Cercospora leaf blight (CLB) and purple seed stain (PSS) are common soybean diseases in the Gulf South of the United States (USA). For nearly a century, <i>Cercospora kikuchii</i> has been considered as the only pathogen causing these diseases. However, previous reports of genetic diversity among isolates collected throughout Louisiana suggested the presence of multiple lineages or species. Recent systematic studies classified species of <i>Cercospora</i> using a taxonomic system based on phylogenetic analysis of five nuclear loci (legacy genes). Using a similar approach, cercosporoid fungi tentatively identified as <i>C. kikuchii</i> were evaluated along with 53 other species of <i>Cercospora</i>. No isolates from this study were nested within the clade including the ex-type strain of <i>C. kikuchii</i>. Five isolates grouped with <i>C.</i> cf. <i>sigesbeckiae</i> and all others were part of <i>C.</i> cf. <i>flagellaris</i>. Several isolates of <i>C.</i> cf. <i>flagellaris</i> were also obtained from <i>Gossypyium hirsutum</i> and <i>Phytolacca americana</i>. These results suggest that <i>C. kikuchii</i> is not the organism responsible for causing CLB or PSS in the Gulf South and other areas of the USA.
Multiple haplotypes were observed at each locus and individual genes varied in their resolving power. Most species were monophyletic in concatenated analyses, but reciprocal monophyly was generally not observed within individual gene trees. Furthermore, node support values were generally low across all topologies, indicating that the phylogenetic markers most commonly used for systematic studies of <i>Cercospora</i> are limited to answering shallow-level taxonomic questions. However, existing genome sequence data provided an excellent opportunity to develop new markers with stronger phylogenetic signal to better understand the evolutionary history of <i>Cercospora</i>. Sixty-three exon-flanked intergenic regions, syntenic between the genomes of <i>C.</i> cf <i>sigesbeckiae</i> and <i>C. canescens</i>, were extracted and aligned, then ranked and filtered according to several metrics to assess their phylogenetic utility. Candidate markers were validated by PCR on 24 <i>Cercospora</i> species, including 16 type strains. Assessment of phylogenetic informativeness profiles and phylogenetic analyses showed that all of the new markers provide greater interspecific resolution than the legacy genes and offer new options for identifying cryptic species in complex clades like <i>C.</i> cf. <i>flagellaris</i>.
| Identifer | oai:union.ndltd.org:LSU/oai:etd.lsu.edu:etd-11122015-232818 |
| Date | 07 December 2015 |
| Creators | Albu, Sebastian |
| Contributors | Schneider, Raymond, Doyle, Vinson, Clark, Christopher, Cao, Quang, Aime, M. Catherine |
| Publisher | LSU |
| Source Sets | Louisiana State University |
| Language | English |
| Detected Language | English |
| Type | text |
| Format | application/pdf |
| Source | http://etd.lsu.edu/docs/available/etd-11122015-232818/ |
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