Abstract
Bipolaris cookei (=Bipolaris sorghicola) causes target leaf spot, one of the most prevalent foliar diseases of sorghum. Little is known about the molecular basis of pathogenesis in B. cookei, in large part due to a paucity of resources for molecular genetics, such as a reference genome. Here, a draft genome sequence of B. cookei was obtained and analyzed. A hybrid assembly strategy utilizing Illumina and Pacific Biosciences sequencing technologies produced a draft nuclear genome of 36.1 Mb, organized into 321 scaffolds with L50 of 31 and N50 of 378 kb, from which 11,189 genes were predicted. Additionally, a finished mitochondrial genome sequence of 135,790 bp was obtained, which contained 75 predicted genes. Comparative genomics revealed that B. cookei possessed substantially fewer carbohydrate-active enzymes and secreted proteins than closely related Bipolaris species. Novel genes involved in secondary metabolism, including genes implicated in ophiobolin biosynthesis, were identified. Among 37 B. cookei genes induced during sorghum infection, one encodes a putative effector with a limited taxonomic distribution among plant pathogenic fungi. The draft genome sequence of B. cookei provided novel insights into target leaf spot of sorghum and is an important resource for future investigation.
Highlights
Sorghum (Sorghum bicolor (L.)) was domesticated in northeast Africa 4–5000 years ago, anthropological records indicate it has been consumed by humans as early as 8000 BC1,2
14% of the B. cookei draft genome sequence was comprised of transposable elements (TEs)
Comparative genomic analyses with the mitochondrial gene cob from Cercospora beticola[25] indicated that the mutation G143A, which is associated with resistance to QoI fungicides, is not present in B. cookei strain LSLP18.3 (Supplementary Fig. S4)
Summary
Sorghum (Sorghum bicolor (L.)) was domesticated in northeast Africa 4–5000 years ago, anthropological records indicate it has been consumed by humans as early as 8000 BC1,2. In warm, humid growing areas, is hindered by a wide variety of fungal foliar diseases[8]. Noteworthy in the southeastern U.S is target leaf spot, caused by Bipolaris cookei [=B. sorghicola = Drechslera sorghicola = Helminthosporium sorghicola9]. Within two decades after its first reported observation on grain sorghum in Mississippi in 198614, target leaf spot has become widespread in the lower Mississippi river valley. Quantitative trait loci underlying resistance to target leaf spot have been explored to some extent[17,18]. Comparative transcriptomics during infection of resistant and susceptible hybrids with B. cookei identified both plant and fungal genes 12 and 24 hr after infection[21,22]. Novel genes were identified that could play important roles in pathogenicity
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