many cotton-producing regions, including the Republic of Uzbekistan. Since the Soviet era, cotton production in Uzbekistan has been vital to the nation’s economy as Uzbekistan is among the world’s largest producers of cotton. This study aimed to genetically characterize FO f. sp vasinfectum race 4 (FOV4) isolates, which is causing disease in the main cotton-producing region of Uzbekistan, and to compare them with FOV4 isolates from California and Texas. To this end, short read Illumina sequencing was performed with low genome coverage (1-2X) on 15 Fusarium isolates from Uzbekistan. A BLAST database was created from each of these sequencing files and used to validate the presence of effector genes. To generate a composite genome representing of 10 FOV4 isolates with identical EF1-alpha sequence (Uzbk-21, Uzbk-25, Uzbk-26, Uzbk-27, Uzbk-28, Uzbk-31, Uzbk-32, Uzbk-34, Uzbk-35, and Uzbk-37), the Illumina short reads generated for each individual isolate were concatenated into a single FASTQ file containing approximately 20.8 million reads (4,215 Mb of combined sequence), representing >50 fold coverage of the expected genome size. A guided assembly was generated using the Tm2 (FOV4 N biotype) as the reference. The resulting composite genome was composed of 1,165 contigs with a total size of approximately 57.8 Mb. Among which, the mean contig length was 49,598 bp, the minimum contig length was 502 bp, and the maximum contig length was 4,003,644 bp. The GC content was 47.9%. This genome composite was referred as the Uzbk-FOV4C (standing for Uzbekistan FOV4 composite) genome. Uzbk-FOV4C should play a crucial role in facilitating identification of genes (effectors and receptors) and alleles important in host-plant interactions, and in improving selection signatures relevant for resistance to diseases such as Fusarium wilt.