Monilinia fructicola (MFRC), Monilinia laxa (MLAX) and Monilinia fructigena (MFRG) are the main causal agents of brown rot on stone and pome fruits. Genomic and transcriptomic data for the three fungal species have so far remained largely unexplored. The complete transcriptomes of MFRC (GenBank accession GGAK00000000), MLAX (GGAL00000000) and MFRG (GGAM00000000) was sequenced (Illumina technology), de-novo assembled and annotated1. Comparative analyses among orthologous transcripts led to identify 65 transcripts significantly over-expressed or unique in MFRC, 30 in MLAX and 31 in MFRG. They represent sets of potential key genes associated with fungal morphogenesis and development, secondary metabolism and host-microbiota-pathogen interactions. High-quality draft genomes of M. fructicola Mfrc123 strain (VICG00000000)2, M. laxa Mlax316 strain (VIGI00000000)3 and M. fructigena Mfrg269 strain (QKRW00000000)4 were obtained through a hybrid and hierarchical de-novo assembly strategy using both Illumina and PacBio sequencing technologies. They consisted of 20 (MFRC), 49 (MLAX) and 131 (MFRG) scaffolds, with a total length of 44.05, 42.81 and 43.125 Mb and a scaffold N50 of 2,592, 2,449 and 768 kb, respectively. Genome annotations identified a total of 12,118 (MFRC), 11,163 (MLAX) and 10,502 (MFRG) genes and 13,749, 12,424 and 9,960 proteins, respectively. These newly generated reference genomes improve current available resources in terms of contiguity, gap-free sequences, and read mappability and provide structural and functional annotations of the genomes. They are expected to significantly contribute to comparative analysis of genome biology and evolution within Monilinia species. 1 De Miccolis Angelini et al. (2018). BMC Genomics 19:436 2 De Miccolis Angelini et al. (2019). Genome Biol Evol 11:2850–2855 3 Landi et al. (2019). Mol Plant Microbe Interact (Epub ahead of print) 4 Landi et al. (2018). BMC Res Notes 11:758
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