Genome analysis of Spiroplasma citri strains from different host plants and its leafhopper vectors

Authors: RATTNER, RACHEL - Cooperative Agricultural Support Services; THAPA, SHREE - University Of California, Davis; DANG, TYLER - University Of California; OSMAN, FATIMA - University Of California, Davis; SELVARAJ, VIJAYANANDRAJ - Foreign Agricultural Service (FAS, USDA); MAHESHWARI, YOGITA - Foreign Agricultural Service (FAS, USDA); PAGLIACCIA, DEBORAH - University Of California; ESPINDOLA, ANDRES - Oklahoma State University; HAJERI, SUBHAS - Central California Tristeza Eradication Agency; Chen, Jianchi; COAKER, GITTA - University Of California, Davis; VIDALAKIS, GEORGIOS - University Of California; Yokomi, Raymond - Ray

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/21/2021
Publication Date: 5/22/2021
Citation: Rattner, R., Thapa, S.P., Dang, T., Osman, F., Selvaraj, V., Maheshwari, Y., Pagliaccia, D., Espindola, A.S., Hajeri, S., Chen, J., Coaker, G., Vidalakis, G., Yokomi, R.K. 2021. Genome analysis of Spiroplasma citri strains from different host plants and its leafhopper vectors. BMC Genomics. 22:373. https://doi.org/10.1186/s12864-021-07637-8.
DOI: https://doi.org/10.1186/s12864-021-07637-8

Interpretive Summary: Spiroplasma citri is a plant pathogenic bacterium with a complex lifestyle involving multiple plant and insect hosts and causes diseases such as citrus stubborn, carrot purple leaf, brittle root of horseradish, among others. The bacterium is transmitted by leafhoppers that become infected for life when feeding on infected plants and spreads the pathogen to other plants as it disperses and feeds. The resultant genetic diversity of the bacterium was examined by whole genome sequencing of seven S. citri strains collected from different hosts and timeframes. The bacterium’s circular chromosome was found to range from 1.58 to 1.74 Mbp, likely due to invasions of repetitive plectroviral sequences in the genome, as well as a variable number of plasmids. This diversity is being used to further study the evolution of S. citri as it diverged from other spiroplasmas with commensal, mutualistic, and pathogenic relationships with arthropods, plants, and animals. These data contribute to the fundamental knowledge on how S. citri spreads and induce diseases and are important for developing new control strategies.

Technical Abstract: The Spiroplasma citri species complex is a bacterium that causes economically important diseases of citrus and other crops and ornamentals. The pathogen is transmitted by leafhoppers and when infected, can transmit the bacterium for its life. This complex lifestyle serves as drivers of genetic diversity. Using long-read sequencing technology, complete genomes of seven strains of S. citri, isolated from different plant and insect hosts, were assembled. S. citri’s circularized chromosome ranged in size from 1.58 to 1.74 Mbp, due to various insertions of repetitive plectroviral sequences. Notable differences were found in number of plasmids present (ranging from one to ten). All strains contained a plasmid with high similarity to plasmid pSci6 from S. citri strain GII3-3X known to confer insect transmissibility. These extrachromosomal plasmids and viral sequences inserted throughout the genome of S. citri likely contribute to its spread and adaptation to different hosts. These findings further our understanding of genetic diversity and evolution in S. citri.