Draft genome sequences and comparative analyses of Spiroplasma citri strains from various hosts.

Spiroplasma citri is a plant pathogenic bacterium that infects a wide range of hosts. In Iran, S. citri is responsible for causing several important diseases, including citrus stubborn, sesame yellows, and safflower necrotic yellows. The beet leafhopper Circulifer haematoceps is a common vector for S. citri transmission in the Mediterranean and Middle Eastern regions. For the first time, we sequenced the whole genome of three Iranian strains D10, D12, and D4 isolated from plants (citrus and sesame) and the insect hosts, originating from Fars Province, for a better understanding of their genetics, and differences and evolution. We compared genomes of these strains and several other S. citri whole genomes from the NCBI database to discover single/multiple nucleotide variations (SNVs/MNVs), deletions, insertions and replacements and so on. Analyses showed that strain D10 from citrus had 99.49, 99.45, 98.79 and 98.78% whole genome similarity with strains C189, R8-A2T, D4 (from leafhopper) and D12 (from sesame), respectively. Iranian strain D10 had the lowest and D12 had the highest number of detected SNVs and MNVs compared to the strain R8-A2T. In a whole-genome comparison of the three studied strains rather R8-A2T showed the lowest amount of rearrangement. On the other hand, a comparison of the whole genome of S. citri and its close relative S. melliferum showed extensive rearrangement in blocks of genomes. We found a high level of genetic changes within three Iranian strains. While there was no indication of the presence of mutS, mutL (DNA mismatch repair loci) and recA genes throughout the annotated genomes, there was a highlighted presence of repeated regions and transposase genes. The lack of universal DNA mismatch repair and the recA gene, and the abundance of mobile genetic elements, may account for the high rate of genetic changes. The fructose, trehalose and triacylglycerol metabolism operons predicted can be responsible for Spiroplasma pathogenic pathways. This study expands a better understanding of S. citri genetics and evolution in the hosts. Our findings provide valuable insights into the molecular mechanisms underlying S. citri pathogenesis and transmission, which could aid in the development of new strategies for disease control.