Draft genome of Cercospora zeina, Fusarium pininemorale, Hawksworthiomyces lignivorus, Huntiella decipiens and Ophiostoma ips

Abstract

The genomes of Cercospora zeina, Fusarium pininemorale, Hawksworthiomyces lignivorus, Huntiella decipiens, and Ophiostoma ips are presented in this genome announcement. Three of these genomes are from plant pathogens and otherwise economically important fungal species. Fusarium pininemorale and H. decipiens are not known to cause significant disease but are closely related to species of economic importance. The genome sizes range from 25.99 Mb in the case of O. ips to 4.82 Mb for H. lignivorus. These genomes include the first reports of a genome from the genus Hawksworthiomyces. The availability of these genome data will allow the resolution of longstanding questions regarding the taxonomy of these species. In addition these genome sequences through comparative studies with closely related organisms will increase our understanding of how these species or close relatives cause disease.

Repeat-Induced Point Mutations Drive Divergence between Fusarium circinatum and Its Close Relatives

“…The whole divergence process can be enhanced even further by a range of additional factors; e.g., chromosome loss or large genomic rearrangements can interfere with complementary base pairing during homologous recombination [63], while geographical isolation becomes a physical barrier to gene flow [64]. Other large inter-chromosomal inversions, such as those observed among American clade species of the FFSC [5,14,65], likely also hamper recombination and gene flow between populations.…”

IMA Genome-F 11

“…For example, the head blight pathogen Fusarium graminearum (genome size: 36.5 Mb) has approximately 14 164 genes (King et al 2015), the pine needle blight pathogen Dothistroma septosporum (genome size: 31. Wingfield et al 2016a;Wingfield et al 2017;Molano et al 2018;Vanderpool et al 2018;Wingfield et al 2018a). The annotation of the C. fimbriata genome sequence presented in this study is the first manually curated genome including additional RNA evidence, for any species in the Ceratocystidaceae.…”

“…The assembled draft genome of Fusarium xylarioides was estimated to be 55.24 Mb with a coverage of 61x, corresponding to 424 scaffolds larger than 500 bp with an N50 value of 250 204 bp, and an average GC content of 43.4%. Among the FFSC species for which genomes sequences are available, F. xylarioides thus has the largest predicted genome size, i.e., the genomes of F. circinatum is 43.43 Mb, F. temperatum 45.46 Mb, F. fracticaudum 46.29 Mb, F. pininemorale 47.83 Mb, and F. nygamai is 51.61 Mb (Wingfield et al 2015a(Wingfield et al , 2015b(Wingfield et al , 2017(Wingfield et al , 2018a. The predicted size of our sequenced genome was similar to that of another F. xylarioides strain K1 (55.11 Mb), whose genome sequence has recently been made available on NCBI under nucleotide accession number GCA_004329255.…”

De novo Assembly of Transcriptomes From a B73 Maize Line Introgressed With a QTL for Resistance to Gray Leaf Spot Disease Reveals a Candidate Allele of a Lectin Receptor-Like Kinase

“…This method is particularly effective if the background carrying the QTL introgression has a well-annotated genome sequence, such as the maize inbred line B73 (Jiao et al, 2017). For applications in molecular plant pathology, it is also helpful if the pathogen genome sequence is also available, as was the case for C. zeina (Wingfield et al, 2017). This allows mapping of RNAseq reads to both host and pathogen genomes simultaneously to identify unmapped reads that can be de novo assembled and annotated to find candidates from the QTL locus (Figure 1).…”

“…The functional annotations of the differentially expressed genes (FDR < 0.05) were determined by comparing them to the B73 v.4 (Jiao et al, 2017) and C. zeina (Wingfield et al, 2017) reference genomes using BLAT (RRID:SCR_011919) (Kent, 2002). Transcripts were classified as B73 or C. zeina genes if they had at least 80% identity across 90% of the transcript's length, which was determined using a custom AWK script.…”